*>>>>>>>> Developmental Residue Topology File for Proteins <<<<< *>>>>>>>>>>>>>>>>> Using All Hydrogens (ALLH) <<<<<<<<<<<<<<<<<< *>>>>>>>>>>>>>>>>>>>>>>> May 1993 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<< *>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< *>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< * These files are a beta release; additional parameter development * and testing may lead to alteration of the contents. * * * * * Original file: top_all22_prot_b5.inp. * * IMPROPER dihedrals, some from toph19.inp, were added to this library to * make it more useful for MODELLER (Andrej Sali). Note that this is * only necessary when MODELLER's non-hydrogen topology is used; * presumably, the H-related energy terms in the all-hydrogen topology * would restrain peptide bonds, ring planarities, and chiralities (?) * sufficiently and would obviate the need for these impropers. * * Specifically, the following impropers were added: * * IMPR CA N C CB for mainchain of all residues but GLY; * ring impropers for Phe, Tyr, Hsd (His on 1/25/03), Hsp, Hse, and Trp. * * the chirality constraints for the chiral and pro-chiral * centers in sidechains of ILE, LEU, THR, VAL; note that * the toph19.inp IMPR for LEU had to be changed to allow * for the swapped CD1/CD2 LEU labels (that was changed back on 1/25/03). * * IMPR NE CD CZ HE for ARG. * * Trp appeared to have too many improper dih restraints so the optimizer * got caught in a deep local minimum too easily. I made them sparser * relative to toph19 and also introduced two new 180 degree impropers * across the two rings. * * The IC entries added to allow amino-acid residue creation without patches: * * IC N CA C O 1.4592 114.4400 0.0000 122.5200 1.2297 * IC HN N CA C 0.9996 115.4200 0.0000 114.4400 1.5390 * * Only the 20 standard residue types were modified. * * No changes were done for cis/trans prolines. * * PA, PB, and UNDF atom types were added. * * GDP and GTP residue types were added. * * Pro pucker is enforced by an additional explicit CP1 CP2 CP2 CP3 term. * * * This file was obtained by editing the H naming conventions in top.lib * (1/25/03) to conform to those of PDB, which now conforms to IUPAC. In * addition, the models.lib file had to be edited, and the source code changed * in iupac_model.F90. I ran program PDB-H/conver-top on * the original top.lib and edited special cases manually as follows: * DECL HN --> H * RESI ASX copied to be the same as ASN * RESI GLX copied to be the same as GLN * RESI CYS old HG1 is non-conforming, renamed to HG per PDB * RESI CSS was edited manually based on the new CYS (copy CYS, delete all * references to HG) * PRES DISU, edit lots of H names to match the new CYS, CSS. * RESI UNK is like GLY, so copy GLY to it. * RESI ILE: edit HD1/2/3 to 1HD1/2/3 * RESI SER: HG1 -> HG * RESI HSE: keep it as edited by the program thinking it is HIS, * even though HE2 is undefined in PDB (keep it as HE2) * RESI HSP: the same as HSE * PRES NTER, GLYP, PROP: all these N-terminals are edited manually into 1H, * 2H, 3H * PRES ASPP edited to reflect new ASP (HB1 and HB2 into 1HB and 2HB) * PRES GLUP the same as ASPP * PRES HS2 not edited, won't work, so it was just deleted * * While renaming the hydrogens, I also renamed here a few other atoms to make * them conform to PDB and simplify the source code (dihedral_routines.F90, * atom_residue_routines.F90, iupac_model.F90): * RESI ILE CD --> CD1; and resdih.lib was changed accordingly * RESI LEU CD1 and CD2 were swapped back (in the IMPR entry), and * resdih.lib was changed accordingly. * RESI HSD --> HIS, to conform to PDB; (restyp and resdih libs changed * accordingly). * PRES CTER OT1 and OT2 were changed to O and OXT, respectively, to conform * to PDB * RESI TIP3, OH2 --> O, to conform to PDB * * Additionally modified 08/25/2008 to conform to remediated PDB (v3): * new atom naming for nucleic acids, NAD, GDP, GTP, ions. New deoxy nucleic * acid types DADE, DCYT, DGUA, DTHY, DURA. All hydrogen names now start * with H, not a digit. * * Modified 09/18/2008 to add elements to MASS lines, to conform to newer * CHARMM format and to allow writing out new-style PDB output. * * Note that MODELLER special-cases the peptide bond (C +N) and the * associated improper (C CA +N O). Ordinarily it will warn if some of * the atoms in a bond are missing, but it will suppress this for the two * bonds above for the last residue in a chain (obviously the +N atom * cannot be found in this case). It will also suppress creating the bond * entirely if the residue containing +N is a HETATM and does not appear * to be a modified amino acid (for this, a simple heuristic is used - * the residue must also contain a carbon CA atom). This prevents the creation * of spurious bonds to ligands that happen to contain an atom called "N". * * MODELLER topology.submodel = 1 22 1 MASS 1 H 1.00800 H ! polar H MASS 2 HC 1.00800 H ! N-ter H MASS 3 HA 1.00800 H ! nonpolar H MASS 4 HT 1.00800 H ! TIPS3P WATER HYDROGEN MASS 5 HP 1.00800 H ! aromatic H MASS 6 HB 1.00800 H ! backbone H MASS 7 HR1 1.00800 H ! his he1, (+) his HG,HD2 MASS 8 HR2 1.00800 H ! (+) his HE1 MASS 9 HR3 1.00800 H ! neutral his HG, HD2 MASS 10 HS 1.00800 H ! thiol hydrogen MASS 11 HA1 1.00800 H ! for alkene; RHC=CR MASS 12 HA2 1.00800 H ! for alkene; H2C=CR MASS 13 C 12.01100 C ! carbonyl C, peptide backbone MASS 14 CA 12.01100 C ! aromatic C MASS 15 CT1 12.01100 C ! aliphatic sp3 C for CH MASS 16 CT2 12.01100 C ! aliphatic sp3 C for CH2 MASS 17 CT3 12.01100 C ! aliphatic sp3 C for CH3 MASS 18 CPH1 12.01100 C ! his CG and CD2 carbons MASS 19 CPH2 12.01100 C ! his CE1 carbon MASS 20 CPT 12.01100 C ! trp C between rings MASS 21 CY 12.01100 C ! TRP C in pyrrole ring MASS 22 CP1 12.01100 C ! tetrahedral C (proline CA) MASS 23 CP2 12.01100 C ! tetrahedral C (proline CB/CG) MASS 24 CP3 12.01100 C ! tetrahedral C (proline CD) MASS 25 CC 12.01100 C ! carbonyl C, asn,asp,gln,glu,cter,ct2 MASS 26 CD 12.01100 C ! carbonyl C, pres aspp,glup,ct1 MASS 27 CPA 12.01100 C ! heme alpha-C MASS 28 CPB 12.01100 C ! heme beta-C MASS 29 CPM 12.01100 C ! heme meso-C MASS 30 CM 12.01100 C ! heme CO carbon MASS 31 CS 12.01100 C ! thiolate carbon MASS 32 CE1 12.01100 C ! for alkene; RHC=CR MASS 33 CE2 12.01100 C ! for alkene; H2C=CR MASS 34 N 14.00700 N ! proline N MASS 35 NR1 14.00700 N ! neutral his protonated ring nitrogen MASS 36 NR2 14.00700 N ! neutral his unprotonated ring nitrogen MASS 37 NR3 14.00700 N ! charged his ring nitrogen MASS 38 NH1 14.00700 N ! peptide nitrogen MASS 39 NH2 14.00700 N ! amide nitrogen MASS 40 NH3 14.00700 N ! ammonium nitrogen MASS 41 NC2 14.00700 N ! guanidinium nitroogen MASS 42 NY 14.00700 N ! TRP N in pyrrole ring MASS 43 NP 14.00700 N ! Proline ring NH2+ (N-terminal) MASS 44 NPH 14.00700 N ! heme pyrrole N MASS 45 NP1 14.00700 N ! heme pyrrole N ! Roberto MASS 46 PA 30.97400 P ! PA ! Andrej MASS 47 PB 30.97400 P ! PB ! Andrej MASS 48 O 15.99900 O ! carbonyl oxygen MASS 49 OB 15.99900 O ! carbonyl oxygen in acetic acid MASS 50 OC 15.99900 O ! carboxylate oxygen MASS 51 OH1 15.99900 O ! hydroxyl oxygen MASS 52 OS 15.99940 O ! ester oxygen MASS 53 OT 15.99940 O ! TIPS3P WATER OXYGEN MASS 54 OM 15.99900 O ! heme CO/O2 oxygen MASS 55 S 32.06000 S ! sulphur MASS 56 SM 32.06000 S ! sulfur C-S-S-C type MASS 57 SS 32.06000 S ! thiolate sulfur MASS 58 HE 4.00260 HE ! helium MASS 59 NE 20.17970 NE ! neon MASS 60 CAL 40.08000 CA ! calcium 2+ MASS 61 ZN 65.37000 ZN ! zinc (II) cation MASS 62 FE 55.84700 FE ! heme iron 56 MASS 63 UNDF 55.84700 X ! undefined Andrej ! nucleic acid section !MASS 104 HT 1.008000 H ! TIPS3P WATER HYDROGEN MASS 64 HN1 1.008000 H ! Nucleic acid amine proton MASS 65 HN2 1.008000 H ! Nucleic acid ring nitrogen proton MASS 66 HN3 1.008000 H ! Nucleic acid aromatic carbon proton MASS 67 HN4 1.008000 H ! Nucleic acid phosphate hydroxyl proton MASS 68 HN5 1.008000 H ! Nucleic acid ribose hydroxyl proton MASS 69 HN6 1.008000 H ! Nucleic acid ribose aliphatic proton MASS 70 HN7 1.008000 H ! Nucleic acid proton (equivalent to protein HA) MASS 71 HN3B 1.008000 H ! NAD+ aromatic hydrogen MASS 72 CN1 12.011000 C ! Nucleic acid carbonyl carbon MASS 73 CN2 12.011000 C ! Nucleic acid aromatic carbon to amide MASS 74 CN3 12.011000 C ! Nucleic acid aromatic carbon MASS 75 CN4 12.011000 C ! Nucleic acid purine C8 and ADE C2 MASS 76 CN5 12.011000 C ! Nucleic acid purine C4 and C5 MASS 77 CN6 12.011000 C ! Nucleic acid sp3 ribose ring carbon MASS 78 CN6B 12.011000 C ! Nucleic acid sp3 ribose ring carbon, C1' MASS 79 CN6C 12.011000 C ! Nucleic acid sp3 deoxyribose ring carbon, C2' MASS 80 CN7 12.011000 C ! Nucleic acid carbon (equivalent to protein CT1) MASS 81 CN8 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2) MASS 82 CN9 12.011000 C ! Nucleic acid carbon (equivalent to protein CT3) MASS 83 CN3A 12.011000 C ! NAD+ aromatic carbon MASS 84 CN3B 12.011000 C ! NAD+ aromatic carbon MASS 85 CN3C 12.011000 C ! NADH aromatic carbon MASS 86 CN3D 12.011000 C ! Nucleic acid aromatic carbon for 5MC MASS 87 CN1A 12.011000 C ! NAD+/NADH amide carbonyl carbon MASS 88 NN1 14.007000 N ! Nucleic acid amide nitrogen MASS 89 NN2 14.007000 N ! Nucleic acid protonated ring nitrogen MASS 90 NN2U 14.007000 N ! Nucleic acid protonated ring nitrogen, ura N3 MASS 91 NN2G 14.007000 N ! Nucleic acid protonated ring nitrogen, gua N1 MASS 92 NN3 14.007000 N ! Nucleic acid unprotonated ring nitrogen MASS 93 NN4 14.007000 N ! Nucleic acid purine N7 MASS 94 NN5 14.007000 N ! Nucleic acid sp2 amine nitrogen MASS 95 NN3A 14.007000 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3 MASS 96 NN3I 14.007000 N ! Nucleic acid unprotonated ring nitrogen, inosine N3 !MASS 164 OT 15.999400 O ! TIPS3P WATER OXYGEN MASS 97 ON1 15.999400 O ! Nucleic acid carbonyl oxygen MASS 98 ON1C 15.999400 O ! Nucleic acid carbonyl oxygen, cyt O2 MASS 99 ON2 15.999400 O ! Nucleic acid phosphate ester oxygen MASS 100 ON3 15.999400 O ! Nucleic acid =O in phosphate MASS 101 ON4 15.999400 O ! Nucleic acid phosphate hydroxyl oxygen MASS 102 ON5 15.999400 O ! Nucleic acid ribose hydroxyl oxygen MASS 103 ON6 15.999400 O ! Nucleic acid ribose ring oxygen MASS 104 ON2B 15.999400 O ! Nucleic acid phosphate ester oxygen, tyr-phosphate MASS 105 P 30.974000 P ! phosphorus MASS 106 P2 30.974000 P ! pyrophosphate phosphorus MASS 107 SOD 22.989770 NA ! Sodium Ion MASS 108 MG 24.305000 MG ! Magnesium Ion MASS 109 DUM 0.001 X ! dummy atom DECL -CA DECL -C DECL -O DECL +N DECL +H DECL +CA DEFA FIRS NTER LAST CTER AUTO ANGLES DIHE RESI ALA 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM H H 0.31 ! H-N ATOM CA CT1 0.07 ! | HB1 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB2 ATOM CB CT3 -0.27 ! | \ ATOM HB1 HA 0.09 ! | HB3 ATOM HB2 HA 0.09 ! O=C ATOM HB3 HA 0.09 ! | GROUP ! ATOM C C 0.51 ATOM O O -0.51 BOND CB CA N H N CA O C BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 IMPR N -C CA H C CA +N O IMPR CA N C CB DONOR H N ACCEPTOR O C IC -C CA *N H 1.3551 126.4900 180.0000 115.4200 0.9996 IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114 IC N CA C O 1.4300 107.0000 0.0000 122.5200 1.2297 IC H N CA C 0.9996 115.4200 0.0000 114.4400 1.4900 RESI ARG 1.00 GROUP ATOM N NH1 -0.47 ! | HH11 ATOM H H 0.31 ! H-N | ATOM CA CT1 0.07 ! | HB2 HG2 HD2 HE NH1-HH12 ATOM HA HB 0.09 ! | | | | | / GROUP ! HA-CA--CB--CG--CD--NE--CZ ATOM CB CT2 -0.18 ! | | | | \ ATOM HB3 HA 0.09 ! | HB3 HG3 HD3 NH2-HH21 ATOM HB2 HA 0.09 ! O=C | GROUP ! | HH22 ATOM CG CT2 -0.18 ATOM HG3 HA 0.09 ATOM HG2 HA 0.09 GROUP ATOM CD CT2 0.20 ATOM HD3 HA 0.09 ATOM HD2 HA 0.09 ATOM NE NC2 -0.70 ATOM HE HC 0.44 ATOM CZ C 0.64 ATOM NH1 NC2 -0.80 ATOM HH11 HC 0.46 ATOM HH12 HC 0.46 ATOM NH2 NC2 -0.80 ATOM HH21 HC 0.46 ATOM HH22 HC 0.46 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG NE CD CZ NE BOND NH1 CZ NH2 CZ N H N CA BOND O C C CA C +N CA HA CB HB3 BOND CB HB2 CG HG3 CG HG2 CD HD3 CD HD2 BOND NE HE NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22 IMPR N -C CA H C CA +N O IMPR CZ NH1 NH2 NE IMPR CA N C CB IMPR NE CD CZ HE DONOR H N DONOR HE NE DONOR HH11 NH1 DONOR HH12 NH1 DONOR HH21 NH2 DONOR HH22 NH2 ACCEPTOR O C IC -C CA *N H 1.3496 122.4500 180.0000 116.6700 0.9973 IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227 IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511 IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271 IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565 IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552 IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836 IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475 IC CG CA *CB HB3 1.5475 115.9500 120.0500 106.4000 1.1163 IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124 IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384 IC CD CB *CG HG3 1.5384 114.0100 125.2000 108.5500 1.1121 IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143 IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034 IC NE CG *CD HD3 1.5034 107.0900 120.6900 109.4100 1.1143 IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150 IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401 IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065 IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311 IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903 IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023 IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292 IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899 IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914 RESI ASN 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM H H 0.31 ! H-N ATOM CA CT1 0.07 ! | HB2 OD1 HD21 (cis to OD1) ATOM HA HB 0.09 ! | | || / GROUP ! HA-CA--CB--CG--ND2 ATOM CB CT2 -0.18 ! | | \ ATOM HB3 HA 0.09 ! | HB3 HD22 (trans to OD1) ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CC 0.55 ATOM OD1 O -0.55 GROUP ATOM ND2 NH2 -0.62 ATOM HD22 H 0.32 ATOM HD21 H 0.30 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB OD1 CG ND2 CG BOND N H N CA O C C CA C +N BOND CA HA CB HB3 CB HB2 ND2 HD22 ND2 HD21 IMPR N -C CA H C CA +N O IMPR CG ND2 CB OD1 CG CB ND2 OD1 IMPR ND2 CG HD22 HD21 ND2 CG HD21 HD22 IMPR CA N C CB DONOR H N DONOR HD22 ND2 DONOR HD21 ND2 ACCEPTOR OD1 CG ACCEPTOR O C IC -C CA *N H 1.3480 124.0500 180.0000 114.4900 0.9992 IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245 IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467 IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282 IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528 IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627 IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848 IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319 IC CG CA *CB HB3 1.5319 114.3000 119.1700 107.8200 1.1120 IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091 IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323 IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521 IC CB CG ND2 HD22 1.5319 116.1500 -179.2600 117.3500 0.9963 IC HD22 CG *ND2 HD21 0.9963 117.3500 178.0200 120.0500 0.9951 RESI ASX 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM H H 0.31 ! H-N ATOM CA CT1 0.07 ! | HB1 OD1 HD1 (cis to OD1) ATOM HA HB 0.09 ! | | || / GROUP ! HA-CA--CB--CG--ND2 ATOM CB CT2 -0.18 ! | | \ ATOM HB2 HA 0.09 ! | HB2 HD2 (trans to OD1) ATOM HB1 HA 0.09 ! O=C GROUP ! | ATOM CG CC 0.55 ATOM OD1 O -0.55 GROUP ATOM ND2 NH2 -0.62 ATOM HD2 H 0.32 ATOM HD1 H 0.30 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB OD1 CG ND2 CG BOND N H N CA O C C CA C +N BOND CA HA CB HB2 CB HB1 ND2 HD2 ND2 HD1 IMPR N -C CA H C CA +N O IMPR CG ND2 CB OD1 CG CB ND2 OD1 IMPR ND2 CG HD2 HD1 ND2 CG HD1 HD2 IMPR CA N C CB DONOR H N DONOR HD2 ND2 DONOR HD2 ND2 ACCEPTOR OD1 CG ACCEPTOR O C IC -C CA *N H 1.3480 124.0500 180.0000 114.4900 0.9992 IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245 IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467 IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282 IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528 IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627 IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848 IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319 IC CG CA *CB HB2 1.5319 114.3000 119.1700 107.8200 1.1120 IC CG CA *CB HB1 1.5319 114.3000 -123.7400 110.3400 1.1091 IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323 IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521 IC CB CG ND2 HD2 1.5319 116.1500 -179.2600 117.3500 0.9963 IC HD2 CG *ND2 HD1 0.9963 117.3500 178.0200 120.0500 0.9951 RESI ASP -1.00 GROUP ATOM N NH1 -0.47 ! | ATOM H H 0.31 ! H-N ATOM CA CT1 0.07 ! | HB2 OD1 ATOM HA HB 0.09 ! | | // GROUP ! HA-CA--CB--CG ATOM CB CT2 -0.28 ! | | \\ ATOM HB3 HA 0.09 ! | HB3 OD2 ATOM HB2 HA 0.09 ! O=C ATOM CG CC 0.62 ! | ATOM OD1 OC -0.76 ATOM OD2 OC -0.76 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB OD1 CG OD2 CG BOND N H N CA O C C CA C +N BOND CA HA CB HB3 CB HB2 IMPR N -C CA H C CA +N O IMPR OD1 CB OD2 CG IMPR CA N C CB DONOR H N ACCEPTOR OD1 CG ACCEPTOR OD2 CG ACCEPTOR O C IC -C CA *N H 1.3465 125.3100 180.0000 112.9400 0.9966 IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315 IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478 IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330 IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484 IC N C *CA CB 1.4490 105.6300 122.3300 114.1000 1.5619 IC N C *CA HA 1.4490 105.6300 -116.4000 106.7700 1.0841 IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218 IC CG CA *CB HB3 1.5218 112.6000 119.2200 109.2300 1.1086 IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080 IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565 IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541 RESI CYS 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM H H 0.31 ! H-N ATOM CA CT1 0.07 ! | HB2 ATOM HA HB 0.09 ! | | GROUP ! HA-CA--CB--SG ATOM CB CT2 -0.11 ! | | \ ATOM HB3 HA 0.09 ! | HB3 HG ATOM HB2 HA 0.09 ! O=C ATOM SG S -0.23 ! | ATOM HG HS 0.16 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA SG CB N H N CA BOND O C C CA C +N CA HA CB HB3 BOND CB HB2 SG HG IMPR N -C CA H C CA +N O IMPR CA N C CB DONOR H N DONOR HG SG ACCEPTOR O C IC -C CA *N H 1.3479 123.9300 180.0000 114.7700 0.9982 IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 IC SG CA *CB HB3 1.8359 113.8700 119.9100 107.2400 1.1134 IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 IC CA CB SG HG 1.5584 113.8700 176.9600 97.1500 1.3341 RESI CSS 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM H H 0.31 ! H-N ATOM CA CT1 0.07 ! | HB2 ATOM HA HB 0.09 ! | | GROUP ! HA-CA--CB--SG ATOM CB CT2 -0.11 ! | | ATOM HB3 HA 0.09 ! | HB3 ATOM HB2 HA 0.09 ! O=C ATOM SG S -0.23 ! | GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA SG CB N H N CA BOND O C C CA C +N CA HA CB HB2 BOND CB HB3 IMPR N -C CA H C CA +N O IMPR CA N C CB DONOR H N ACCEPTOR O C IC -C CA *N H 1.3479 123.9300 180.0000 114.7700 0.9982 IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 IC SG CA *CB HB3 1.8359 113.8700 119.9100 107.2400 1.1134 IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 RESI GLN 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM H H 0.31 ! H-N ATOM CA CT1 0.07 ! | HB2 HG2 OE1 HE21 (cis to OE1) ATOM HA HB 0.09 ! | | | || / GROUP ! HA-CA--CB--CG--CD--NE2 ATOM CB CT2 -0.18 ! | | | \ ATOM HB3 HA 0.09 ! | HB3 HG3 HE22 (trans to OE1) ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CT2 -0.18 ATOM HG3 HA 0.09 ATOM HG2 HA 0.09 GROUP ATOM CD CC 0.55 ATOM OE1 O -0.55 GROUP ATOM NE2 NH2 -0.62 ATOM HE22 H 0.32 ATOM HE21 H 0.30 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG OE1 CD NE2 CD BOND N H N CA O C C CA BOND C +N CA HA CB HB3 CB HB2 CG HG3 BOND CG HG2 NE2 HE22 NE2 HE21 IMPR N -C CA H C CA +N O IMPR CD NE2 CG OE1 CD CG NE2 OE1 IMPR NE2 CD HE22 HE21 NE2 CD HE21 HE22 IMPR CA N C CB DONOR H N DONOR HE22 NE2 DONOR HE21 NE2 ACCEPTOR OE1 CD ACCEPTOR O C IC -C CA *N H 1.3477 123.9300 180.0000 114.4500 0.9984 IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180 IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463 IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291 IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461 IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538 IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832 IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534 IC CG CA *CB HB3 1.5534 115.5200 120.9300 106.8000 1.1147 IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140 IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320 IC CD CB *CG HG3 1.5320 112.5000 118.6900 110.4100 1.1112 IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094 IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294 IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530 IC CG CD NE2 HE22 1.5320 116.8400 -179.7200 116.8600 0.9959 IC HE22 CD *NE2 HE21 0.9959 116.8600 -178.9100 119.8300 0.9943 RESI GLX 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM H H 0.31 ! H-N ATOM CA CT1 0.07 ! | HB1 HG1 OE1 HE21 (cis to OE1) ATOM HA HB 0.09 ! | | | || / GROUP ! HA-CA--CB--CG--CD--NE2 ATOM CB CT2 -0.18 ! | | | \ ATOM HB2 HA 0.09 ! | HB2 HG2 HE22 (trans to OE1) ATOM HB1 HA 0.09 ! O=C GROUP ! | ATOM CG CT2 -0.18 ATOM HG2 HA 0.09 ATOM HG1 HA 0.09 GROUP ATOM CD CC 0.55 ATOM OE1 O -0.55 GROUP ATOM NE2 NH2 -0.62 ATOM HE22 H 0.32 ATOM HE21 H 0.30 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG OE1 CD NE2 CD BOND N H N CA O C C CA BOND C +N CA HA CB HB2 CB HB1 CG HG2 BOND CG HG1 NE2 HE22 NE2 HE21 IMPR N -C CA H C CA +N O IMPR CD NE2 CG OE1 CD CG NE2 OE1 IMPR NE2 CD HE22 HE21 NE2 CD HE21 HE22 IMPR CA N C CB DONOR H N DONOR HE22 NE2 DONOR HE21 NE2 ACCEPTOR OE1 CD ACCEPTOR O C IC -C CA *N H 1.3477 123.9300 180.0000 114.4500 0.9984 IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180 IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463 IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291 IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461 IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538 IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832 IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534 IC CG CA *CB HB2 1.5534 115.5200 120.9300 106.8000 1.1147 IC CG CA *CB HB1 1.5534 115.5200 -124.5800 109.3400 1.1140 IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320 IC CD CB *CG HG2 1.5320 112.5000 118.6900 110.4100 1.1112 IC CD CB *CG HG1 1.5320 112.5000 -121.9100 110.7400 1.1094 IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294 IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530 IC CG CD NE2 HE22 1.5320 116.8400 -179.7200 116.8600 0.9959 IC HE22 CD *NE2 HE21 0.9959 116.8600 -178.9100 119.8300 0.9943 RESI GLU -1.00 GROUP ATOM N NH1 -0.47 ! | ATOM H H 0.31 ! H-N ATOM CA CT1 0.07 ! | HB2 HG2 OE1 ATOM HA HB 0.09 ! | | | // GROUP ! HA-CA--CB--CG--CD ATOM CB CT2 -0.18 ! | | | \\ ATOM HB3 HA 0.09 ! | HB3 HG3 OE2 ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CT2 -0.28 ATOM HG3 HA 0.09 ATOM HG2 HA 0.09 ATOM CD CC 0.62 ATOM OE1 OC -0.76 ATOM OE2 OC -0.76 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG OE1 CD OE2 CD BOND N H N CA O C C CA BOND C +N CA HA CB HB3 CB HB2 CG HG3 BOND CG HG2 IMPR N -C CA H C CA +N O IMPR OE1 CG OE2 CD IMPR CA N C CB DONOR H N ACCEPTOR OE1 CD ACCEPTOR OE2 CD ACCEPTOR O C IC -C CA *N H 1.3471 124.4500 180.0000 113.9900 0.9961 IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516 IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828 IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557 IC CG CA *CB HB3 1.5557 115.6900 121.2200 108.1600 1.1145 IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307 IC CD CB *CG HG3 1.5307 115.7300 117.3800 109.5000 1.1053 IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081 IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590 IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532 RESI GLY 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM H H 0.31 ! N-H ATOM CA CT2 -0.02 ! | ATOM HA3 HB 0.09 ! | ATOM HA2 HB 0.09 ! HA2-CA-HA3 GROUP ! | ATOM C C 0.51 ! | ATOM O O -0.51 ! C=O ! | BOND N H N CA O C C CA BOND C +N CA HA3 CA HA2 IMPR N -C CA H C CA +N O DONOR H N ACCEPTOR O C IC -C CA *N H 1.3475 122.8200 180.0000 115.6200 0.9992 IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971 IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479 IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289 IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560 IC N C *CA HA3 1.4553 108.9400 117.8600 108.0300 1.0814 IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817 PATCHING FIRS GLYP RESI UNK 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM H H 0.31 ! N-H ATOM CA CT2 -0.02 ! | ATOM HA3 HB 0.09 ! | ATOM HA2 HB 0.09 ! HA2-CA-HA3 GROUP ! | ATOM C C 0.51 ! | ATOM O O -0.51 ! C=O ! | BOND N H N CA O C C CA BOND C +N CA HA3 CA HA2 IMPR N -C CA H C CA +N O DONOR H N ACCEPTOR O C IC -C CA *N H 1.3475 122.8200 180.0000 115.6200 0.9992 IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971 IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479 IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289 IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560 IC N C *CA HA3 1.4553 108.9400 117.8600 108.0300 1.0814 IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817 PATCHING FIRS GLYP RESI HIS 0.00 ! neutral HIS, proton on ND1 GROUP ATOM N NH1 -0.47 ! | HD1 HE1 ATOM H H 0.31 ! H-N | / ATOM CA CT1 0.07 ! | HB2 ND1--CE1 ATOM HA HB 0.09 ! | | / | GROUP ! HA-CA--CB--CG | ATOM ND1 NR1 -0.36 ! | | \ | ATOM HD1 H 0.32 ! | HB3 CD2--NE2 ATOM CG CPH1 -0.05 ! O=C | ATOM CB CT2 -0.09 ! | HD2 ATOM HB3 HA 0.09 ATOM HB2 HA 0.09 GROUP ATOM NE2 NR2 -0.70 ATOM CD2 CPH1 0.22 ATOM HD2 HR3 0.10 ATOM CE1 CPH2 0.25 ATOM HE1 HR1 0.13 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB ND1 CG CD2 CG CE1 ND1 BOND NE2 CD2 N H N CA O C BOND C CA C +N NE2 CE1 CA HA CB HB3 BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 IMPR ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 IMPR ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 IMPR N -C CA H C CA +N O IMPR CA N C CB IMPR CG ND1 CD2 CB CG ND1 CE1 NE2 IMPR ND1 CE1 NE2 CD2 CE1 NE2 CD2 CG NE2 CD2 CG ND1 IMPR CD2 CG ND1 CE1 DONOR H N DONOR HD1 ND1 ACCEPTOR NE2 ACCEPTOR O C IC -C CA *N H 1.3475 123.2700 180.0000 115.2100 0.9988 IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166 IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509 IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273 IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545 IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519 IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830 IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041 IC CG CA *CB HB3 1.5041 114.0500 121.1700 109.0100 1.1118 IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121 IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783 IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597 IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549 IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817 IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932 IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005 IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834 RESI HSE 0.00 ! neutral His, proton on NE2 GROUP ATOM N NH1 -0.47 ! | HE1 ATOM H H 0.31 ! H-N / ATOM CA CT1 0.07 ! | HB2 ND1--CE1 ATOM HA HB 0.09 ! | | / | GROUP ! HA-CA--CB--CG | ATOM NE2 NR1 -0.36 ! | | \ | ATOM HE2 H 0.32 ! | HB3 CD2--NE2 ATOM CD2 CPH1 -0.05 ! O=C | \ ATOM HD2 HR3 0.09 ! | HD2 HE2 GROUP ATOM ND1 NR2 -0.70 ATOM CG CPH1 0.22 ATOM CE1 CPH2 0.25 ATOM HE1 HR1 0.13 ATOM CB CT2 -0.08 ATOM HB3 HA 0.09 ATOM HB2 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB ND1 CG CD2 CG CE1 ND1 BOND NE2 CD2 N H N CA O C BOND C CA C +N NE2 CE1 CA HA CB HB3 BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1 IMPR NE2 CD2 CE1 HE2 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 IMPR NE2 CE1 CD2 HE2 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 IMPR N -C CA H C CA +N O IMPR CA N C CB IMPR CG ND1 CD2 CB CG ND1 CE1 NE2 IMPR ND1 CE1 NE2 CD2 CE1 NE2 CD2 CG NE2 CD2 CG ND1 IMPR CD2 CG ND1 CE1 DONOR H N DONOR HE2 NE2 ACCEPTOR ND1 ACCEPTOR O C IC -C CA *N H 1.3472 124.1600 180.0000 114.3600 0.9991 IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166 IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446 IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290 IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505 IC N C *CA CB 1.4532 106.4300 123.5200 111.6700 1.5578 IC N C *CA HA 1.4532 106.4300 -116.4900 107.0800 1.0833 IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109 IC CG CA *CB HB3 1.5109 116.9400 119.8000 107.9100 1.1114 IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101 IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859 IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596 IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170 IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782 IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929 IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996 IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809 RESI HSP 1.00 ! Protonated His GROUP ATOM N NH1 -0.47 ! | HD1 HE1 ATOM H H 0.31 ! H-N | / ATOM CA CT1 0.07 ! | HB2 ND1--CE1 ATOM HA HB 0.09 ! | | / | GROUP ! HA-CA--CB--CG | ATOM ND1 NR3 -0.51 ! | | \ | ATOM HD1 H 0.44 ! | HB3 CD2--NE2 ATOM NE2 NR3 -0.51 ! O=C | \ ATOM HE2 H 0.44 ! | HD2 HE2 ATOM CE1 CPH2 0.32 ATOM HE1 HR2 0.18 GROUP ATOM CD2 CPH1 0.19 ATOM HD2 HR1 0.13 ATOM CG CPH1 0.19 ATOM CB CT2 -0.05 ATOM HB3 HA 0.09 ATOM HB2 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB ND1 CG CD2 CG CE1 ND1 BOND NE2 CD2 N H N CA O C BOND C CA C +N NE2 CE1 CA HA CB HB3 BOND CB HB2 ND1 HD1 NE2 HE2 CD2 HD2 CE1 HE1 IMPR HD1 CG CE1 ND1 IMPR HD1 CE1 CG ND1 IMPR HE2 CD2 CE1 NE2 HE2 CE1 CD2 NE2 IMPR N -C CA H C CA +N O IMPR CA N C CB IMPR CG ND1 CD2 CB CG ND1 CE1 NE2 IMPR ND1 CE1 NE2 CD2 CE1 NE2 CD2 CG NE2 CD2 CG ND1 IMPR CD2 CG ND1 CE1 DONOR H N DONOR HD1 ND1 DONOR HE2 NE2 ACCEPTOR O C IC -C CA *N H 1.3489 123.9300 180.0000 118.8000 1.0041 IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225 IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464 IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284 IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521 IC N C *CA CB 1.4548 112.0300 125.1300 109.3800 1.5533 IC N C *CA HA 1.4548 112.0300 -119.2000 106.7200 1.0832 IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168 IC CG CA *CB HB3 1.5168 114.1800 122.5000 108.9900 1.1116 IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132 IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718 IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549 IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262 IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727 IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799 IC CE1 CD2 *NE2 HE2 1.3256 108.8200 -172.9400 125.5200 1.0020 IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018 IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867 RESI ILE 0.00 GROUP ATOM N NH1 -0.47 ! | HG21 HG22 ATOM H H 0.31 ! H-N | / ATOM CA CT1 0.07 ! | CG2--HG23 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB HD11 ATOM CB CT1 -0.09 ! | \ / ATOM HB HA 0.09 ! | CG1--CD1--HD12 GROUP ! O=C / \ \ ATOM CG1 CT2 -0.18 ! | HG12 HG13 HD13 ATOM HG13 HA 0.09 ATOM HG12 HA 0.09 GROUP ATOM CG2 CT3 -0.27 ATOM HG21 HA 0.09 ATOM HG22 HA 0.09 ATOM HG23 HA 0.09 GROUP ATOM CD1 CT3 -0.27 ATOM HD11 HA 0.09 ATOM HD12 HA 0.09 ATOM HD13 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG1 CB CG2 CB CD1 CG1 BOND N H N CA O C C CA C +N BOND CA HA CB HB CG1 HG13 CG1 HG12 CG2 HG21 BOND CG2 HG22 CG2 HG23 CD1 HD11 CD1 HD12 CD1 HD13 IMPR N -C CA H C CA +N O IMPR CA N C CB IMPR CB CG1 CG2 CA DONOR H N ACCEPTOR O C IC -C CA *N H 1.3470 124.1600 180.0000 114.1900 0.9978 IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190 IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465 IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300 IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467 IC N C *CA CB 1.4542 106.3500 124.2200 112.9300 1.5681 IC N C *CA HA 1.4542 106.3500 -115.6300 106.8100 1.0826 IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498 IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195 IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452 IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100 IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102 IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105 IC CA CB CG1 CD1 1.5681 113.6300 180.0000 114.0900 1.5381 IC CD1 CB *CG1 HG13 1.5381 114.0900 122.3600 109.7800 1.1130 IC CD1 CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141 IC CB CG1 CD1 HD11 1.5498 114.0900 -176.7800 110.3100 1.1115 IC HD11 CG1 *CD1 HD12 1.1115 110.3100 119.7500 110.6500 1.1113 IC HD11 CG1 *CD1 HD13 1.1115 110.3100 -119.7000 111.0200 1.1103 RESI LEU 0.00 GROUP ATOM N NH1 -0.47 ! | HD11 HD12 ATOM H H 0.31 ! H-N | / ATOM CA CT1 0.07 ! | HB2 CD1--HD13 ATOM HA HB 0.09 ! | | / GROUP ! HA-CA--CB--CG-HG ATOM CB CT2 -0.18 ! | | \ ATOM HB3 HA 0.09 ! | HB3 CD2--HD23 ATOM HB2 HA 0.09 ! O=C | \ GROUP ! | HD21 HD22 ATOM CG CT1 -0.09 ATOM HG HA 0.09 GROUP ATOM CD1 CT3 -0.27 ATOM HD11 HA 0.09 ATOM HD12 HA 0.09 ATOM HD13 HA 0.09 GROUP ATOM CD2 CT3 -0.27 ATOM HD21 HA 0.09 ATOM HD22 HA 0.09 ATOM HD23 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD1 CG CD2 CG BOND N H N CA O C C CA C +N BOND CA HA CB HB3 CB HB2 CG HG CD1 HD11 BOND CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23 IMPR N -C CA H C CA +N O IMPR CA N C CB IMPR CG CD2 CD1 CB DONOR H N ACCEPTOR O C IC -C CA *N H 1.3474 124.3100 180.0000 114.2600 0.9979 IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184 IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463 IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299 IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467 IC N C *CA CB 1.4508 106.0500 121.5200 112.1200 1.5543 IC N C *CA HA 1.4508 106.0500 -116.5000 107.5700 1.0824 IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472 IC CG CA *CB HB3 1.5472 117.4600 120.9800 107.1700 1.1145 IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126 IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361 IC CD1 CB *CG CD2 1.5361 110.4800 -123.7500 112.5700 1.5360 IC CD1 CB *CG HG 1.5361 110.4800 116.6300 108.6800 1.1168 IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111 IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112 IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108 IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116 IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086 IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115 RESI LYS 1.00 GROUP ATOM N NH1 -0.47 ! | ATOM H H 0.31 ! N-N ATOM CA CT1 0.07 ! | HB2 HG2 HD2 HE2 HZ1 ATOM HA HB 0.09 ! | | | | | / GROUP ! HA-CA--CB--CG--CD--CE--NZ--HZ2 ATOM CB CT2 -0.18 ! | | | | | \ ATOM HB3 HA 0.09 ! | HB3 HG3 HD3 HE3 HZ3 ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CT2 -0.18 ATOM HG3 HA 0.09 ATOM HG2 HA 0.09 GROUP ATOM CD CT2 -0.18 ATOM HD3 HA 0.09 ATOM HD2 HA 0.09 GROUP ATOM CE CT2 0.21 ATOM HE3 HA 0.05 ATOM HE2 HA 0.05 ATOM NZ NH3 -0.30 ATOM HZ1 HC 0.33 ATOM HZ2 HC 0.33 ATOM HZ3 HC 0.33 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG CE CD NZ CE BOND N H N CA O C C CA BOND C +N CA HA CB HB3 CB HB2 CG HG3 BOND CG HG2 CD HD3 CD HD2 CE HE3 CE HE2 BOND NZ HZ1 NZ HZ2 NZ HZ3 IMPR N -C CA H C CA +N O IMPR CA N C CB DONOR H N DONOR HZ1 NZ DONOR HZ2 NZ DONOR HZ3 NZ ACCEPTOR O C IC -C CA *N H 1.3482 123.5700 180.0000 115.1100 0.9988 IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 IC CG CA *CB HB3 1.5435 115.7600 120.9000 107.1100 1.1146 IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 IC CD CB *CG HG3 1.5397 113.2800 120.7400 109.1000 1.1138 IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 IC CE CG *CD HD3 1.5350 112.3300 122.2500 108.4100 1.1141 IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 IC NZ CD *CE HE3 1.4604 110.4600 119.9100 110.5100 1.1128 IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123 IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402 IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401 RESI MET 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM H H 0.31 ! H-N ATOM CA CT1 0.07 ! | HB2 HG2 HE1 ATOM HA HB 0.09 ! | | | | GROUP ! HA-CA--CB--CG--SD--CE--HE3 ATOM CB CT2 -0.18 ! | | | | ATOM HB3 HA 0.09 ! | HB3 HG3 HE2 ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CT2 -0.14 ATOM HG3 HA 0.09 ATOM HG2 HA 0.09 ATOM SD S -0.09 ATOM CE CT3 -0.22 ATOM HE1 HA 0.09 ATOM HE2 HA 0.09 ATOM HE3 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB SD CG CE SD BOND N H N CA O C C CA C +N BOND CA HA CB HB3 CB HB2 CG HG3 CG HG2 BOND CE HE1 CE HE2 CE HE3 IMPR N -C CA H C CA +N O IMPR CA N C CB DONOR H N ACCEPTOR O C IC -C CA *N H 1.3478 124.2100 180.0000 114.3900 0.9978 IC -C N CA C 1.3478 124.2100 180.0000 106.3100 1.5195 IC N CA C +N 1.4510 106.3100 180.0000 117.7400 1.3471 IC +N CA *C O 1.3471 117.7400 180.0000 120.6400 1.2288 IC CA C +N +CA 1.5195 117.7400 180.0000 124.5200 1.4471 IC N C *CA CB 1.4510 106.3100 121.6200 111.8800 1.5546 IC N C *CA HA 1.4510 106.3100 -116.9800 107.5700 1.0832 IC N CA CB CG 1.4510 111.2500 180.0000 115.9200 1.5460 IC CG CA *CB HB3 1.5460 115.9200 120.5600 106.9000 1.1153 IC CG CA *CB HB2 1.5460 115.9200 -124.8000 109.3800 1.1129 IC CA CB CG SD 1.5546 115.9200 180.0000 110.2800 1.8219 IC SD CB *CG HG3 1.8219 110.2800 120.5000 110.3400 1.1106 IC SD CB *CG HG2 1.8219 110.2800 -121.1600 109.6400 1.1119 IC CB CG SD CE 1.5460 110.2800 180.0000 98.9400 1.8206 IC CG SD CE HE1 1.8219 98.9400 -179.4200 110.9100 1.1111 IC HE1 SD *CE HE2 1.1111 110.9100 119.9500 111.0300 1.1115 IC HE1 SD *CE HE3 1.1111 110.9100 -119.9500 111.0900 1.1112 RESI PHE 0.00 GROUP ATOM N NH1 -0.47 ! | HD1 HE1 ATOM H H 0.31 ! H-N | | ATOM CA CT1 0.07 ! | HB2 CD1--CE1 ATOM HA HB 0.09 ! | | / \ GROUP ! HA-CA--CB--CG CZ--HZ ATOM CB CT2 -0.18 ! | | \ / ATOM HB3 HA 0.09 ! | HB3 CD2--CE2 ATOM HB2 HA 0.09 ! O=C | | GROUP ! | HD2 HE2 ATOM CG CA 0.00 GROUP ATOM CD1 CA -0.115 ATOM HD1 HP 0.115 GROUP ATOM CD2 CA -0.115 ATOM HD2 HP 0.115 GROUP ATOM CE1 CA -0.115 ATOM HE1 HP 0.115 GROUP ATOM CE2 CA -0.115 ATOM HE2 HP 0.115 GROUP ATOM CZ CA -0.115 ATOM HZ HP 0.115 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 N H BOND N CA O C C CA C +N CA HA BOND CB HB3 CB HB2 CD1 HD1 CD2 HD2 CE1 HE1 BOND CE2 HE2 CZ HZ IMPR N -C CA H C CA +N O IMPR CA N C CB IMPR CB CG CD1 CE1 CG CD1 CE1 CZ CD1 CE1 CZ CE2 IMPR CE1 CZ CE2 CD2 CZ CE2 CD2 CG CE2 CD2 CG CB DONOR H N ACCEPTOR O C IC -C CA *N H 1.3476 123.8900 180.0000 114.4700 0.9987 IC -C N CA C 1.3476 123.8900 180.0000 106.3800 1.5229 IC N CA C +N 1.4504 106.3800 180.0000 117.6500 1.3483 IC +N CA *C O 1.3483 117.6500 180.0000 120.4900 1.2287 IC CA C +N +CA 1.5229 117.6500 180.0000 124.1000 1.4523 IC N C *CA CB 1.4504 106.3800 122.4900 112.4500 1.5594 IC N C *CA HA 1.4504 106.3800 -115.6300 107.0500 1.0832 IC N CA CB CG 1.4504 111.6300 180.0000 112.7600 1.5109 IC CG CA *CB HB3 1.5109 112.7600 118.2700 109.1000 1.1119 IC CG CA *CB HB2 1.5109 112.7600 -123.8300 111.1100 1.1113 IC CA CB CG CD1 1.5594 112.7600 90.0000 120.3200 1.4059 IC CD1 CB *CG CD2 1.4059 120.3200 -177.9600 120.7600 1.4062 IC CB CG CD1 CE1 1.5109 120.3200 -177.3700 120.6300 1.4006 IC CE1 CG *CD1 HD1 1.4006 120.6300 179.7000 119.6500 1.0814 IC CB CG CD2 CE2 1.5109 120.7600 177.2000 120.6200 1.4002 IC CE2 CG *CD2 HD2 1.4002 120.6200 -178.6900 119.9900 1.0811 IC CG CD1 CE1 CZ 1.4059 120.6300 -0.1200 119.9300 1.4004 IC CZ CD1 *CE1 HE1 1.4004 119.9300 -179.6900 120.0100 1.0808 IC CZ CD2 *CE2 HE2 1.4000 119.9600 -179.9300 119.8700 1.0811 IC CE1 CE2 *CZ HZ 1.4004 119.9800 179.5100 119.9700 1.0807 RESI PRO 0.00 GROUP ! HD2 HD3 ATOM N N -0.29 ! | \ / ATOM CA CP1 0.02 ! N---CD HG2 ATOM HA HB 0.09 ! | \ / ATOM CD CP3 0.00 ! | CG ATOM HD3 HA 0.09 ! | / \ ATOM HD2 HA 0.09 ! HA-CA--CB HG3 GROUP ! | / \ ATOM CB CP2 -0.18 ! | HB2 HB3 ATOM HB3 HA 0.09 ! O=C ATOM HB2 HA 0.09 ! | GROUP ATOM CG CP2 -0.18 ATOM HG3 HA 0.09 ATOM HG2 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND O C C CA C +N BOND N CA CA CB CB CG CG CD N CD BOND HA CA HG3 CG HG2 CG HD3 CD HD2 CD HB3 CB HB2 CB IMPR N -C CA CD IMPR C CA +N O IMPR CA N C CB ACCEPTOR O C IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624 IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399 IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569 IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316 IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517 IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399 IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837 IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322 IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317 IC N CA CB HB3 1.4585 102.5600 -84.9400 109.0200 1.1131 IC N CA CB HB2 1.4585 102.5600 153.9300 112.7400 1.1088 IC CA CB CG HG3 1.5399 104.3900 -156.7200 112.9500 1.1077 IC CA CB CG HG2 1.5399 104.3900 81.2600 109.2200 1.1143 IC CB CG CD HD3 1.5322 103.2100 -93.5500 110.0300 1.1137 IC CB CG CD HD2 1.5322 103.2100 144.5200 110.0000 1.1144 PATCHING FIRS PROP RESI SER 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM H H 0.31 ! H-N ATOM CA CT1 0.07 ! | HB2 ATOM HA HB 0.09 ! | | GROUP ! HA-CA--CB--OG ATOM CB CT2 0.05 ! | | \ ATOM HB3 HA 0.09 ! | HB3 HG ATOM HB2 HA 0.09 ! O=C ATOM OG OH1 -0.66 ! | ATOM HG H 0.43 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA OG CB N H N CA BOND O C C CA C +N CA HA CB HB3 BOND CB HB2 OG HG IMPR N -C CA H C CA +N O IMPR CA N C CB DONOR H N DONOR HG OG ACCEPTOR OG ACCEPTOR O C IC -C CA *N H 1.3474 124.3700 180.0000 114.1800 0.9999 IC -C N CA C 1.3474 124.3700 180.0000 105.8100 1.5166 IC N CA C +N 1.4579 105.8100 180.0000 117.7200 1.3448 IC +N CA *C O 1.3448 117.7200 180.0000 120.2500 1.2290 IC CA C +N +CA 1.5166 117.7200 180.0000 124.6300 1.4529 IC N C *CA CB 1.4579 105.8100 124.7500 111.4000 1.5585 IC N C *CA HA 1.4579 105.8100 -115.5600 107.3000 1.0821 IC N CA CB OG 1.4579 114.2800 180.0000 112.4500 1.4341 IC OG CA *CB HB3 1.4341 112.4500 119.3200 108.1000 1.1140 IC OG CA *CB HB2 1.4341 112.4500 -123.8600 110.3800 1.1136 IC CA CB OG HG 1.5585 112.4500 165.9600 107.0800 0.9655 RESI THR 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM H H 0.31 ! H-N ATOM CA CT1 0.07 ! | OG1--HG1 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB ATOM CB CT1 0.14 ! | \ ATOM HB HA 0.09 ! | CG2--HG21 ATOM OG1 OH1 -0.66 ! O=C / \ ATOM HG1 H 0.43 ! | HG23 HG22 GROUP ATOM CG2 CT3 -0.27 ATOM HG21 HA 0.09 ATOM HG22 HA 0.09 ATOM HG23 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA OG1 CB CG2 CB N H BOND N CA O C C CA C +N CA HA BOND CB HB OG1 HG1 CG2 HG21 CG2 HG22 CG2 HG23 IMPR N -C CA H C CA +N O IMPR CA N C CB IMPR CB OG1 CG2 CA DONOR H N DONOR HG1 OG1 ACCEPTOR OG1 ACCEPTOR O C IC -C CA *N H 1.3471 124.1200 180.0000 114.2600 0.9995 IC -C N CA C 1.3471 124.1200 180.0000 106.0900 1.5162 IC N CA C +N 1.4607 106.0900 180.0000 117.6900 1.3449 IC +N CA *C O 1.3449 117.6900 180.0000 120.3000 1.2294 IC CA C +N +CA 1.5162 117.6900 180.0000 124.6600 1.4525 IC N C *CA CB 1.4607 106.0900 126.4600 112.7400 1.5693 IC N C *CA HA 1.4607 106.0900 -114.9200 106.5300 1.0817 IC N CA CB OG1 1.4607 114.8100 180.0000 112.1600 1.4252 IC OG1 CA *CB HB 1.4252 112.1600 116.3900 106.1100 1.1174 IC OG1 CA *CB CG2 1.4252 112.1600 -124.1300 115.9100 1.5324 IC CA CB OG1 HG1 1.5693 112.1600 -179.2800 105.4500 0.9633 IC CA CB CG2 HG21 1.5693 115.9100 -173.6500 110.8500 1.1104 IC HG21 CB *CG2 HG22 1.1104 110.8500 119.5100 110.4100 1.1109 IC HG21 CB *CG2 HG23 1.1104 110.8500 -120.3900 111.1100 1.1113 RESI TRP 0.00 GROUP ATOM N NH1 -0.47 ! | HE3 ATOM H H 0.31 ! H-N | ATOM CA CT1 0.07 ! | HB2 CE3 ATOM HA HB 0.09 ! | | / \ GROUP ! HA-CA--CB---CG-----CD2 CZ3-HZ3 ATOM CB CT2 -0.18 ! | | | | | ATOM HB3 HA 0.09 ! | HB3 CD1 CE2 CH2-HH2 ATOM HB2 HA 0.09 ! O=C / \ / \ / GROUP ! | HD1 NE1 CZ2 ATOM CG CY -0.03 ! | | ATOM CD2 CPT -0.02 ! HE1 HZ2 ATOM CD1 CA 0.035 ATOM HD1 HP 0.115 ATOM NE1 NY -0.61 ATOM HE1 H 0.38 ATOM CE2 CPT 0.13 GROUP ATOM CE3 CA -0.115 ATOM HE3 HP 0.115 GROUP ATOM CZ2 CA -0.115 ATOM HZ2 HP 0.115 GROUP ATOM CZ3 CA -0.115 ATOM HZ3 HP 0.115 GROUP ATOM CH2 CA -0.115 ATOM HH2 HP 0.115 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD1 CG CD2 CG NE1 CD1 BOND CE2 CD2 CZ2 CE2 CZ3 CE3 CH2 CZ2 BOND N H N CA O C C CA C +N BOND CZ3 CH2 CD2 CE3 NE1 CE2 CA HA CB HB3 BOND CB HB2 CD1 HD1 NE1 HE1 CE3 HE3 CZ2 HZ2 BOND CZ3 HZ3 CH2 HH2 IMPR N -C CA H C CA +N O IMPR CA N C CB NE1 CD1 CE2 HE1 IMPR CG CD1 CD2 CB CE3 CD2 CE2 CZ2 CZ2 CH2 CZ3 CE3 IMPR CG CD1 NE1 CE2 NE1 CE2 CD2 CG NE1 CE2 CZ2 CH2 IMPR CG CD2 CE3 CZ3 DONOR H N DONOR HE1 NE1 ACCEPTOR O C IC -C CA *N H 1.3482 123.5100 180.0000 115.0200 0.9972 IC -C N CA C 1.3482 123.5100 180.0000 107.6900 1.5202 IC N CA C +N 1.4507 107.6900 180.0000 117.5700 1.3505 IC +N CA *C O 1.3505 117.5700 180.0000 121.0800 1.2304 IC CA C +N +CA 1.5202 117.5700 180.0000 124.8800 1.4526 IC N C *CA CB 1.4507 107.6900 122.6800 111.2300 1.5560 IC N C *CA HA 1.4507 107.6900 -117.0200 106.9200 1.0835 IC N CA CB CG 1.4507 111.6800 180.0000 115.1400 1.5233 IC CG CA *CB HB3 1.5233 115.1400 119.1700 107.8400 1.1127 IC CG CA *CB HB2 1.5233 115.1400 -124.7300 109.8700 1.1118 IC CA CB CG CD2 1.5560 115.1400 90.0000 123.9500 1.4407 IC CD2 CB *CG CD1 1.4407 123.9500 -172.8100 129.1800 1.3679 IC CD1 CG CD2 CE2 1.3679 106.5700 -0.0800 106.6500 1.4126 IC CG CD2 CE2 NE1 1.4407 106.6500 0.1400 107.8700 1.3746 IC CE2 CG *CD2 CE3 1.4126 106.6500 179.2100 132.5400 1.4011 IC CE2 CD2 CE3 CZ3 1.4126 120.8000 -0.2000 118.1600 1.4017 IC CD2 CE3 CZ3 CH2 1.4011 118.1600 0.1000 120.9700 1.4019 IC CE3 CZ3 CH2 CZ2 1.4017 120.9700 0.0100 120.8700 1.4030 IC CZ3 CD2 *CE3 HE3 1.4017 118.1600 -179.6200 121.8400 1.0815 IC CH2 CE3 *CZ3 HZ3 1.4019 120.9700 -179.8200 119.4500 1.0811 IC CZ2 CZ3 *CH2 HH2 1.4030 120.8700 -179.9200 119.5700 1.0811 IC CE2 CH2 *CZ2 HZ2 1.3939 118.4200 179.8700 120.0800 1.0790 IC CD1 CE2 *NE1 HE1 1.3752 108.8100 177.7800 124.6800 0.9767 IC CG NE1 *CD1 HD1 1.3679 110.1000 178.1000 125.4300 1.0820 RESI TYR 0.00 GROUP ATOM N NH1 -0.47 ! | HD1 HE1 ATOM H H 0.31 ! H-N | | ATOM CA CT1 0.07 ! | HB2 CD1--CE1 ATOM HA HB 0.09 ! | | / \ GROUP ! HA-CA--CB--CG CZ--OH ATOM CB CT2 -0.18 ! | | \ / \ ATOM HB3 HA 0.09 ! | HB3 CD2--CE2 HH ATOM HB2 HA 0.09 ! O=C | | GROUP ! | HD2 HE2 ATOM CG CA 0.00 GROUP ATOM CD1 CA -0.115 ATOM HD1 HP 0.115 GROUP ATOM CD2 CA -0.115 ATOM HD2 HP 0.115 GROUP ATOM CE1 CA -0.115 ATOM HE1 HP 0.115 GROUP ATOM CE2 CA -0.115 ATOM HE2 HP 0.115 GROUP ATOM CZ CA 0.11 ATOM OH OH1 -0.54 ATOM HH H 0.43 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD1 CG CD2 CG CE1 CD1 BOND CE2 CD2 CZ CE1 CZ CE2 OH CZ BOND N H N CA O C C CA C +N BOND CA HA CB HB3 CB HB2 CD1 HD1 CD2 HD2 BOND CE1 HE1 CE2 HE2 OH HH IMPR N -C CA H C CA +N O IMPR CA N C CB IMPR CB CG CD1 CE1 CG CD1 CE1 CZ CD1 CE1 CZ CE2 IMPR CE1 CZ CE2 CD2 CZ CE2 CD2 CG CE2 CD2 CG CB IMPR CD1 CE1 CZ OH CD2 CE2 CZ OH DONOR H N DONOR HH OH ACCEPTOR OH ACCEPTOR O C IC -C CA *N H 1.3476 123.8100 180.0000 114.5400 0.9986 IC -C N CA C 1.3476 123.8100 180.0000 106.5200 1.5232 IC N CA C +N 1.4501 106.5200 180.0000 117.3300 1.3484 IC +N CA *C O 1.3484 117.3300 180.0000 120.6700 1.2287 IC CA C +N +CA 1.5232 117.3300 180.0000 124.3100 1.4513 IC N C *CA CB 1.4501 106.5200 122.2700 112.3400 1.5606 IC N C *CA HA 1.4501 106.5200 -116.0400 107.1500 1.0833 IC N CA CB CG 1.4501 111.4300 180.0000 112.9400 1.5113 IC CG CA *CB HB3 1.5113 112.9400 118.8900 109.1200 1.1119 IC CG CA *CB HB2 1.5113 112.9400 -123.3600 110.7000 1.1115 IC CA CB CG CD1 1.5606 112.9400 90.0000 120.4900 1.4064 IC CD1 CB *CG CD2 1.4064 120.4900 -176.4600 120.4600 1.4068 IC CB CG CD1 CE1 1.5113 120.4900 -175.4900 120.4000 1.4026 IC CE1 CG *CD1 HD1 1.4026 120.4000 178.9400 119.8000 1.0814 IC CB CG CD2 CE2 1.5113 120.4600 175.3200 120.5600 1.4022 IC CE2 CG *CD2 HD2 1.4022 120.5600 -177.5700 119.9800 1.0813 IC CG CD1 CE1 CZ 1.4064 120.4000 -0.1900 120.0900 1.3978 IC CZ CD1 *CE1 HE1 1.3978 120.0900 179.6400 120.5800 1.0799 IC CZ CD2 *CE2 HE2 1.3979 119.9200 -178.6900 119.7600 1.0798 IC CE1 CE2 *CZ OH 1.3978 120.0500 -178.9800 120.2500 1.4063 IC CE1 CZ OH HH 1.3978 119.6800 175.4500 107.4700 0.9594 RESI VAL 0.00 GROUP ATOM N NH1 -0.47 ! | HG11 HG12 ATOM H H 0.31 ! H-N | / ATOM CA CT1 0.07 ! | CG1--HG13 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB ATOM CB CT1 -0.09 ! | \ ATOM HB HA 0.09 ! | CG2--HG21 GROUP ! O=C / \ ATOM CG1 CT3 -0.27 ! | HG23 HG22 ATOM HG11 HA 0.09 ATOM HG12 HA 0.09 ATOM HG13 HA 0.09 GROUP ATOM CG2 CT3 -0.27 ATOM HG21 HA 0.09 ATOM HG22 HA 0.09 ATOM HG23 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG1 CB CG2 CB N H BOND N CA O C C CA C +N CA HA BOND CB HB CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21 BOND CG2 HG22 CG2 HG23 IMPR N -C CA H C CA +N O IMPR CA N C CB IMPR CB CG2 CG1 CA DONOR H N ACCEPTOR O C IC -C CA *N H 1.3482 124.5700 180.0000 114.4100 0.9966 IC -C N CA C 1.3482 124.5700 180.0000 105.5400 1.5180 IC N CA C +N 1.4570 105.5400 180.0000 117.8300 1.3471 IC +N CA *C O 1.3471 117.8300 180.0000 120.7000 1.2297 IC CA C +N +CA 1.5180 117.8300 180.0000 124.0800 1.4471 IC N C *CA CB 1.4570 105.5400 122.9500 111.2300 1.5660 IC N C *CA HA 1.4570 105.5400 -117.2400 107.4600 1.0828 IC N CA CB CG1 1.4570 113.0500 180.0000 113.9700 1.5441 IC CG1 CA *CB CG2 1.5441 113.9700 123.9900 112.1700 1.5414 IC CG1 CA *CB HB 1.5441 113.9700 -119.1700 107.5700 1.1178 IC CA CB CG1 HG11 1.5660 113.9700 177.8300 110.3000 1.1114 IC HG11 CB *CG1 HG12 1.1114 110.3000 119.2500 111.6700 1.1097 IC HG11 CB *CG1 HG13 1.1114 110.3000 -119.4900 110.7000 1.1110 IC CA CB CG2 HG21 1.5660 112.1700 -177.7800 110.7100 1.1108 IC HG21 CB *CG2 HG22 1.1108 110.7100 120.0800 110.5600 1.1115 IC HG21 CB *CG2 HG23 1.1108 110.7100 -119.5500 111.2300 1.1098 DEFA FIRS NONE LAST NONE RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral GROUP ATOM O OT -0.834 ATOM H1 HT 0.417 ATOM H2 HT 0.417 BOND O H1 O H2 H1 H2 ! the last bond is needed for shake ANGLE H1 O H2 ! required ACCEPTOR O PATCHING FIRS NONE LAST NONE RESI CAL 2.00 ! Calcium ion GROUP ATOM CA CAL 2.00 PATCHING FIRST NONE LAST NONE RESI ZN2 2.00 ! Zinc ion GROUP ATOM ZN ZN 2.00 PATCHING FIRST NONE LAST NONE RESI HEME -2.00 ! 6-liganded planar heme GROUP ATOM FE FE 0.24 ! O2A O1A O2D O1D ATOM NA NPH -0.18 ! \\ // \\ // ATOM NB NP1 -0.18 ! CGA CGD ATOM NC NPH -0.18 ! | | ATOM ND NP1 -0.18 ! HBA1--CBA--HBA2 HHA HBD1--CBD--HBD2 ATOM C1A CPA 0.12 ! | | | ATOM C2A CPB -0.06 ! HAA1--CAA-HAA2 _CHA_ HAD1--CAD--HAD2 ATOM C3A CPB -0.06 ! | / \ | ATOM C4A CPA 0.12 ! C2A---C1A C4D---C3D ATOM C1B CPA 0.12 ! | | | | ATOM C2B CPB -0.06 !HMA1\ | | | | /HMD1 ATOM C3B CPB -0.06 !HMA2-CMA--C3A NA ND C2D--CMD-HMD2 ATOM C4B CPA 0.12 !HMA3/ \ / \ / \ / \HMD3 ATOM C1C CPA 0.12 ! C4A \ / C1D ATOM C2C CPB -0.06 ! / \ / \ ATOM C3C CPB -0.06 ! HHB--CHB FE CHD--HHD ATOM C4C CPA 0.12 ! \ / \ / ATOM C1D CPA 0.12 ! C1B / \ C4C HAC ATOM C2D CPB -0.06 !HMB1\ / \ / \ / \ / ATOM C3D CPB -0.06 !HMB2-CMB--C2B NB NC C3C--CAC ATOM C4D CPA 0.12 !HMB3/ | | | | \\ /HBC1 GROUP ! | | | | CBC ATOM CHA CPM -0.10 ! C3B---C4B C1C---C2C \HBC2 ATOM HHA HA 0.10 ! | \_CHC_/ | GROUP ! CAB | CMC--HMC3 ATOM CHB CPM -0.10 ! // \ HHC / | ATOM HHB HA 0.10 ! CBB HAB HMC1 HMC2 GROUP ! / \ ATOM CHC CPM -0.10 ! HBB1 HBB2 ATOM HHC HA 0.10 ! GROUP ATOM CHD CPM -0.10 ATOM HHD HA 0.10 GROUP ATOM CMA CT3 -0.27 ATOM HMA1 HA 0.09 ATOM HMA2 HA 0.09 ATOM HMA3 HA 0.09 GROUP ATOM CAA CT2 -0.18 ATOM HAA1 HA 0.09 ATOM HAA2 HA 0.09 GROUP ATOM CBA CT2 -0.28 ATOM HBA1 HA 0.09 ATOM HBA2 HA 0.09 ATOM CGA CC 0.62 ATOM O1A OC -0.76 ATOM O2A OC -0.76 GROUP ATOM CMB CT3 -0.27 ATOM HMB1 HA 0.09 ATOM HMB2 HA 0.09 ATOM HMB3 HA 0.09 GROUP ATOM CAB C -0.20 ATOM HAB HA 0.20 GROUP ATOM CBB C -0.20 ATOM HBB1 HA 0.10 ATOM HBB2 HA 0.10 GROUP ATOM CMC CT3 -0.27 ATOM HMC1 HA 0.09 ATOM HMC2 HA 0.09 ATOM HMC3 HA 0.09 GROUP ATOM CAC C -0.20 ATOM HAC HA 0.20 GROUP ATOM CBC C -0.20 ATOM HBC1 HA 0.10 ATOM HBC2 HA 0.10 GROUP ATOM CMD CT3 -0.27 ATOM HMD1 HA 0.09 ATOM HMD2 HA 0.09 ATOM HMD3 HA 0.09 GROUP ATOM CAD CT2 -0.18 ATOM HAD1 HA 0.09 ATOM HAD2 HA 0.09 GROUP ATOM CBD CT2 -0.28 ATOM HBD1 HA 0.09 ATOM HBD2 HA 0.09 ATOM CGD CC 0.62 ATOM O1D OC -0.76 ATOM O2D OC -0.76 BOND FE NA FE NB FE NC FE ND NA C1A BOND C1A C2A C2A C3A C3A C4A NA C4A C2A CAA BOND CAA CBA CBA CGA CGA O1A CGA O2A C3A CMA BOND CHB C4A CHB C1B NB C1B C1B C2B C2B C3B BOND C3B C4B NB C4B C2B CMB C3B CAB CAB CBB BOND CHC C4B CHC C1C NC C1C C1C C2C C2C C3C BOND C3C C4C NC C4C C2C CMC C3C CAC CAC CBC BOND CHD C4C CHD C1D ND C1D C1D C2D C2D C3D BOND C3D C4D ND C4D C2D CMD C3D CAD CAD CBD BOND CBD CGD CGD O1D CGD O2D CHA C4D CHA C1A BOND CHA HHA CHB HHB CHC HHC CHD HHD BOND CAA HAA1 CAA HAA2 CBA HBA1 CBA HBA2 BOND CMA HMA1 CMA HMA2 CMA HMA3 BOND CMB HMB1 CMB HMB2 CMB HMB3 BOND CAB HAB CBB HBB1 CBB HBB2 BOND CMC HMC1 CMC HMC2 CMC HMC3 BOND CAC HAC CBC HBC1 CBC HBC2 BOND CMD HMD1 CMD HMD2 CMD HMD3 BOND CAD HAD1 CAD HAD2 CBD HBD1 CBD HBD2 IMPR C2A C1A C3A CAA C3A C2A C4A CMA C2B C1B C3B CMB IMPR C3B C2B C4B CAB C2C C1C C3C CMC C3C C2C C4C CAC IMPR C2D C1D C3D CMD C3D C2D C4D CAD O1A CBA O2A CGA IMPR O1D CBD O2D CGD IMPR C4A NA C1A C2A C1A NA C4A C3A IMPR C4B NB C1B C2B C1B NB C4B C3B IMPR C4C NC C1C C2C C1C NC C4C C3C IMPR C4D ND C1D C2D C1D ND C4D C3D IMPR NA C1A C2A C3A NA C4A C3A C2A IMPR NB C1B C2B C3B NB C4B C3B C2B IMPR NC C1C C2C C3C NC C4C C3C C2C IMPR ND C1D C2D C3D ND C4D C3D C2D IMPR NA C1A CHA C4D NA C4A CHB C1B IMPR NB C1B CHB C4A NB C4B CHC C1C IMPR NC C1C CHC C4B NC C4C CHD C1D IMPR ND C1D CHD C4C ND C4D CHA C1A IMPR CHA C1A C4D HHA IMPR CHB C1B C4A HHB IMPR CHC C1C C4B HHC IMPR CHD C1D C4C HHD IMPR C1A C2A CHA NA C4A C3A CHB NA IMPR C1B C2B CHB NB C4B C3B CHC NB IMPR C1C C2C CHC NC C4C C3C CHD NC IMPR C1D C2D CHD ND C4D C3D CHA ND IMPR NA C1A C4A FE IMPR NB C1B C4B FE IMPR NC C1C C4C FE IMPR ND C1D C4D FE IMPR CAB CBB C3B HAB HAB CAB CBB HBB2 CAB CBB HBB2 HBB1 IMPR CAC CBC C3C HAC HAC CAC CBC HBC2 CAC CBC HBC2 HBC1 ACCEPTOR NA ACCEPTOR O1A ! CGA ACCEPTOR O2A ! CGA ACCEPTOR NB ACCEPTOR NC ACCEPTOR ND ACCEPTOR O1D ! CGD ACCEPTOR O2D ! CGD IC FE NA C4A C3A 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3A C4A NA C1A 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NA C1A C2A 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4A NA FE NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC NA FE NB C1B 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NB C1B C2B 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2B C1B NB C4B 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NB C4B C3B 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4B NB FE NC 0.0000 0.0000 0.0000 0.0000 0.0000 IC NB FE NC C1C 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NC C1C C2C 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2C C1C NC C4C 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NC C4C C3C 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4C NC FE ND 0.0000 0.0000 0.0000 0.0000 0.0000 IC NC FE ND C1D 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE ND C1D C2D 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2D C1D ND C4D 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE ND C4D C3D 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4A NA FE CHB 0.0000 0.0000 0.0000 0.0000 0.0000 IC NA FE CHB HHB 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4B NB FE CHC 0.0000 0.0000 0.0000 0.0000 0.0000 IC NB FE CHC HHC 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4C NC FE CHD 0.0000 0.0000 0.0000 0.0000 0.0000 IC NC FE CHD HHD 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4D ND FE CHA 0.0000 0.0000 0.0000 0.0000 0.0000 IC ND FE CHA HHA 0.0000 0.0000 0.0000 0.0000 0.0000 IC C3B C1B *C2B CMB 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4B C2B *C3B CAB 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2B C3B CAB CBB 0.0000 0.0000 -45.0000 0.0000 0.0000 ! PREVENTS VINYL COLLISION IC CHC C1C C2C CMC 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4C C2C *C3C CAC 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2C C3C CAC CBC 0.0000 0.0000 -45.0000 0.0000 0.0000 ! PREVENTS VINYL COLLISION IC C4D C2D *C3D CAD 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3D C1D *C2D CMD 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2D C3D CAD CBD 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C3D CAD CBD CGD 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAD CBD CGD O1D 0.0000 0.0000 0.0000 0.0000 0.0000 IC CAD CBD CGD O2D 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4A C2A *C3A CMA 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3A C1A *C2A CAA 0.0000 0.0000 180.0000 0.0000 0.0000 IC C1A C2A CAA CBA 0.0000 0.0000 120.0000 0.0000 0.0000 IC C2A CAA CBA CGA 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAA CBA CGA O1A 0.0000 0.0000 0.0000 0.0000 0.0000 IC CAA CBA CGA O2A 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3C C1C *C2C CMC 0.0000 0.0000 180.0000 0.0000 0.0000 IC CBA O1A *CGA O2A 0.0000 0.0000 180.0000 0.0000 0.0000 IC CBD O1D *CGD O2D 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2A C3A CMA HMA1 0.0000 0.0000 0.0000 0.0000 0.0000 IC C2A C3A CMA HMA2 0.0000 0.0000 120.0000 0.0000 0.0000 IC C2A C3A CMA HMA3 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C3A C2A CAA HAA1 0.0000 0.0000 -60.0000 0.0000 0.0000 IC C3A C2A CAA HAA2 0.0000 0.0000 60.0000 0.0000 0.0000 IC C2A CAA CBA HBA1 0.0000 0.0000 -60.0000 0.0000 0.0000 IC C2A CAA CBA HBA2 0.0000 0.0000 60.0000 0.0000 0.0000 IC C3B C2B CMB HMB1 0.0000 0.0000 0.0000 0.0000 0.0000 IC C3B C2B CMB HMB2 0.0000 0.0000 120.0000 0.0000 0.0000 IC C3B C2B CMB HMB3 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C2B C3B CAB HAB 0.0000 0.0000 120.0000 0.0000 0.0000 IC C3B CAB CBB HBB1 0.0000 0.0000 60.0000 0.0000 0.0000 IC C3B CAB CBB HBB2 0.0000 0.0000 -60.0000 0.0000 0.0000 IC C1C C2C CMC HMC1 0.0000 0.0000 0.0000 0.0000 0.0000 IC C1C C2C CMC HMC2 0.0000 0.0000 120.0000 0.0000 0.0000 IC C1C C2C CMC HMC3 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C2C C3C CAC HAC 0.0000 0.0000 120.0000 0.0000 0.0000 IC C3C CAC CBC HBC1 0.0000 0.0000 60.0000 0.0000 0.0000 IC C3C CAC CBC HBC2 0.0000 0.0000 -60.0000 0.0000 0.0000 IC C1D C2D CMD HMD1 0.0000 0.0000 0.0000 0.0000 0.0000 IC C1D C2D CMD HMD2 0.0000 0.0000 120.0000 0.0000 0.0000 IC C1D C2D CMD HMD3 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C2D C3D CAD HAD1 0.0000 0.0000 60.0000 0.0000 0.0000 IC C2D C3D CAD HAD2 0.0000 0.0000 -60.0000 0.0000 0.0000 IC C3D CAD CBD HBD1 0.0000 0.0000 60.0000 0.0000 0.0000 IC C3D CAD CBD HBD2 0.0000 0.0000 -60.0000 0.0000 0.0000 PATCHING FIRS NONE LAST NONE PRES NTER 1.00 ! standard N-terminus GROUP ! use in generate statement ATOM N NH3 -0.30 ! ATOM H HC 0.33 ! H ATOM H2 HC 0.33 ! / ATOM H3 HC 0.33 ! --CA--N--H2 ATOM CA CT1 0.21 ! | \ ATOM HA HB 0.10 ! HA H3 BOND H2 N H3 N DONOR H2 N DONOR H3 N IC H N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC H2 CA *N H 0.0000 0.0000 120.0000 0.0000 0.0000 IC H3 CA *N H2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES GLYP 1.00 ! Glycine N-terminus GROUP ! use in generate statement ATOM N NH3 -0.30 ! ATOM H HC 0.33 ! HA2 H ATOM H2 HC 0.33 ! | / ATOM H3 HC 0.33 ! --CA--N--H2 ATOM CA CT2 0.13 ! | \ ATOM HA2 HB 0.09 ! HA3 H3 ATOM HA3 HB 0.09 ! BOND H2 N H3 N DONOR H2 N DONOR H3 N IC H2 CA *N H 0.0000 0.0000 120.0000 0.0000 0.0000 IC H3 CA *N H2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES PROP 1.00 ! Proline N-Terminal GROUP ! use in generate statement ATOM N NP -0.07 ! HA ATOM H1 HC 0.24 ! | ATOM H2 HC 0.24 ! -CA H1 ATOM CD CP3 0.16 ! / \ / ATOM CA CP1 0.16 ! N ATOM HA HB 0.09 ! / \ ATOM HD2 HA 0.09 ! -CD H2 ATOM HD3 HA 0.09 ! | \ BOND H1 N H2 N ! HD2 HD3 DONOR H1 N DONOR H2 N IC H1 CA *N CD 0.0000 0.0000 120.0000 0.0000 0.0000 IC H2 CA *N H1 0.0000 0.0000 120.0000 0.0000 0.0000 PRES ACE 0.00 ! acetylated N-terminus GROUP ! use in generate statement ATOM CAY CT3 -0.27 ! ATOM HY1 HA 0.09 ! HY1 HY2 HY3 ATOM HY2 HA 0.09 ! \ | / ATOM HY3 HA 0.09 ! CAY GROUP ! | ATOM CY C 0.51 ! CY=OY ATOM OY O -0.51 ! | ! BOND CY CAY OY CY CY N CAY HY1 CAY HY2 CAY HY3 IMPR CY CAY N OY IMPR N CY CA HN ACCEPTOR OY CY IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 PRES ACP 0.00 ! acetylated N-terminus for proline GROUP ! use in generate statement ATOM CAY CT3 -0.27 ! ATOM HY1 HA 0.09 ! HY1 HY2 HY3 ATOM HY2 HA 0.09 ! \ | / ATOM HY3 HA 0.09 ! CAY GROUP ! | ATOM CY C 0.51 ! CY=OY ATOM OY O -0.51 ! | ! BOND CY CAY OY CY CY N CAY HY1 CAY HY2 CAY HY3 IMPR CY CAY N OY IMPR N CY CA CD ACCEPTOR OY CY IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 IC CY CA *N CD 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 PRES CTER -1.00 ! standard C-terminus GROUP ! use in generate statement ATOM C CC 0.34 ! O ATOM O OC -0.67 ! // ATOM OXT OC -0.67 ! -C ! DELETE ATOM O ! \\ BOND C OXT ! OXT IMPR O CA OXT C ACCEPTOR O C ACCEPTOR OXT C IC N CA C OXT 0.0000 0.0000 180.0000 0.0000 0.0000 IC OXT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 PRES CT1 0.00 ! methylated C-terminus from methyl acetate GROUP ! use in generate statement ATOM N NH1 -0.47 ! ATOM HN H 0.31 ! OT1 ATOM CA CT1 0.17 ! | // ATOM HA HB 0.09 ! -N--CA--C HT1 ATOM C CD 0.63 ! | | \ / ATOM OT1 OB -0.52 ! HN HA OT2--CT--HT2 ATOM OT2 OS -0.34 ! \ ATOM CT CT3 -0.14 ! HT3 ATOM HT1 HA 0.09 ! ATOM HT2 HA 0.09 ! ATOM HT3 HA 0.09 ! DELETE ATOM O BOND C OT1 C OT2 OT2 CT BOND CT HT1 CT HT2 CT HT3 IMPR OT1 CA OT2 C ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA C OT2 CT 0.0000 0.0000 180.0000 0.0000 0.0000 IC C OT2 CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000 IC C OT2 CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000 IC C OT2 CT HT3 0.0000 0.0000 240.0000 0.0000 0.0000 PRES CT2 0.00 ! amidated C-terminus GROUP ! use in generate statement ATOM C CC 0.55 ! ATOM O O -0.55 ! | GROUP ! O=C ATOM NT NH2 -0.62 ! | ATOM HT1 H 0.32 ! NT ATOM HT2 H 0.30 ! / \ BOND C NT ! HT1 HT2 BOND NT HT1 NT HT2 ! DIHE CA C NT HT2 ! (HT1 is cis to O) IMPR C NT CA O C CA NT O IMPR NT C HT1 HT2 NT C HT2 HT1 DONOR HT1 NT DONOR HT2 NT IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA C NT HT1 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT1 C *NT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 PRES CT3 0.00 ! N-Methylamide C-terminus GROUP ! use in generate statement ATOM C C 0.51 ! ATOM O O -0.51 ! | GROUP ! C=O ATOM NT NH1 -0.47 ! | ATOM HNT H 0.31 ! NT-HNT ATOM CAT CT3 -0.11 ! | ATOM HT1 HA 0.09 ! HT1-CAT-HT3 ATOM HT2 HA 0.09 ! | ATOM HT3 HA 0.09 ! HT2 ! BOND C NT NT HNT NT CAT CAT HT1 CAT HT2 CAT HT3 DIHE CA C NT CAT IMPR NT C CAT HNT C CA NT O DONOR HNT NT IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC C CAT *NT HNT 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA C NT CAT 0.0000 0.0000 180.0000 0.0000 0.0000 IC C NT CAT HT1 0.0000 0.0000 60.0000 0.0000 0.0000 IC C NT CAT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC C NT CAT HT3 0.0000 0.0000 -60.0000 0.0000 0.0000 PRES ASPP 0.00 ! patch for protonated aspartic acid, proton on od2 GROUP ! via acetic acid, use in a patch statement ATOM CB CT2 -0.21 ! ATOM HB2 HA 0.09 ! HB2 OD1 ATOM HB3 HA 0.09 ! | // ATOM CG CD 0.75 ! -CB--CG ATOM OD1 OB -0.55 ! | \ ATOM OD2 OH1 -0.61 ! HB3 OD2-HD2 ATOM HD2 H 0.44 ! BOND OD2 HD2 ANGLE HD2 OD2 CG DIHE HD2 OD2 CG OD1 HD2 OD2 CG CB DONOR HD2 OD2 IC HD2 OD2 CG OD1 0.0000 0.0000 0.0000 0.0000 0.0000 PRES GLUP 0.00 ! patch for protonated glutamic acid, proton on oe2 GROUP ! via acetic acid, use in a patch statement ATOM CG CT2 -0.21 ! ATOM HG2 HA 0.09 ! HG2 OE1 ATOM HG3 HA 0.09 ! | // ATOM CD CD 0.75 ! -CG--CD ATOM OE1 OB -0.55 ! | \ ATOM OE2 OH1 -0.61 ! HG3 OE2-HE2 ATOM HE2 H 0.44 ! BOND OE2 HE2 ANGLE HE2 OE2 CD DIHE HE2 OE2 CD OE1 HE2 OE2 CD CG DONOR HE2 OE2 IC HE2 OE2 CD OE1 0.0000 0.0000 0.0000 0.0000 0.0000 PRES LINK 0.00 ! linkage for IMAGES or for joining segments ! 1 refers to previous (N terminal) ! 2 refers to next (C terminal) ! use in a patch statement BOND 1:C 2:N ANGLE 1:C 2:N 2:CA 1:CA 1:C 2:N ANGLE 1:O 1:C 2:N 1:C 2:N 2:HN DIHE 1:C 2:N 2:CA 2:C 1:C 2:N 2:CA 2:HA 1:C 2:N 2:CA 2:CB DIHE 1:HA 1:CA 1:C 2:N 1:N 1:CA 1:C 2:N 1:CB 1:CA 1:C 2:N DIHE 1:CA 1:C 2:N 2:HN 1:CA 1:C 2:N 2:CA DIHE 1:O 1:C 2:N 2:HN 1:O 1:C 2:N 2:CA IMPR 2:N 1:C 2:CA 2:HN 1:C 1:CA 2:N 1:O IC 1:N 1:CA 1:C 2:N 0.0000 0.0000 180.0000 0.0000 0.0000 IC 2:N 1:CA 1:*C 1:O 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1:CA 1:C 2:N 2:CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1:C 2:N 2:CA 2:C 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1:C 2:CA 2:*N 2:HN 0.0000 0.0000 180.0000 0.0000 0.0000 PRES DISU -0.36 ! patch for disulfides. Patch must be 1-CYS and 2-CYS. GROUP ! use in a patch statement ATOM 1:CB CT2 -0.10 ! ATOM 1:SG SM -0.08 ! 2:SG--2:CB-- GROUP ! / ATOM 2:SG SM -0.08 ! -1:CB--1:SG ATOM 2:CB CT2 -0.10 ! DELETE ATOM 1:HG DELETE ATOM 2:HG BOND 1:SG 2:SG ANGLE 1:CB 1:SG 2:SG 1:SG 2:SG 2:CB DIHE 1:HB2 1:CB 1:SG 2:SG 1:HB3 1:CB 1:SG 2:SG DIHE 2:HB2 2:CB 2:SG 1:SG 2:HB3 2:CB 2:SG 1:SG DIHE 1:CA 1:CB 1:SG 2:SG 1:SG 2:SG 2:CB 2:CA DIHE 1:CB 1:SG 2:SG 2:CB IC 1:CA 1:CB 1:SG 2:SG 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1:CB 1:SG 2:SG 2:CB 0.0000 0.0000 90.0000 0.0000 0.0000 IC 1:SG 2:SG 2:CB 2:CA 0.0000 0.0000 180.0000 0.0000 0.0000 RESI O2 0.00 ! O2 ligand for heme GROUP ATOM O1 OM 0.021 ATOM O2 OM -0.021 BOND O1 O2 PATCHING FIRS NONE LAST NONE RESI CO 0.00 ! CO ligand for heme GROUP ATOM C CM 0.021 ATOM O OM -0.021 BOND C O PATCHING FIRS NONE LAST NONE PRES FHEM 0.00 ! FIX UP THE HEME BY DELETING UNWANTED AUTOGENERATED ANGLES ! unliganded heme patch DELETE ANGLE 1NA 1FE 1NC 1NB 1FE 1ND PRES PHEM 0.00 ! Patch for HEME to His link. ! Patch residues must be 1-HIS, and 2-HEME. DELETE ANGLE 2:NA 2:FE 2:NC 2:NB 2:FE 2:ND BOND 1:NE2 2:FE ANGLE 1:CD2 1:NE2 2:FE 1:CE1 1:NE2 2:FE 1:NE2 2:FE 2:NA 1:NE2 2:FE 2:NB ANGLE 1:NE2 2:FE 2:NC 1:NE2 2:FE 2:ND IC 1:CD2 1:NE2 2:FE 2:NA 0.0000 0.0000 0.0000 0.0000 0.0000 IC 1:CD2 1:NE2 2:FE 2:NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 1:CD2 1:NE2 2:FE 2:NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 1:CD2 1:NE2 2:FE 2:NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 1:CE1 1:NE2 2:FE 2:NA 0.0000 0.0000 0.0000 0.0000 0.0000 PRES PLO2 0.00 ! Patch residue for Heme ligand. Residues must be ! 1-O2 , 2-HEME , and 3-HIS ! O1 of the oxygen is bonded to the iron. BOND 1:O1 2:FE ANGLE 1:O2 1:O1 2:FE 1:O1 2:FE 2:NA 1:O1 2:FE 2:NB ANGLE 1:O1 2:FE 2:NC 1:O1 2:FE 2:ND DIHE 1:O2 1:O1 2:FE 2:NA IC 1:O2 1:O1 2:FE 2:NA 0.0000 0.0000 0.0000 0.0000 0.0000 IC 1:O2 1:O1 2:FE 3:NE2 0.0000 0.0000 0.0000 0.0000 0.0000 PRES PLIG 0.00 ! Patch residue for Heme ligand. Residues must be, ! 1-CO , 2-HEME , and 3-HIS BOND 1:C 2:FE ANGLE 1:C 2:FE 3:NE2 ANGLE 1:O 1:C 2:FE 1:C 2:FE 2:NA 1:C 2:FE 2:NB ANGLE 1:C 2:FE 2:NC 1:C 2:FE 2:ND IC 1:O 1:C 2:FE 2:NA 0.0000 0.0000 0.0000 0.0000 0.0000 IC 1:O 1:C 2:FE 3:NE2 0.0000 0.0000 0.0000 0.0000 0.0000 ! patches for cyclic peptides PRES LIG1 0.00000 ! linkage for cyclic peptide ! 1 refers to the C terminus which is a glycine ! 2 refers to the N terminus ! use in a patch statement, perform initial ! generation using first NONE last NONE BOND 1:C 2:N ANGLE 1:C 2:N 2:CA 1:CA 1:C 2:N ANGLE 1:O 1:C 2:N 1:C 2:N 2:HN DIHE 1:C 2:N 2:CA 2:C 1:C 2:N 2:CA 2:HA 1:C 2:N 2:CA 2:CB DIHE 1:HA1 1:CA 1:C 2:N 1:N 1:CA 1:C 2:N 1:HA2 1:CA 1:C 2:N DIHE 1:CA 1:C 2:N 2:HN 1:CA 1:C 2:N 2:CA DIHE 1:O 1:C 2:N 2:HN 1:O 1:C 2:N 2:CA DIHE 1:CA 1:C 2:N 2:CA IMPR 2:N 1:C 2:CA 2:HN 1:C 1:CA 2:N 1:O IC 1:N 1:CA 1:C 2:N 0.0000 0.0000 180.0000 0.0000 0.0000 IC 2:N 1:CA 1:*C 1:O 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1:CA 1:C 2:N 2:CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1:C 2:N 2:CA 2:C 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1:C 2:CA 2:*N 2:HN 0.0000 0.0000 180.0000 0.0000 0.0000 PRES LIG2 0.00000 ! linkage for cyclic peptide ! 1: refers to the C terminus ! 2: refers to the N terminus which is a glycine ! use in a patch statement, perform initial ! generation using first NONE last NONE BOND 1:C 2:N ANGLE 1:C 2:N 2:CA 1:CA 1:C 2:N ANGLE 1:O 1:C 2:N 1:C 2:N 2:HN DIHE 1:C 2:N 2:CA 2:C 1:C 2:N 2:CA 2:HA1 1:C 2:N 2:CA 2:HA2 DIHE 1:HA 1:CA 1:C 2:N 1:N 1:CA 1:C 2:N 1:CB 1:CA 1:C 2:N DIHE 1:CA 1:C 2:N 2:HN 1:CA 1:C 2:N 2:CA DIHE 1:O 1:C 2:N 2:HN 1:O 1:C 2:N 2:CA DIHE 1:CA 1:C 2:N 2:CA IMPR 2:N 1:C 2:CA 2:HN 1:C 1:CA 2:N 1:O IC 1:N 1:CA 1:C 2:N 0.0000 0.0000 1:80.0000 0.0000 0.0000 IC 2:N 1:CA 1:*C 1:O 0.0000 0.0000 1:80.0000 0.0000 0.0000 IC 1:CA 1:C 2:N 2:CA 0.0000 0.0000 1:80.0000 0.0000 0.0000 IC 1:C 2:N 2:CA 2:C 0.0000 0.0000 1:80.0000 0.0000 0.0000 IC 1:C 2:CA 2:*N 2:HN 0.0000 0.0000 1:80.0000 0.0000 0.0000 PRES LIG3 0.00000 ! linkage for cyclic peptide ! 1: refers to the C terminus which is a glycine ! 2: refers to the N terminus which is a glycine ! use in a patch statement, perform initial ! generation using first NONE last NONE BOND 1:C 2:N ANGLE 1:C 2:N 2:CA 1:CA 1:C 2:N ANGLE 1:O 1:C 2:N 1:C 2:N 2:HN DIHE 1:C 2:N 2:CA 2:C 1:C 2:N 2:CA 2:HA1 1:C 2:N 2:CA 2:HA2 DIHE 1:HA1 1:CA 1:C 2:N 1:N 1:CA 1:C 2:N 1:HA2 1:CA 1:C 2:N DIHE 1:CA 1:C 2:N 2:HN 1:CA 1:C 2:N 2:CA DIHE 1:O 1:C 2:N 2:HN 1:O 1:C 2:N 2:CA DIHE 1:CA 1:C 2:N 2:CA IMPR 2:N 1:C 2:CA 2:HN 1:C 1:CA 2:N 1:O IC 1:N 1:CA 1:C 2:N 0.0000 0.0000 1:80.0000 0.0000 0.0000 IC 2:N 1:CA 1:*C 1:O 0.0000 0.0000 1:80.0000 0.0000 0.0000 IC 1:CA 1:C 2:N 2:CA 0.0000 0.0000 1:80.0000 0.0000 0.0000 IC 1:C 2:N 2:CA 2:C 0.0000 0.0000 1:80.0000 0.0000 0.0000 IC 1:C 2:CA 2:*N 2:HN 0.0000 0.0000 1:80.0000 0.0000 0.0000 RESI GDP -2.000 GROUP ATOM PB PB 0.000 ! correct charge ATOM O1B OT -0.650 ATOM O2B OT -0.650 ATOM O3B OT -0.650 ATOM PA PA 0.000 ! correct charge ATOM O1A OT -0.650 ATOM O2A OT -0.650 ATOM O3A OS -0.670 ATOM O5' OS -0.670 ATOM C5' CT1 -0.103 ATOM C4' CT1 0.062 ATOM O4' OS -0.370 ATOM C3' CT1 0.248 ATOM O3' OT -0.650 ATOM C2' CT1 0.198 ATOM O2' OT -0.650 ATOM C1' CT1 0.163 ATOM N9 NY -0.300 ATOM C8 CT1 0.298 ATOM N7 NY -0.300 ATOM C5 CT1 0.047 ATOM C6 CT1 -0.153 ATOM O6 OS -0.650 ATOM N1 NY -0.300 ATOM C2 CT1 0.298 ATOM N2 NY -0.300 ATOM N3 NY -0.300 ATOM C4 CT1 0.298 ATOM HOB2 H 0.400 ATOM HOB3 H 0.400 ATOM HOA2 H 0.400 ATOM H5' HA 0.047 ATOM H5'' HA 0.047 ATOM H4' HA 0.032 ATOM H3' HA -0.003 ATOM HO3' H 0.400 ATOM H2' HA 0.117 ATOM HO2' H 0.400 ATOM H1' HA 0.032 ATOM H8 HA 0.047 ATOM HN1 H 0.150 ATOM HN21 H 0.150 ATOM HN22 H 0.150 BOND PB O1B ! missing parameter for bond distance BOND PB O2B ! missing parameter for bond distance BOND PB O3B ! missing parameter for bond distance BOND PB O3A ! missing parameter for bond distance BOND PA O1A ! missing parameter for bond distance BOND PA O2A ! missing parameter for bond distance BOND PA O3A ! missing parameter for bond distance BOND PA O5' ! missing parameter for bond distance BOND O5' C5' BOND C5' C4' BOND C4' O4' BOND C4' C3' BOND O4' C1' BOND C3' O3' BOND C3' C2' BOND C2' O2' BOND C2' C1' BOND C1' N9 BOND N9 C8 BOND N9 C4 BOND C8 N7 BOND N7 C5 BOND C5 C6 BOND C5 C4 BOND C6 O6 BOND C6 N1 BOND N1 C2 BOND N1 HN1 BOND C2 N2 BOND C2 N3 BOND N3 C4 BOND O2B HOB2 BOND O3B HOB3 BOND O2A HOA2 BOND C5' H5' BOND C5' H5'' BOND C4' H4' BOND C3' H3' BOND O3' HO3' BOND C2' H2' BOND O2' HO2' BOND C1' H1' BOND C8 H8 BOND N2 HN21 BOND N2 HN22 IC O1B PB O2B HOB2 1.48 118.32 -180.00 109.47 1.09 IC O3B PB O2B HOB2 1.52 106.55 -54.45 109.47 1.09 IC O3A PB O2B HOB2 1.57 105.52 56.07 109.47 1.09 IC O1B PB O3B HOB3 1.48 110.82 180.00 109.47 1.09 IC O2B PB O3B HOB3 1.48 106.55 50.02 109.47 1.09 IC O3A PB O3B HOB3 1.57 104.33 -61.33 109.47 1.09 IC O1B PB O3A PA 1.48 110.27 -110.29 132.38 1.60 IC O2B PB O3A PA 1.48 105.52 18.57 132.38 1.60 IC O3B PB O3A PA 1.52 104.33 130.66 132.38 1.60 IC PB O3A PA O1A 1.57 132.38 60.12 109.45 1.46 IC PB O3A PA O2A 1.57 132.38 -71.12 107.10 1.46 IC PB O3A PA O5' 1.57 132.38 176.57 99.21 1.59 IC O1A PA O2A HOA2 1.46 119.75 -180.00 109.47 1.09 IC O3A PA O2A HOA2 1.60 107.10 -54.75 109.47 1.09 IC O5' PA O2A HOA2 1.59 108.13 51.32 109.47 1.09 IC O1A PA O5' C5' 1.46 111.18 41.22 124.45 1.43 IC O2A PA O5' C5' 1.46 108.13 174.59 124.45 1.43 IC O3A PA O5' C5' 1.60 99.21 -73.90 124.45 1.43 IC PA O5' C5' C4' 1.59 124.45 -127.26 110.03 1.55 IC PA O5' C5' H5' 1.59 124.45 112.65 109.33 1.09 IC PA O5' C5' H5'' 1.59 124.45 -7.12 109.32 1.09 IC O5' C5' C4' O4' 1.43 110.03 -71.36 108.30 1.42 IC H5' C5' C4' O4' 1.09 109.33 48.73 108.30 1.42 IC H5'' C5' C4' O4' 1.09 109.39 168.54 108.30 1.42 IC O5' C5' C4' C3' 1.43 110.03 46.98 117.95 1.54 IC O5' C5' C4' H4' 1.43 110.03 169.98 107.91 1.09 IC C5' C4' O4' C1' 1.55 108.30 127.41 111.37 1.44 IC C3' C4' O4' C1' 1.54 104.53 0.85 111.37 1.44 IC H4' C4' O4' C1' 1.09 109.68 -115.06 111.37 1.44 IC C4' O4' C1' C2' 1.42 111.37 -21.10 106.08 1.50 IC C4' O4' C1' N9 1.42 111.37 -142.28 105.27 1.47 IC C4' O4' C1' H1' 1.42 111.37 98.49 111.21 1.09 IC O4' C1' C2' C3' 1.44 106.08 31.82 101.68 1.51 IC N9 C1' C2' C3' 1.47 114.02 147.19 101.68 1.51 IC H1' C1' C2' C3' 1.09 110.00 -88.55 101.68 1.51 IC O4' C1' C2' O2' 1.44 106.08 155.82 112.70 1.42 IC O4' C1' C2' H2' 1.44 106.08 -83.79 109.67 1.09 IC O2' C2' C3' C4' 1.42 115.28 -153.32 105.38 1.54 IC C1' C2' C3' C4' 1.50 101.68 -31.08 105.38 1.54 IC H2' C2' C3' C4' 1.09 109.30 84.81 105.38 1.54 IC O2' C2' C3' O3' 1.42 115.28 -35.58 109.89 1.41 IC O2' C2' C3' H3' 1.42 115.28 86.62 110.85 1.09 IC O3' C3' C4' C5' 1.41 109.38 141.09 117.95 1.55 IC C2' C3' C4' C5' 1.51 105.38 -100.83 117.95 1.55 IC H3' C3' C4' C5' 1.09 110.91 19.20 117.95 1.55 IC O3' C3' C4' O4' 1.41 109.38 -98.61 104.53 1.42 IC O3' C3' C4' H4' 1.41 109.38 18.27 108.28 1.09 IC C4' C3' O3' HO3' 1.54 109.38 -180.00 109.47 1.09 IC C2' C3' O3' HO3' 1.51 109.89 64.77 109.47 1.09 IC H3' C3' O3' HO3' 1.09 110.31 -57.75 109.47 1.09 IC C3' C2' O2' HO2' 1.51 115.28 -180.00 109.47 1.09 IC C1' C2' O2' HO2' 1.50 112.70 63.87 109.47 1.09 IC H2' C2' O2' HO2' 1.09 108.03 -57.45 109.47 1.09 IC O4' C1' N9 C8 1.44 105.27 66.14 128.27 1.37 IC C2' C1' N9 C8 1.50 114.02 -49.70 128.27 1.37 IC H1' C1' N9 C8 1.09 110.12 -173.90 128.27 1.37 IC O4' C1' N9 C4 1.44 105.27 -109.35 126.75 1.38 IC C1' C8 *N9 C4 1.47 128.27 176.26 104.86 1.38 IC C1' N9 C8 N7 1.47 128.27 -176.76 115.21 1.30 IC C4 N9 C8 N7 1.38 104.86 -0.49 115.21 1.30 IC C1' N9 C8 H8 1.47 128.27 -55.55 108.19 1.09 IC N9 C8 N7 C5 1.37 115.21 0.26 102.97 1.40 IC H8 C8 N7 C5 1.09 108.21 -120.93 102.97 1.40 IC C8 N7 C5 C6 1.30 102.97 179.93 129.85 1.42 IC C8 N7 C5 C4 1.30 102.97 0.07 111.01 1.37 IC N7 C5 C6 O6 1.40 129.85 0.48 127.67 1.23 IC C4 C5 C6 O6 1.37 119.14 -179.68 127.67 1.23 IC N7 C5 C6 N1 1.40 129.85 -179.42 112.19 1.38 IC C5 C6 N1 C2 1.42 112.19 -0.57 124.92 1.37 IC O6 C6 N1 C2 1.23 120.14 179.53 124.92 1.37 IC C5 C6 N1 HN1 1.42 112.19 -122.42 105.39 1.09 IC C6 C2 *N1 HN1 1.38 124.92 121.85 105.39 1.09 IC C6 N1 C2 N2 1.38 124.92 -179.59 117.54 1.32 IC HN1 N1 C2 N2 1.09 105.39 -57.74 117.54 1.32 IC C6 N1 C2 N3 1.38 124.92 0.72 123.83 1.33 IC N1 C2 N2 HN22 1.37 117.54 60.00 109.47 1.09 IC N3 C2 N2 HN22 1.33 118.63 -120.29 109.47 1.09 IC N1 C2 N2 HN21 1.37 117.54 -180.00 109.47 1.09 IC C2 HN21 *N2 HN22 1.32 109.47 120.00 109.47 1.09 IC N1 C2 N3 C4 1.37 123.83 -0.62 112.15 1.36 IC N2 C2 N3 C4 1.32 118.63 179.70 112.15 1.36 IC C2 N3 C4 N9 1.33 112.15 -179.75 126.28 1.38 IC C2 N3 C4 C5 1.33 112.15 0.53 127.77 1.37 IC C5 C4 N9 C1' 1.37 105.95 176.83 126.75 1.47 IC N3 C4 N9 C1' 1.36 126.28 -2.94 126.75 1.47 IC C5 C4 N9 C8 1.37 105.95 0.49 104.86 1.37 IC N9 C4 C5 N7 1.38 105.95 -0.36 111.01 1.40 IC N3 C4 C5 N7 1.36 127.77 179.40 111.01 1.40 IC N9 C4 C5 C6 1.38 105.95 179.76 119.14 1.42 PATCHING FIRS NONE LAST NONE RESI GTP -2.000 GROUP ATOM PG PB 0.000 ATOM O3B OS -0.670 ATOM O1G OT -0.300 ATOM O2G OT -0.650 ATOM O3G OT -0.650 ATOM PB PA 0.000 ATOM O1B OT -0.650 ATOM O2B OT -0.650 ATOM PA PA 0.000 ATOM O1A OT -0.650 ATOM O2A OT -0.650 ATOM O3A OS -0.670 ATOM O5' OS -0.670 ATOM C5' CT1 -0.070 ATOM C4' CT1 0.095 ATOM O4' OS -0.370 ATOM C3' CT1 0.280 ATOM O3' OT -0.650 ATOM C2' CT1 0.230 ATOM O2' OT -0.650 ATOM C1' CT1 0.195 ATOM N9 NY -0.300 ATOM C8 CT1 0.330 ATOM N7 NY -0.300 ATOM C5 CT1 0.080 ATOM C6 CT1 -0.120 ATOM O6 OT -0.650 ATOM N1 NY -0.300 ATOM C2 CT1 0.330 ATOM N2 NY -0.300 ATOM N3 NY -0.300 ATOM C4 CT1 0.330 ATOM HOG2 H 0.400 ATOM HOG3 H 0.400 ATOM HOB2 H 0.400 ATOM HOA2 H 0.400 ATOM H5' HA 0.080 ATOM H5'' HA 0.080 ATOM H4' HA 0.065 ATOM H3' HA 0.030 ATOM HO3' H 0.400 ATOM H2' HA 0.150 ATOM HO2' H 0.400 ATOM H1' HA 0.065 ATOM H8 HA 0.080 ATOM HN1 H 0.150 ATOM HN21 H 0.150 ATOM HN22 H 0.150 BOND PG O3B ! missing parameter for bond distance BOND PG O1G ! missing parameter for bond distance BOND PG O2G ! missing parameter for bond distance BOND PG O3G ! missing parameter for bond distance BOND O3B PB ! missing parameter for bond distance BOND PB O1B ! missing parameter for bond distance BOND PB O2B ! missing parameter for bond distance BOND PB O3A ! missing parameter for bond distance BOND PA O1A ! missing parameter for bond distance BOND PA O2A ! missing parameter for bond distance BOND PA O3A ! missing parameter for bond distance BOND PA O5' ! missing parameter for bond distance BOND O5' C5' BOND C5' C4' BOND C4' O4' BOND C4' C3' BOND O4' C1' BOND C3' O3' BOND C3' C2' BOND C2' O2' BOND C2' C1' BOND C1' N9 BOND N9 C8 BOND N9 C4 BOND C8 N7 BOND N7 C5 BOND C5 C6 BOND C5 C4 BOND C6 O6 BOND C6 N1 BOND N1 C2 BOND C2 N2 BOND C2 N3 BOND N3 C4 BOND O2G HOG2 BOND O3G HOG3 BOND O2B HOB2 BOND O2A HOA2 BOND C5' H5' BOND C5' H5'' BOND C4' H4' BOND C3' H3' BOND O3' HO3' BOND C2' H2' BOND O2' HO2' BOND C1' H1' BOND C8 H8 BOND N1 HN1 BOND N2 HN21 BOND N2 HN22 IC O1G PG O3B PB 1.88 104.53 169.46 132.71 1.59 IC O2G PG O3B PB 1.45 109.17 -70.94 132.71 1.59 IC O3G PG O3B PB 1.50 99.70 48.54 132.71 1.59 IC PG O3B PB O1B 1.63 132.71 -83.55 110.98 1.47 IC PG O3B PB O2B 1.63 132.71 53.97 111.58 1.45 IC PG O3B PB O3A 1.63 132.71 164.67 104.87 1.63 IC O3B PB O2B HOB2 1.59 111.58 -180.00 109.47 1.09 IC O1B PB O2B HOB2 1.47 120.58 -47.09 109.47 1.09 IC O3A PB O2B HOB2 1.63 102.90 68.05 109.47 1.09 IC O3B PB O3A PA 1.59 104.87 -93.55 138.39 1.62 IC O1B PB O3A PA 1.47 104.05 149.81 138.39 1.62 IC O2B PB O3A PA 1.45 102.90 23.27 138.39 1.62 IC PB O3A PA O1A 1.63 138.39 -70.73 107.13 1.47 IC PB O3A PA O2A 1.63 138.39 62.36 110.26 1.47 IC PB O3A PA O5' 1.63 138.39 179.05 92.83 1.65 IC O1A PA O2A HOA2 1.47 120.70 -180.00 109.47 1.09 IC O3A PA O2A HOA2 1.62 110.26 54.25 109.47 1.09 IC O5' PA O2A HOA2 1.65 113.81 -48.49 109.47 1.09 IC O1A PA O5' C5' 1.47 108.39 159.08 120.69 1.46 IC O2A PA O5' C5' 1.47 113.81 21.80 120.69 1.46 IC O3A PA O5' C5' 1.62 92.83 -91.83 120.69 1.46 IC PA O5' C5' C4' 1.65 120.69 -117.03 111.69 1.58 IC PA O5' C5' H5' 1.65 120.69 122.65 108.91 1.09 IC PA O5' C5' H5'' 1.65 120.69 3.39 108.99 1.09 IC O5' C5' C4' O4' 1.46 111.69 -64.31 102.84 1.40 IC H5' C5' C4' O4' 1.09 108.91 56.02 102.84 1.40 IC H5'' C5' C4' O4' 1.09 108.94 175.24 102.84 1.40 IC O5' C5' C4' C3' 1.46 111.69 51.44 122.05 1.53 IC O5' C5' C4' H4' 1.46 111.69 178.10 108.34 1.09 IC C5' C4' O4' C1' 1.58 102.84 134.24 113.79 1.40 IC C3' C4' O4' C1' 1.53 103.96 6.11 113.79 1.40 IC H4' C4' O4' C1' 1.09 111.02 -110.08 113.79 1.40 IC C4' O4' C1' C2' 1.40 113.79 -25.68 101.87 1.49 IC C4' O4' C1' N9 1.40 113.79 -146.29 105.71 1.47 IC C4' O4' C1' H1' 1.40 113.79 93.08 112.38 1.09 IC O4' C1' C2' C3' 1.40 101.87 34.71 104.45 1.48 IC N9 C1' C2' C3' 1.47 115.08 148.53 104.45 1.48 IC H1' C1' C2' C3' 1.09 110.93 -85.08 104.45 1.48 IC O4' C1' C2' O2' 1.40 101.87 164.93 111.77 1.41 IC O4' C1' C2' H2' 1.40 101.87 -78.73 107.86 1.09 IC O2' C2' C3' C4' 1.41 119.22 -157.24 103.58 1.53 IC C1' C2' C3' C4' 1.49 104.45 -31.57 103.58 1.53 IC H2' C2' C3' C4' 1.09 106.86 82.57 103.58 1.53 IC O2' C2' C3' O3' 1.41 119.22 -41.28 111.13 1.39 IC O2' C2' C3' H3' 1.41 119.22 82.57 111.28 1.09 IC O3' C3' C4' C5' 1.39 108.20 143.13 122.05 1.58 IC C2' C3' C4' C5' 1.48 103.58 -98.86 122.05 1.58 IC H3' C3' C4' C5' 1.09 111.73 21.02 122.05 1.58 IC O3' C3' C4' O4' 1.39 108.20 -101.68 103.96 1.40 IC O3' C3' C4' H4' 1.39 108.20 16.43 108.25 1.09 IC C4' C3' O3' HO3' 1.53 108.20 180.00 109.47 1.09 IC C2' C3' O3' HO3' 1.48 111.13 66.92 109.47 1.09 IC H3' C3' O3' HO3' 1.09 110.69 -57.26 109.47 1.09 IC C3' C2' O2' HO2' 1.48 119.22 -180.00 109.47 1.09 IC C1' C2' O2' HO2' 1.49 111.77 57.91 109.47 1.09 IC H2' C2' O2' HO2' 1.09 106.16 -59.46 109.47 1.09 IC O4' C1' N9 C8 1.40 105.71 63.50 128.74 1.38 IC C2' C1' N9 C8 1.49 115.08 -48.06 128.74 1.38 IC H1' C1' N9 C8 1.09 110.51 -174.66 128.74 1.38 IC O4' C1' N9 C4 1.40 105.71 -115.56 126.06 1.41 IC C1' C8 *N9 C4 1.47 128.74 179.22 105.20 1.41 IC C1' N9 C8 N7 1.47 128.74 -179.59 114.76 1.30 IC C4 N9 C8 N7 1.41 105.20 -0.37 114.76 1.30 IC C1' N9 C8 H8 1.47 128.74 -58.53 108.29 1.09 IC N9 C8 N7 C5 1.38 114.76 -0.15 104.38 1.41 IC H8 C8 N7 C5 1.09 108.26 -121.23 104.38 1.41 IC C8 N7 C5 C6 1.30 104.38 179.35 130.61 1.45 IC C8 N7 C5 C4 1.30 104.38 0.63 110.26 1.39 IC N7 C5 C6 O6 1.41 130.61 2.20 129.60 1.24 IC C4 C5 C6 O6 1.39 119.12 -179.18 129.60 1.24 IC N7 C5 C6 N1 1.41 130.61 -178.21 111.86 1.41 IC C5 C6 N1 C2 1.45 111.86 -0.53 124.81 1.39 IC O6 C6 N1 C2 1.24 118.54 179.11 124.81 1.39 IC C5 C6 N1 HN1 1.45 111.86 -122.38 105.42 1.09 IC C6 C2 *N1 HN1 1.41 124.81 121.84 105.42 1.09 IC C6 N1 C2 N2 1.41 124.81 -179.26 114.66 1.31 IC HN1 N1 C2 N2 1.09 105.42 -57.42 114.66 1.31 IC C6 N1 C2 N3 1.41 124.81 0.72 124.86 1.35 IC N1 C2 N2 HN22 1.39 114.66 60.00 109.47 1.09 IC N3 C2 N2 HN22 1.35 120.47 -119.98 109.47 1.09 IC N1 C2 N2 HN21 1.39 114.66 180.00 109.47 1.09 IC C2 HN21 *N2 HN22 1.31 109.47 120.00 109.47 1.09 IC N1 C2 N3 C4 1.39 124.86 -0.65 111.51 1.40 IC N2 C2 N3 C4 1.31 120.47 179.33 111.51 1.40 IC C2 N3 C4 N9 1.35 111.51 179.66 126.76 1.41 IC C2 N3 C4 C5 1.35 111.51 0.57 127.84 1.39 IC C5 C4 N9 C1' 1.39 105.39 179.97 126.06 1.47 IC N3 C4 N9 C1' 1.40 126.76 0.72 126.06 1.47 IC C5 C4 N9 C8 1.39 105.39 0.72 105.20 1.38 IC N9 C4 C5 N7 1.41 105.39 -0.86 110.26 1.41 IC N3 C4 C5 N7 1.40 127.84 178.38 110.26 1.41 IC N9 C4 C5 C6 1.41 105.39 -179.74 119.12 1.45 IC O3B PG O2G HOG2 1.63 109.17 -180.00 109.47 1.09 IC O1G PG O2G HOG2 1.88 111.67 -64.92 109.47 1.09 IC O3G PG O2G HOG2 1.50 113.76 69.64 109.47 1.09 IC O3B PG O3G HOG3 1.63 99.70 -180.00 109.47 1.09 IC O1G PG O3G HOG3 1.88 116.61 68.27 109.47 1.09 IC O2G PG O3G HOG3 1.45 113.76 -63.95 109.47 1.09 PATCHING FIRS NONE LAST NONE RESI DUM 0.00 ! DUMMY ATOM GROUP ATOM DUM DUM 0.00 PATCHING FIRST NONE LAST NONE ! The following patches for phosphotyrosine must be used with a ! parameter file containing both the protein and nucleic acid parameters. ! In addition, the commented parameters listed below must be included ! in the combined parameter file ! PRES TP1 -1.00 ! convert tyrosine to monoanionic phosphotyrosine ! use in a patch statement as follows ! ! patch to convert tyrosine to phenolphosphate !PATCH TP1 TYR 1 SETUP WARN ! ! this patch requires that the use of the following ! !1) protein topology file that contains mass list of atoms in both ! the protein and nucleic acid topology files and ! ! add to the topology file !MASS 179 ON2b 15.999400 O ! Nucleic acid phosphate ester oxygen (pres tp1/tp2) ! !2) parameter file that contains both the protein and nucleic acid ! parameters plus the parameters listed below ! ! parameters to be added to the protein/nucleic acid parameter file ! !bonds !CA ON2b 340.0 1.38 !phenol phosphate, 6/94, adm jr. !ON2b P 270.0 1.61 !phenol phosphate, 6/94, adm jr. !angles !CA CA ON2b 75.0 120.0 !phenol phosphate, 6/94, adm jr. !CA ON2b P 90.0 120.0 20. 2.30 !phenol phosphate, 6/94, adm jr. !ON4 P ON2b 48.1 108.0 !phenol phosphate, 6/94, adm jr. !ON3 P ON2b 98.9 103.0 !phenol phosphate, 6/94, adm jr. !dihedrals !CA CA CA ON2b 3.10 2 180.0 !phenol phosphate, 6/94, adm jr. !HP CA CA ON2b 4.20 2 180.0 !phenol phosphate, 6/94, adm jr. !CA CA ON2b P 1.40 2 180.0 !phenol phosphate, 6/94, adm jr. !CA CA ON2b P 0.20 3 180.0 !phenol phosphate, 6/94, adm jr. !CA ON2b P ON4 0.95 2 0.0 !phenol phosphate, 6/94, adm jr. !CA ON2b P ON4 0.50 3 0.0 !phenol phosphate, 6/94, adm jr. !CA ON2b P ON3 0.10 3 0.0 !phenol phosphate, 6/94, adm jr. !nonbonded !ON2b 0.0 -0.1521 1.77 ! ! end of parameters to be added DELE ATOM HH GROUP ATOM CE1 CA -0.21 ATOM HE1 HP 0.21 GROUP ATOM CE2 CA -0.21 ATOM HE2 HP 0.21 GROUP ATOM CZ CA -0.16 ATOM OH ON2B -0.36 ! NA ATOM TYPE ATOM P1 P 1.40 ! NA ATOM TYPE ATOM O2 ON4 -0.76 ! NA ATOM TYPE ATOM H2 HN4 0.40 ! NA ATOM TYPE ATOM O3 ON3 -0.76 ! NA ATOM TYPE ATOM O4 ON3 -0.76 ! NA ATOM TYPE BOND P1 OH P1 O2 P1 O3 P1 O4 BOND O2 H2 ANGL CZ OH P1 ANGL OH P1 O2 OH P1 O3 OH P1 O4 ANGL O2 P1 O3 O2 P1 O4 O3 P1 O4 ANGL P1 O2 H2 DIHE CE1 CZ OH P1 CE2 CZ OH P1 DIHE CZ OH P1 O2 CZ OH P1 O3 CZ OH P1 O4 DIHE OH P1 O2 H2 O3 P1 O2 H2 O4 P1 O2 H2 BILD CE1 CZ OH P1 0.0000 000.00 0.00 000.00 0.0000 BILD CZ OH P1 O2 0.0000 000.00 180.00 000.00 0.0000 BILD O2 OH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 BILD O2 OH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 BILD H2 O2 P1 OH 0.0000 000.00 180.00 000.00 0.0000 PRES TP1A -1.00 ! patch to convert tyrosine to ! monoanionic phenol-phosphate model compound ! use in patch statement DELE ATOM N DELE ATOM HN DELE ATOM CA DELE ATOM HA DELE ATOM CB DELE ATOM HB2 DELE ATOM HB3 DELE ATOM C DELE ATOM O DELE ATOM HH GROUP ATOM CG CA -0.115 ATOM HG HP 0.115 GROUP ATOM CE1 CA -0.21 ATOM HE1 HP 0.21 GROUP ATOM CE2 CA -0.21 ATOM HE2 HP 0.21 GROUP ATOM CZ CA -0.16 ATOM OH ON2B -0.36 ! NA ATOM TYPE ATOM P1 P 1.40 ! NA ATOM TYPE ATOM O2 ON4 -0.76 ! NA ATOM TYPE ATOM H2 HN4 0.40 ! NA ATOM TYPE ATOM O3 ON3 -0.76 ! NA ATOM TYPE ATOM O4 ON3 -0.76 ! NA ATOM TYPE BOND P1 OH P1 O2 P1 O3 P1 O4 BOND O2 H2 BOND CG HG ANGL CZ OH P1 ANGL OH P1 O2 OH P1 O3 OH P1 O4 ANGL O2 P1 O3 O2 P1 O4 O3 P1 O4 ANGL P1 O2 H2 ANGL HG CG CD1 HG CG CD2 DIHE CE1 CZ OH P1 CE2 CZ OH P1 DIHE CZ OH P1 O2 CZ OH P1 O3 CZ OH P1 O4 DIHE OH P1 O2 H2 O3 P1 O2 H2 O4 P1 O2 H2 DIHE HG CG CD1 CE1 HG CG CD1 HD1 DIHE HG CG CD2 CE2 HG CG CD2 HD2 BILD CE1 CZ OH P1 0.0000 000.00 0.00 000.00 0.0000 BILD CZ OH P1 O2 0.0000 000.00 180.00 000.00 0.0000 BILD O2 OH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 BILD O2 OH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 BILD H2 O2 P1 OH 0.0000 000.00 180.00 000.00 0.0000 BILD CD1 CD2 *CG HG 1.3978 120.09 179.64 120.58 1.0799 PRES TP2 -2.00 ! patch to convert tyrosine to ! dianionic phosphotyrosine ! use in patch statement ! ! see PRES TP1 for proper preparation of the topology and ! parameter files ! DELE ATOM HH GROUP ATOM CE1 CA -0.21 ATOM HE1 HP 0.21 GROUP ATOM CE2 CA -0.21 ATOM HE2 HP 0.21 GROUP ATOM CZ CA -0.28 ATOM OH ON2B -0.28 ! NA ATOM TYPE ATOM P1 P 1.44 ! NA ATOM TYPE ATOM O2 ON3 -0.96 ! NA ATOM TYPE ATOM O3 ON3 -0.96 ! NA ATOM TYPE ATOM O4 ON3 -0.96 ! NA ATOM TYPE BOND P1 OH P1 O2 P1 O3 P1 O4 ANGL CZ OH P1 ANGL OH P1 O2 OH P1 O3 OH P1 O4 ANGL O2 P1 O3 O2 P1 O4 O3 P1 O4 DIHE CE1 CZ OH P1 CE2 CZ OH P1 DIHE CZ OH P1 O2 CZ OH P1 O3 CZ OH P1 O4 BILD CE1 CZ OH P1 0.0000 000.00 0.00 000.00 0.0000 BILD CZ OH P1 O2 0.0000 000.00 180.00 000.00 0.0000 BILD O2 OH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 BILD O2 OH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 PRES TP2A -2.00 ! patch to convert tyrosine to ! dianionic phosphotyrosine ! use in patch statement ! ! this converts a single tyrosine to a phenol phosphate ! see PRES TP1 for proper preparation of the topology and ! parameter files DELE ATOM N DELE ATOM HN DELE ATOM CA DELE ATOM HA DELE ATOM CB DELE ATOM HB2 DELE ATOM HB3 DELE ATOM C DELE ATOM O DELE ATOM HH GROUP ATOM CG CA -0.115 ATOM HG HP 0.115 GROUP ATOM CE1 CA -0.21 ATOM HE1 HP 0.21 GROUP ATOM CE2 CA -0.21 ATOM HE2 HP 0.21 GROUP ATOM CZ CA -0.28 ATOM OH ON2B -0.28 ! NA ATOM TYPE ATOM P1 P 1.44 ! NA ATOM TYPE ATOM O2 ON3 -0.96 ! NA ATOM TYPE ATOM O3 ON3 -0.96 ! NA ATOM TYPE ATOM O4 ON3 -0.96 ! NA ATOM TYPE BOND P1 OH P1 O2 P1 O3 P1 O4 BOND CG HG ANGL CZ OH P1 ANGL OH P1 O2 OH P1 O3 OH P1 O4 ANGL O2 P1 O3 O2 P1 O4 O3 P1 O4 ANGL HG CG CD1 HG CG CD2 DIHE CE1 CZ OH P1 CE2 CZ OH P1 DIHE CZ OH P1 O2 CZ OH P1 O3 CZ OH P1 O4 DIHE HG CG CD1 CE1 HG CG CD1 HD1 DIHE HG CG CD2 CE2 HG CG CD2 HD2 BILD CE1 CZ OH P1 0.0000 000.00 0.00 000.00 0.0000 BILD CZ OH P1 O2 0.0000 000.00 180.00 000.00 0.0000 BILD O2 OH *P1 O3 0.0000 000.00 -115.82 000.00 0.0000 BILD O2 OH *P1 O4 0.0000 000.00 115.90 000.00 0.0000 BILD CD1 CD2 *CG HG 1.3978 120.09 179.64 120.58 1.0799 !nucleic acid section RESI GUA -1.00 ATOM P P 1.50 ! O6 ATOM OP1 ON3 -0.80 ! || ATOM OP2 ON3 -0.80 ! C6 ATOM O5' ON2 -0.55 ! / \ ! H1-N1 C5--N7\\ ATOM C5' CN8 -0.08 ! | || C8-H8 ATOM H5' HN7 0.09 ! C2 C4--N9/ ATOM H5'' HN7 0.09 ! / \\ / \ GROUP ! H21-N2 N3 \ ATOM C4' CN6 0.11 ! | \ ATOM H4' HN6 0.09 ! H22 \ ATOM O4' ON6 -0.40 ! \ ATOM C1' CN6B 0.11 ! OP1 H5' H4' O4' \ ATOM H1' HN6 0.09 ! | | \ / \ \ GROUP ! -P-O5'-C5'---C4' C1' ATOM N9 NN2 -0.14 ! | | \ / \ ATOM C4 CN5 0.14 ! OP2 H5'' C3'--C2' H1' GROUP ! / \ / \ ATOM N3 NN3A -0.66 ! O3' H3' O2' H2' ATOM C2 CN2 0.76 ! | | ATOM N1 NN2G -0.38 ! HO2' ATOM H1 HN2 0.28 ! GROUP ATOM N2 NN1 -0.64 ATOM H21 HN1 0.31 ATOM H22 HN1 0.33 GROUP ATOM C6 CN1 0.55 ATOM O6 ON1 -0.47 ATOM C5 CN5 -0.08 GROUP ATOM N7 NN4 -0.69 ATOM C8 CN4 0.41 ATOM H8 HN3 0.28 GROUP ATOM C2' CN6 0.14 ATOM H2' HN6 0.09 ATOM O2' ON5 -0.66 ATOM HO2' HN5 0.43 GROUP ATOM C3' CN6 0.01 ATOM H3' HN6 0.09 ATOM O3' ON2 -0.55 BOND P OP1 P OP2 P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C4 C5 N3 C2 C2 N2 C2 N1 N2 H21 BOND N2 H22 N1 H1 N1 C6 C6 O6 C6 C5 BOND C5 N7 N7 C8 C2' C3' C3' O3' O3' +P BOND C2' O2' O2' HO2' BOND C1' H1' C2' H2' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 ! repeat dihedrals for phosphate multiple periodicities ! for CHARMM21 and previous versions !DIHE -O3' P O5' C5' C3' O3' +P +O5' ! Sugar Gauche Term !DIHE C1' C2' C3' O3' IMPH N2 N3 N1 C2 H1 C2 C6 N1 O6 N1 C5 C6 IMPH H8 N7 N9 C8 H22 H21 C2 N2 DONO H21 N2 DONO H22 N2 DONO H1 N1 DONO HO2' O2' ACCE O6 C6 ACCE N3 ACCE N7 ACCE OP1 P ACCE OP2 P ACCE O2' ACCE O3' ACCE O4' ACCE O5' BILD -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 BILD -O3' O5' *P OP1 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P OP2 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 BILD O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 BILD C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 BILD C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 BILD C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 BILD C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 BILD O4' C1' N9 C4 1.5251 113.71 -96.0 125.59 1.3783 BILD C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 BILD C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 BILD C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 BILD N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 BILD C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 BILD C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 BILD N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 BILD N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 BILD H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 BILD N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 BILD C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 BILD C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 BILD HO2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 RESI ADE -1.00 ! ATOM P P 1.50 ! H61 H62 ATOM OP1 ON3 -0.80 ! \ / ATOM OP2 ON3 -0.80 ! N6 ATOM O5' ON2 -0.55 ! | ! C6 ATOM C5' CN8 -0.08 ! // \ ATOM H5' HN7 0.09 ! N1 C5--N7\\ ATOM H5'' HN7 0.09 ! | || C8-H8 GROUP ! C2 C4--N9/ ATOM C4' CN6 0.11 ! / \\ / \ ATOM H4' HN6 0.09 ! H2 N3 \ ATOM O4' ON6 -0.40 ! \ ATOM C1' CN6B 0.11 ! \ ATOM H1' HN6 0.09 ! \ GROUP ! OP1 H5' H4' O4' \ ATOM C5 CN5 0.23 ! | | \ / \ \ ATOM N7 NN4 -0.63 ! -P-O5'-C5'---C4' C1' ATOM C8 CN4 0.38 ! | | \ / \ ATOM H8 HN3 0.18 ! OP2 H5'' C3'--C2' H1' ATOM N9 NN2 -0.16 ! / \ / \ GROUP ! O3' H3' O2' H2' ATOM N1 NN3A -0.74 ! | | ATOM C2 CN4 0.53 ! HO2' ATOM H2 HN3 0.16 ! ATOM N3 NN3A -0.69 ATOM C4 CN5 0.31 ATOM C6 CN2 0.43 GROUP ATOM N6 NN1 -0.80 ATOM H61 HN1 0.40 ATOM H62 HN1 0.40 GROUP ATOM C2' CN6 0.14 ATOM H2' HN6 0.09 ATOM O2' ON5 -0.66 ATOM HO2' HN5 0.43 GROUP ATOM C3' CN6 0.01 ATOM H3' HN6 0.09 ATOM O3' ON2 -0.55 BOND P OP1 P OP2 P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C4 C5 N3 C2 C2 N1 N1 C6 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 N7 C8 BOND C2' C3' C2' O2' O2' HO2' C3' O3' O3' +P BOND C1' H1' C2' H2' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 C2 H2 ! repeat dihedrals for phosphate multiple periodicities ! for CHARMM21 and previous versions !DIHE -O3' P O5' C5' C3' O3' +P +O5' ! Sugar Gauche Term !DIHE C1' C2' C3' O3' IMPH H62 C6 H61 N6 N6 N1 C5 C6 H2 N1 N3 C2 IMPH H8 N7 N9 C8 DONO H61 N6 DONO H62 N6 DONO HO2' O2' ACCE N3 ACCE N7 ACCE N1 ACCE OP1 P ACCE OP2 P ACCE O2' ACCE O3' ACCE O4' ACCE O5' BILD -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 BILD -O3' O5' *P OP1 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P OP2 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 BILD O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 BILD C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 BILD C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 BILD C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 BILD C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 BILD O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 BILD C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 BILD C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 BILD C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 BILD C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 BILD N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 BILD C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 BILD N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 BILD C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 BILD N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 BILD H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 BILD C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 BILD N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 BILD H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 BILD N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 BILD HO2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 RESI CYT -1.00 ATOM P P 1.50 ! ATOM OP1 ON3 -0.80 ! ATOM OP2 ON3 -0.80 ! H42 H41 ATOM O5' ON2 -0.55 ! \ / ! N4 ATOM C5' CN8 -0.08 ! | ATOM H5' HN7 0.09 ! C4 ATOM H5'' HN7 0.09 ! / \\ GROUP ! H5-C5 N3 ATOM C4' CN6 0.11 ! || | ATOM H4' HN6 0.09 ! H6-C6 C2 ATOM O4' ON6 -0.40 ! \ / \\ ATOM C1' CN6B 0.11 ! N1 O2 ATOM H1' HN6 0.09 ! \ GROUP ! \ ATOM N1 NN2 -0.16 ! \ ATOM C6 CN3 0.11 ! OP1 H5' H4' O4' \ ATOM H6 HN3 0.05 ! | | \ / \ \ GROUP ! -P-O5'-C5'---C4' C1' ATOM C2 CN1 0.53 ! | | \ / \ ATOM O2 ON1C -0.48 ! OP2 H5'' C3'--C2' H1' ATOM N3 NN3 -0.67 ! / \ / \ ATOM C4 CN2 0.62 ! O3' H3' O2' H2' GROUP ! | | ATOM N4 NN1 -0.58 ! HO2' ATOM H41 HN1 0.31 ! ATOM H42 HN1 0.27 GROUP ATOM C5 CN3 -0.10 ATOM H5 HN3 0.10 GROUP ATOM C2' CN6 0.14 ATOM H2' HN6 0.09 ATOM O2' ON5 -0.66 ATOM HO2' HN5 0.43 GROUP ATOM C3' CN6 0.01 ATOM H3' HN6 0.09 ATOM O3' ON2 -0.55 BOND P OP1 P OP2 P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 BOND C2 N3 N3 C4 C4 N4 N4 H41 N4 H42 BOND C4 C5 C5 C6 C2' C3' C3' O3' O3' +P BOND C2' O2' O2' HO2' BOND C1' H1' C2' H2' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C5 H5 C6 H6 ! repeat dihedrals for phosphate multiple periodicities ! for CHARMM21 and previous versions !DIHE -O3' P O5' C5' C3' O3' +P +O5' ! Sugar Gauche Term !DIHE C1' C2' C3' O3' IMPH O2 N1 N3 C2 N4 N3 C5 C4 IMPH H5 C4 C6 C5 H6 C5 N1 C6 IMPH H42 C4 H41 N4 DONO H42 N4 DONO HO2' O2' DONO H41 N4 ACCE O2 C2 ACCE N3 ACCE OP1 P ACCE OP2 P ACCE O2' ACCE O3' ACCE O4' ACCE O5' BILD -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 BILD -O3' O5' *P OP1 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P OP2 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 BILD O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 BILD C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 BILD C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 BILD C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 BILD C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 BILD O4' C1' N1 C2 1.5251 113.71 -96.0 117.79 1.399 BILD C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 BILD C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 BILD C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 BILD N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 BILD N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 BILD C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 BILD N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 BILD H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 BILD HO2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 RESI THY -1.00 ! ATOM P P 1.50 ! H71 O4 ATOM OP1 ON3 -0.80 ! | || ATOM OP2 ON3 -0.80 ! H72-C7 C4 H3 ATOM O5' ON2 -0.55 ! | \ / \ / ! H73 C5 N3 ATOM C5' CN8 -0.08 ! || | ATOM H5' HN7 0.09 ! H6-C6 C2 ATOM H5'' HN7 0.09 ! \ / \\ GROUP ! N1 O2 ATOM C4' CN6 0.11 ! \ ATOM H4' HN6 0.09 ! \ ATOM O4' ON6 -0.40 ! \ ATOM C1' CN6B 0.11 ! OP1 H5' H4' O4' \ ATOM H1' HN6 0.09 ! | | \ / \ \ GROUP ! -P-O5'-C5'---C4' C1' ATOM N1 NN2 -0.30 ! | | \ / \ ATOM C6 CN3 0.17 ! OP2 H5'' C3'--C2' H1' ATOM H6 HN3 0.13 ! / \ / \ GROUP ! O3' H3' O2' H2' ATOM C2 CN1 0.57 ! | | ATOM O2 ON1 -0.47 ! HO2' ATOM N3 NN2U -0.46 ! ATOM H3 HN2 0.36 GROUP ATOM C4 CN1 0.54 ATOM O4 ON1 -0.49 ATOM C5 CN3 -0.15 ATOM C7 CN9 -0.11 ATOM H71 HN7 0.07 ATOM H72 HN7 0.07 ATOM H73 HN7 0.07 GROUP ATOM C2' CN6 0.14 ATOM H2' HN6 0.09 ATOM O2' ON5 -0.66 ATOM HO2' HN5 0.43 GROUP ATOM C3' CN6 0.01 ATOM H3' HN6 0.09 ATOM O3' ON2 -0.55 BOND P OP1 P OP2 P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 BOND C5 C7 C5 C6 C2' C3' C3' O3' O3' +P BOND C2' O2' O2' HO2' BOND C1' H1' C2' H2' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C6 H6 C7 H71 C7 H72 C7 H73 ! repeat dihedrals for phosphate multiple periodicities ! for CHARMM21 and previous versions !DIHE -O3' P O5' C5' C3' O3' +P +O5' ! Sugar Gauche Terms !DIHE C1' C2' C3' O3' IMPH O2 N1 N3 C2 H3 C2 C4 N3 IMPH O4 N3 C5 C4 H6 N1 C5 C6 IMPH C7 C4 C6 C5 DONO H3 N3 DONO HO2' O2' ACCE O2 C2 ACCE O4 C4 ACCE OP1 P ACCE OP2 P ACCE O2' ACCE O3' ACCE O4' ACCE O5' BILD -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 BILD -O3' O5' *P OP1 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P OP2 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 BILD O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 BILD C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 BILD C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 BILD C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 BILD C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 BILD O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 BILD C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 BILD C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 BILD C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 BILD N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 BILD N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 BILD C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 BILD C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 BILD C4 C6 *C5 C7 1.4439 120.78 -179.94 121.63 1.5000 BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 BILD C6 C5 C7 H71 0.0 0.0 0.0 0.0 0.0 BILD C5 H71 *C7 H72 0.0 0.0 115.0 0.0 0.0 BILD H71 H72 *C7 H73 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 BILD HO2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0. 115.0 0.0 0.0 RESI URA -1.00 ! ATOM P P 1.50 ! O4 ATOM OP1 ON3 -0.80 ! || ATOM OP2 ON3 -0.80 ! C4 H3 ATOM O5' ON2 -0.55 ! / \ / ! H5-C5 N3 ATOM C5' CN8 -0.08 ! || | ATOM H5' HN7 0.09 ! H6-C6 C2 ATOM H5'' HN7 0.09 ! \ / \\ GROUP ! N1 O2 ATOM C4' CN6 0.11 ! \ ATOM H4' HN6 0.09 ! \ ATOM O4' ON6 -0.40 ! \ ATOM C1' CN6B 0.11 ! OP1 H5' H4' O4' \ ATOM H1' HN6 0.09 ! | | \ / \ \ GROUP ! -P-O5'-C5'---C4' C1' ATOM N1 NN2 -0.30 ! | | \ / \ ATOM C6 CN3 0.17 ! OP2 H5'' C3'--C2' H1' ATOM H6 HN3 0.13 ! / \ / \ GROUP ! O3' H3' O2' H2' ATOM C2 CN1 0.57 ! | | ATOM O2 ON1 -0.47 ! HO2' ATOM N3 NN2U -0.46 ! ATOM H3 HN2 0.36 GROUP ATOM C4 CN1 0.54 ATOM O4 ON1 -0.49 ATOM C5 CN3 -0.15 ATOM H5 HN3 0.10 GROUP ATOM C2' CN6 0.14 ATOM H2' HN6 0.09 ATOM O2' ON5 -0.66 ATOM HO2' HN5 0.43 GROUP ATOM C3' CN6 0.01 ATOM H3' HN6 0.09 ATOM O3' ON2 -0.55 BOND P OP1 P OP2 P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 BOND C5 C6 C2' C3' C3' O3' O3' +P BOND C2' O2' O2' HO2' BOND C1' H1' C2' H2' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C5 H5 C6 H6 ! repeat dihedrals for phosphate multiple periodicities ! for CHARMM21 and previous versions !DIHE -O3' P O5' C5' C3' O3' +P +O5' ! Sugar Gauche Term !DIHE C1' C2' C3' O3' IMPH O2 N1 N3 C2 H3 C2 C4 N3 H5 C4 C6 C5 IMPH O4 N3 C5 C4 H6 N1 C5 C6 DONO H3 N3 DONO HO2' O2' ACCE O2 C2 ACCE O4 C4 ACCE OP1 P ACCE OP2 P ACCE O2' ACCE O3' ACCE O4' ACCE O5' BILD -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 BILD -O3' O5' *P OP1 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P OP2 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 BILD O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 BILD C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 BILD C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 BILD C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 BILD C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 BILD O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 BILD C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379 BILD C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338 BILD C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373 BILD N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218 BILD N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383 BILD C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227 BILD C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03 BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 BILD HO2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 !DNA bases (RNA bases with the DEO1 patch applied) RESI DGUA -1.00 ATOM P P 1.50 ! O6 ATOM OP1 ON3 -0.80 ! || ATOM OP2 ON3 -0.80 ! C6 ATOM O5' ON2 -0.55 ! / \ ! H1-N1 C5--N7\\ ATOM C5' CN8 -0.08 ! | || C8-H8 ATOM H5' HN7 0.09 ! C2 C4--N9/ ATOM H5'' HN7 0.09 ! / \\ / \ GROUP ! H21-N2 N3 \ ATOM C4' CN6 0.11 ! | \ ATOM H4' HN6 0.09 ! H22 \ ATOM O4' ON6 -0.40 ! \ ATOM C1' CN6B 0.11 ! OP1 H5' H4' O4' \ ATOM H1' HN6 0.09 ! | | \ / \ \ GROUP ! -P-O5'-C5'---C4' C1' ATOM N9 NN2 -0.14 ! | | \ / \ ATOM C4 CN5 0.14 ! OP2 H5'' C3'--C2' H1' GROUP ! / \ / \ ATOM N3 NN3A -0.66 ! O3' H3' H2'' H2' ATOM C2 CN2 0.76 ! | ATOM N1 NN2G -0.38 ! ATOM H1 HN2 0.28 ! GROUP ATOM N2 NN1 -0.64 ATOM H21 HN1 0.31 ATOM H22 HN1 0.33 GROUP ATOM C6 CN1 0.55 ATOM O6 ON1 -0.47 ATOM C5 CN5 -0.08 GROUP ATOM N7 NN4 -0.69 ATOM C8 CN4 0.41 ATOM H8 HN3 0.28 GROUP ATOM C2' CN6C -0.18 ATOM H2'' HN6 0.09 ATOM H2' HN6 0.09 GROUP ATOM C3' CN6 0.01 ATOM H3' HN6 0.09 ATOM O3' ON2 -0.55 BOND P OP1 P OP2 P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C4 C5 N3 C2 C2 N2 C2 N1 N2 H21 BOND N2 H22 N1 H1 N1 C6 C6 O6 C6 C5 BOND C5 N7 N7 C8 C2' C3' C3' O3' O3' +P BOND C1' H1' C2' H2' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 C2' H2'' THET C1' C2' H2'' C3' C2' H2'' H2'' C2' H2' DIHE H2'' C2' C1' O4' H2''' C2' C1' N1 H2'' C2' C1' H1' DIHE H2'' C2' C3' C4' H2'' C2' C3' O3' H2'' C2' C3' H3' ! repeat dihedrals for phosphate multiple periodicities ! for CHARMM21 and previous versions !DIHE -O3' P O5' C5' C3' O3' +P +O5' ! Sugar Gauche Term !DIHE C1' C2' C3' O3' IMPH N2 N3 N1 C2 H1 C2 C6 N1 O6 N1 C5 C6 IMPH H8 N7 N9 C8 H22 H21 C2 N2 DONO H21 N2 DONO H22 N2 DONO H1 N1 ACCE O6 C6 ACCE N3 ACCE N7 ACCE OP1 P ACCE OP2 P ACCE O3' ACCE O4' ACCE O5' BILD -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 BILD -O3' O5' *P OP1 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P OP2 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 BILD O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 BILD C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 BILD C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 BILD C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 BILD C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 BILD O4' C1' N9 C4 1.5251 113.71 -96.0 125.59 1.3783 BILD C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 BILD C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 BILD C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 BILD N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 BILD C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 BILD C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 BILD N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 BILD N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 BILD H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 BILD N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 BILD C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 BILD C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 BILD C1' C3' *C2' H2'' 0.0 0.0 -115.0 0.0 0.0 RESI DADE -1.00 ! ATOM P P 1.50 ! H61 H62 ATOM OP1 ON3 -0.80 ! \ / ATOM OP2 ON3 -0.80 ! N6 ATOM O5' ON2 -0.55 ! | ! C6 ATOM C5' CN8 -0.08 ! // \ ATOM H5' HN7 0.09 ! N1 C5--N7\\ ATOM H5'' HN7 0.09 ! | || C8-H8 GROUP ! C2 C4--N9/ ATOM C4' CN6 0.11 ! / \\ / \ ATOM H4' HN6 0.09 ! H2 N3 \ ATOM O4' ON6 -0.40 ! \ ATOM C1' CN6B 0.11 ! \ ATOM H1' HN6 0.09 ! \ GROUP ! OP1 H5' H4' O4' \ ATOM C5 CN5 0.23 ! | | \ / \ \ ATOM N7 NN4 -0.63 ! -P-O5'-C5'---C4' C1' ATOM C8 CN4 0.38 ! | | \ / \ ATOM H8 HN3 0.18 ! OP2 H5'' C3'--C2' H1' ATOM N9 NN2 -0.16 ! / \ / \ GROUP ! O3' H3' H2'' H2' ATOM N1 NN3A -0.74 ! | ATOM C2 CN4 0.53 ! ATOM H2 HN3 0.16 ! ATOM N3 NN3A -0.69 ATOM C4 CN5 0.31 ATOM C6 CN2 0.43 GROUP ATOM N6 NN1 -0.80 ATOM H61 HN1 0.40 ATOM H62 HN1 0.40 GROUP ATOM C2' CN6C -0.18 ATOM H2'' HN6 0.09 ATOM H2' HN6 0.09 GROUP ATOM C3' CN6 0.01 ATOM H3' HN6 0.09 ATOM O3' ON2 -0.55 BOND P OP1 P OP2 P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C4 C5 N3 C2 C2 N1 N1 C6 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 N7 C8 BOND C2' C3' C2' O2' O2' HO2' C3' O3' O3' +P BOND C1' H1' C2' H2' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 C2 H2 C2' H2'' THET C1' C2' H2'' C3' C2' H2'' H2'' C2' H2' DIHE H2'' C2' C1' O4' H2''' C2' C1' N1 H2'' C2' C1' H1' DIHE H2'' C2' C3' C4' H2'' C2' C3' O3' H2'' C2' C3' H3' ! repeat dihedrals for phosphate multiple periodicities ! for CHARMM21 and previous versions !DIHE -O3' P O5' C5' C3' O3' +P +O5' ! Sugar Gauche Term !DIHE C1' C2' C3' O3' IMPH H62 C6 H61 N6 N6 N1 C5 C6 H2 N1 N3 C2 IMPH H8 N7 N9 C8 DONO H61 N6 DONO H62 N6 ACCE N3 ACCE N7 ACCE N1 ACCE OP1 P ACCE OP2 P ACCE O3' ACCE O4' ACCE O5' BILD -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 BILD -O3' O5' *P OP1 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P OP2 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 BILD O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 BILD C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 BILD C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 BILD C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 BILD C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 BILD O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 BILD C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 BILD C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 BILD C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 BILD C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 BILD N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 BILD C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 BILD N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 BILD C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 BILD N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 BILD H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 BILD C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 BILD N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 BILD H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 BILD N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 BILD C1' C3' *C2' H2'' 0.0 0.0 -115.0 0.0 0.0 RESI DCYT -1.00 ATOM P P 1.50 ! ATOM OP1 ON3 -0.80 ! ATOM OP2 ON3 -0.80 ! H42 H41 ATOM O5' ON2 -0.55 ! \ / ! N4 ATOM C5' CN8 -0.08 ! | ATOM H5' HN7 0.09 ! C4 ATOM H5'' HN7 0.09 ! / \\ GROUP ! H5-C5 N3 ATOM C4' CN6 0.11 ! || | ATOM H4' HN6 0.09 ! H6-C6 C2 ATOM O4' ON6 -0.40 ! \ / \\ ATOM C1' CN6B 0.11 ! N1 O2 ATOM H1' HN6 0.09 ! \ GROUP ! \ ATOM N1 NN2 -0.16 ! \ ATOM C6 CN3 0.11 ! OP1 H5' H4' O4' \ ATOM H6 HN3 0.05 ! | | \ / \ \ GROUP ! -P-O5'-C5'---C4' C1' ATOM C2 CN1 0.53 ! | | \ / \ ATOM O2 ON1C -0.48 ! OP2 H5'' C3'--C2' H1' ATOM N3 NN3 -0.67 ! / \ / \ ATOM C4 CN2 0.62 ! O3' H3' H2'' H2' GROUP ! | ATOM N4 NN1 -0.58 ! ATOM H41 HN1 0.31 ! ATOM H42 HN1 0.27 GROUP ATOM C5 CN3 -0.10 ATOM H5 HN3 0.10 GROUP ATOM C2' CN6C -0.18 ATOM H2'' HN6 0.09 ATOM H2' HN6 0.09 GROUP ATOM C3' CN6 0.01 ATOM H3' HN6 0.09 ATOM O3' ON2 -0.55 BOND P OP1 P OP2 P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 BOND C2 N3 N3 C4 C4 N4 N4 H41 N4 H42 BOND C4 C5 C5 C6 C2' C3' C3' O3' O3' +P BOND C1' H1' C2' H2' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C5 H5 C6 H6 C2' H2'' THET C1' C2' H2'' C3' C2' H2'' H2'' C2' H2' DIHE H2'' C2' C1' O4' H2''' C2' C1' N1 H2'' C2' C1' H1' DIHE H2'' C2' C3' C4' H2'' C2' C3' O3' H2'' C2' C3' H3' ! repeat dihedrals for phosphate multiple periodicities ! for CHARMM21 and previous versions !DIHE -O3' P O5' C5' C3' O3' +P +O5' ! Sugar Gauche Term !DIHE C1' C2' C3' O3' IMPH O2 N1 N3 C2 N4 N3 C5 C4 IMPH H5 C4 C6 C5 H6 C5 N1 C6 IMPH H42 C4 H41 N4 DONO H42 N4 DONO H41 N4 ACCE O2 C2 ACCE N3 ACCE OP1 P ACCE OP2 P ACCE O3' ACCE O4' ACCE O5' BILD -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 BILD -O3' O5' *P OP1 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P OP2 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 BILD O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 BILD C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 BILD C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 BILD C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 BILD C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 BILD O4' C1' N1 C2 1.5251 113.71 -96.0 117.79 1.399 BILD C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 BILD C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 BILD C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 BILD N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 BILD N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 BILD C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 BILD N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 BILD H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 BILD C1' C3' *C2' H2'' 0.0 0.0 -115.0 0.0 0.0 RESI DTHY -1.00 ! ATOM P P 1.50 ! H71 O4 ATOM OP1 ON3 -0.80 ! | || ATOM OP2 ON3 -0.80 ! H72-C7 C4 H3 ATOM O5' ON2 -0.55 ! | \ / \ / ! H73 C5 N3 ATOM C5' CN8 -0.08 ! || | ATOM H5' HN7 0.09 ! H6-C6 C2 ATOM H5'' HN7 0.09 ! \ / \\ GROUP ! N1 O2 ATOM C4' CN6 0.11 ! \ ATOM H4' HN6 0.09 ! \ ATOM O4' ON6 -0.40 ! \ ATOM C1' CN6B 0.11 ! OP1 H5' H4' O4' \ ATOM H1' HN6 0.09 ! | | \ / \ \ GROUP ! -P-O5'-C5'---C4' C1' ATOM N1 NN2 -0.30 ! | | \ / \ ATOM C6 CN3 0.17 ! OP2 H5'' C3'--C2' H1' ATOM H6 HN3 0.13 ! / \ / \ GROUP ! O3' H3' H2'' H2' ATOM C2 CN1 0.57 ! | ATOM O2 ON1 -0.47 ! ATOM N3 NN2U -0.46 ! ATOM H3 HN2 0.36 GROUP ATOM C4 CN1 0.54 ATOM O4 ON1 -0.49 ATOM C5 CN3 -0.15 ATOM C7 CN9 -0.11 ATOM H71 HN7 0.07 ATOM H72 HN7 0.07 ATOM H73 HN7 0.07 GROUP ATOM C2' CN6C -0.18 ATOM H2'' HN6 0.09 ATOM H2' HN6 0.09 GROUP ATOM C3' CN6 0.01 ATOM H3' HN6 0.09 ATOM O3' ON2 -0.55 BOND P OP1 P OP2 P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 BOND C5 C7 C5 C6 C2' C3' C3' O3' O3' +P BOND C1' H1' C2' H2' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C6 H6 C7 H71 C7 H72 C7 H73 BOND C2' H2'' THET C1' C2' H2'' C3' C2' H2'' H2'' C2' H2' DIHE H2'' C2' C1' O4' H2''' C2' C1' N1 H2'' C2' C1' H1' DIHE H2'' C2' C3' C4' H2'' C2' C3' O3' H2'' C2' C3' H3' ! repeat dihedrals for phosphate multiple periodicities ! for CHARMM21 and previous versions !DIHE -O3' P O5' C5' C3' O3' +P +O5' ! Sugar Gauche Terms !DIHE C1' C2' C3' O3' IMPH O2 N1 N3 C2 H3 C2 C4 N3 IMPH O4 N3 C5 C4 H6 N1 C5 C6 IMPH C7 C4 C6 C5 DONO H3 N3 ACCE O2 C2 ACCE O4 C4 ACCE OP1 P ACCE OP2 P ACCE O3' ACCE O4' ACCE O5' BILD -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 BILD -O3' O5' *P OP1 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P OP2 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 BILD O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 BILD C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 BILD C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 BILD C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 BILD C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 BILD O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 BILD C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 BILD C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 BILD C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 BILD N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 BILD N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 BILD C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 BILD C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 BILD C4 C6 *C5 C7 1.4439 120.78 -179.94 121.63 1.5000 BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 BILD C6 C5 C7 H71 0.0 0.0 0.0 0.0 0.0 BILD C5 H71 *C7 H72 0.0 0.0 115.0 0.0 0.0 BILD H71 H72 *C7 H73 0.0 0.0 -115.0 0.0 0.0 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0. 115.0 0.0 0.0 BILD C1' C3' *C2' H2'' 0.0 0.0 -115.0 0.0 0.0 RESI DURA -1.00 ! ATOM P P 1.50 ! O4 ATOM OP1 ON3 -0.80 ! || ATOM OP2 ON3 -0.80 ! C4 H3 ATOM O5' ON2 -0.55 ! / \ / ! H5-C5 N3 ATOM C5' CN8 -0.08 ! || | ATOM H5' HN7 0.09 ! H6-C6 C2 ATOM H5'' HN7 0.09 ! \ / \\ GROUP ! N1 O2 ATOM C4' CN6 0.11 ! \ ATOM H4' HN6 0.09 ! \ ATOM O4' ON6 -0.40 ! \ ATOM C1' CN6B 0.11 ! OP1 H5' H4' O4' \ ATOM H1' HN6 0.09 ! | | \ / \ \ GROUP ! -P-O5'-C5'---C4' C1' ATOM N1 NN2 -0.30 ! | | \ / \ ATOM C6 CN3 0.17 ! OP2 H5'' C3'--C2' H1' ATOM H6 HN3 0.13 ! / \ / \ GROUP ! O3' H3' H2'' H2' ATOM C2 CN1 0.57 ! | ATOM O2 ON1 -0.47 ! ATOM N3 NN2U -0.46 ! ATOM H3 HN2 0.36 GROUP ATOM C4 CN1 0.54 ATOM O4 ON1 -0.49 ATOM C5 CN3 -0.15 ATOM H5 HN3 0.10 GROUP ATOM C2' CN6C -0.18 ATOM H2'' HN6 0.09 ATOM H2' HN6 0.09 GROUP ATOM C3' CN6 0.01 ATOM H3' HN6 0.09 ATOM O3' ON2 -0.55 BOND P OP1 P OP2 P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2 BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 BOND C5 C6 C2' C3' C3' O3' O3' +P BOND C1' H1' C2' H2' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C5 H5 C6 H6 C2' H2'' THET C1' C2' H2'' C3' C2' H2'' H2'' C2' H2' DIHE H2'' C2' C1' O4' H2''' C2' C1' N1 H2'' C2' C1' H1' DIHE H2'' C2' C3' C4' H2'' C2' C3' O3' H2'' C2' C3' H3' ! repeat dihedrals for phosphate multiple periodicities ! for CHARMM21 and previous versions !DIHE -O3' P O5' C5' C3' O3' +P +O5' ! Sugar Gauche Term !DIHE C1' C2' C3' O3' IMPH O2 N1 N3 C2 H3 C2 C4 N3 H5 C4 C6 C5 IMPH O4 N3 C5 C4 H6 N1 C5 C6 DONO H3 N3 ACCE O2 C2 ACCE O4 C4 ACCE OP1 P ACCE OP2 P ACCE O3' ACCE O4' ACCE O5' BILD -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 BILD -O3' O5' *P OP1 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P OP2 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 BILD O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 BILD C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 BILD C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 BILD C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 BILD C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 BILD O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 BILD C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379 BILD C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338 BILD C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373 BILD N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218 BILD N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383 BILD C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227 BILD C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03 BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 BILD C1' C3' *C2' H2'' 0.0 0.0 -115.0 0.0 0.0 RESI DMPA -1.00 ! Dimethylphosphate GROUP ! ATOM P1 P 1.500 ! ATOM O3 ON3 -0.800 ! ATOM O4 ON3 -0.800 ! H11 ATOM O1 ON2 -0.550 ! | ATOM O2 ON2 -0.550 ! H13- C1-H12 ! \ ATOM C1 CN9 -0.170 ! O3 O1 ATOM H11 HN7 0.090 ! \\ / ATOM H12 HN7 0.090 ! (-) P1 ATOM H13 HN7 0.090 ! // \ ! O4 O2 ATOM C2 CN9 -0.170 ! / ATOM H21 HN7 0.090 ! H23-C2-H22 ATOM H22 HN7 0.090 ! | ATOM H23 HN7 0.090 ! H21 ! BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 O2 C2 BOND C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 C2 H23 ! repeat dihedrals for multiple periodicities ! for CHARMM21 and previous versions !DIHE O1 P1 O2 C2 O2 P1 O1 C1 ! IC FOR THE g,g conformation (3-21G* opt. structure) IC O3 P1 O1 C1 1.4723 107.31 000.0 117.79 1.4356 IC O4 P1 O2 C2 1.4722 000.0 000.0 117.79 1.4357 IC O1 P1 O2 C2 1.6343 000.0 73.8 117.79 1.4357 IC O2 P1 O1 C1 1.6344 000.0 73.7 117.79 1.4356 IC H11 C1 O1 P1 1.0827 107.8 174.8 117.79 1.6343 IC H12 C1 O1 P1 1.0800 110.4 54.1 117.79 1.6343 IC H13 C1 O1 P1 1.0848 110.7 294.3 117.79 1.6343 IC H21 C2 O2 P1 1.0827 107.9 174.7 117.79 1.6344 IC H22 C2 O2 P1 1.0800 110.4 54.1 117.79 1.6344 IC H23 C2 O2 P1 1.0848 110.7 294.2 117.79 1.6344 RESI MP_0 0.00 ! Methylphosphate, neutral GROUP ! ! atom order for molvib ATOM C1 CN9 -0.17 ! ATOM O1 ON2 -0.56 ! H11 ATOM P1 P 1.50 ! | ATOM O2 ON4 -0.63 ! H13--C1--H12 ATOM O3 ON4 -0.63 ! | ATOM O4 ON3 -0.64 ! O1 ATOM H11 HN7 0.09 ! | ATOM H12 HN7 0.09 ! O4==P1--O3 ATOM H13 HN7 0.09 ! | \ ATOM H2 HN4 0.43 ! O2 H3 ATOM H3 HN4 0.43 ! \ ! H2 ! BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 BOND C1 H11 C1 H12 C1 H13 O2 H2 O3 H3 ! ester multiple dihedral term ! for CHARMM21 and previous versions !DIHE C1 O1 P1 O2 ! IC IC O3 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 IC O4 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 IC O2 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 IC H1 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 IC H12 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 IC H13 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 IC H2 O2 P1 O1 0.0000 000.00 180.0 000.00 0.0000 IC H3 O3 P1 O1 0.0000 000.00 180.0 000.00 0.0000 ! dummies to analyze cetain angles IC O3 P1 O4 O1 0.0 0.0 0.0 0.0 0.0 RESI MP_1 -1.00 ! Methylphosphate, anionic GROUP ! ! atom order for molvib ATOM C1 CN9 -0.170 ! ATOM O1 ON2 -0.620 ! H11 ATOM P1 P 1.500 ! | ATOM O2 ON4 -0.680 ! H13--C1--H12 ATOM O3 ON3 -0.820 ! | ATOM O4 ON3 -0.820 ! O1 ATOM H11 HN7 0.090 ! | ATOM H12 HN7 0.090 ! O4==P1==O3 (-) ATOM H13 HN7 0.090 ! | ATOM H2 HN4 0.340 ! O2 ! \ ! H2 ! BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 BOND C1 H11 C1 H12 C1 H13 O2 H2 ! ester multiple dihedral term ! for CHARMM21 and previous versions !DIHE C1 O1 P1 O2 ! IC IC O3 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 IC O4 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 IC O2 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 IC H11 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 IC H12 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 IC H13 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 IC H2 O2 P1 O1 0.0000 000.00 000.0 000.00 0.0000 ! dummies to analyze cetain angles IC O3 P1 O4 O1 0.0 0.0 0.0 0.0 0.0 RESI MP_2 -2.00 ! Methylphosphate, dianionic GROUP ! ATOM P1 P 1.100 ! ATOM O1 ON2 -0.400 ! H11 ATOM O2 ON3 -0.900 ! | ATOM O3 ON3 -0.900 ! H13--C1--H12 ATOM O4 ON3 -0.900 ! | GROUP ! O1 ATOM C1 CN9 -0.270 ! | ATOM H11 HN7 0.090 ! (-) O4==P1==O3 (-) ATOM H12 HN7 0.090 ! || ATOM H13 HN7 0.090 ! O2 ! BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 BOND C1 H11 C1 H12 C1 H13 ! ester multiple dihedral term ! for CHARMM21 and previous versions !DIHE C1 O1 P1 O2 ! IC IC O3 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 IC O4 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 IC O2 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 IC H11 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 IC H12 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 IC H13 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 ! dummies to analyze cetain angles IC O3 P1 O4 O1 0.0 0.0 0.0 0.0 0.0 !RESI TIP3 0.00 ! TIPS3P WATER MODEL ! ! GENERATE USING NOANGLE NODIHEDRAL !GROUP !ATOM OH2 OT -0.834 !ATOM H1 HT 0.417 !ATOM H2 HT 0.417 !BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE !ANGLE H1 OH2 H2 ! REQUIRED !ACCEPTOR OH2 !PATCHING FIRS NONE LAST NONE RESI SOD 1.00 ! Sodium Ion GROUP ATOM NA SOD 1.00 PATCHING FIRST NONE LAST NONE RESI MG 2.00 ! Magnesium Ion GROUP ATOM MG MG 2.00 PATCHING FIRST NONE LAST NONE PRES DEO1 0.000 ! Patch to make DEOXYribose in PYRIMIDINES DELETE ATOM O2' ! necessary due to auto-generate dihedrals DELETE ATOM HO2' ! and N1 versus N9 atom in glycosidac link ! use in patch statement GROUP ATOM C2' CN6C -0.18 ATOM H2'' HN6 0.09 ATOM H2' HN6 0.09 BOND C2' H2'' THET C1' C2' H2'' C3' C2' H2'' H2'' C2' H2' DIHE H2'' C2' C1' O4' H2''' C2' C1' N1 H2'' C2' C1' H1' DIHE H2'' C2' C3' C4' H2'' C2' C3' O3' H2'' C2' C3' H3' BILD C1' C3' *C2' H2'' 0.0 0.0 -115.0 0.0 0.0 PRES DEO2 0.000 ! Patch to make DEOXYribose in PURINES DELETE ATOM O2' ! necessary due to auto-generate dihedrals DELETE ATOM HO2' ! and N1 versus N9 atom in glycosidac link ! use in patch statement GROUP ATOM C2' CN6C -0.18 ATOM H2'' HN6 0.09 ATOM H2' HN6 0.09 BOND C2' H2'' THET C1' C2' H2'' C3' C2' H2'' H2'' C2' H2' DIHE H2'' C2' C1' O4' H2'' C2' C1' N9 H2'' C2' C1' H1' DIHE H2'' C2' C3' C4' H2'' C2' C3' O3' H2'' C2' C3' H3' BILD C1' C3' *C2' H2'' 0.0 0.0 -115.0 0.0 0.0 PRES PYRC 0.00 ! Patch to generate CYTOSINE (pyrimidine) ! use in generate statement ! DELETE PHOSPHATE AND RIBOSE ATOMS DELE ATOM P DELE ATOM OP1 DELE ATOM OP2 DELE ATOM O5' DELE ATOM C5' DELE ATOM H5' DELE ATOM H5'' DELE ATOM C4' DELE ATOM H4' DELE ATOM O4' DELE ATOM C1' DELE ATOM H1' DELE ATOM C2' DELE ATOM H2' DELE ATOM O2' DELE ATOM HO2' DELE ATOM C3' DELE ATOM O3' DELE ATOM H3' GROUP ATOM N1 NN2 -0.57 ATOM H1 HN2 0.41 ATOM C6 CN3 0.11 ATOM H6 HN3 0.05 BOND N1 H1 IMPH H1 C6 C2 N1 BILD C5 C6 N1 H1 0.0 0.0 180.0 0.0 0.0 PRES PYRU 0.00 ! Patch to generate URACIL or THYMINE (pyrimidine) ! use in generate statement ! DELETE PHOSPHATE AND RIBOSE ATOMS DELE ATOM P DELE ATOM OP1 DELE ATOM OP2 DELE ATOM O5' DELE ATOM C5' DELE ATOM H5' DELE ATOM H5'' DELE ATOM C4' DELE ATOM H4' DELE ATOM O4' DELE ATOM C1' DELE ATOM H1' DELE ATOM C2' DELE ATOM H2' DELE ATOM O2' DELE ATOM HO2' DELE ATOM C3' DELE ATOM O3' DELE ATOM H3' GROUP ATOM N1 NN2 -0.76 ATOM H1 HN2 0.46 ATOM C6 CN3 0.17 ATOM H6 HN3 0.13 BOND N1 H1 IMPH H1 C6 C2 N1 BILD C5 C6 N1 H1 0.0 0.0 180.0 0.0 0.0 PRES PURG 0.00 ! Patch to generate GUANINE (purine) ! use in generate statement ! DELETE PHOSPHATE AND RIBOSE ATOMS DELE ATOM P DELE ATOM OP1 DELE ATOM OP2 DELE ATOM O5' DELE ATOM C5' DELE ATOM H5' DELE ATOM H5'' DELE ATOM C4' DELE ATOM H4' DELE ATOM O4' DELE ATOM C1' DELE ATOM H1' DELE ATOM C2' DELE ATOM H2' DELE ATOM O2' DELE ATOM HO2' DELE ATOM C3' DELE ATOM O3' DELE ATOM H3' GROUP ATOM N9 NN2 -0.55 ATOM C4 CN5 0.14 ATOM H9 HN2 0.41 BOND N9 H9 IMPH H9 C8 C4 N9 BILD C5 C4 N9 H9 0.0 0.0 180.0 0.0 0.0 PRES PURA 0.00 ! Patch to generate ADENINE (purine) ! use in generate statement ! DELETE PHOSPHATE AND RIBOSE ATOMS DELE ATOM P DELE ATOM OP1 DELE ATOM OP2 DELE ATOM O5' DELE ATOM C5' DELE ATOM H5' DELE ATOM H5'' DELE ATOM C4' DELE ATOM H4' DELE ATOM O4' DELE ATOM C1' DELE ATOM H1' DELE ATOM C2' DELE ATOM H2' DELE ATOM O2' DELE ATOM HO2' DELE ATOM C3' DELE ATOM O3' DELE ATOM H3' GROUP ATOM C5 CN5 0.23 ATOM N7 NN4 -0.63 ATOM C8 CN4 0.38 ATOM H8 HN3 0.18 ATOM N9 NN2 -0.55 ATOM H9 HN2 0.39 BOND N9 H9 IMPH H9 C8 C4 N9 BILD C5 C4 N9 H9 0.0 0.0 180.0 0.0 0.0 PRES 5TER 0.00 ! 5'-terminal HYDROXYL patch, from MeOH ! use in generate statement GROUP ATOM HO5' HN5 0.43 ATOM O5' ON5 -0.66 ATOM C5' CN8 0.05 ATOM H5' HN7 0.09 ATOM H5'' HN7 0.09 ! DELETE ATOM P DELETE ATOM OP1 DELETE ATOM OP2 ! BOND HO5' O5' DONO HO5' O5' BILD HO5' O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 PRES 5MET 0.00 ! 5'-ribose METHYL patch ! use in generate statement GROUP ATOM C5' CN9 -0.27 ATOM H5' HN7 0.09 ATOM H5'' HN7 0.09 ATOM H5'3 HN7 0.09 ! Can't use ''' and avoid conflict with THY ! DELETE ATOM O5' DELETE ATOM P DELETE ATOM OP1 DELETE ATOM OP2 ! BOND C5' H5'3 PRES 5PHO -1.00 ! 5'terminal PHOSPHATE patch ! use in generate statement GROUP ATOM C5' CN8 -0.08 ATOM H5' HN7 0.09 ATOM H5'' HN7 0.09 ATOM P P 1.50 ATOM OP1 ON3 -0.82 ATOM OP2 ON3 -0.82 ATOM O5' ON2 -0.62 ATOM OP3 ON4 -0.68 ATOM HOP3 HN4 0.34 BOND OP3 P HOP3 OP3 ! ester multiple dihedral term !DIHE C5' O5' P OP3 DONO HOP3 OP3 BILD C4' C5' O5' P 0.0000 000.00 180.00 000.00 0.0000 BILD C5' O5' P OP3 0.0000 000.00 -39.52 000.00 0.0000 BILD OP3 O5' *P OP1 0.0000 000.00 -115.82 000.00 0.0000 BILD OP3 O5' *P OP2 0.0000 000.00 115.90 000.00 0.0000 BILD HOP3 OP3 P O5' 0.0000 000.00 180.00 000.00 0.0000 PRES 3TER 0.00 ! 3'terminal HYDROXYL patch, from MeOH ! use in generate statement GROUP ATOM C3' CN6 0.14 ATOM H3' HN6 0.09 ATOM O3' ON5 -0.66 ATOM HO3' HN5 0.43 BOND O3' HO3' DONO HO3' O3' BILD HO3' O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 PRES 3PHO -1.00 ! 3'terminal PHOSPHATE patch ! use in generate statement GROUP ATOM C3' CN6 0.01 ATOM H3' HN6 0.09 ATOM P3 P 1.50 ATOM OP31 ON3 -0.82 ATOM OP32 ON3 -0.82 ATOM O3' ON2 -0.62 ATOM OP33 ON4 -0.68 ATOM H3T HN4 0.34 BOND O3' P3 P3 OP31 P3 OP31 P3 OP33 OP33 H3T ! ester multiple dihedral term !DIHE C3' O3' P3 OP33 DONO H3T OP33 ACCE OP33 ACCE OP31 ACCE OP32 BILD C4' C3' O3' P3 0.0000 000.00 180.00 000.00 0.0000 BILD C3' O3' P3 OP33 0.0000 000.00 -39.52 000.00 0.0000 BILD OP33 O3' *P3 OP31 0.0000 000.00 -115.82 000.00 0.0000 BILD OP33 O3' *P3 OP32 0.0000 000.00 115.90 000.00 0.0000 BILD H3T OP33 P3 O3' 0.0000 000.00 180.00 000.00 0.0000 PRES 25P1 -1.00 ! patch to convert a 3'-5' phosphodiester ! linkage to a 2'-5' in deoxy species ! for PYRIMIDINES due to N1/N9 conflict ! Note: groups from this patch are NOT correct DELE ATOM 1:O3' DELE ATOM 1:H2'' ! alpha versus beta must be checked ! H2' is normally beta GROUP ATOM 1:C3' CN6 -0.18 ATOM 1:H3' HN6 0.09 ATOM 1:H3'' HN6 0.09 GROUP ATOM 1:C2' CN6 0.01 ATOM 1:H2' HN6 0.09 ATOM 1:O2' ON2 -0.55 ATOM 2:P P 1.50 ATOM 2:OP1 ON3 -0.80 ATOM 2:OP2 ON3 -0.80 ATOM 2:O5' ON2 -0.55 ATOM 2:C5' CN8 -0.08 ATOM 2:H5' HN7 0.09 ATOM 2:H5'' HN7 0.09 BOND 1:C3' 1:H3'' BOND 1:C2' 1:O2' 1:O2' 2:P ANGL 1:H3'' 1:C3' 1:C2' 1:H3'' 1:C3' 1:C4' 1:H3'' 1:C3' 1:H3' ANGL 1:O2' 1:C2' 1:H2' 1:O2' 1:C2' 1:C1' 1:O2' 1:C2' 1:C3' ANGL 1:C2' 1:O2' 2:P ANGL 1:O2' 2:P 2:OP1 1:O2' 2:P 2:OP2 1:O2' 2:P 2:O5' DIHE 1:H3'' 1:C3' 1:C2' 1:C1' 1:H3'' 1:C3' 1:C2' 1:H2' DIHE 1:H3'' 1:C3' 1:C2' 1:O2' 1:H3'' 1:C3' 1:C4' 1:O4' DIHE 1:H3'' 1:C3' 1:C4' 1:H4' 1:H3'' 1:C3' 1:C4' 1:C5' DIHE 1:O2' 1:C2' 1:C1' 1:O4' 1:O2' 1:C2' 1:C1' 1:H1' ! this term requires separate purine/pyrmidine patches DIHE 1:O2' 1:C2' 1:C1' 1:N1 DIHE 1:O2' 1:C2' 1:C3' 1:H3' 1:O2' 1:C2' 1:C3' 1:H3'' DIHE 1:O2' 1:C2' 1:C3' 1:C4' 1:C1' 1:C2' 1:O2' 2:P DIHE 1:C3' 1:C2' 1:O2' 2:P 1:H2' 1:C2' 1:O2' 2:P DIHE 1:C2' 1:O2' 2:P 2:OP1 1:C2' 1:O2' 2:P 2:OP2 DIHE 1:C2' 1:O2' 2:P 2:O5' 1:O2' 2:P 2:O5' 2:C5' IC 1:C2' 1:C4' 1:*C3' 1:H3'' 0.0000 000.00 -124.08 000.00 0.0000 PRES 25P2 -1.00 ! patch to convert a 3'-5' phosphodiester ! linkage to a 2'-5' in deoxy compounds ! for PURINES due to N1/N9 conflict ! Note: groups from this patch are NOT correct DELE ATOM 1:O3' DELE ATOM 1:H2'' ! alpha versus beta must be checked ! H2' is normally beta GROUP ATOM 1:C3' CN6 -0.18 ATOM 1:H3' HN6 0.09 ATOM 1:H3'' HN6 0.09 GROUP ATOM 1:C2' CN6 0.01 ATOM 1:H2' HN6 0.09 ATOM 1:O2' ON2 -0.55 ATOM 2:P P 1.50 ATOM 2:OP1 ON3 -0.80 ATOM 2:OP2 ON3 -0.80 ATOM 2:O5' ON2 -0.55 ATOM 2:C5' CN8 -0.08 ATOM 2:H5' HN7 0.09 ATOM 2:H5'' HN7 0.09 BOND 1:C3' 1:H3'' BOND 1:C2' 1:O2' 1:O2' 2:P ANGL 1:H3'' 1:C3' 1:C2' 1:H3'' 1:C3' 1:C4' 1:H3'' 1:C3' 1:H3' ANGL 1:O2' 1:C2' 1:H2' 1:O2' 1:C2' 1:C1' 1:O2' 1:C2' 1:C3' ANGL 1:C2' 1:O2' 2:P ANGL 1:O2' 2:P 2:OP1 1:O2' 2:P 2:OP2 1:O2' 2:P 2:O5' DIHE 1:H3'' 1:C3' 1:C2' 1:C1' 1:H3'' 1:C3' 1:C2' 1:H2' DIHE 1:H3'' 1:C3' 1:C2' 1:O2' 1:H3'' 1:C3' 1:C4' 1:O4' DIHE 1:H3'' 1:C3' 1:C4' 1:H4' 1:H3'' 1:C3' 1:C4' 1:C5' DIHE 1:O2' 1:C2' 1:C1' 1:O4' 1:O2' 1:C2' 1:C1' 1:H1' ! this term requires separate purine/pyrmidine patches DIHE 1:O2' 1:C2' 1:C1' 1:N9 DIHE 1:O2' 1:C2' 1:C3' 1:H3' 1:O2' 1:C2' 1:C3' 1:H3'' DIHE 1:O2' 1:C2' 1:C3' 1:C4' 1:C1' 1:C2' 1:O2' 2:P DIHE 1:C3' 1:C2' 1:O2' 2:P 1:H2' 1:C2' 1:O2' 2:P DIHE 1:C2' 1:O2' 2:P 2:OP1 1:C2' 1:O2' 2:P 2:OP2 DIHE 1:C2' 1:O2' 2:P 2:O5' 1:O2' 2:P 2:O5' 2:C5' IC 1:C2' 1:C4' 1:*C3' 1:H3'' 0.0000 000.00 -124.08 000.00 0.0000 PRES 9MG 0.000 ! 9-Methyl guanine patch ! use in generate statement ! DELETE PHOSPHATE AND RIBOSE ATOMS DELE ATOM P DELE ATOM OP1 DELE ATOM OP2 DELE ATOM O5' DELE ATOM C5' DELE ATOM H5' DELE ATOM H5'' DELE ATOM C4' DELE ATOM H4' DELE ATOM O4' DELE ATOM C1' DELE ATOM H1' DELE ATOM C2' DELE ATOM H2' DELE ATOM O2' DELE ATOM HO2' DELE ATOM C3' DELE ATOM O3' DELE ATOM H3' GROUP ATOM C9 CN9 -0.27 ATOM H91 HN7 0.09 ATOM H92 HN7 0.09 ATOM H93 HN7 0.09 BOND N9 C9 C9 H91 C9 H92 C9 H93 BILD C8 C4 *N9 C9 0.0 0.0 180.0 0.0 0.0 BILD C8 N9 C9 H91 0.0 0.0 180.0 0.0 0.0 BILD N9 H91 *C9 H92 0.0 0.0 -115.0 0.0 0.0 BILD H91 H92 *C9 H93 0.0 0.0 115.0 0.0 0.0 PRES 9EG 0.000 ! 9-Ethyl guanine patch ! use in generate statement ! DELETE PHOSPHATE AND RIBOSE ATOMS DELE ATOM P DELE ATOM OP1 DELE ATOM OP2 DELE ATOM O5' DELE ATOM C5' DELE ATOM H5' DELE ATOM H5'' DELE ATOM C4' DELE ATOM H4' DELE ATOM O4' DELE ATOM C1' DELE ATOM H1' DELE ATOM C2' DELE ATOM H2' DELE ATOM O2' DELE ATOM HO2' DELE ATOM C3' DELE ATOM O3' DELE ATOM H3' GROUP ATOM C9 CN8 -0.18 ATOM H91 HN7 0.09 ATOM H92 HN7 0.09 GROUP ATOM C9B CN9 -0.27 ATOM H9B1 HN7 0.09 ATOM H9B2 HN7 0.09 ATOM H9B3 HN7 0.09 BOND N9 C9 C9 H91 C9 H92 C9 H93 BOND C9 C9B C9B H9B1 C9B H9B2 C9B H9B3 BILD C8 C4 *N9 C9 0.0 0.0 180.0 0.0 0.0 BILD C8 N9 C9 C9B 0.0 0.0 0.0 0.0 0.0 BILD N9 C9B *C9 H91 0.0 0.0 -115.0 0.0 0.0 BILD C9B H91 *C9 H92 0.0 0.0 115.0 0.0 0.0 BILD N9 C9 C9B H9B1 0.0 0.0 180.0 0.0 0.0 BILD C9 H9B1 *C9B H9B2 0.0 0.0 -115.0 0.0 0.0 BILD H9B1 H9B2 *C9B H9B3 0.0 0.0 115.0 0.0 0.0 PRES 9MA 0.00 ! 9-Methyl adenine patch ! use in generate statement ! DELETE PHOSPHATE AND RIBOSE ATOMS DELE ATOM P DELE ATOM OP1 DELE ATOM OP2 DELE ATOM O5' DELE ATOM C5' DELE ATOM H5' DELE ATOM H5'' DELE ATOM C4' DELE ATOM H4' DELE ATOM O4' DELE ATOM C1' DELE ATOM H1' DELE ATOM C2' DELE ATOM H2' DELE ATOM O2' DELE ATOM HO2' DELE ATOM C3' DELE ATOM O3' DELE ATOM H3' GROUP ATOM C9 CN9 -0.27 ATOM H91 HN7 0.09 ATOM H92 HN7 0.09 ATOM H93 HN7 0.09 BOND N9 C9 C9 H91 C9 H92 C9 H93 BILD C8 C4 *N9 C9 0.0 0.0 180.0 0.0 0.0 BILD C4 N9 C9 H91 0.0 0.0 180.0 0.0 0.0 BILD N9 H91 *C9 H92 0.0 0.0 -115.0 0.0 0.0 BILD H91 H92 *C9 H93 0.0 0.0 115.0 0.0 0.0 PRES 1MC 0.000 ! 1-Methyl Cytosine patch ! use in generate statement ! DELETE PHOSPHATE AND RIBOSE ATOMS DELE ATOM P DELE ATOM OP1 DELE ATOM OP2 DELE ATOM O5' DELE ATOM C5' DELE ATOM H5' DELE ATOM H5'' DELE ATOM C4' DELE ATOM H4' DELE ATOM O4' DELE ATOM C1' DELE ATOM H1' DELE ATOM C2' DELE ATOM H2' DELE ATOM O2' DELE ATOM HO2' DELE ATOM C3' DELE ATOM O3' DELE ATOM H3' GROUP ATOM C1 CN9 -0.27 ATOM H11 HN7 0.09 ATOM H12 HN7 0.09 ATOM H13 HN7 0.09 BOND N1 C1 C1 H11 C1 H12 C1 H13 BILD C6 C2 *N1 C1 0.0 0.0 180.0 0.0 0.0 BILD C2 N1 C1 H11 0.0 0.0 180.0 0.0 0.0 BILD N1 H11 *C1 H12 0.0 0.0 -115.0 0.0 0.0 BILD H11 H12 *C1 H13 0.0 0.0 115.0 0.0 0.0 PRES 5MC1 0.00 ! Patch to generate 5-methylcytosine (base only) ! use in generate statement ! DELETE PHOSPHATE AND RIBOSE ATOMS DELE ATOM P DELE ATOM OP1 DELE ATOM OP2 DELE ATOM O5' DELE ATOM C5' DELE ATOM H5' DELE ATOM H5'' DELE ATOM C4' DELE ATOM H4' DELE ATOM O4' DELE ATOM C1' DELE ATOM H1' DELE ATOM C2' DELE ATOM H2' DELE ATOM O2' DELE ATOM HO2' DELE ATOM C3' DELE ATOM O3' DELE ATOM H3' DELE ATOM H5 GROUP ATOM N1 NN2 -0.57 ATOM H1 HN2 0.41 ATOM C6 CN3 0.11 ATOM H6 HN3 0.05 GROUP ATOM C5 CN3D -0.05 ATOM C7 CN9 -0.22 ATOM H5M1 HN7 0.09 ATOM H5M2 HN7 0.09 ATOM H5M3 HN7 0.09 BOND N1 H1 BOND C5 C7 C7 H5M1 C7 H5M2 C7 H5M3 IMPH H1 C6 C2 N1 BILD C5 C6 N1 H1 0.0 0.0 180.0 0.0 0.0 BILD C6 C4 *C5 C7 0.0 0.0 180.0 0.0 0.0 BILD C4 C5 C7 H5M1 0.0 0.0 180.0 0.0 0.0 BILD C5 H5M1 *C7 H5M2 0.0 0.0 -115.0 0.0 0.0 BILD H5M1 H5M2 *C7 H5M3 0.0 0.0 115.0 0.0 0.0 PRES 5MC2 0.00 ! Patch to convert cytosine to 5-methylcytosine ! use in PATCH statement DELE ATOM H5 GROUP ATOM C5 CN3D -0.05 ATOM C7 CN9 -0.22 ATOM H5M1 HN7 0.09 ATOM H5M2 HN7 0.09 ATOM H5M3 HN7 0.09 BOND C5 C7 C7 H5M1 C7 H5M2 C7 H5M3 ANGL C4 C5 C7 C6 C5 C7 ANGL C5 C7 H5M1 C5 C7 H5M2 C5 C7 H5M3 ANGL H5M1 C7 H5M2 H5M1 C7 H5M3 H5M2 C7 H5M3 DIHE C7 C5 C4 N3 C7 C5 C4 N4 DIHE C7 C5 C6 H6 C7 C5 C6 N1 DIHE H5M1 C7 C5 C4 H5M1 C7 C5 C6 DIHE H5M2 C7 C5 C4 H5M2 C7 C5 C6 DIHE H5M3 C7 C5 C4 H5M3 C7 C5 C6 BILD C6 C4 *C5 C7 0.0 0.0 180.0 0.0 0.0 BILD C4 C5 C7 H5M1 0.0 0.0 180.0 0.0 0.0 BILD C5 H5M1 *C7 H5M2 0.0 0.0 -115.0 0.0 0.0 BILD H5M1 H5M2 *C7 H5M3 0.0 0.0 115.0 0.0 0.0 PRES INO1 0.00 ! patch to convert guanine to inosine ! use in patch statement DELE ATOM N2 DELE ATOM H21 DELE ATOM H22 GROUP ATOM N3 NN3I -0.64 ATOM C2 CN4 0.59 ATOM H2 HN3 0.09 ATOM N1 NN2G -0.29 ATOM H1 HN2 0.25 BOND C2 H2 ANGL N1 C2 H2 N3 C2 H2 DIHE H1 N1 C2 H2 C6 N1 C2 H2 C4 N3 C2 H2 IMPR H2 N1 N3 C2 BILD N1 N3 *C2 H2 1.375 124.0 180.0 119.7 1.341 PRES 1MT 0.00 ! 1-Methyl Thymine patch ! use in generate statement ! DELETE PHOSPHATE AND RIBOSE ATOMS DELE ATOM P DELE ATOM OP1 DELE ATOM OP2 DELE ATOM O5' DELE ATOM C5' DELE ATOM H5' DELE ATOM H5'' DELE ATOM C4' DELE ATOM H4' DELE ATOM O4' DELE ATOM C1' DELE ATOM H1' DELE ATOM C2' DELE ATOM H2' DELE ATOM O2' DELE ATOM HO2' DELE ATOM C3' DELE ATOM O3' DELE ATOM H3' GROUP ATOM C1 CN9 -0.27 ATOM H11 HN7 0.09 ATOM H12 HN7 0.09 ATOM H13 HN7 0.09 BOND N1 C1 C1 H11 C1 H12 C1 H13 BILD C6 C2 *N1 C1 0.0 0.0 180.0 0.0 0.0 BILD C2 N1 C1 H11 0.0 0.0 180.0 0.0 0.0 BILD N1 H11 *C1 H12 0.0 0.0 -115.0 0.0 0.0 BILD H11 H12 *C1 H13 0.0 0.0 115.0 0.0 0.0 RESI RIBT 0.00 ! RIBOSE, Wilma Olsen's dihedral model ! which has a 1'amino and a 5'methyl group (as in her paper) GROUP ATOM C5' CN9 -0.27 ! H5'1 HN11 HN12 ATOM H5'1 HN7 0.09 ! | \ / ATOM H5'2 HN7 0.09 ! H5'2- C5' O4' N1 ATOM H5'3 HN7 0.09 ! / \ / \ / GROUP ! H5'3 C4' C1' ATOM N1 NN5 -0.20 ! / | | \ ATOM HN11 HN1 0.10 ! H4' C3'-----C2' H1' ATOM HN12 HN1 0.10 ! / \ / \ GROUP ! O3' H3' H2' O2' ATOM C2' CN6 0.14 ! | | ATOM H2' HN6 0.09 ! HO3' HO2' ATOM O2' ON5 -0.66 ! ATOM HO2' HN5 0.43 GROUP ATOM C3' CN6 0.14 ATOM H3' HN6 0.09 ATOM O3' ON5 -0.66 ATOM HO3' HN5 0.43 GROUP ATOM C1' CN6B 0.11 ATOM H1' HN6 0.09 ATOM C4' CN6 0.11 ATOM H4' HN6 0.09 ATOM O4' ON6 -0.40 BOND C1' O4' C1' H1' C1' N1 N1 HN11 N1 HN12 BOND C1' C2' BOND C2' H2' C2' O2' O2' HO2' C2' C3' C3' H3' BOND C3' O3' O3' HO3' C3' C4' C4' O4' C4' H4' BOND C4' C5' C5' H5'1 C5' H5'2 C5' H5'3 ! GAUCHE TERM ! for CHARMM21 and previous versions !DIHE O3' C3' C2' C1' ! ribose model compound C2*endo minimu IC C4' O4' C1' C2' 1.4525 109.84 0.01 106.85 1.5501 IC O4' C1' C2' C3' 1.4284 106.85 23.59 102.37 1.5478 IC C1' C2' C3' C4' 1.5501 102.37 -36.26 100.54 1.5386 IC C2' C3' C4' O4' 1.5478 100.54 37.42 105.04 1.4525 IC C3' C4' O4' C1' 1.5386 105.04 -24.05 109.84 1.4284 IC N1 C1' C2' C3' 1.4718 115.03 142.01 102.37 1.5478 IC H1' C1' C2' C3' 1.1015 109.14 -92.19 102.37 1.5478 IC C5' C4' O4' C1' 1.5235 108.26 102.92 109.84 1.4284 IC H4' C4' O4' C1' 1.1015 107.70 -140.23 109.84 1.4284 IC O2' C2' C3' C4' 1.4293 111.84 -157.09 100.54 1.5386 IC HO2' O2' C2' C3' 0.9681 103.92 14.18 111.84 1.5478 IC H2' C2' C3' C4' 1.1014 109.54 80.48 100.54 1.5386 IC O3' C3' C4' O4' 1.4352 111.98 -83.02 105.04 1.4525 IC HO3' O3' C3' C4' 0.9650 105.47 38.18 111.98 1.5386 IC H3' C3' C4' O4' 1.1007 110.59 153.45 105.04 1.4525 IC HN11 N1 C1' C2' 1.0098 111.38 68.43 115.03 1.5501 IC HN12 N1 C1' C2' 1.0096 111.07 -173.22 115.03 1.5501 IC H5'1 C5' C4' O4' 1.1110 111.00 -59.60 108.26 1.4525 IC H5'2 C5' C4' O4' 1.1107 110.76 179.64 108.26 1.4525 IC H5'3 C5' C4' O4' 1.1119 110.14 59.84 108.26 1.4525 PATC FIRS NONE LAST NONE RESI DEOT 0.00 ! DEOXYRIBOSE, Wilma Olsen's dihedral model ! 1' amino and 5' methyl group GROUP ATOM C5' CN9 -0.27 ! H5'1 HN11 HN12 ATOM H5'1 HN7 0.09 ! | \ / ATOM H5'2 HN7 0.09 ! H5'2- C5' O4' N1 ATOM H5'3 HN7 0.09 ! / \ / \ / GROUP ! H5'3 C4' C1' ATOM N1 NN5 -0.20 ! / | | \ ATOM HN11 HN1 0.10 ! H4' C3'-----C2' H1' ATOM HN12 HN1 0.10 ! / \ / \ GROUP ! O3' H3' H2'1 H2'2 ATOM C2' CN6C -0.18 ! | ATOM H2'1 HN6 0.09 ! HO3' ATOM H2'2 HN6 0.09 ! GROUP ATOM C3' CN6 0.14 ATOM H3' HN6 0.09 ATOM O3' ON5 -0.66 ATOM HO3' HN5 0.43 GROUP ATOM C1' CN6B 0.11 ATOM H1' HN6 0.09 ATOM C4' CN6 0.11 ATOM H4' HN6 0.09 ATOM O4' ON6 -0.40 BOND C1' O4' C1' H1' C1' N1 N1 HN11 N1 HN12 BOND C1' C2' BOND C2' H2'1 C2' H2'2 C2' C3' C3' H3' BOND C3' O3' O3' HO3' C3' C4' C4' O4' C4' H4' BOND C4' C5' C5' H5'1 C5' H5'2 C5' H5'3 ! GAUCHE TERM ! for CHARMM21 and previous versions !DIHE O3' C3' C2' C1' ! deoxyribose model compound C2*endo minimum IC C4' O4' C1' C2' 1.4556 110.31 -14.32 105.78 1.5315 IC O4' C1' C2' C3' 1.4200 105.78 32.55 102.71 1.5248 IC C1' C2' C3' C4' 1.5315 102.71 -36.74 101.19 1.5432 IC C2' C3' C4' O4' 1.5248 101.19 29.12 105.88 1.4556 IC C3' C4' O4' C1' 1.5432 105.88 -9.56 110.31 1.4200 IC N1 C1' C2' C3' 1.4659 114.38 150.08 102.71 1.5248 IC HN11 N1 C1' C2' 1.0091 111.57 51.56 114.38 1.5315 IC HN12 N1 C1' C2' 1.0093 110.86 -66.78 114.38 1.5315 IC H1' C1' C2' C3' 1.1024 109.82 -83.66 102.71 1.5248 IC C5' C4' O4' C1' 1.5227 107.90 116.96 110.31 1.4200 IC H5'1 C5' C4' O4' 1.1110 110.65 -60.61 107.90 1.4556 IC H5'2 C5' C4' O4' 1.1106 110.69 178.86 107.90 1.4556 IC H5'3 C5' C4' O4' 1.1117 110.22 58.93 107.90 1.4556 IC H4' C4' O4' C1' 1.1012 107.70 -126.13 110.31 1.4200 IC H2'1 C2' C3' C4' 1.0992 111.36 -156.17 101.19 1.5432 IC H2'2 C2' C3' C4' 1.0994 109.88 81.56 101.19 1.5432 IC O3' C3' C4' O4' 1.4238 112.68 -88.97 105.88 1.4556 IC HO3' O3' C3' C4' 0.9616 105.23 49.32 112.68 1.5432 IC H3' C3' C4' O4' 1.1016 110.76 146.70 105.88 1.4556 PATC FIRS NONE LAST NONE RESI NIC 1.00 ! oxidized nicotinamide, jjp1/adm jr. ! ! ! HN71 ! \ ! HN72-N7 H4 ! \ | ! C7 C4 ! / \ / \ ! O7 C3 C5-H5 ! | | ! H2-C2 C6-H6 ! \+ / ! N1 ! | ! H1 ! ! GROUP ATOM H1 HN2 0.45 ATOM N1 NN2 -0.52 ATOM C6 CN3B 0.16 ATOM H6 HN3B 0.19 ATOM C5 CN3 -0.10 ATOM H5 HN3B 0.16 ATOM C4 CN3A -0.05 ATOM H4 HN3B 0.16 ATOM C3 CN3 0.05 ATOM C2 CN3B 0.18 ATOM H2 HN3B 0.16 ATOM C7 CN1A 0.68 ATOM O7 ON1 -0.40 ATOM N7 NN1 -0.82 ATOM HN71 HN1 0.34 ! trans to O7 ATOM HN72 HN1 0.36 ! cis to O7 BOND N1 H1 N1 C6 C6 H6 C6 C5 C5 H5 BOND C5 C4 C4 H4 C4 C3 C3 C2 N1 C2 BOND C2 H2 C3 C7 C7 O7 C7 N7 N7 HN71 N7 HN72 ! amide impropers IMPH C7 N7 C3 O7 C7 C3 N7 O7 IMPH N7 C7 HN72 HN71 N7 C7 HN71 HN72 ! ring hydrogen impropers IMPH H1 C2 C6 N1 H6 N1 C5 C6 H5 C6 C4 C5 IMPH H4 C5 C3 C4 H2 C3 N1 C2 ! ic table for analysis IC N1 C6 C5 C4 0.0000 000.00 000.00 000.00 0.000 IC C6 C5 C4 C3 0.0000 000.00 000.00 000.00 0.000 IC C5 C4 C3 C2 0.0000 000.00 000.00 000.00 0.000 IC C4 C3 C2 N1 0.0000 000.00 000.00 000.00 0.000 IC C4 C3 C2 H2 0.0000 000.00 000.00 000.00 0.000 IC C3 C2 N1 C6 0.0000 000.00 000.00 000.00 0.000 IC C2 N1 C6 C5 0.0000 000.00 000.00 000.00 0.000 IC C3 C2 N1 H1 0.0000 000.00 000.00 000.00 0.000 IC C2 N1 C6 H6 0.0000 000.00 000.00 000.00 0.000 IC N1 C6 C5 H5 0.0000 000.00 000.00 000.00 0.000 IC C6 C5 C4 H4 0.0000 000.00 000.00 000.00 0.000 IC C5 C4 C3 C7 0.0000 000.00 000.00 000.00 0.000 IC N1 C2 C3 C7 0.0000 000.00 000.00 000.00 0.000 IC C4 C3 C7 O7 0.0000 000.00 000.00 000.00 0.000 IC C4 C3 C7 N7 0.0000 000.00 000.00 000.00 0.000 IC O7 C7 N7 HN71 0.0000 000.00 000.00 000.00 0.000 IC O7 C7 N7 HN72 0.0000 000.00 000.00 000.00 0.000 PATCH FIRST NONE LAST NONE RESI NICH 0.00 ! reduced nicotinamide, jjp1/adm jr. ! ! H15 ! \ ! H16-N14 H8 H17 ! \ \ / ! C12 C7 ! / \ / \ ! O13 C9 C5-H6 ! | | ! H11-C10 C3-H4 ! \ / ! N2 ! | ! H1 ! ! entire molecule is one group GROUP ATOM H1 HN2 0.42 ATOM N2 NN2 -0.69 ATOM C3 CN3C -0.06 ATOM H4 HN3 0.17 ATOM C5 CN3 -0.18 ATOM H6 HN3 0.14 ATOM C7 CN8 -0.28 ATOM H8 HN7 0.09 ATOM H17 HN7 0.09 ATOM C10 CN3C -0.10 ATOM H11 HN3 0.14 ATOM C9 CN3 0.36 ! ATOM C12 CN1A 0.55 ! ATOM O13 ON1 -0.51 ! ATOM N14 NN1 -0.72 ! ATOM H15 HN1 0.26 ! trans to O13 ATOM H16 HN1 0.32 ! cis to O13 BOND N2 H1 N2 C3 C3 H4 C3 C5 C5 H6 BOND C5 C7 C7 H8 C7 H17 C7 C9 C9 C10 N2 C10 BOND C10 H11 C9 C12 C12 O13 C12 N14 N14 H15 N14 H16 ! amide impropers IMPH C12 N14 C9 O13 C12 C9 N14 O13 IMPH N14 C12 H16 H15 N14 C12 H15 H16 ! ring hydrogen impropers IMPH H1 C10 C3 N2 H4 N2 C5 C3 H6 C3 C7 C5 IMPH H11 C9 N2 C10 ! ic table for analysis IC N2 C3 C5 C7 0.0000 000.00 000.00 000.00 0.000 IC C3 C5 C7 C9 0.0000 000.00 000.00 000.00 0.000 IC C5 C7 C9 C10 0.0000 000.00 000.00 000.00 0.000 IC C7 C9 C10 N2 0.0000 000.00 000.00 000.00 0.000 IC C9 C10 N2 C3 0.0000 000.00 000.00 000.00 0.000 IC C10 N2 C3 C5 0.0000 000.00 000.00 000.00 0.000 IC C9 C10 N2 H1 0.0000 000.00 000.00 000.00 0.000 IC C10 N2 C3 H4 0.0000 000.00 000.00 000.00 0.000 IC N2 C3 C5 H6 0.0000 000.00 000.00 000.00 0.000 IC C3 C5 C7 H8 0.0000 000.00 000.00 000.00 0.000 IC C3 C5 C7 H17 0.0000 000.00 000.00 000.00 0.000 IC C5 C7 C9 C12 0.0000 000.00 000.00 000.00 0.000 IC N2 C10 C9 C12 0.0000 000.00 000.00 000.00 0.000 IC C7 C9 C12 O13 0.0000 000.00 000.00 000.00 0.000 IC C7 C9 C12 N14 0.0000 000.00 000.00 000.00 0.000 IC O13 C12 N14 H15 0.0000 000.00 000.00 000.00 0.000 IC O13 C12 N14 H16 0.0000 000.00 000.00 000.00 0.000 PATCH FIRST NONE LAST NONE RESI PPI1 -3.00 ! Inorganic phosphate, jjp1/adm jr. GROUP ! ATOM C1 CN9 -0.17 ! ATOM O11 ON2 -0.62 ! ATOM P1 P 1.50 ! H11 ATOM O12 ON2 -0.74 ! | ATOM O13 ON3 -0.82 ! H13--C1--H12 ATOM O14 ON3 -0.82 ! | ! O11 ATOM P2 P2 1.10 ! | ATOM O22 ON3 -0.90 ! O14==P1==O13 (-) ATOM O23 ON3 -0.90 ! | ATOM O24 ON3 -0.90 ! O12 ! | ATOM H11 HN7 0.09 ! (-) O24==P2==O23 (-) ATOM H12 HN7 0.09 ! || ATOM H13 HN7 0.09 ! O22 BOND P1 O11 P1 O12 P1 O13 P1 O14 O11 C1 BOND C1 H11 C1 H12 C1 H13 BOND O12 P2 P2 O22 P2 O23 P2 O24 ! IC Table IC C1 O11 P1 O12 0.0000 000.00 180.0 000.00 0.0000 IC O11 P1 O12 P2 0.0000 000.00 180.0 000.00 0.0000 IC P1 O12 P2 O22 0.0000 000.00 180.0 000.00 0.0000 IC C1 O11 P1 O13 0.0000 000.00 60.0 000.00 0.0000 IC C1 O11 P1 O14 0.0000 000.00 -60.0 000.00 0.0000 IC P1 O12 P2 O23 0.0000 000.00 60.0 000.00 0.0000 IC P1 O12 P2 O24 0.0000 000.00 -60.0 000.00 0.0000 IC P1 O11 C1 H11 0.0000 000.00 180.0 000.00 0.0000 IC P1 O11 C1 H12 0.0000 000.00 60.0 000.00 0.0000 IC P1 O11 C1 H13 0.0000 000.00 -60.0 000.00 0.0000 PATC FIRS NONE LAST NONE RESI ADP -3.00 ! adenosine diphosphate, jjp1/adm jr. ! atom names correspond to pdb nomenclature GROUP ATOM C4' CN6 0.11 ! HN61 HN62 ATOM H4' HN6 0.09 ! \ / ATOM O4' ON6 -0.40 ! N6 ATOM C1' CN6B 0.11 ! | ATOM H1' HN6 0.09 ! C6 GROUP ! // \ ATOM C5 CN5 0.23 ! N1 C5--N7\\ ATOM N7 NN4 -0.63 ! | || C8-H8 ATOM C8 CN4 0.38 ! C2 C4--N9/ ATOM H8 HN3 0.18 ! / \\ / \ ATOM N9 NN2 -0.16 ! H2 N3 \ GROUP ! \ ATOM N1 NN3A -0.74 ! \ ATOM C2 CN4 0.53 ! \ ATOM H2 HN3 0.16 ! O3B O1A H5'1 H4' O4' \ ATOM N3 NN3A -0.69 ! | | | \ / \ \ ATOM C4 CN5 0.31 ! O1B=PB-O3A--PA-O5'-C5'---C4' C1' ATOM C6 CN2 0.43 ! | | | \ / \ GROUP ! O2B O2A H5'2 C3'--C2' H1' ATOM N6 NN1 -0.80 ! / \ / \ ATOM HN61 HN1 0.40 ! O3' H3' O2' H2' ATOM HN62 HN1 0.40 ! | | GROUP ! HO3' HO2' ATOM C2' CN6 0.14 ! ATOM H2' HN6 0.09 ATOM O2' ON5 -0.66 ATOM HO2' HN5 0.43 GROUP ATOM C3' CN6 0.14 ATOM H3' HN6 0.09 ATOM O3' ON5 -0.66 ATOM HO3' HN5 0.43 GROUP ATOM C5' CN8 -0.08 ATOM H5'1 HN7 0.09 ATOM H5'2 HN7 0.09 ATOM O5' ON2 -0.62 ATOM PA P 1.50 ATOM O1A ON3 -0.82 ATOM O2A ON3 -0.82 ATOM O3A ON2 -0.74 ATOM PB P2 1.10 ATOM O1B ON3 -0.90 ATOM O2B ON3 -0.90 ATOM O3B ON3 -0.90 BOND PB O3A PB O1B PB O2B PB O3B O3A PA BOND PA O1A PA O2A PA O5' O3' HO3' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C4 C5 N3 C2 C2 N1 N1 C6 C6 N6 BOND N6 HN61 N6 HN62 C6 C5 C5 N7 N7 C8 BOND C2' C3' C2' O2' O2' HO2' C3' O3' BOND C1' H1' C2' H2' C3' H3' C4' H4' C5' H5'1 BOND C5' H5'2 C8 H8 C2 H2 IMPH HN62 C6 HN61 N6 N6 N1 C5 C6 H2 N1 N3 C2 IMPH H8 N7 N9 C8 DONO HN61 N6 DONO HN62 N6 DONO HO2' O2' ACCE N3 ACCE N7 ACCE N1 ACCE O1A PA ACCE O2A PA ACCE O2' ACCE O3' ACCE O4' ACCE O5' ACCE O3A ACCE O3B ACCE O2B ACCE O1B IC PB O3A PA O2A 0.0000 0.0000 0.0000 0.0000 0.0000 IC PA O3A PB O1B 0.0000 0.0000 0.0000 0.0000 0.0000 IC PB O3A PA O5' 0.0000 0.0000 0.0000 0.0000 0.0000 IC C5' O5' PA O1A 0.0000 000.00 60.0 000.00 0.0000 IC C5' O5' PA O2A 0.0000 000.00 -60.0 000.00 0.0000 IC PA O3A PB O2B 0.0000 000.00 60.0 000.00 0.0000 IC PA O3A PB O3B 0.0000 000.00 -60.0 000.00 0.0000 IC PA O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 IC HO3' O3' C3' C4' 0.9650 105.47 38.18 111.98 1.5386 IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 HN61 1.337 121.2 0.0 119.0 1.01 IC HN61 C6 *N6 HN62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 HN61 1.337 119.0 0.0 119.0 1.01 IC HN61 C6 *N6 HN62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 IC HO2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'1 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'2 0.0 0.0 115.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI ATP -4.00 !adenosine triphosphate , jjp1/adm jr. !atom names correspond to pdb nomenclature ! GROUP ATOM C4' CN6 0.11 ! HN61 HN62 ATOM H4' HN6 0.09 ! \ / ATOM O4' ON6 -0.40 ! N6 ATOM C1' CN6B 0.11 ! | ATOM H1' HN6 0.09 ! C6 GROUP ! // \ ATOM C5 CN5 0.23 ! N1 C5--N7\\ ATOM N7 NN4 -0.63 ! | || C8-H8 ATOM C8 CN4 0.38 ! C2 C4--N9/ ATOM H8 HN3 0.18 ! / \\ / \ ATOM N9 NN2 -0.16 ! H2 N3 \ GROUP ! \ ATOM N1 NN3A -0.74 ! \ ATOM C2 CN4 0.53 ! \ ATOM H2 HN3 0.16 ! (-)O3G O2B O1A H5'1 H4' O4' \ ATOM N3 NN3A -0.69 ! | | | | \ / \ \ ATOM C4 CN5 0.31 !O1G=PG-O3B-PB-O3A-PA-O5*-C5*---C4' C1' ATOM C6 CN2 0.43 ! | | | | \ / \ GROUP ! (-)O2G (-)O1B (-)O2A H5'2 C3'--C2' H1' ATOM N6 NN1 -0.80 ! / \ / \ ATOM HN61 HN1 0.40 ! O3' H3' O2' H2' ATOM HN62 HN1 0.40 ! | | GROUP ! HO3' HO2' ATOM C2' CN6 0.14 ! ATOM H2' HN6 0.09 ATOM O2' ON5 -0.66 ATOM HO2' HN5 0.43 GROUP ATOM C3' CN6 0.14 ATOM H3' HN6 0.09 ATOM O3' ON5 -0.66 ATOM HO3' HN5 0.43 GROUP ATOM C5' CN8 -0.08 ATOM H5'1 HN7 0.09 ATOM H5'2 HN7 0.09 ATOM O5' ON2 -0.62 ATOM PA P 1.50 ATOM O1A ON3 -0.82 ATOM O2A ON3 -0.82 ATOM O3A ON2 -0.74 ATOM PB P2 1.50 ATOM O1B ON3 -0.82 ATOM O2B ON3 -0.82 ATOM O3B ON2 -0.86 ! charge adjusted to yield total triP of -4.0 ATOM PG P2 1.10 ATOM O1G ON3 -0.90 ATOM O2G ON3 -0.90 ATOM O3G ON3 -0.90 BOND O5' C5' O5' PA PA O1A PA O2A PA O3A BOND O3A PB PB O1B PB O2B PB O3B O3B PG BOND PG O1G PG O2G PG O3G BOND C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C4 C5 N3 C2 C2 N1 N1 C6 C6 N6 BOND N6 HN61 N6 HN62 C6 C5 C5 N7 N7 C8 BOND C2' C3' C2' O2' O2' HO2' C3' O3' O3' HO3' BOND C1' H1' C2' H2' C3' H3' C4' H4' C5' H5'1 BOND C5' H5'2 C8 H8 C2 H2 IMPH HN62 C6 HN61 N6 N6 N1 C5 C6 H2 N1 N3 C2 IMPH H8 N7 N9 C8 DONO HN61 N6 DONO HN62 N6 DONO HO2' O2' ACCE N3 ACCE N7 ACCE N1 ACCE O1A PA ACCE O2A PA ACCE O2' ACCE O3' ACCE O4' ACCE O5' ACCE O3A ACCE O2B ACCE O1B ACCE O3B ACCE O3G ACCE O2G ACCE O2G IC PB O3A PA O2A 0.0000 0.0000 0.0000 0.0000 0.0000 IC PA O3A PB O1B 0.0000 0.0000 0.0000 0.0000 0.0000 IC PB O3A PA O5' 0.0000 0.0000 0.0000 0.0000 0.0000 IC PA O3A PB O3B 0.0000 000.00 180.0 000.00 0.0000 IC O3A PB O3B PG 0.0000 000.00 180.0 000.00 0.0000 IC PB O3B PG O1G 0.0000 000.00 180.0 000.00 0.0000 IC C5' O5' PA O1A 0.0000 000.00 60.0 000.00 0.0000 IC C5' O5' PA O2A 0.0000 000.00 -60.0 000.00 0.0000 IC PA O3A PB O1B 0.0000 000.00 60.0 000.00 0.0000 IC PA O3A PB O2B 0.0000 000.00 -60.0 000.00 0.0000 IC PB O3B PG O2G 0.0000 000.00 60.0 000.00 0.0000 IC PB O3B PG O3G 0.0000 000.00 -60.0 000.00 0.0000 IC PA O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 IC HO3' O3' C3' C4' 0.9650 105.47 38.18 111.98 1.5386 IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 HN61 1.337 121.2 0.0 119.0 1.01 IC HN61 C6 *N6 HN62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 HN61 1.337 119.0 0.0 119.0 1.01 IC HN61 C6 *N6 HN62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 IC HO2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'1 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'2 0.0 0.0 115.0 0.0 0.0 PATC FIRS NONE LAST NONE PRES 5DP -3.00 ! patch to create 5' diphosphate on nucleotides, jjp1/adm jr. ! as in ADP, use in generate statement GROUP ATOM C5' CN8 -0.08 ATOM H5'1 HN7 0.09 ATOM H5'2 HN7 0.09 ATOM O5' ON2 -0.62 ATOM P P 1.50 ATOM OP1 ON3 -0.82 ATOM OP2 ON3 -0.82 ATOM O13 ON2 -0.74 ATOM P2 P2 1.10 ATOM O21 ON3 -0.90 ATOM O22 ON3 -0.90 ATOM O23 ON3 -0.90 BOND P O13 O13 P2 BOND P2 O21 P2 O22 P2 O23 ACCE O13 ACCE O21 ACCE O22 ACCE O23 IC C5' O5' P O13 0.0000 000.00 180.0 000.00 0.0000 IC O5' P O13 P2 0.0000 000.00 180.0 000.00 0.0000 IC P O13 P2 O21 0.0000 000.00 180.0 000.00 0.0000 IC P O13 P2 O22 0.0000 000.00 60.0 000.00 0.0000 IC P O13 P2 O23 0.0000 000.00 -60.0 000.00 0.0000 PATC FIRS NONE LAST NONE RESI NAD -1.00 ! oxidized nicotinamide adenine dinucleotide, jjp1/adm jr. ! atom names correspond to pdb nomenclature ! GROUP ! ATOM C4B CN6 0.11 ! H61A H62A ATOM H4B HN6 0.09 ! \ / ATOM O4B ON6 -0.40 ! N6A ATOM C1B CN6B 0.11 ! | ATOM H1B HN6 0.09 ! C6A GROUP ! // \ ATOM C5A CN5 0.23 ! N1A C5A--N7A\\ ATOM N7A NN4 -0.63 ! | || C8A-H8A ATOM C8A CN4 0.38 ! C2A C4A--N9A/ ATOM H8A HN3 0.18 ! / \\ / \ ATOM N9A NN2 -0.16 ! H2A N3A \ GROUP ! \ ATOM N1A NN3A -0.74 ! \ ATOM C2A CN4 0.53 ! \ ATOM H2A HN3 0.16 ! O1N O1A H51A H4B O4B \ ATOM N3A NN3A -0.69 ! | | | \ / \ \ ATOM C4A CN5 0.31 ! O5D-PN-O3--PA-O5B--C5B--C4B C1B ATOM C6A CN2 0.43 ! \ | | | \ / \ GROUP ! \ O2N O2A H52A C3B--C2B H1B ATOM N6A NN1 -0.80 ! \ / \ / \ ATOM H61A HN1 0.40 ! \ O3B H3B O2B H2B ATOM H62A HN1 0.40 ! \ | | GROUP ! \ HO3A HO2A ATOM C2B CN6 0.14 ! \ H71N ATOM H2B HN6 0.09 ! \ \ ATOM O2B ON5 -0.66 ! \ H72N-N7N H4N ATOM HO2A HN5 0.43 ! \ \ | GROUP ! \ C7N C4N ATOM C3B CN6 0.14 ! \ / \ / \ ATOM H3B HN6 0.09 ! \ O7N C3N C5N-H5N ATOM O3B ON5 -0.66 ! \ | | ATOM HO3A HN5 0.43 ! \ H51N H4D O4D H2N-C2N C6N-H6N GROUP ! \ | \ / \ \+ / ATOM C5B CN8 -0.08 ! C5D---C4D C1D----------N1N ATOM H52A HN7 0.09 ! | \ / \ ATOM H51A HN7 0.09 ! H52N C3D--C2D H1D ATOM PA P 1.50 ! / \ / \ ATOM O1A ON3 -0.82 ! O3D H3D O2D H2D ATOM O2A ON3 -0.82 ! | | ATOM O5B ON2 -0.62 ! HO3N HO2N ATOM O3 ON2 -0.68 ATOM PN P 1.50 ATOM O1N ON3 -0.82 ATOM O2N ON3 -0.82 ATOM O5D ON2 -0.62 ATOM C5D CN9 -0.08 ATOM H51N HN7 0.09 ATOM H52N HN7 0.09 GROUP ATOM C2D CN6 0.14 ATOM H2D HN6 0.09 ATOM O2D ON5 -0.66 ATOM HO2N HN5 0.43 GROUP ATOM C3D CN6 0.14 ATOM H3D HN6 0.09 ATOM O3D ON5 -0.66 ATOM HO3N HN5 0.43 GROUP ATOM C1D CN6B 0.11 ATOM H1D HN6 0.09 ATOM C4D CN6 0.11 ATOM H4D HN6 0.09 ATOM O4D ON6 -0.40 GROUP ATOM N1N NN2 -0.07 ATOM C6N CN3B 0.16 ATOM H6N HN3B 0.19 ATOM C5N CN3 -0.10 ATOM H5N HN3B 0.16 ATOM C4N CN3A -0.05 ATOM H4N HN3B 0.16 ATOM C3N CN3 0.05 ATOM C2N CN3B 0.18 ATOM H2N HN3B 0.16 ATOM C7N CN1A 0.68 ATOM O7N ON1 -0.40 ATOM N7N NN1 -0.82 ATOM H71N HN1 0.34 ! trans to amide O ATOM H72N HN1 0.36 ! cis to amide O BOND N1A C2A C2A N3A N3A C4A C4A C5A C5A C6A BOND C6A N6A C6A N1A C5A N7A N7A C8A C8A N9A BOND N9A C4A C2A H2A N6A H61A N6A H62A C8A H8A BOND N9A C1B C1B C2B C2B C3B C3B C4B C4B O4B BOND O4B C1B C1B H1B C2B O2B O2B HO2A C2B H2B BOND C3B H3B C3B O3B O3B HO3A C4B H4B C4B C5B BOND C5B H51A C5B H52A C5B O5B O5B PA PA O1A BOND PA O2A PA O3 O3 PN PN O1N PN NO2 BOND PN O5D O5D C5D C5D H51N C5D H52N C5D C4D BOND C4D O4D O4D C1D C1D C2D C2D C3D C3D C4D BOND C1D H1D C2D H2D C2D O2D O2D HO2N C3D H3D BOND C3D O3D O3D HO3N C4D H4D C1D N1N N1N C2N BOND C2N C3N C3N C4N C4N C5N C5N C6N C6N N1N BOND C2N H2N C3N C7N C7N O7N C7N N7N N7N H71N BOND N7N H72N C4N H4N C5N H5N C6N H6N O2N PN ! adenine impropers IMPH H62A C6A H61A N6A N6A N1A C5A C6A H2A N1A N3A AC2 IMPH H8A N7A N9A AC8 ! amide impropers IMPH C7N N7N C3N O7N C7N C3N N7N O7N IMPH N7N C7N H71N H72N N7N C7N H72N H71N ! ring hydrogen impropers IMPH H6N N1N C5N C6N H5N C6N C4N C5N IMPH H4N C5N C3N C4N H2N C3N N1N C2N DONO H61A N6A DONO H62A N6A DONO HO2A O2B DONO HO3A O3B ACCE N1A ACCE AN3 ACCE AN7 ACCE O4B ACCE O2B ACCE O3B ACCE O5B ACCE O1A PA ACCE O2A PA ACCE O3 ACCE O1N PN ACCE O2N PN ACCE O5D ACCE O4D ACCE O3D ACCE O2D ACCE O7N DONO HO2N O2D DONO HO3N O3D DONO H71N N7N DONO H72N N7N IC PN O3 PA O1A 0.0000 0.000 0.0000 0.0000 0.0000 IC PN O3 PA O2A 0.0000 0.000 0.0000 0.0000 0.0000 IC PN O3 PA O5B 0.0000 0.000 0.0000 0.0000 0.0000 IC H52A C5B C4B C3B 0.0000 0.000 0.0000 0.0000 0.0000 IC O5B C5B C4B O4B 0.0000 0.000 0.0000 0.0000 0.0000 IC O4B C1B N9A C8A 0.0000 0.000 0.0000 0.0000 0.0000 IC PA O3 PN O5D 1.4863 65.28 -169.00 98.59 1.5977 IC C5B O5B PA O3 1.4232 127.31 -165.10 103.27 1.4863 IC C5B O5B PA O2A 1.4232 127.31 73.33 111.48 1.4836 IC H51A C5B C4B C3B 0.9935 120.00 -58.20 111.58 1.6942 IC PA O3 PN O1N 1.4863 65.28 78.51 108.97 1.4756 IC PA O3 PN O2N 1.4863 65.28 -54.29 112.88 1.4636 IC PA O5B C5B C4B 1.5901 127.31 121.29 111.63 1.5491 IC O1A PA O5B C5B 1.5901 127.31 121.29 127.31 1.4232 IC O5B C5B C4B C3B 1.4232 111.63 -58.20 111.58 1.6942 IC C5B C4B C3B O3B 1.5491 111.58 128.42 114.19 1.4337 IC HO3A O3B C3B C4B 0.9671 98.77 147.40 114.19 1.6942 IC O4B C3B *C4A C5B 1.8868 112.95 -118.10 111.58 1.5491 IC C2B C4B *C3B O3B 1.5097 93.22 -117.72 114.19 1.4337 IC C4B C3B C2B C1B 1.6942 93.22 -12.93 117.82 1.5415 IC C3B C2B C1B N9A 1.5097 117.82 135.56 115.01 1.4847 IC O4B C1B N9A C4A 1.3646 95.44 -90.72 125.96 1.4013 IC C1B C4A *N9A C8A 1.4847 125.96 -176.52 105.34 1.3777 IC C4A N9A C8A N7A 1.4013 105.34 -0.07 114.01 1.3282 IC C8A N9A C4A C5A 1.3777 105.34 0.11 105.06 1.3782 IC C8A N7A C5A C6A 1.3282 103.21 -179.92 130.78 1.4146 IC N7A C5A C6A N1A 1.3814 130.78 -179.94 117.85 1.3482 IC C5A C6A N1A C2A 1.4146 117.85 -0.14 118.87 1.3300 IC N9A C5A *C4A N3A 1.4013 105.06 -179.67 126.14 1.3648 IC C5A N1A *C6A N6A 1.4146 117.85 179.89 119.69 1.3419 IC N1A C6A N6A H61A 1.3482 119.69 -0.39 116.60 0.9912 IC H61A C6A *N6A H62A 0.9912 116.60 -179.02 116.94 0.9978 IC C5A N1A *C6A N6A 1.4146 117.85 179.89 119.69 1.3419 IC N1A C6A N6A H61A 1.3482 119.69 -0.39 116.60 0.9912 IC H61A C6A *N6A H62A 0.9912 116.60 -179.02 116.94 0.9978 IC N9A N7A *C8A H8A 1.3777 114.01 -179.37 126.34 1.0962 IC N1A N3A *C2A H2A 1.3300 129.42 179.97 114.82 1.0928 IC C1B C3B *C2A O2B 1.5415 117.82 -145.06 114.13 1.4294 IC H2B O2B C2B C3B 2.0386 31.12 -93.63 114.13 1.5097 IC HO2A O2B C2B C3B 0.9953 99.36 -93.63 114.13 1.5097 IC O4B C2B *C1B H1B 1.3646 120.77 -114.99 109.65 1.1105 IC C1B C3B *C2A H2B 1.5415 117.82 108.23 86.44 1.0999 IC C2B C4B *C3B H3B 1.5097 93.22 117.28 111.94 1.1110 IC C3B O4B *C4A H4B 1.6942 112.95 -140.26 57.99 1.0000 IC C4B O5B *C5A H52A 1.5491 111.63 -123.75 111.23 1.1111 IC C4B O5B *C5A H52A 1.5491 111.63 -123.75 111.23 1.1111 IC C5D O5D PN O2N 1.4451 128.40 -49.72 108.83 1.4636 IC H51N C5D O5D PN 1.1110 109.50 115.00 128.40 1.5977 IC H52N C5D O5D PN 1.1110 109.50 -115.00 128.40 1.5977 IC PN O5D C5D C4D 1.5977 128.40 0.00 110.10 1.5160 IC O5D C5D C4D C3D 1.4451 110.10 0.00 108.50 1.5160 IC C5D C4D C3D C2D 1.5160 108.50 0.00 111.00 1.5160 IC C4D C3D C2D C1D 1.5160 111.00 0.00 105.50 1.5270 IC C3D C2D C1D O4D 1.5160 105.50 0.00 105.00 1.4100 IC C2D C1D O4D C4D 1.5270 105.00 0.00 117.86 1.4712 IC O2D C2D C1D O4D 1.4200 110.10 180.00 105.00 1.4100 IC HO2N O2D C2D C1D 0.9600 106.00 180.00 110.10 1.5270 IC O4D C2D *C1D H1D 1.4100 105.00 -115.00 110.10 1.1110 IC C1D C3D *C2N H2D 1.5270 105.50 115.00 110.10 1.1110 IC C2D C4D *C3N H3D 1.5160 111.00 115.00 110.10 1.1110 IC C3D O4D *C4N H4D 1.5160 100.64 -115.00 107.24 1.1110 IC C4D O5D *C5N H52N 1.5160 110.10 -115.00 109.50 1.1110 IC C4D O5D *C5N H51N 1.5160 110.10 115.00 109.50 1.1110 IC C3D C2D C1D N1N 1.5160 105.50 0.00 113.70 1.4800 IC O3D C3D C2D C1D 1.4200 110.10 180.00 105.50 1.5270 IC HO3N O3D C3D C2D 0.9600 106.00 180.00 110.10 1.5160 IC C2D C1D N1N C2N 1.5270 113.70 0.00 121.70 1.3150 IC C1D N1N C2N C3N 1.4800 121.70 0.00 122.00 1.3500 IC N1N C2N C3N C4N 1.3150 122.00 0.00 118.00 1.3600 IC C2N C3N C4N C5N 1.3500 118.00 0.00 118.00 1.3600 IC C3N C4N C5N C6N 1.3600 118.00 0.00 118.00 1.3500 IC C4N C5N C6N N1N 1.3600 118.00 0.00 124.51 1.2199 IC C5N C6N N1N C2N 1.3500 124.51 0.00 119.49 1.3150 IC N1N C2N C3N C7N 1.3150 122.00 0.00 131.80 1.4800 IC C2N C3N C7N O7N 1.3500 131.80 0.00 118.50 1.2300 IC C2N C3N C7N N7N 1.3500 131.80 0.00 113.00 1.3600 IC O7N C7N N7N H71N 1.2300 0.00 180.00 120.00 1.0000 IC O7N C7N N7N H72N 1.2300 0.00 0.00 120.00 1.0000 IC C2N C3N C4N H4N 1.3500 118.00 0.00 121.00 1.0900 IC C3N C4N C5N H5N 1.3600 118.00 0.00 119.00 1.0900 IC C4N C5N C6N H6N 1.3600 118.00 0.00 120.50 1.0900 IC C6N N1N C2N H2N 1.2199 119.49 0.00 117.50 1.0900 PATCH FIRST NONE LAST NONE RESI NADH -2.00 ! reduced nicotinamide adenine dinucleotide, jjp1/adm jr. ! atom names correspond to pdb nomenclature ! GROUP ! ATOM C4B CN6 0.11 ! H61A H62A ATOM H4B HN6 0.09 ! \ / ATOM O4B ON6 -0.40 ! N6A ATOM C1B CN6B 0.11 ! | ATOM H1B HN6 0.09 ! C6A GROUP ! // \ ATOM C5A CN5 0.23 ! N1A C5A--N7A\\ ATOM N7A NN4 -0.63 ! | || C8A-H8A ATOM C8A CN4 0.38 ! C2A C4A--N9A/ ATOM H8A HN3 0.18 ! / \\ / \ ATOM N9A NN2 -0.16 ! H2A N3A \ GROUP ! \ ATOM N1A NN3A -0.74 ! \ ATOM C2A CN4 0.53 ! \ ATOM H2A HN3 0.16 ! O1N O1A H51A H4B O4B \ ATOM N3A NN3A -0.69 ! | | | \ / \ \ ATOM C4A CN5 0.31 ! O5D-PN-O3--PA-O5B--C5B--C4B C1B ATOM C6A CN2 0.43 ! \ | | | \ / \ GROUP ! \ O2N O2A H52A C3B--C2B H1B ATOM N6A NN1 -0.80 ! \ / \ / \ ATOM H61A HN1 0.40 ! \ O3B H3B O2B H2B ATOM H62A HN1 0.40 ! \ | | GROUP ! \ HO3A HO2A ATOM C2B CN6 0.14 ! \ H71N ATOM H2B HN6 0.09 ! \ \ ATOM O2B ON5 -0.66 ! \ H72N-N7N H4N H42N ATOM HO2A HN5 0.43 ! \ \ \ / GROUP ! \ C7N C4N ATOM C3B CN6 0.14 ! \ / \ / \ ATOM H3B HN6 0.09 ! \ O7N C3N C5N-H5N ATOM O3B ON5 -0.66 ! \ | | ATOM HO3A HN5 0.43 ! \ H51N H4D O4D H2N-C2N C6N-H6N GROUP ! \ | \ / \ \ / ATOM C5B CN8 -0.08 ! C5D---C4D C1D----------N1N ATOM H52A HN7 0.09 ! | \ / \ ATOM H51A HN7 0.09 ! H52N C3D--C2D H1D ATOM PA P 1.50 ! / \ / \ ATOM O1A ON3 -0.82 ! O3D H3D O2D H2D ATOM O2A ON3 -0.82 ! | | ATOM O5B ON2 -0.62 ! HO3N HO2N ATOM O3 ON2 -0.68 ATOM PN P 1.50 ATOM O1N ON3 -0.82 ATOM O2N ON3 -0.82 ATOM O5D ON2 -0.62 ATOM C5D CN9 -0.08 ATOM H51N HN7 0.09 ATOM H52N HN7 0.09 GROUP ATOM C2D CN6 0.14 ATOM H2D HN6 0.09 ATOM O2D ON5 -0.66 ATOM HO2N HN5 0.43 GROUP ATOM C3D CN6 0.14 ATOM H3D HN6 0.09 ATOM O3D ON5 -0.66 ATOM HO3N HN5 0.43 GROUP ATOM C1D CN6B 0.11 ATOM H1D HN6 0.09 ATOM C4D CN6 0.11 ATOM H4D HN6 0.09 ATOM O4D ON6 -0.40 GROUP ATOM N1N NN2 -0.27 !N2 ATOM C6N CN3C -0.06 !C3 ATOM H6N HN3 0.17 !H4 ATOM C5N CN3 -0.18 !C5 ATOM H5N HN3 0.14 !H6 ATOM C4N CN8 -0.28 !C7 ATOM H4N HN7 0.09 !H8 ATOM H42N HN7 0.09 !H17 ATOM C3N CN3 0.36 !C9 ATOM C2N CN3C -0.10 !C10 ATOM H2N HN3 0.14 !H11 ATOM C7N CN1A 0.55 !C12 ATOM O7N ON1 -0.51 !O13 ATOM N7N NN1 -0.72 !N14 ATOM H71N HN1 0.26 !H15 ! trans to amide O ATOM H72N HN1 0.32 !H16 ! cis to amide O BOND N1A C2A C2A N3A N3A C4A C4A C5A C5A C6A BOND C6A N6A C6A N1A C5A N7A N7A C8A C8A N9A BOND N9A C4A C2A H2A N6A H61A N6A H62A C8A H8A BOND N9A C1B C1B C2B C2B C3B C3B C4B C4B O4B BOND O4B C1B C1B H1B C2B O2B O2B HO2A C2B H2B BOND C3B H3B C3B O3B O3B HO3A C4B H4B C4B C5B BOND C5B H51A C5B H52A C5B O5B O5B PA PA O1A BOND PA O2A PA O3 O3 PN PN O1N PN NO2 BOND PN O5D O5D C5D C5D H51N C5D H52N C5D C4D BOND C4D O4D O4D C1D C1D C2D C2D C3D C3D C4D BOND C1D H1D C2D H2D C2D O2D O2D HO2N C3D H3D BOND C3D O3D O3D HO3N C4D H4D C1D N1N N1N C2N BOND C2N C3N C3N C4N C4N C5N C5N C6N C6N N1N BOND C2N H2N C3N C7N C7N O7N C7N N7N N7N H71N BOND N7N H72N C4N H4N C4N H42N C5N H5N C6N H6N ! adenine impropers IMPH H62A C6A H61A N6A N6A N1A C5A C6A H2A N1A N3A AC2 IMPH H8A N7A N9A AC8 ! amide impropers IMPH C7N N7N C3N O7N C7N C3N N7N O7N IMPH N7N C7N H71N H72N N7N C7N H72N H71N ! ring hydrogen impropers IMPH H6N N1N C5N C6N H5N C6N C4N C5N IMPH H4N C5N C3N C4N H2N C3N N1N C2N DONO H61A N6A DONO H62A N6A DONO HO2A O2B DONO HO3A O3B ACCE N1A ACCE N3A ACCE N7A ACCE O4B ACCE O2B ACCE O3B ACCE O5B ACCE O1A PA ACCE O2A PA ACCE O3 ACCE O1N PN ACCE O2N PN ACCE O5D ACCE O4D ACCE O3D ACCE O2D ACCE O7N DONO HO2N O2D DONO HO3N O3D DONO H71N N7N DONO H72N N7N IC PA O3 PN O5D 1.5477 110.11 175.47 98.59 1.5945 IC C5B O5B PA O3 1.4379 124.23 -120.69 96.29 1.5477 IC C5B O5B PA O2A 1.4379 124.23 -4.20 104.25 1.4838 IC H51A C5B C4B C3B 1.1127 107.45 -172.00 111.64 1.5309 IC PA O3 PN O1N 1.5477 110.11 63.14 114.14 1.4739 IC PA O3 PN O2N 1.5477 110.11 -73.96 111.08 1.4835 IC PA O5B C5B C4B 1.5968 124.23 104.17 111.45 1.5366 IC O1A PA O5B C5B 1.4736 106.06 122.59 124.23 1.4379 IC O5B C5B C4B C3B 1.4379 111.45 -54.02 111.64 1.5309 IC C5B C4B C3B O3B 1.5366 111.64 117.91 108.23 1.4176 IC HO3A O3B C3B C4B 0.9780 101.86 -77.83 108.23 1.5309 IC O4B C3B *C4A C5B 3.7210 30.68 12.44 22.46 6.0953 IC C2B C4B *C3B O3B 1.5171 107.22 -123.00 108.23 1.4176 IC C4B C3B C2B C1B 1.5309 107.22 -27.93 98.01 1.5397 IC C3B C2B C1B N9A 1.5171 98.01 168.03 114.25 1.4756 IC O4B C1B N9A C4A 1.4308 112.85 -160.05 123.87 1.3958 IC C1B C4A *N9A C8A 1.4756 123.87 160.62 105.30 1.3614 IC C4A N9A C8A N7A 1.3958 105.30 2.73 114.72 1.3222 IC C8A N9A C4A C5A 1.3614 105.30 -0.85 105.33 1.3777 IC C8A N7A C5A C6A 1.3222 102.89 -175.73 131.43 1.4163 IC N7A C5A C6A N1A 1.3877 131.43 177.76 117.35 1.3499 IC C5A C6A N1A C2A 1.4163 117.35 0.19 119.36 1.3330 IC N9A C5A *C4A N3A 1.3958 105.33 -177.76 126.56 1.3567 IC C5A N1A *C6A N6A 1.4163 117.35 178.91 119.82 1.3439 IC N1A C6A N6A H61A 1.3499 119.82 -2.82 115.89 0.9932 IC H61A C6A *N6A H62A 0.9932 115.89 -173.48 118.52 0.9961 IC C5A N1A *C6A N6A 1.4163 117.35 178.91 119.82 1.3439 IC N1A C6A N6A H61A 1.3499 119.82 -2.82 115.89 0.9932 IC H61A C6A *N6A H62A 0.9932 115.89 -173.48 118.52 0.9961 IC N9A N7A *C8A H8A 1.3614 114.72 173.63 127.58 1.0942 IC N1A N3A *C2A H2A 1.3330 128.86 179.26 114.95 1.0940 IC C1B C3B *C2A O2B 4.3577 16.73 79.16 23.49 5.5426 IC H2B O2B C2B C3B 2.0992 29.77 125.89 110.79 1.5171 IC HO2A O2B C2B C3B 0.9759 105.90 7.59 110.79 1.5171 IC O4B C2B *C1B H1B 1.4308 104.32 -114.05 107.95 1.1153 IC C1B C3B *C2A H2B 4.3577 16.73 138.52 14.56 4.3331 IC C2B C4B *C3B H3B 1.5171 107.22 118.77 114.33 1.1023 IC C3B O4B *C4A H4B 4.6236 30.68 55.38 18.92 5.2267 IC C4B O5B *C5A H52A 5.8410 8.40 125.34 12.50 6.6777 IC C4B O5B *C5A H52A 5.8410 8.40 125.34 12.50 6.6777 IC C5D O5D PN O2N 1.4351 125.31 34.31 105.69 1.4835 IC H51N C5D O5D PN 1.1087 111.20 -6.79 125.31 1.5945 IC H52N C5D O5D PN 1.1115 107.95 108.24 125.31 1.5945 IC PN O5D C5D C4D 1.5945 125.31 -133.06 113.61 1.5644 IC O5D C5D C4D C3D 1.4351 113.61 37.01 114.92 1.5111 IC C5D C4D C3D C2D 1.5644 114.92 71.49 99.06 1.5369 IC C4D C3D C2D C1D 1.5111 99.06 54.76 97.08 1.5500 IC C3D C2D C1D O4D 1.5369 97.08 -39.12 103.14 1.4628 IC C2D C1D O4D C4D 1.5500 103.14 9.47 109.09 1.4960 IC O2D C2D C1D O4D 1.4207 114.02 -166.39 103.14 1.4628 IC HO2N O2D C2D C1D 0.9638 100.52 -89.37 114.02 1.5500 IC O4D C2D *C1D H1D 1.4628 103.14 -111.22 105.40 1.1096 IC C1D C3D *C2N H2D 2.4663 46.96 -41.97 34.01 3.9460 IC C2D C4D *C3N H3D 3.9136 23.54 -115.76 16.12 3.6674 IC C3D O4D *C4N H4D 5.4003 24.61 -39.21 14.97 6.7904 IC C4D O5D *C5N H52N 5.9665 13.65 -41.47 15.17 7.7670 IC C4D O5D *C5N H51N 5.9665 13.65 -87.41 13.92 6.7251 IC C3D C2D C1D N1N 1.5369 97.08 88.64 116.58 1.5502 IC O3D C3D C2D C1D 1.4176 119.76 -172.52 97.08 1.5500 IC HO3N O3D C3D C2D 0.9717 103.61 17.81 119.76 1.5369 IC C2D C1D N1N C2N 1.5500 116.58 -19.65 116.34 1.3499 IC C1D N1N C2N C3N 1.5502 116.34 134.66 130.57 1.3607 IC N1N C2N C3N C4N 1.3499 130.57 5.82 111.74 1.5356 IC C2N C3N C4N C5N 1.3607 111.74 -1.05 119.26 1.5319 IC C3N C4N C5N C6N 1.5356 119.26 -1.26 113.69 1.3745 IC C4N C5N C6N N1N 1.5319 113.69 -0.29 128.15 1.3388 IC C5N C6N N1N C2N 1.3745 128.15 4.14 116.26 1.3499 IC N1N C2N C3N C7N 1.3499 130.57 -147.46 122.72 1.5282 IC C2N C3N C7N O7N 1.3607 122.72 -140.47 119.41 1.2169 IC C2N C3N C7N N7N 1.3607 122.72 46.61 116.68 1.3621 IC O7N C7N N7N H71N 1.2169 123.49 -177.07 120.21 1.0093 IC O7N C7N N7N H72N 1.2169 123.49 -4.94 119.16 1.0014 IC C2N C3N C4N H4N 1.3607 111.74 -135.39 112.16 1.1099 IC C2N C3N C4N H42N 1.3607 111.74 114.48 103.52 1.1129 IC C3N C4N C5N H5N 1.5356 119.26 -171.18 122.65 1.0912 IC C4N C5N C6N H6N 1.5319 113.69 179.92 118.00 1.0878 IC C6N N1N C2N H2N 1.3388 116.26 162.03 117.47 1.0731 PATCH FIRST NONE LAST NONE END