*>>>>>>>>>> Developmental Parameter 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: par_all22_prot_b5.inp. * * Several IMPROPER dihedrals from param19.inp were added to this library to * make it more useful for MODELLER (Andrej Sali). Search for Andrej. * See top.lib for more information. * * NH1 CT[12] C were enforced from k=50 to k=80 * * BONDS C C 600.000 1.3350 ! ALLOW ARO HEM ! Heme vinyl substituent (KK, from propene (JCS)) CA CA 305.000 1.3750 ! ALLOW ARO ! benzene, JES 8/25/89 CE1 CE1 440.000 1.3400 ! ! for butene; from propene, yin/adm jr., 12/95 CE1 CE2 500.000 1.3420 ! ! for propene, yin/adm jr., 12/95 CE1 CT2 365.000 1.5020 ! ! for butene; from propene, yin/adm jr., 12/95 CE1 CT3 383.000 1.5040 ! ! for butene, yin/adm jr., 12/95 CE2 CE2 510.000 1.3300 ! ! for ethene, yin/adm jr., 12/95 CP1 C 250.000 1.4900 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP1 CC 250.000 1.4900 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP1 CD 200.000 1.4900 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP1 222.500 1.5270 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP2 222.500 1.5370 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 CP2 222.500 1.5370 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CPB C 450.000 1.3800 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CPB CPA 299.800 1.4432 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPB CPB 340.700 1.3464 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPH1 CPH1 410.000 1.3600 ! ALLOW ARO ! histidine, adm jr., 6/27/90 CPM CPA 360.000 1.3716 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPT CA 305.000 1.3680 ! ALLOW ARO ! adm jr., 12/30/91, for jwk CPT CPT 360.000 1.4000 ! ALLOW ARO !adm jr., 12/30/91, for jwk CT1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) CT1 CC 200.000 1.5220 ! ALLOW POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT1 CD 200.000 1.5220 ! ALLOW POL ! adm jr. 5/02/91, acetic acid pure solvent CT1 CT1 222.500 1.5000 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT2 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) CT2 CA 230.000 1.4900 ! ALLOW ALI ARO ! phe,tyr, JES 8/25/89 CT2 CC 200.000 1.5220 ! ALLOW POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT2 CD 200.000 1.5220 ! ALLOW POL ! adm jr. 5/02/91, acetic acid pure solvent CT2 CPB 230.000 1.4900 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT2 CPH1 229.630 1.5000 ! ALLOW ARO ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals CT2 CT1 222.500 1.5380 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT2 CT2 222.500 1.5300 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) CT3 CA 230.000 1.4900 ! ALLOW ALI ARO ! toluene, adm jr. 3/7/92 CT3 CC 200.000 1.5220 ! ALLOW POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT3 CD 200.000 1.5220 ! ALLOW POL ! adm jr. 5/02/91, acetic acid pure solvent CT3 CPB 230.000 1.4900 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT3 CPH1 229.630 1.5000 ! ALLOW ARO ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals CT3 CS 190.000 1.5310 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 CT3 CT1 222.500 1.5380 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT2 222.500 1.5280 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT3 222.500 1.5300 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CY CA 350.000 1.3650 ! ALLOW ARO !adm jr., 5/08/91, indole CCDB structure search CY CPT 350.000 1.4400 ! ALLOW ARO !adm jr., 12/30/91, for jwk CY CT2 230.000 1.5100 ! ALLOW ARO !JWK Kb from alkane freq.. b0 from TRP crystal FE CM 258.000 1.9000 ! ALLOW HEM ! Heme (6-liganded): CO ligand (KK 05/13/91) FE CPM 0.000 3.3814 ! ALLOW HEM ! Heme (6-liganded): for "ic para" only (KK 05/13/91) H CD 330.000 1.1100 ! ALLOW PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent HA C 330.000 1.1000 ! ALLOW ARO HEM ! Heme vinyl substituent (KK, from propene (JCS)) HA CA 340.000 1.0830 ! ALLOW ARO ! trp, adm jr., 10/02/89 HA CC 317.130 1.1000 ! ALLOW POL ! adm jr., 5/13/91, formamide geometry and vibrations HA CP2 309.000 1.1110 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP3 309.000 1.1110 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CPM 367.600 1.0900 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) HA CS 300.000 1.1110 ! ALLOW SUL ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 HA CT1 309.000 1.1110 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT2 309.000 1.1110 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 322.000 1.1110 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CY 330.000 1.0800 ! ALLOW ARO ! JWK 05/14/91 new r0 from indole HA1 CE1 360.500 1.1000 ! ! for propene, yin/adm jr., 12/95 HA2 CE2 365.000 1.1000 ! ! for ethene, yin/adm jr., 12/95 HB CP1 330.000 1.0800 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CT1 330.000 1.0800 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT2 330.000 1.0800 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT3 330.000 1.0800 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HP CA 340.000 1.0800 ! ALLOW ARO ! phe,tyr JES 8/25/89 HP CY 350.000 1.0800 ! ALLOW ARO !adm jr., 12/30/91, for jwk HR1 CPH1 375.000 1.0830 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH2 340.000 1.0900 ! ALLOW ARO ! his, adm jr., 6/28/29 HR2 CPH2 333.000 1.0700 ! ALLOW ARO ! his, adm jr., 6/27/90 HR3 CPH1 365.000 1.0830 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HT HT 0.000 1.5139 ! ALLOW WAT ! FROM TIPS3P GEOMETRY (FOR SHAKE/W PARAM) N C 260.000 1.3000 ! ALLOW PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP1 320.000 1.4340 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP3 320.000 1.4550 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NC2 C 463.000 1.3650 ! ALLOW PEP POL ARO ! 403.0->463.0, 1.305->1.365 guanidinium (KK) NC2 CT2 261.000 1.4900 ! ALLOW ALI POL ! arg, (DS) NC2 CT3 261.000 1.4900 ! ALLOW ALI POL ! methylguanidinium, adm jr., 3/26/92 NC2 HC 455.000 1.0000 ! ALLOW POL ! 405.0->455.0 GUANIDINIUM (KK) NH1 C 370.000 1.3450 ! ALLOW PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) NH1 CT1 320.000 1.4300 ! ALLOW ALI PEP POL ARO ! NMA Gas & Liquid Phase IR Spectra (LK) NH1 CT2 320.000 1.4300 ! ALLOW ALI PEP POL ARO ! NMA Gas & Liquid Phase IR Spectra (LK) NH1 CT3 320.000 1.4300 ! ALLOW ALI PEP POL ARO ! NMA Gas & Liquid Phase IR Spectra (LK) NH1 H 440.000 0.9970 ! ALLOW PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) NH1 HC 405.000 0.9800 ! ALLOW PEP POL ARO ! (DS) NH2 CC 430.000 1.3600 ! ALLOW PEP POL ARO ! adm jr. 4/10/91, acetamide NH2 CT3 240.000 1.4550 ! ALLOW POL ! methylamine geom/freq, adm jr., 6/2/92 NH2 H 480.000 1.0000 ! ALLOW POL ! adm jr. 8/13/90 acetamide geometry and vibrations NH2 HC 460.000 1.0000 ! ALLOW POL ! methylamine geom/freq, adm jr., 6/2/92 NH3 CT1 200.000 1.4800 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) NH3 CT2 200.000 1.4800 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) NH3 CT3 200.000 1.4800 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) NH3 HC 403.000 1.0400 ! ALLOW POL ! new stretch and bend; methylammonium (KK 03/10/92) NP CP1 320.000 1.4850 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP3 320.000 1.5020 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP HC 460.000 1.0060 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NPH CPA 377.200 1.3757 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NPH FE 270.200 1.9580 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NR1 CPH1 400.000 1.3800 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR1 CPH2 400.000 1.3600 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR1 H 466.000 1.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR2 CPH1 400.000 1.3800 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR2 CPH2 400.000 1.3200 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR2 FE 65.000 2.2000 ! ALLOW HEM ! Heme (6-liganded): His ligand (KK 05/13/91) NR3 CPH1 380.000 1.3700 ! ALLOW ARO ! his, adm jr., 6/28/90 NR3 CPH2 380.000 1.3200 ! ALLOW ARO ! his, adm jr., 6/27/90 NR3 H 453.000 1.0000 ! ALLOW ARO ! his, adm jr., 6/27/90 NY CA 270.000 1.3700 ! ALLOW ARO !adm jr., 12/30/91, for jwk NY CPT 270.000 1.3750 ! ALLOW ARO !adm jr., 12/30/91, for jwk NY H 465.000 0.9760 ! ALLOW ARO ! indole JWK 08/28/89 O C 620.000 1.2300 ! ALLOW PEP POL ARO ! Peptide geometry, condensed phase (LK) O CC 650.000 1.2300 ! ALLOW PEP POL ARO ! adm jr. 4/10/91, acetamide OB CC 750.000 1.2200 ! ALLOW PEP POL ARO ! adm jr., 10/17/90, acetic acid vibrations and geom. OB CD 750.000 1.2200 ! ALLOW PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent OC CA 525.000 1.2600 ! ALLOW PEP POL ARO ION ! adm jr. 8/27/91, phenoxide OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION ! adm jr. 7/23/91, acetic acid OC CT2 450.000 1.3300 ! ALLOW ALC ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 OC CT3 450.000 1.3300 ! ALLOW ALC ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 OH1 CA 334.300 1.4110 ! ALLOW ARO ALC ! MeOH, EMB 10/10/89, OH1 CD 230.000 1.4000 ! ALLOW PEP POL ARO ALC ! adm jr. 5/02/91, acetic acid pure solvent OH1 CT1 428.000 1.4200 ! ALLOW ALI ALC ARO ! methanol vib fit EMB 11/21/89 OH1 CT2 428.000 1.4200 ! ALLOW ALI ALC ARO ! methanol vib fit EMB 11/21/89 OH1 CT3 428.000 1.4200 ! ALLOW ALI ALC ARO ! methanol vib fit EMB 11/21/89 OH1 H 545.000 0.9600 ! ALLOW ALC ARO ! EMB 11/21/89 methanol vib fit OM CM 1115.000 1.1280 ! ALLOW HEM ! Heme (6-liganded): CO ligand (KK 05/13/91) OM FE 250.000 1.8000 ! ALLOW HEM ! Heme (6-liganded): O2 ligand (KK 05/13/91) OM OM 600.000 1.2300 ! ALLOW HEM ! Heme (6-liganded): O2 ligand (KK 05/13/91) OS CD 150.000 1.3340 ! ALLOW POL PEP ! adm jr. 5/02/91, acetic acid pure solvent OS CT3 340.000 1.4300 ! ALLOW POL PEP ! adm jr., 4/05/91, for PRES CT1 from methylacetate OT HT 450.000 0.9572 ! ALLOW WAT ! FROM TIPS3P GEOM S CT2 198.000 1.8180 ! ALLOW ALI SUL ION ! fitted to C-S s 9/26/92 (FL) S CT3 240.000 1.8160 ! ALLOW ALI SUL ION ! fitted to C-S s 9/26/92 (FL) S HS 275.000 1.3250 ! ALLOW SUL ION ! methanethiol pure solvent, adm jr., 6/22/92 SM CT2 214.000 1.8160 ! ALLOW SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) SM CT3 214.000 1.8160 ! ALLOW SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) SM SM 173.000 2.0290 ! ALLOW SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) SS CS 205.000 1.8360 ! ALLOW SUL ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 NP1 CPA 377.200 1.3757 ! ALLOW HEM correct for N-Fe-N angles MJS NP1 FE 270.200 1.9580 ! ALLOW HEM correct for N-Fe-N angles MJS ! nucleic acid section CN1 CN3 302.0 1.425 !U,T, par_a4 JWK 9/30/91 CN1A CN3 302.0 1.480 !nad/ppi, jjp1/adm jr. 7/95 CN1 CN5 302.0 1.360 !G, JWK, adm jr., 7/24/91 CN1A NN1 560.0 1.360 !nad/ppi, jjp1/adm jr. 7/95 CN1 NN2 302.0 1.400 !U, JWK, adm jr., 7/24/91 CN1 NN2G 340.0 1.410 !G, par_a4 JWK 9/30/91 CN1 NN2U 340.0 1.410 !U, par_a4 JWK 9/30/91 CN1 NN3 400.0 1.358 !C, par_a6 JWK 9/30/91 CN1 ON1 620.0 1.235 !U,A,G par_a4 adm jr., 10/2/91 CN1A ON1 860.0 1.230 !nad/ppi, jjp1/adm jr. 7/95 CN1 ON1C 620.0 1.245 !C, adm jr., 10/2/91 CN2 CN3 302.0 1.420 !C, JWK, adm jr., 7/24/91 CN2 CN3D 260.0 1.405 !5mc, adm jr., 9/9/93, from cn2 cn3 CN2 CN5 302.0 1.360 !A, JWK, adm jr., 10/2/91 CN2 NN1 400.0 1.365 !C,A,G JWK, adm jr., 10/2/91 CN2 NN2G 400.0 1.400 !G JWK, adm jr., 7/24/91 CN2 NN3 400.0 1.340 !C par_a6 JWK 9/30/91 CN2 NN3A 320.0 1.340 !A par_a8 JWK 9/30/91 CN3 CN3 560.0 1.335 ! par_a4 JWK 9/30/91 CN3A CN3 450.0 1.360 !nad/ppi, jjp1/adm jr. 7/95 CN3B CN3 420.0 1.350 !nad/ppi, jjp1/adm jr. 7/95 CN3C CN3 420.0 1.320 !nadh/ppi, jjp1/adm jr. 7/95 CN3D CN3 560.0 1.335 !5mc, adm jr., 9/9/93, from cn3 cn3 CN3 CN8 222.5 1.490 !nadh/ppi, jjp1/adm jr. 7/95 CN3 CN9 230.0 1.480 !T, par_51, adm jr., 7/24/91 CN3D CN9 230.0 1.480 !5mc, adm jr., 9/9/93, from cn3 cn9 CN3 HN3 350.0 1.09 !C,U, JWK CN3 HN3B 350.0 1.09 !nad/ppi, jjp1/adm jr. 7/95 CN3A HN3B 350.0 1.09 !nad/ppi, jjp1/adm jr. 7/95 CN3B HN3B 350.0 1.09 !nad/ppi, jjp1/adm jr. 7/95 CN3C HN3 374.0 1.09 !nadh/ppi, jjp1/adm jr. 7/95 CN3 NN2 302.0 1.365 !C,U, JWK, adm jr., 7/24/91 CN3B NN2 420.0 1.315 !nad/ppi, jjp1/adm jr. 7/95 CN3C NN2 420.0 1.355 !nadh/ppi, jjp1/adm jr. 7/95 CN4 HN3 380.0 1.09 !G,A, JWK par_a7 9/30/91 CN4 NN2 300.0 1.365 !G,A, JWK, adm jr., 7/24/91 CN4 NN2G 350.0 1.365 !Inosine, adm jr., 2/94 CN4 NN3A 310.0 1.310 !A, JWK, par_a7 9/30/91 CN4 NN3I 450.0 1.295 !Inosine, adm jr., 2/94 CN4 NN4 400.0 1.308 !G,A, JWK par_a8 9/30/91 CN5 CN5 320.0 1.370 !G,A, JWK par_a8 9/30/91 CN5 NN2 302.0 1.408 !G,A, JWK, adm jr., 7/24/91 CN5 NN3A 350.0 1.336 !A, JWK par_a8 9/30/91 CN5 NN3I 350.0 1.346 !Inosine, adm jr., 2/94 CN5 NN4 350.0 1.360 !G,A, JWK, par_a8 9/30/91 CN6 CN6 222.5 1.516 !RIBOSE, ADM Jr. CN6 CN6B 222.5 1.527 !RIBOSE, ADM Jr. CN6 CN6C 222.5 1.537 !RIBOSE, ADM Jr. CN6B CN6C 222.5 1.527 !RIBOSE, ADM Jr. CN6 CN7 222.5 1.516 !RIBOSE, ADM Jr. CN6 CN8 222.5 1.516 !RIBOSE, ADM Jr. CN6 CN9 222.5 1.516 !RIBOSE, ADM Jr. CN6 HN6 309.0 1.111 !RIBOSE, ADM Jr. CN6B HN6 309.0 1.111 !RIBOSE, ADM Jr. CN6C HN6 309.0 1.111 !RIBOSE, ADM Jr. CN6B NN2 300.0 1.48 !RIBOSE, ADM Jr. CN6B NN1 300.0 1.48 !RIBOSE, ADM Jr. CN6 ON2 340.0 1.43 !from CN7 ON2, ADM Jr. CN6 ON5 428.0 1.420 !RIBOSE, MeOH CN6 ON6 296.7 1.445 !RIBOSE, ADM Jr. CN6B ON6 296.7 1.41 !RIBOSE, ADM Jr. CN7 CN7 222.50 1.500 !Alkanes, sacred CN7 CN8 222.50 1.538 !Alkanes, free CN7 CN9 222.50 1.538 !Alkanes, sacred CN7 HN7 309.0 1.111 !Alkanes, sacred CN8 CN9 222.50 1.528 !Alkanes, sacred CN8 HN7 309.0 1.111 !Alkanes, sacred CN8 NN2 400.0 1.460 !9-E-GUA, ADM JR. CN8 ON2 340.0 1.43 !DMP, ADM Jr. CN8 ON5 428.0 1.42 !RIBOSE, MeOH CN9 HN7 322.0 1.111 !Alkanes, sacred CN9 NN2 400.0 1.460 !FOR 9-M-ADE(THY), ADM JR. CN9 ON2 340.0 1.43 !DMP, ADM Jr. HN1 NN1 488.0 1.00 !A,C,G, JWK, adm jr., 7/24/91 HN2 NN2 474.0 1.01 !C,U, JWK HN2 NN2G 471.0 1.01 !G, JWK, par_a12 9/30/91 HN2 NN2U 474.0 1.01 !U, JWK, adm jr., 7/24/91 HN4 ON4 545.0 0.960 !MP_1, ADM Jr. HN5 ON5 545.0 0.960 !RIBOSE, MeOH !HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM) !HT OT 450.0 0.9572 ! from TIPS3P geometry ON2 P 270.0 1.60 !DMP, ADM Jr. ON3 P 580.0 1.48 !DMP, ADM Jr. ON4 P 237.0 1.58 !MP_1, ADM Jr. ON2 P2 300.0 1.68 !nad/ppi, jjp1/adm jr. 7/95 ON3 P2 480.0 1.53 !nad/ppi, jjp1/adm jr. 7/95 NN5 HN1 460. 1.01 !sugar model, adm jr. NN5 CN6B 240. 1.47 !sugar model, adm jr. 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 CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO ! JES 8/25/89 CE1 CE1 CT3 48.00 123.50 ! ! for 2-butene, yin/adm jr., 12/95 CE1 CT2 CT3 32.00 112.20 ! ! for 1-butene; from propene, yin/adm jr., 12/95 CE2 CE1 CT2 48.00 126.00 ! ! for 1-butene; from propene, yin/adm jr., 12/95 CE2 CE1 CT3 47.00 125.20 ! ! for propene, yin/adm jr., 12/95 CP1 N C 60.000 117.0000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP1 C 52.000 112.3000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP1 CC 52.000 112.3000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP1 CD 50.000 112.3000 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP2 CP1 70.000 108.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 CP2 CP2 70.000 108.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N C 60.000 117.0000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N CP1 100.000 114.2000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 NP CP1 100.000 111.0000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CPA CPB C 70.000 126.7400 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CPA CPM CPA 94.200 125.1200 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPA NPH CPA 139.300 103.9000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPB C C 70.000 121.5000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CPB CPB C 70.000 126.7500 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CPB CPB CPA 30.800 106.5100 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPH2 NR1 CPH1 130.000 107.5000 ! ALLOW ARO ! his, adm jr., 6/27/90 CPH2 NR2 CPH1 130.000 104.0000 ! ALLOW ARO ! his, adm jr., 6/27/90 CPH2 NR3 CPH1 145.000 108.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 CPM CPA CPB 61.600 124.0700 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPT CA CA 60.000 118.0000 ! ALLOW ARO !adm jr., 12/30/91, for jwk CPT CPT CA 60.000 122.0000 ! ALLOW ARO !adm jr., 12/30/91, for jwk CPT CY CA 120.000 107.40 25.00 2.26100 ! ALLOW ARO !adm jr., 12/30/91, for jwk CPT NY CA 110.000 108.0000 ! ALLOW ARO !adm jr., 12/30/91, for jwk CT1 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) CT1 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT1 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT1 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO ! PARALLH19 (JES) CT1 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT1 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent CT1 CT2 CPH1 58.350 113.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted CT1 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) CT1 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) CT2 CA CA 45.800 122.3000 ! ALLOW ALI ARO ! PARALLH19 (JES) CT2 CPB CPA 65.000 126.7400 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT2 CPB CPB 65.000 126.7500 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT2 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS CT2 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) CT2 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT2 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent CT2 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT2 CT2 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! from CT2 CT1 C, for lactams, adm jr. CT2 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters CT2 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent CT2 CT2 CPB 70.000 113.0000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT2 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) CT2 CT2 CT2 58.350 113.60 11.16 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT2 CT3 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) CT2 CY CA 45.800 129.4000 ! ALLOW ARO !adm jr., 5/08/91, indole CCDB structure search CT2 CY CPT 45.800 124.0000 ! ALLOW ARO !adm jr., 5/08/91, indole CCDB structure search CT2 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO ! 107.5->120.0 to make planar Arg (KK) CT2 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) CT2 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP ! adm jr. 5/02/91, acetic acid pure solvent CT3 CA CA 45.800 122.3000 ! ALLOW ALI ARO ! toluene, adm jr., 3/7/92 CT3 CPB CPA 65.000 126.7400 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT3 CPB CPB 65.000 126.7500 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT3 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS CT3 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/09/92, for ALA cter CT3 CT1 CT1 53.350 108.50 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT1 CT2 53.350 114.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT1 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO ! ethylbenzene, adm jr., 3/7/92 CT3 CT2 CPH1 58.350 113.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted CT3 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) CT3 CT2 CT2 58.000 115.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 CT2 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CT3 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO ! methylguanidinium, adm jr., 3/26/92 CT3 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) CT3 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP ! adm jr. 5/02/91, acetic acid pure solvent CT3 S CT2 34.000 95.0000 ! ALLOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) CY CPT CA 160.000 130.6000 ! ALLOW ARO !adm jr., 12/30/91, for jwk CY CPT CPT 110.000 107.4000 ! ALLOW ARO !adm jr., 12/30/91, for jwk CY CT2 CT1 58.350 114.0000 ! ALLOW ARO ! from TRP crystal, JWK CY CT2 CT3 58.350 114.0000 ! ALLOW ARO ! from TRP crystal, JWK FE NPH CPA 96.150 128.0500 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) FE NR2 CPH1 30.000 133.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) FE NR2 CPH2 30.000 123.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) H NH1 C 34.000 123.0000 ! ALLOW PEP POL ARO ! NMA Vib Modes (LK) H NH1 CT1 35.000 117.0000 ! ALLOW PEP POL ARO ALI ! NMA Vibrational Modes (LK) H NH1 CT2 35.000 117.0000 ! ALLOW PEP POL ARO ALI ! NMA Vibrational Modes (LK) H NH1 CT3 35.000 117.0000 ! ALLOW PEP POL ARO ALI ! NMA Vibrational Modes (LK) H NH2 CC 50.000 120.0000 ! ALLOW POL PEP ARO ! his, adm jr. 8/13/90 acetamide geometry and vibrations H NH2 H 23.000 120.0000 ! ALLOW POL ! adm jr. 8/13/90 acetamide geometry and vibrations H NR1 CPH1 30.000 125.50 20.00 2.15000 ! ALLOW ARO ! his, adm jr., 6/27/90 H NR1 CPH2 30.000 127.00 20.00 2.14000 ! ALLOW ARO ! his, adm jr., 6/27/90 H NR3 CPH1 25.000 126.00 15.00 2.13000 ! ALLOW ARO ! his, adm jr., 6/27/90 H NR3 CPH2 25.000 126.00 15.00 2.09000 ! ALLOW ARO ! his, adm jr., 6/27/90 H NY CA 28.000 126.0000 ! ALLOW ARO !adm jr., 12/30/91, for jwk H NY CPT 28.000 126.0000 ! ALLOW ARO !adm jr., 12/30/91, for jwk H OH1 CA 65.000 108.0000 ! ALLOW ALC ARO ! JES 8/25/89 phenol H OH1 CD 55.000 115.0000 ! ALLOW ALC ARO PEP POL ! adm jr. 5/02/91, acetic acid pure solvent H OH1 CT1 57.500 106.0000 ! ALLOW ALC ARO ALI ! methanol vib fit EMB 11/21/89 H OH1 CT2 57.500 106.0000 ! ALLOW ALC ARO ALI ! methanol vib fit EMB 11/21/89 H OH1 CT3 57.500 106.0000 ! ALLOW ALC ARO ALI ! methanol vib fit EMB 11/21/89 HA C C 50.000 120.5000 ! ALLOW PEP POL ARO ! Heme vinyl substituent (KK from propene (JCS)) HA C CPB 50.000 120.0000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) HA C HA 50.000 118.0000 ! ALLOW PEP POL ARO ! Heme vinyl substituent (KK from propene (JCS)) HA CA CA 29.000 120.00 25.00 2.15250 ! ALLOW ARO ! trp, adm jr., 10/02/89 HA CA CPT 41.000 122.0000 ! ALLOW ARO !adm jr., 5/08/91, indole CCDB structure search HA CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole HA CP2 CP1 33.430 110.10 22.53 2.17900 ! ALLOW ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP2 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP2 CP3 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP3 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP3 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CPM CPA 12.700 117.4400 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) HA CPM FE 0.000 180.0000 ! ALLOW HEM ! Heme (6-liganded): for "ic para" only (KK 05/13/91) HA CS CT3 34.600 110.10 22.53 2.17900 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 HA CS HA 35.500 108.40 14.00 1.77500 ! ALLOW SUL ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 HA CT1 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 HA CT1 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent HA CT1 CT1 34.500 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT1 CT2 34.500 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT1 CT3 34.500 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT1 HA 35.500 109.00 5.40 1.80200 ! TEST for test cpd ! based on HA CT2 HA HA CT2 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 HA CT2 CA 49.300 107.5000 ! ALLOW ALI ARO ! PARALLH19 (JES) HA CT2 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters HA CT2 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent HA CT2 CE1 45.00 111.50 ! ! for 1-butene; from propene, yin/adm jr., 12/95 HA CT2 CPB 50.000 109.5000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) HA CT2 CPH1 33.430 109.5000 ! ALLOW ARO ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED HA CT2 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) HA CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT2 CT3 34.600 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT2 CY 33.430 109.5000 ! ALLOW ARO ! ADM JR., 10/02/89, from CT2CT2HA (U-B OMITTED), FOR JOANNA HA CT2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 HA CT3 CA 49.300 107.5000 ! ALLOW ALI ARO ! toluene, adm jr. 3/7/92 HA CT3 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! adm jr. 4/05/91, for asn,asp,gln,glu and cters HA CT3 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent HA CT3 CE1 42.00 111.50 ! ! for 2-butene, yin/adm jr., 12/95 HA CT3 CPB 50.000 109.5000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) HA CT3 CPH1 33.430 109.5000 ! ALLOW ARO ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED HA CT3 CS 34.600 110.10 22.53 2.17900 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 HA CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI ! alkane frequencies (MJF), alkane geometries (SF) HA CT3 CT2 34.600 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 CT3 37.500 110.10 22.53 2.17900 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CT3 HA 35.500 108.40 5.40 1.80200 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 HA CY CA 20.000 126.40 25.00 2.18600 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole HA CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole HA1 CE1 CE1 52.00 119.50 ! ! for 2-butene, yin/adm jr., 12/95 HA1 CE1 CE2 42.00 118.00 ! ! for propene, yin/adm jr., 12/95 HA1 CE1 CT2 40.00 116.00 ! ! for 1-butene; from propene, yin/adm jr., 12/95 HA1 CE1 CT3 22.00 117.00 ! ! for propene, yin/adm jr., 12/95 HA2 CE2 CE1 45.00 120.50 ! ! for propene, yin/adm jr., 12/95 HA2 CE2 CE2 55.50 120.50 ! ! for ethene, yin/adm jr., 12/95 HA2 CE2 HA2 19.00 119.00 ! ! for propene, yin/adm jr., 12/95 HB CP1 C 50.000 112.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CP1 CC 50.000 112.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CP1 CD 50.000 112.0000 ! ALLOW PEP POL PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CP1 CP2 35.000 118.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CT1 C 50.000 109.5000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT1 CC 50.000 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters HB CT1 CD 50.000 109.5000 ! ALLOW PEP POL ! adm jr. 5/02/91, acetic acid pure solvent HB CT1 CT1 35.000 111.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT1 CT2 35.000 111.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT1 CT3 35.000 111.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT2 C 50.000 109.5000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT2 CC 50.000 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters HB CT2 CD 50.000 109.5000 ! ALLOW PEP POL ! adm jr. 5/02/91, acetic acid pure solvent HB CT2 HB 36.000 115.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT3 C 50.000 109.5000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HC NC2 C 49.000 120.0000 ! ALLOW POL PEP ARO ! 35.3->49.0 GUANIDINIUM (KK) HC NC2 CT2 40.400 120.0000 ! ALLOW POL ALI ! 107.5->120.0 to make planar Arg (KK) HC NC2 CT3 40.400 120.0000 ! ALLOW POL ALI ! methylguanidinium, adm jr., 3/26/92 HC NC2 HC 25.000 120.0000 ! ALLOW POL ! 40.0->25.0 GUANIDINIUM (KK) HC NH2 CT3 50.000 111.0000 ! ALLOW POL ! methylamine geom/freq, adm jr., 6/2/92 HC NH2 HC 39.000 106.5000 ! ALLOW POL ! 40.0->25.0 GUANIDINIUM (KK) HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI ! new stretch and bend; methylammonium (KK 03/10/92) HC NH3 CT2 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI ! new stretch and bend; methylammonium (KK 03/10/92) HC NH3 CT3 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI ! new stretch and bend; methylammonium (KK 03/10/92) HC NH3 HC 44.000 109.5000 ! ALLOW POL ! new stretch and bend; methylammonium (KK 03/10/92) HC NP CP1 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP3 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP HC 51.000 107.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HP CA CA 30.000 120.00 22.00 2.15250 ! ALLOW ARO ! JES 8/25/89 benzene HP CA CPT 30.000 122.00 22.00 2.14600 ! ALLOW ARO !adm jr., 12/30/91, for jwk HP CA CY 32.000 125.00 25.00 2.17300 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole HP CY CA 32.000 126.40 25.00 2.18600 ! ALLOW ARO !adm jr., 12/30/91, for jwk HP CY CPT 32.000 126.40 25.00 2.25500 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole HR1 CPH1 CPH1 22.000 130.00 15.00 2.21500 ! ALLOW ARO ! adm jr., 6/27/90, his HR3 CPH1 CPH1 25.000 130.00 20.00 2.20000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HS S CT2 38.800 95.0000 ! ALLOW SUL ION ALI ! methanethiol pure solvent, adm jr., 6/22/92 HS S CT3 43.000 95.0000 ! ALLOW SUL ION ALI ! methanethiol pure solvent, adm jr., 6/22/92 HT OT HT 55.000 104.5200 ! ALLOW WAT ! TIP3P GEOMETRY, ADM JR. N C CP1 20.000 112.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT1 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT2 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT3 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP1 C 50.000 108.2000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP1 CC 50.000 108.2000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP1 CD 50.000 108.2000 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP1 CP2 70.000 110.8000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP1 HB 48.000 112.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP3 CP2 70.000 110.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CP3 HA 48.000 108.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NC2 C NC2 52.000 120.00 90.00 2.36420 ! ALLOW POL PEP ARO ! changed from 60.0/120.3 for guanidinium (KK) NC2 CT2 CT2 67.700 107.5000 ! ALLOW ALI POL ! arg, (DS) NC2 CT2 HA 51.500 107.5000 ! ALLOW ALI POL ! arg, (DS) NC2 CT3 HA 51.500 107.5000 ! ALLOW ALI POL ! methylguanidinium, adm jr., 3/26/92 NH1 C CP1 80.000 116.5000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH1 C CT1 80.000 116.5000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) NH1 C CT2 80.000 116.5000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) NH1 C CT3 80.000 116.5000 ! ALLOW ALI PEP POL ARO ! NMA Vib Modes (LK) NH1 CT1 C 80.000 107.0000 ! ALLOW PEP POL ARO ALI ! Andrej Sali; Alanine Dipeptide ab initio calc's (LK) NH1 CT1 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 4/05/91, for asn,asp,gln,glu and cters NH1 CT1 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 5/02/91, acetic acid pure solvent NH1 CT1 CT1 70.000 113.5000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) NH1 CT1 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) NH1 CT1 CT3 70.000 113.5000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) NH1 CT1 HB 48.000 108.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) NH1 CT2 C 80.000 107.0000 ! ALLOW PEP POL ARO ALI ! Alanine Dipeptide ab initio calc's (LK) NH1 CT2 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 5/20/92, for asn,asp,gln,glu and cters NH1 CT2 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 5/02/91, acetic acid pure solvent NH1 CT2 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO ! from NH1 CT1 CT2, for lactams, adm jr. NH1 CT2 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO ! from NH1 CT3 HA, for lactams, adm jr. NH1 CT2 HB 48.000 108.0000 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) NH1 CT3 HA 51.500 109.5000 ! ALLOW ALI PEP POL ARO ! NMA crystal (JCS) NH2 CC CP1 80.000 112.5000 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH2 CC CT1 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO ! adm jr. 8/13/90 acetamide geometry and vibrations NH2 CC CT2 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO ! adm jr. 8/13/90 acetamide geometry and vibrations NH2 CC CT3 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO ! adm jr. 8/13/90 acetamide geometry and vibrations NH2 CC HA 44.000 111.00 50.00 1.98000 ! ALLOW POL ! adm jr., 5/13/91, formamide geometry and vibrations NH2 CT3 HA 38.000 109.50 50.00 2.14000 ! ALLOW POL ! methylamine geom/freq, adm jr., 6/2/92 NH3 CT1 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI ! new aliphatics, adm jr., 2/3/92 NH3 CT1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 4/05/91, for asn,asp,gln,glu and cters NH3 CT1 CT1 67.700 110.0000 ! ALLOW ALI POL ! new aliphatics, adm jr., 2/3/92 NH3 CT1 CT2 67.700 110.0000 ! ALLOW ALI POL ! new aliphatics, adm jr., 2/3/92 NH3 CT1 CT3 67.700 110.0000 ! ALLOW ALI POL ! new aliphatics, adm jr., 2/3/92 NH3 CT1 HB 51.500 107.5000 ! ALLOW ALI POL PEP ! new aliphatics, adm jr., 2/3/92 NH3 CT2 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI ! alanine (JCS) NH3 CT2 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 4/05/91, for asn,asp,gln,glu and cters NH3 CT2 CD 43.700 110.0000 ! ALLOW PEP POL ARO ALI ! adm jr. 5/02/91, acetic acid pure solvent NH3 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL ! alanine (JCS) NH3 CT2 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) NH3 CT2 HB 51.500 107.5000 ! ALLOW ALI POL PEP ! for use on NTER -- from NH3 CT2HA (JCS) -- (LK) NH3 CT3 HA 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL ! new stretch and bend; methylammonium (KK 03/10/92) NP CP1 C 50.000 106.0000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP1 CC 50.000 106.0000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP1 CD 50.000 106.0000 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP1 CP2 70.000 108.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP1 HB 51.500 107.5000 ! ALLOW ALI POL PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP3 CP2 70.000 108.5000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP3 HA 51.500 109.1500 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NPH CPA CPB 122.000 111.5400 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NPH CPA CPM 88.000 124.3900 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NPH FE CM 50.000 90.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) NPH FE CPM 0.000 45.0000 ! ALLOW HEM ! Heme (6-liganded): for "ic para" only (KK 05/13/91) NPH FE NPH 14.390 180.0000 ! ALLOW HEM correct for N-Fe-N angles MJS ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NR1 CPH1 CPH1 130.000 106.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR1 CPH1 CT2 45.800 124.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC FROM CA CT2CT NR1 CPH1 CT3 45.800 124.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC FROM CA CT2CT NR1 CPH1 HR3 25.000 124.00 20.00 2.14000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params NR1 CPH2 HR1 25.000 122.50 20.00 2.14000 ! ALLOW ARO ! his, adm jr., 6/27/90 NR2 CPH1 CPH1 130.000 110.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR2 CPH1 CT2 45.800 120.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC FROM CA CT2CT NR2 CPH1 HR3 25.000 120.00 20.00 2.14000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params NR2 CPH2 HR1 25.000 125.00 20.00 2.12000 ! ALLOW ARO ! his, adm jr., 6/27/90 NR2 CPH2 NR1 130.000 112.5000 ! ALLOW ARO ! his, adm jr., 6/27/90 NR2 FE CM 50.000 180.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) NR2 FE NPH 50.000 90.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) NR3 CPH1 CPH1 145.000 108.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR3 CPH1 CT2 45.800 122.0000 ! ALLOW ARO ! his, ADM JR., 7/22/89, FC FROM CA CT2CT NR3 CPH1 HR1 22.000 122.00 15.00 2.18000 ! ALLOW ARO ! his, adm jr., 6/27/90 NR3 CPH2 HR2 32.000 126.00 25.00 2.14000 ! ALLOW ARO ! his, adm jr., 6/27/90 NR3 CPH2 NR3 145.000 108.0000 ! ALLOW ARO ! his, ADM JR., 7/20/89 NY CA CY 120.000 110.00 25.00 2.24000 ! ALLOW ARO !adm jr., 12/30/91, for jwk NY CA HA 32.000 125.00 25.00 2.17700 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole NY CA HP 32.000 125.00 25.00 2.17700 ! ALLOW ARO ! JWK 05/14/91 new theta0 and r0UB from indole NY CPT CA 160.000 130.6000 ! ALLOW ARO !adm jr., 12/30/91, for jwk NY CPT CPT 110.000 107.4000 ! ALLOW ARO !adm jr., 12/30/91, for jwk O C CP1 80.000 118.0000 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C CT1 80.000 121.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) O C CT2 80.000 121.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) O C CT3 80.000 121.0000 ! ALLOW ALI PEP POL ARO ! Alanine Dipeptide ab initio calc's (LK) O C H 50.000 121.7000 ! ALLOW PEP POL ARO ! acetaldehyde (JCS) O C N 80.000 122.5000 ! ALLOW PRO PEP POL ARO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C NH1 80.000 122.5000 ! ALLOW PEP POL ARO ! NMA Vib Modes (LK) O CC CP1 80.000 118.0000 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O CC CT1 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/10/91, acetamide update ! Angle strengthened to better balance with Modeller sidechain restraints ! without generating poor stereochemistry for GLN OE1/ASN OD1 O CC CT2 70.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/10/91, acetamide update O CC CT3 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO ! adm jr. 4/10/91, acetamide update O CC HA 44.000 122.0000 ! ALLOW POL ! adm jr., 5/13/91, formamide geometry and vibrations O CC NH2 75.000 122.50 50.00 2.37000 ! ALLOW POL PEP ARO ! adm jr. 4/10/91, acetamide update OB CD CP1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 OB CD CT1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent OB CD CT2 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent OB CD CT3 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO ! adm jr. 5/02/91, acetic acid pure solvent OC CA CA 40.000 120.0000 ! ALLOW POL ARO ! adm jr. 8/27/91, phenoxide OC CC CP1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION ! adm jr. 7/23/91, correction, ACETATE (KK) OC CC CT2 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION ! adm jr. 7/23/91, correction, ACETATE (KK) OC CC CT3 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION ! adm jr. 7/23/91, correction, ACETATE (KK) OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO ! adm jr. 7/23/91, correction, ACETATE (KK) OC CT2 CT3 65.000 122.0000 ! ALLOW ALC ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 OC CT2 HA 65.000 118.3000 ! ALLOW ALC ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 OC CT3 HA 65.000 118.3000 ! ALLOW ALC ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 OH1 CA CA 45.200 120.0000 ! ALLOW ARO ALC ! PARALLH19 WITH [122.3] (JES) OH1 CD CT2 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC ! adm jr, 10/17/90, acetic acid vibrations OH1 CD CT3 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC ! adm jr, 10/17/90, acetic acid vibrations OH1 CD OB 50.000 123.00 210.00 2.26200 ! ALLOW PEP POL ARO ALC ! adm jr, 10/17/90, acetic acid vibrations OH1 CT1 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT1 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT1 HA 45.900 108.8900 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT2 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT2 CT2 75.700 110.1000 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT2 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT2 HA 45.900 108.8900 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OH1 CT3 HA 45.900 108.8900 ! ALLOW ALI ALC ARO ! MeOH, EMB, 10/10/89 OM CM FE 35.000 180.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) OM FE NPH 5.000 90.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) OM OM FE 0.000 180.0000 ! ALLOW HEM ! Heme (6-liganded): ligand links (KK 05/13/91) OS CD CP1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 OS CD CT1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP ! adm jr., 4/05/91, for PRES CT1 from methylacetate OS CD CT2 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP ! adm jr., 4/05/91, for PRES CT1 from methylacetate OS CD CT3 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP ! adm jr., 4/05/91, for PRES CT1 from methylacetate OS CD OB 90.000 125.90 160.00 2.25760 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate OS CT2 HA 60.000 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for PRES CT1 from methyl acetate OS CT3 HA 60.000 109.5000 ! ALLOW PEP POL ! adm jr. 4/05/91, for PRES CT1 from methyl acetate S CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION ! as in expt.MeEtS & DALC crystal, 5/15/92 S CT2 CT2 58.000 114.5000 ! ALLOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) S CT2 CT3 58.000 114.5000 ! ALLOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) S CT2 HA 46.100 111.3000 ! ALLOW ALI SUL ION ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 S CT3 HA 46.100 111.3000 ! ALLOW ALI SUL ION ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 SM CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION ! as in expt.MeEtS & DALC crystal, 5/15/92 SM CT2 HA 38.000 111.0000 ! ALLOW ALI SUL ION ! new S-S atom type 8/24/90 SM CT3 HA 38.000 111.0000 ! ALLOW ALI SUL ION ! new S-S atom type 8/24/90 SM SM CT2 72.500 103.3000 ! ALLOW ALI SUL ION ! expt. dimethyldisulfide, 3/26/92 (FL) SM SM CT3 72.500 103.3000 ! ALLOW ALI SUL ION ! expt. dimethyldisulfide, 3/26/92 (FL) SS CS CT3 55.000 118.0000 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 SS CS HA 40.000 112.3000 ! ALLOW SUL ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 CPA NP1 CPA 139.300 103.9000 ! ALLOW HEM correct for N-Fe-N angles MJS FE NP1 CPA 96.150 128.0500 ! ALLOW HEM correct for N-Fe-N angles MJS NP1 CPA CPB 122.000 111.5400 ! ALLOW HEM correct for N-Fe-N angles MJS NP1 CPA CPM 88.000 124.3900 ! ALLOW HEM correct for N-Fe-N angles MJS NP1 FE CM 50.000 90.0000 ! ALLOW HEM correct for N-Fe-N angles MJS NP1 FE CPM 0.000 45.0000 ! ALLOW HEM correct for N-Fe-N angles MJS NP1 FE NP1 14.390 180.0000 ! ALLOW HEM correct for N-Fe-N angles MJS NPH FE NP1 14.390 90.0000 ! ALLOW HEM correct for N-Fe-N angles MJS ! nucleic acids section CN3 CN1 NN2U 67.0 113.4 !U,T, JWK, adm jr., 7/24/91 CN3 CN1A NN1 85.0 113.0 80.0 2.46 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN1 ON1 100.0 124.7 !U,T, par_a3 JWK 9/30/91 CN3 CN1A ON1 85.0 118.5 20.0 2.43 !nad/ppi, jjp1/adm jr. 7/95 CN5 CN1 NN2G 67.0 109.4 !G, JWK, adm jr., 7/24/91 CN5 CN1 ON1 100.0 125.6 !G, par_a3 adm jr., 10/2/91 NN1 CN1A ON1 85.0 128.5 20.0 2.17 !nad/ppi, jjp1/adm jr. 7/95 NN2 CN1 NN2U 67.0 114.6 !U,T, JWK, adm jr., 7/24/91 NN2 CN1 NN3 70.0 116.4 !C, JWK, adm jr., 7/24/91 NN2 CN1 ON1 100.0 123.5 !C,U,G par_a3 JWK 9/30/91 NN2 CN1 ON1C 100.0 121.5 !C, adm jr., 10/2/91 NN2G CN1 ON1 100.0 125.0 !G par_a4 adm jr., 10/2/91 NN2U CN1 ON1 100.0 121.9 !U, par_a3 JWK 9/30/91 NN3 CN1 ON1C 100.0 122.1 !C, par_a3 JWK 9/30/91 CN3 CN2 NN1 70.0 117.9 !C, JWK, adm jr., 7/24/91 CN3D CN2 NN1 110.0 116.4 !5mc, adm jr., 9/9/93 CN3 CN2 NN3 70.0 119.8 !C, JWK, adm jr., 7/24/91 CN3D CN2 NN3 30.0 121.3 !5mc, adm jr., 9/9/93 CN5 CN2 NN1 70.0 119.1 !A, adm jr., 6/7/92 CN5 CN2 NN3A 80.0 112.6 !A, JWK par_a9 9/30/91 NN1 CN2 NN2G 70.0 114.8 20. 2.30 !G, JWK, adm jr., 7/24/91 NN1 CN2 NN3 70.0 122.3 !C JWK, adm jr., 7/24/91 NN1 CN2 NN3A 70.0 128.3 !A adm jr., 6/7/92 NN2G CN2 NN3A 70.0 122.9 !G, JWK par_49, par_a11 9/30/91 CN1 CN3 CN3 125.0 118.0 !U,T, JWK, adm jr., 7/24/91 CN1A CN3 CN3C 5.0 107.8 !nad/ppi, jjp1/adm jr. 7/95 CN1A CN3 CN8 125.0 124.2 !nadh/ppi, jjp1/adm jr. 7/95 CN1 CN3 CN9 70.0 118.3 !T, JWK, adm jr., 7/24/91 CN1 CN3 HN3 30.0 120.0 !C,U, JWK, adm jr., 7/24/91 CN2 CN3 CN3 125.0 119.3 !C, JWK, adm jr., 7/24/91 CN2 CN3D CN3 100.0 117.8 !5mc, adm jr. 9/9/93 CN2 CN3D CN9 40.0 118.0 !5mc, adm jr. 9/9/93 CN2 CN3 HN3 30.0 118.7 !C, JWK, adm jr., 7/24/91 CN3A CN3 CN1A 40.0 110.2 !nad/ppi, jjp1/adm jr. 7/95 CN3B CN3 CN1A 10.0 131.8 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3A CN3 50.0 118.0 !nad/ppi, jjp1/adm jr. 7/95 CN3A CN3 CN3B 40.0 118.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3 CN8 53.5 108.5 !nadh/ppi, jjp1/adm jr. 7/95 CN3B CN3 CN8 53.5 108.5 !nad/ppi, jjp1/adm jr. 7/95 CN3C CN3 CN8 43.5 128.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3 CN9 70.0 123.7 !T, JWK, adm jr., 7/24/91 CN3 CN3D CN9 40.0 124.2 !5mc, adm jr., 9/9/93 CN3 CN3 HN3 30.0 122.0 !C,U, JWK, adm jr., 7/24/91 CN3D CN3 HN3 30.0 122.0 !5mc, adm jr., 9/9/93 CN3B CN3 HN3B 30.0 122.0 !nad/ppi, jjp1/adm jr. 7/95 CN3A CN3 HN3B 30.0 119.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3C HN3 42.0 119.0 !nadh/ppi, jjp1/adm jr. 7/95 CN3C CN3 HN3 42.0 116.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3A HN3B 80.0 121.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3B HN3B 80.0 120.5 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3 NN2 125.0 124.2 !C,U, JWK, adm jr., 7/24/91 CN3 CN3B NN2 120.0 122.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3C NN2 60.0 122.0 !nadh/ppi, jjp1/adm jr. 7/95 CN3D CN3 NN2 100.0 124.2 !5mc, adm jr., 9/9/93 CN8 CN3 HN3 30.0 116.0 !nadh/ppi, jjp1/adm jr. 7/95 HN3 CN3 NN2 30.0 113.8 !C,U, JWK, adm jr., 7/24/91 HN3B CN3B NN2 80.0 117.5 !nad/ppi, jjp1/adm jr. 7/95 HN3 CN3C NN2 42.0 119.0 !nad/ppi, jjp1/adm jr. 7/95 HN3 CN4 NN2 40.0 119.0 !G,A, JWK, par_a9 9/30/91 HN3 CN4 NN3A 35.0 114.75 !A, JWK, par_a9 9/30/91 HN3 CN4 NN3I 35.0 115.75 !Inosine, adm jr., 2/94 HN3 CN4 NN2G 35.0 114.75 !Inosine, adm jr., 2/94 HN3 CN4 NN4 40.0 126.7 !G,A, JWK, par_a9 9/30/91 NN2 CN4 NN4 100.0 114.3 !G,A, JWK, par_a9 9/30/91 NN3A CN4 NN3A 80.0 130.5 !A, JWK, par_a9 9/30/91 NN3I CN4 NN2G 80.0 129.5 !Inosine, adm jr., 2/94 CN1 CN5 CN5 125.0 119.5 !G, JWK, adm jr., 7/24/91 CN1 CN5 NN4 125.0 128.8 !G, JWK, adm jr., 7/24/91 CN2 CN5 CN5 100.0 119.7 !A, JWK, par_a7 9/30/91 CN2 CN5 NN4 120.0 128.6 !A, JWK, par_a9 9/30/91 CN5 CN5 NN2 100.0 105.1 !G,A, JWK, par_a9 9/30/91 CN5 CN5 NN3A 100.0 127.5 !A, JWK, par_a7 9/30/91 CN5 CN5 NN3I 100.0 127.5 !Inosine, adm jr., 2/94 CN5 CN5 NN4 100.0 111.7 !G,A, JWK, par_a7 9/30/91 NN2 CN5 NN3A 140.0 127.4 !A, JWK, par_a9 9/30/91 NN2 CN5 NN3I 140.0 127.4 !Inosine, adm jr., 2/94 CN6 CN6 CN6 53.35 111.0 8.0 2.561 ! Alkanes CN6 CN6 CN6B 53.35 105.5 8.0 2.561 ! Alkanes(new eq geom) CN6 CN6 CN6C 53.35 108.0 8.0 2.561 ! Alkanes(new eq geom) CN6 CN6C CN6B 53.35 105.5 8.0 2.561 ! Alkanes(new eq geom) CN6 CN6 CN8 53.35 108.5 8.0 2.561 ! Alkanes CN6 CN6 CN9 53.35 108.5 8.0 2.561 ! Alkanes CN6 CN6B NN2 70.0 113.7 !RIBOSE, ADM Jr. CN6C CN6B NN2 70.0 113.7 !RIBOSE, ADM Jr. CN6 CN6B NN1 70.0 113.7 !RIBOSE, ADM Jr. CN6 CN6 ON2 75.7 110.1 !RIBOSE, ADM Jr., MeOH CN6B CN6 ON2 75.7 110.1 !RIBOSE, ADM Jr., MeOH CN6C CN6 ON2 75.7 110.1 !RIBOSE, ADM Jr., MeOH CN6 CN6 ON5 75.7 110.1 !RIBOSE, ADM Jr., MeOH CN6B CN6 ON5 75.7 110.1 !RIBOSE, ADM Jr., MeOH CN6C CN6 ON5 75.7 110.1 !RIBOSE, ADM Jr., MeOH CN6 CN6 ON6 110.0 105.0 !RIBOSE, ADM Jr. CN6 CN6B ON6 110.0 105.0 !RIBOSE, ADM Jr. CN6C CN6B ON6 110.0 105.0 !RIBOSE, ADM Jr. CN7 CN6 ON6 110.0 109.0 !RIBOSE, ADM Jr. CN8 CN6 ON6 110.0 109.0 !RIBOSE, ADM Jr. CN9 CN6 ON6 110.0 109.0 !RIBOSE, ADM Jr. HN6 CN6 CN6 34.5 110.1 22.53 2.179 ! Alkanes, sacred HN6 CN6B CN6 34.5 110.1 22.53 2.179 ! Alkanes, sacred HN6 CN6B CN6C 34.5 110.1 22.53 2.179 ! Alkanes, free HN6 CN6C CN6 33.4 110.1 22.53 2.179 ! Alkanes, free HN6 CN6C CN6B 33.4 110.1 22.53 2.179 ! Alkanes, free HN6 CN6 CN6B 34.5 110.1 22.53 2.179 ! Alkanes, sacred HN6 CN6 CN6C 34.5 110.1 22.53 2.179 ! Alkanes, free HN6 CN6 CN7 34.5 110.1 22.53 2.179 ! Alkanes, sacred HN6 CN6 CN8 34.5 110.1 22.53 2.179 ! Alkanes, free HN6 CN6 CN9 34.5 110.1 22.53 2.179 ! Alkanes, sacred HN6 CN6 HN6 35.5 109.0 5.40 1.802 ! Alkanes, free HN6 CN6C HN6 35.5 109.0 5.40 1.802 ! Alkanes, free HN6 CN6B NN2 43.0 111.0 !RIBOSE, ADM Jr. HN6 CN6 ON2 60.0 109.5 !from HN7 CN7 ON2, ADM JR. HN6 CN6 ON5 45.9 108.89 !RIBOSE, ADM Jr., MeOH HN6 CN6 ON6 45.2 107.24 !RIBOSE, ADM Jr. HN6 CN6B ON6 45.2 107.24 !RIBOSE, ADM Jr. ON5 CN6 ON6 92.6 111.55 !RIBOSE, ADM Jr., ribose (with O1') ON6 CN6B NN2 70.0 108.0 !RIBOSE, ADM Jr. ON6 CN6B NN5 70.0 108.0 !GLYCOSIDAC, Arnott + Huckins CN6 CN6B NN5 70.0 113.7 !GLYCOSIDAC, Arnott + Huckins CN6C CN6B NN5 70.0 113.7 !GLYCOSIDAC, Arnott + Huckins NN5 CN6B HN6 38.0 111.0 50. 2.14 ! sugar model, adm jr. CN6 CN7 HN7 34.5 110.1 22.53 2.179 ! Alkanes, sacred CN6 CN7 ON2 75.7 110.10 !RIBOSE, ADM Jr., MeOH CN6 CN7 ON5 75.7 110.10 !RIBOSE, ADM Jr., MeOH CN7 CN7 HN7 34.5 110.10 22.53 2.179 ! Alkanes, sacred CN8 CN7 HN7 34.5 110.10 22.53 2.179 ! Alkanes, free HN7 CN7 ON5 45.9 108.89 !RIBOSE, ADM Jr., MeOH CN3 CN8 CN3 125.0 108.0 !nadh/ppi, jjp1/adm jr. 7/95 CN3 CN8 HN7 55.0 110.10 !nadh/ppi, jjp1/adm jr. 7/95 CN6 CN8 HN7 34.5 110.10 22.53 2.179 ! Alkanes, free CN6 CN8 ON2 75.7 110.10 !RIBOSE, ADM Jr., MeOH CN6 CN8 ON5 75.7 110.10 !RIBOSE, ADM Jr., MeOH CN7 CN8 HN7 34.5 110.10 22.53 2.179 ! Alkanes, free CN8 CN8 HN7 26.5 110.10 22.53 2.179 ! Alkanes, free CN9 CN8 HN7 34.6 110.10 22.53 2.179 ! Alkanes, sacred CN9 CN8 NN2 70.0 113.7 !from CN6 CN6B NN2, adm jr. HN7 CN8 HN7 35.5 109.00 5.40 1.802 ! Alkanes, sacred HN7 CN8 NN2 33.43 110.1 !FOR 9-M-ADE(THY), ADM HN7 CN8 ON2 60.0 109.5 !DMP, ADM Jr. HN7 CN8 ON5 45.9 108.89 !RIBOSE, ADM Jr., MeOH CN3 CN9 HN7 33.43 110.10 22.53 2.179 ! Alkanes, sacred CN3D CN9 HN7 33.43 110.10 22.53 2.179 ! Alkanes, sacred CN6 CN9 HN7 33.43 110.10 22.53 2.179 ! Alkanes, sacred CN6 CN9 ON2 75.7 110.1 !nad/ppi, jjp1/adm jr. 7/95 CN7 CN9 HN7 33.43 110.10 22.53 2.179 ! Alkanes, sacred CN8 CN9 HN7 34.60 110.10 22.53 2.179 ! Alkanes, sacred HN7 CN9 HN7 35.50 108.40 5.40 1.802 ! Alkanes, sacred HN7 CN9 NN2 33.43 110.1 !FOR 9-M-ADE(THY), ADM HN7 CN9 ON2 60.0 109.5 !DMP, ADM Jr. CN1A NN1 HN1 35.0 120.0 !nad/ppi, jjp1/adm jr. 7/95 CN2 NN1 HN1 40.0 120.0 ! par_a6 JWK 9/30/91 HN1 NN1 HN1 32.0 120.0 ! par_a5 JWK 9/30/91 CN1 NN2 CN3 125.0 120.6 !C,U, JWK CN1 NN2 CN6B 70.0 117.7 !from CN1 NN2 CN7, adm jr., 7/24/91 CN1 NN2 CN9 70.0 117.7 !1-M-T XTAL, adm jr., 7/24/91 CN1 NN2 HN2 40.5 122.0 !C,U JWK, adm jr., 7/24/91 CN3B NN2 CN3B 30.0 120.0 !nad/ppi, jjp1/adm jr. 7/95 CN3C NN2 CN3C 20.0 114.0 !nadh/ppi, jjp1/adm jr. 7/95 CN3 NN2 CN6B 70.0 121.7 !from CN3 NN2 CN7, adm jr., 7/24/91 CN3B NN2 CN6B 70.0 121.7 !nad/ppi, jjp1/adm jr. 7/95 CN3C NN2 CN6B 70.0 121.7 !nad/ppi, jjp1/adm jr. 7/95 CN3 NN2 CN9 70.0 121.7 !1-M-T XTAL, adm jr., 7/24/91 CN3 NN2 HN2 32.0 117.4 !C,U, JWK, adm jr., 7/24/91 CN3B NN2 HN2 32.0 117.4 !nad/ppi, jjp1/adm jr. 7/95 CN3C NN2 HN2 39.0 123.0 !nad/ppi, jjp1/adm jr. 7/95 CN4 NN2 CN5 110.0 105.6 !G,A, JWK, par_a9 9/30/91 CN4 NN2 CN6B 70.0 128.4 !from CN4 NN2 CN7, adm jr., 7/24/91 CN4 NN2 CN8 70.0 128.4 !9-E-GUA, adm jr., 7/24/91 CN4 NN2 CN9 70.0 128.4 !9-M-ADE, adm jr., 7/24/91 CN4 NN2 HN2 30.0 125.0 !G,A, JWK, par_a9 9/30/91 CN5 NN2 CN6B 70.0 126.0 !from CN5 NN2 CN7, adm jr., 7/24/91 CN5 NN2 CN8 70.0 126.0 !9-E-GUA, adm jr., 7/24/91 CN5 NN2 CN9 70.0 126.0 !9-M-ADE, adm jr., 7/24/91 CN5 NN2 HN2 30.0 129.4 !G,A, JWK, par_a9 9/30/91 CN1 NN2G CN2 125.0 128.7 !G, JWK, adm jr., 7/24/91 CN1 NN2G CN4 125.0 129.7 !Inosine, adm jr., 2/94 CN1 NN2G HN2 40.5 114.3 !G, adm jr., 7/24/91 CN2 NN2G HN2 40.5 117.0 !G par_49, adm jr., 7/24/91 CN4 NN2G HN2 40.5 116.0 !Inosine, adm jr., 2/94 CN1 NN2U CN1 90.0 129.2 !U,T, par_a4 JWK 9/30/91 CN1 NN2U HN2 40.5 115.4 !T,U, JWK, adm jr., 7/24/91 CN1 NN3 CN2 70.0 119.7 !C, JWK, adm jr., 7/24/91 CN2 NN3A CN5 90.0 112.0 !G, JWK, par_a11 9/30/91 CN2 NN3A CN4 90.0 119.9 !A, JWK, par_a9 9/30/91 CN4 NN3A CN5 90.0 110.3 !A, JWK, par_a9 9/30/91 CN4 NN3I CN5 90.0 110.3 !Inosine, adm jr., 2/94 CN4 NN4 CN5 110.0 103.3 !G,A, JWK, par_a9 9/30/91 CN6B NN5 HN1 50.0 111.5 ! sugar model, adm jr. HN1 NN5 HN1 39.0 106.0 ! sugar model, adm jr. CN6 ON2 P 20.0 120.0 35. 2.33 !DMP, ADM JR. CN8 ON2 P 20.0 120.0 35. 2.33 !DMP, ADM Jr. CN9 ON2 P 20.0 120.0 35. 2.33 !DMP, ADM Jr. CN9 ON2 P2 20.0 120.0 35. 2.33 !nad/ppi, jjp1/adm jr. 7/95 P ON2 P 15.0 140.0 -40.0 2.80 !nad/ppi, jjp1/adm jr. 7/95 P2 ON2 P 15.0 140.0 -40.0 2.80 !nad/ppi, jjp1/adm jr. 7/95 P2 ON2 P2 15.0 140.0 -40.0 2.80 !nad/ppi, jjp1/adm jr. 7/95 HN4 ON4 P 30.0 115.0 40.0 2.35 !MP_1, ADM Jr. HN5 ON5 CN6 57.5 106.0 !RIBOSE, ADM Jr., MeOH HN5 ON5 CN7 57.5 106.0 !RIBOSE, ADM Jr., MeOH HN5 ON5 CN8 57.5 106.0 !RIBOSE, ADM Jr., MeOH HN5 ON5 CN9 57.5 106.0 !RIBOSE, ADM Jr., MeOH CN6 ON6 CN6 110.0 107.5 !RIBOSE, ADM Jr. CN6 ON6 CN6B 110.0 107.5 !RIBOSE, ADM Jr. !HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY ON2 P ON2 80.0 104.3 !DMP, ADM Jr. ON2 P ON3 98.9 111.6 !DMP, ADM Jr. ON2 P ON4 48.1 108.0 !MP_1, ADM Jr. ON3 P ON3 120.0 120.0 !DMP, ADM Jr. ON3 P ON4 98.9 108.23 !MP_1, ADM Jr. ON4 P ON4 98.9 104.0 !MP_0, ADM Jr. ON2 P2 ON2 80.0 104.3 !nad/ppi, jjp1/adm jr. 7/95 ON2 P2 ON3 88.9 111.6 !nad/ppi, jjp1/adm jr. 7/95 ON3 P2 ON3 104.0 120.0 !nad/ppi, jjp1/adm jr. 7/95 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 CP1 CP2 CP2 CP3 10.0000 1 145.41 ! for PRO pucker; Andrej Sali C CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c C CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c C N CP1 C 0.8000 3 0.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CA CA CA CA 3.1000 2 180.00 ! ALLOW ARO ! JES 8/25/89 CA CPT CPT CA 3.1000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CA CT2 CT1 C 0.0400 3 0.00 ! ALLOW ARO ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 CA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 CA NY CPT CA 3.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CC CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CC CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 CC CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c CC CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL ! Alanine dipeptide; NMA; acetate; etc. adm jr., 3/3/93c CD CP1 N C 0.0000 1 180.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CD CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c CD CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL ! Alanine dipeptide; NMA; acetate; etc. backbon adm jr., 3/3/93c CE1 CE1 CT3 HA 0.0300 3 0.00 ! ! for butene, yin/adm jr., 12/95 CE2 CE1 CT2 CT3 0.5000 3 0.00 ! ! for butene, yin/adm jr., 12/95 CE2 CE1 CT2 HA 0.1200 3 0.00 ! ! for butene, yin/adm jr., 12/95 CE2 CE1 CT3 HA 0.0500 3 180.00 ! ! for propene, yin/adm jr., 12/95 CP1 C N CP1 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP1 C N CP1 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP2 CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N C CP1 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N C CP1 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N CP1 C 0.1000 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N CP1 CC 0.1000 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 N CP1 CP2 0.1000 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 NP CP1 C 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CP3 NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CPH2 NR1 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/20/89 CPH2 NR2 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/20/89 CPH2 NR3 CPH1 CPH1 12.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/20/89 CPT CA CA CA 3.1000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CPT CPT CA CA 3.1000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CPT CPT CY CA 4.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CPT CPT NY CA 5.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CT1 C N CP1 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT1 C N CP1 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT1 C N CP3 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT1 C N CP3 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT1 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT1 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT1 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c CT1 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI ! ethylbenzene ethyl rotation, adm jr. 3/7/92 CT1 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 CT1 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 CT1 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 CT1 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO ! from ethylbenzene, adm jr., 3/7/92 CT1 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO ! from ethylbenzene, adm jr., 3/7/92 CT1 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT1 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 C N CP1 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 C N CP1 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 C N CP3 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 C N CP3 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT2 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT2 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT2 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT2 CA CA CA 3.1000 2 180.00 ! ALLOW ARO ! JES 8/25/89 toluene and ethylbenzene CT2 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2 CT2 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/22/89, FROM HA CPH1 NR2 CPH2 CT2 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 CT2 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c CT2 CT2 CPH1 CPH1 0.4000 1 0.00 ! ALLOW ARO ! 4-methylimidazole 4-21G//6-31G* rot bar. ADM JR., 9/4/89 CT2 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92, butane trans/gauche CT2 CT2 NH1 C 1.8000 1 0.00 ! ALLOW PEP ! from CT2 CT1 NH1 C, for lactams, adm jr. CT2 CY CPT CA 3.0000 2 180.00 ! ALLOW ARO ! JWK CT2 CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO !JWK CT2 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT2 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT2 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT2 SM SM CT2 1.0000 1 0.00 ! ALLOW ALI SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) CT2 SM SM CT2 4.1000 2 0.00 ! ALLOW ALI SUL ION ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL) CT2 SM SM CT2 0.9000 3 0.00 ! ALLOW ALI SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) CT3 C N CP1 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT3 C N CP1 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT3 C N CP3 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT3 C N CP3 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT3 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT3 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT3 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP ! for acetylated GLY N-terminus, adm jr. CT3 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP ! for acetylated GLY N-terminus, adm jr. CT3 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT3 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT3 CA CA CA 3.1000 2 180.00 ! ALLOW ARO ! toluene, adm jr., 3/7/92 CT3 CE1 CE2 HA2 5.2000 2 180.00 ! ! for propene, yin/adm jr., 12/95 CT3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2 CT3 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c CT3 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI ! ethylbenzene ethyl rotation, adm jr. 3/7/92 CT3 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 CT3 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 CT3 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 CT3 CT2 CT2 CT2 0.1500 1 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92, butane trans/gauche CT3 CT2 CT2 CT3 0.1500 1 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92, butane trans/gauche CT3 CT2 CY CA 0.2300 2 180.00 ! ALLOW ARO ! from ethylbenzene, adm jr., 3/7/92 CT3 CT2 CY CPT 0.2300 2 180.00 ! ALLOW ARO ! from ethylbenzene, adm jr., 3/7/92 CT3 CT2 S CT3 0.2400 1 180.00 ! ALOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) CT3 CT2 S CT3 0.3700 3 0.00 ! ALOW ALI SUL ION ! DTN 8/24/90 CT3 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT3 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 CT3 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP ! Revised to adjust NMA cis/trans energy difference. (LK) CT3 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) CT3 S CT2 CT2 0.2400 1 180.00 ! ALOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) CT3 S CT2 CT2 0.3700 3 0.00 ! ALOW ALI SUL ION ! expt. MeEtS, 3/26/92 (FL) CT3 SM SM CT3 1.0000 1 0.00 ! ALLOW ALI SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) CT3 SM SM CT3 4.1000 2 0.00 ! ALLOW ALI SUL ION ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL) CT3 SM SM CT3 0.9000 3 0.00 ! ALLOW ALI SUL ION ! improved CSSC dihedral in DMDS 5/15/92 (FL) CY CA NY CPT 5.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CY CPT CA CA 3.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole CY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole H NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 H NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) H NH1 C CT2 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) H NH1 C CT3 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) H NH1 CT1 C 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) H NH1 CT1 CC 0.0000 1 0.00 ! ALLOW PEP POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters H NH1 CT1 CD 0.0000 1 0.00 ! ALLOW PEP POL ! adm jr. 5/02/91, acetic acid pure solvent H NH1 CT1 CT1 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) H NH1 CT1 CT2 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) H NH1 CT1 CT3 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) H NH1 CT2 C 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) H NH1 CT2 CC 0.0000 1 0.00 ! ALLOW PEP POL ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 H NH1 CT2 CD 0.0000 1 0.00 ! ALLOW PEP POL ! adm jr. 5/02/91, acetic acid pure solvent H NH1 CT2 CT2 0.0000 1 0.00 ! ALLOW PEP ! from H NH1 CT2 CT3, for lactams, adm jr. H NH1 CT2 CT3 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) H NH2 CC CT1 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO ! adm jr. 4/10/91, acetamide update H NH2 CC CT2 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO ! adm jr. 4/10/91, acetamide update H NH2 CC CT3 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO ! adm jr. 4/10/91, acetamide update H NH2 CC CP1 2.5000 2 180.00 ! ALLOW PEP POL ARO PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 H NR1 CPH1 CPH1 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 7/20/89 H NR1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H H NR1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H H NR3 CPH1 CPH1 1.4000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 H NR3 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA H NR3 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA H NY CA CY 0.8000 2 180.00 ! ALLOW ARO !adm jr., 12/30/91, for jwk H NY CPT CA 0.8000 2 180.00 ! ALLOW ARO !adm jr., 12/30/91, for jwk H NY CPT CPT 0.8000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole H OH1 CA CA 0.9900 2 180.00 ! ALLOW ARO ALC ! phenol OH rot bar, 3.37 kcal/mole, adm jr. 3/7/92 H OH1 CT1 CT1 1.3300 1 0.00 ! ALLOW ALC ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT1 CT1 0.1800 2 0.00 ! ALLOW ALC ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT1 CT1 0.3200 3 0.00 ! ALLOW ALC ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT1 CT3 1.3300 1 0.00 ! ALLOW ALC ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT1 CT3 0.1800 2 0.00 ! ALLOW ALC ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT1 CT3 0.3200 3 0.00 ! ALLOW ALC ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT1 1.3000 1 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT1 0.3000 2 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT1 0.4200 3 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT2 1.3000 1 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT2 0.3000 2 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT2 0.4200 3 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT3 1.3000 1 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT3 0.3000 2 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 H OH1 CT2 CT3 0.4200 3 0.00 ! ALLOW ALC ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 HA CA CA CA 3.5000 2 180.00 ! ALLOW ARO ! adm jr., 10/02/89 HA CA CA CPT 3.5000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CA CA HA 2.5000 2 180.00 ! ALLOW ARO ! ADM JR., 10/02/89 HA CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO ! TRP (JES) HA CA CPT CY 4.0000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CA CY CPT 1.2000 2 180.00 ! ALLOW ARO ! JWK HA CA CY CT2 1.2000 2 180.00 ! ALLOW ARO ! JWK HA CA NY CPT 3.0000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CA NY H 1.0000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL ! adm jr. 4/10/91, acetamide update HA CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HA CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 HA CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 HA CT2 CY CA 0.2500 2 180.00 ! ALLOW ARO ! JWK HA CT2 CY CPT 0.2500 2 180.00 ! ALLOW ARO ! JWK HA CT2 NH1 C 0.0000 3 0.00 ! ALLOW PEP ! LK for autogenerate dihe, sp2-methyl, no dihedral potential HA CT2 NH1 H 0.0000 3 0.00 ! ALLOW PEP ! LK for autogenerate dihe, sp2-methyl, no dihedral potential HA CT2 S CT3 0.2800 3 0.00 ! ALLOW ALI SUL ION ! DTN 8/24/90 HA CT3 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 HA CT3 CS HA 0.1600 3 0.00 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 HA CT3 CT2 CA 0.0400 3 0.00 ! ALLOW ARO ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 HA CT3 NH1 C 0.0000 3 0.00 ! ALLOW PEP ! LK for autogenerate dihe, sp2-methyl, no dihedral potential HA CT3 NH1 H 0.0000 3 0.00 ! ALLOW PEP ! LK for autogenerate dihe, sp2-methyl, no dihedral potential HA CT3 S CT2 0.2800 3 0.00 ! ALLOW ALI SUL ION ! DTN 8/24/90 HA CY CA CPT 1.2000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CY CA HA 1.2000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CY CPT CA 3.0000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA CY CPT CPT 3.0000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 HA1 CE1 CE2 HA2 5.2000 2 180.00 ! ! for propene, yin/adm jr., 12/95 HA1 CE1 CT2 HA 0.8700 3 0.00 ! ! for butene, yin/adm jr., 12/95 HA1 CE1 CT2 CT3 0.1200 3 0.00 ! ! for butene, yin/adm jr., 12/95 HA1 CE1 CT3 HA 0.3400 3 0.00 ! ! for butene, yin/adm jr., 12/95 HA2 CE2 CE1 CT2 5.2000 2 180.00 ! ! for butene, yin/adm jr., 12/95 HB CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CP1 N CP3 0.1000 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CP1 NP CP3 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HB CT1 NH1 C 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT1 NH1 H 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT2 NH1 C 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT2 NH1 H 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT3 NH1 C 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HB CT3 NH1 H 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) HC NP CP1 C 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP1 HB 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP3 CP2 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HC NP CP3 HA 0.0800 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 HP CA CA CA 4.2000 2 180.00 ! ALLOW ARO ! JES 8/25/89 benzene HP CA CA CPT 3.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole HP CA CA CT2 4.2000 2 180.00 ! ALLOW ARO ! JES 8/25/89 toluene and ethylbenzene HP CA CA CT3 4.2000 2 180.00 ! ALLOW ARO ! toluene, adm jr., 3/7/92 HP CA CA HP 2.4000 2 180.00 ! ALLOW ARO ! JES 8/25/89 benzene HP CA CPT CPT 3.0000 2 180.00 ! ALLOW ARO ! JWK indole 05/14/91 HP CA CPT CY 3.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole HP CA CY CPT 2.0000 2 180.00 ! ALLOW ARO !adm jr., 12/30/91, for jwk HP CA CY CT2 1.2000 2 180.00 ! ALLOW ARO ! JWK indole 05/14/91 HP CA NY CPT 2.0000 2 180.00 ! ALLOW ARO !adm jr., 12/30/91, for jwk HP CA NY H 0.4000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole HP CY CA HP 1.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole HP CY CPT CA 2.8000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole HP CY CPT CPT 2.8000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole HR1 CPH1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH1 CPH1 HR1 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90, his HR1 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH1 NR3 H 3.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH2 NR1 CPH1 3.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR1 CPH2 NR2 CPH1 3.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR2 CPH2 NR3 CPH1 3.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 HR2 CPH2 NR3 H 0.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90, YES, 0.0 HR3 CPH1 CPH1 CT2 2.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 CPH1 CPH1 CT3 2.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 CPH1 CPH1 HR3 2.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 CPH1 NR1 H 1.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HS S CT2 CT1 0.2400 1 0.00 ! ALLOW ALI SUL ION ! methanethiol pure solvent, adm jr., 6/22/92 HS S CT2 CT1 0.1500 2 0.00 ! ALLOW ALI SUL ION ! methanethiol pure solvent, adm jr., 6/22/92 HS S CT2 CT1 0.2700 3 0.00 ! ALLOW ALI SUL ION ! methanethiol pure solvent, adm jr., 6/22/92 HS S CT2 CT3 0.2400 1 0.00 ! ALLOW ALI SUL ION ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 HS S CT2 CT3 0.1500 2 0.00 ! ALLOW ALI SUL ION ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 HS S CT2 CT3 0.2700 3 0.00 ! ALLOW ALI SUL ION ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 HS S CT2 HA 0.2000 3 0.00 ! ALLOW ALI SUL ION ! methanethiol pure solvent, adm jr., 6/22/92 HS S CT3 HA 0.2000 3 0.00 ! ALLOW ALI SUL ION ! methanethiol pure solvent, adm jr., 6/22/92 N C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT1 HB 0.0000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT2 HB 0.0000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N C CT3 HA 0.0000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 N CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 NH1 C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH1 C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH1 C CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH1 C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH1 C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH1 C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH1 C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) NH1 C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) NH1 C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) NH1 C CT1 HB 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) NH1 C CT1 NH1 0.6000 1 0.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 NH1 C CT2 CT2 0.0000 1 0.00 ! ALLOW PEP ! from NH1 C CT1 CT2, for lactams, adm jr. NH1 C CT2 HA 0.0000 3 0.00 ! ALLOW PEP ! LK for autogenerate dihe, sp2-methyl, no dihedral potential NH1 C CT2 HB 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) NH1 C CT2 NH1 0.6000 1 0.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 NH1 C CT3 HA 0.0000 3 0.00 ! ALLOW PEP ! LK for autogenerate dihe, sp2-methyl, no dihedral potential NH1 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH1 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH2 CC CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH2 CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH2 CC CP1 HB 0.4000 1 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH2 CC CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH2 CC CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH2 CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH2 CC CT2 HA 0.0000 3 180.00 ! ALLOW POL ! adm jr., 8/13/90 acetamide geometry and vibrations NH3 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH3 CT1 C NH1 0.6000 1 0.00 ! ALLOW PEP PRO ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 NH3 CT1 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 NH3 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NH3 CT2 C NH1 0.4000 1 0.00 ! ALLOW PEP PRO ! adm jr. 3/24/92, for PRES GLYP NH3 CT2 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 NP CP1 C N 0.3000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP1 C NH1 0.3000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NP CP1 CC NH2 0.3000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NR1 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA NR1 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA NR1 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params NR1 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR1 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR1 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR1 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR1 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR1 CPH2 NR2 CPH1 14.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR2 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA NR2 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA NR2 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params NR2 CPH1 CPH1 NR1 14.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR2 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO ! HIS CB-CG TORSION, NR2 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO ! HIS CB-CG TORSION, NR2 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO ! HIS CB-CG TORSION, NR2 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR2 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR2 CPH2 NR1 CPH1 14.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR2 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR3 CPH1 CPH1 CT2 2.5000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 NR3 CPH1 CPH1 CT3 2.5000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 NR3 CPH1 CPH1 HR1 2.5000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 NR3 CPH1 CPH1 NR3 12.0000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 NR3 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR3 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR3 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR3 CPH1 CT2 HA 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR3 CPH1 CT3 HA 0.1900 3 0.00 ! ALLOW ARO ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 NR3 CPH2 NR3 CPH1 12.0000 2 180.00 ! ALLOW ARO ! his, ADM JR., 7/20/89 NR3 CPH2 NR3 H 1.4000 2 180.00 ! ALLOW ARO ! his, adm jr., 6/27/90 NY CA CY CPT 4.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole NY CA CY CT2 3.5000 2 180.00 ! ALLOW ARO ! JWK NY CA CY HA 3.5000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 NY CA CY HP 3.5000 2 180.00 ! ALLOW ARO ! JWK indole 05/14/91 NY CPT CA CA 2.8000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole NY CPT CA HA 4.0000 2 180.00 ! ALLOW ARO ! JWK 09/05/89 NY CPT CA HP 3.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole NY CPT CPT CA 10.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole NY CPT CPT CY 5.0000 2 180.00 ! ALLOW ARO ! JWK 05/14/91 fit to indole O C CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C CP1 HB 0.4000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C CT1 CT1 1.4000 1 0.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c O C CT1 CT2 1.4000 1 0.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c O C CT1 CT3 1.4000 1 0.00 ! ALLOW PEP ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c O C CT1 HB 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) O C CT1 NH1 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) O C CT1 NH3 0.0000 1 0.00 ! ALLOW PEP PRO ! Backbone parameter set made complete RLD 8/8/90 O C CT2 CT2 1.4000 1 0.00 ! ALLOW PEP ! from O C CT1 CT2, for lactams, adm jr. O C CT2 HA 0.0000 3 180.00 ! ALLOW POL ! adm jr., 8/13/90 acetamide geometry and vibrations O C CT2 HB 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) O C CT2 NH1 0.0000 1 0.00 ! ALLOW PEP ! Alanine Dipeptide ab initio calc's (LK) O C CT2 NH3 0.0000 1 0.00 ! ALLOW PEP PRO ! Backbone parameter set made complete RLD 8/8/90 O C CT3 HA 0.0000 3 180.00 ! ALLOW POL ! adm jr., 8/13/90 acetamide geometry and vibrations O C N CP1 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C N CP1 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C N CP3 2.7500 2 180.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C N CP3 0.3000 4 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) O C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) O C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) O C NH1 H 2.5000 2 180.00 ! ALLOW PEP ! Gives appropriate NMA cis/trans barrier. (LK) O CC CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O CC CP1 HB 0.4000 1 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O CC CP1 HB 0.6000 2 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 O CC CT2 HA 0.0000 3 180.00 ! ALLOW POL ! adm jr. 4/05/91, for asn,asp,gln,glu and cters O CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO ! adm jr. 4/10/91, acetamide update OB CD OS CT2 0.9650 1 180.00 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate OB CD OS CT2 3.8500 2 180.00 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate OB CD OS CT3 0.9650 1 180.00 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate OB CD OS CT3 3.8500 2 180.00 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate OC CA CA CA 3.1000 2 180.00 ! ALLOW ARO ! adm jr. 8/27/91, phenoxide OC CA CA HP 4.2000 2 180.00 ! ALLOW ARO ! adm jr. 8/27/91, phenoxide OC CC CP1 CP2 0.1600 3 0.00 ! ALLOW PEP PRO POL ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 OC CC CP1 HB 0.1600 3 0.00 ! ALLOW PEP PRO POL ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 OC CC CP1 N 0.1600 3 0.00 ! ALLOW PEP PRO POL ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 OC CC CP1 NP 0.1600 3 0.00 ! ALLOW PEP PRO POL ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 OC CC CT1 NH3 3.2000 2 180.00 ! ALLOW PEP PRO ! adm jr. 4/17/94, zwitterionic glycine OC CC CT2 NH3 3.2000 2 180.00 ! ALLOW PEP PRO ! adm jr. 4/17/94, zwitterionic glycine OH1 CA CA CA 3.1000 2 180.00 ! ALLOW ARO ! JES 8/25/89 phenol OH1 CA CA HP 4.2000 2 180.00 ! ALLOW ARO ! JES 8/25/89 phenol S CT2 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION ! DTN 8/24/90 SM CT2 CT2 HA 0.0100 3 0.00 ! ALLOW ALI SUL ION ! DTN 8/24/90 SM SM CT2 CT1 0.3100 3 0.00 ! ALLOW SUL ALI ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 SM SM CT2 CT2 0.3100 3 0.00 ! ALLOW SUL ALI ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 SM SM CT2 HA 0.1580 3 0.00 ! ALLOW ALI SUL ION ! expt. dimethyldisulfide, 3/26/92 (FL) SM SM CT3 HA 0.1580 3 0.00 ! ALLOW ALI SUL ION ! expt. dimethyldisulfide, 3/26/92 (FL) SS CS CT3 HA 0.1500 3 0.00 ! ALLOW SUL ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 X C C X 4.0000 2 180.00 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) X C NC2 X 2.2500 2 180.00 ! ALLOW PEP POL ARO ! 9.0->2.25 GUANIDINIUM (KK) X CD OH1 X 2.0500 2 180.00 ! ALLOW PEP POL ARO ALC ! adm jr, 10/17/90, acetic acid C-Oh rotation barrier X CD OS X 2.0500 2 180.00 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate X CE1 CE1 X 5.2000 2 180.00 ! ! for butene, yin/adm jr., 12/95 X CE2 CE2 X 4.9000 2 180.00 ! ! for ethene, yin/adm jr., 12/95 X CP1 C X 0.0000 6 180.00 ! ALLOW POL PEP PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 X CP1 CC X 0.0000 6 180.00 ! ALLOW POL PEP ! changed to 0.0 RLD 5/19/92 X CP1 CD X 0.0000 6 180.00 ! ALLOW POL PEP ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 X CP1 CP2 X 0.1400 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 X CP2 CP2 X 0.1600 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 X CP3 CP2 X 0.1400 3 0.00 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 X CPA CPB X 0.0000 2 0.00 ! ALLOW HEM ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) X CPA CPM X 0.0000 2 0.00 ! ALLOW HEM ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) X CPB C X 3.0000 2 180.00 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) X CPB CPB X 0.0000 2 0.00 ! ALLOW HEM ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) X CPB CT2 X 0.0000 6 0.00 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) X CPB CT3 X 0.0000 6 0.00 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) X CPT CPT X 0.0000 2 180.00 ! ALLOW ARO ! JWK indole 05/14/91 X CT1 CC X 0.0500 6 180.00 ! ALLOW POL PEP ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) X CT1 CD X 0.0000 6 180.00 ! ALLOW POL PEP ! adm jr. 3/19/92, from lipid methyl acetate X CT1 CT1 X 0.2000 3 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 X CT1 CT3 X 0.2000 3 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 X CT1 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL ! 0.715->0.10 METHYLAMMONIUM (KK) X CT1 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO ! EMB 11/21/89 methanol vib fit X CT1 OS X -0.1000 3 0.00 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate X CT2 CA X 0.0000 6 0.00 ! ALLOW ALI ARO ! toluene, adm jr., 3/7/92 X CT2 CC X 0.0500 6 180.00 ! ALLOW POL PEP ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) X CT2 CD X 0.0000 6 180.00 ! ALLOW POL PEP ! adm jr. 3/19/92, from lipid methyl acetate X CT2 CT2 X 0.1950 3 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 X CT2 CT3 X 0.1600 3 0.00 ! ALLOW ALI ! rotation barrier in Ethane (SF) X CT2 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL ! methylguanidinium, adm jr., 3/26/92 X CT2 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL ! 0.715->0.10 METHYLAMMONIUM (KK) X CT2 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO ! EMB 11/21/89 methanol vib fit X CT2 OS X -0.1000 3 0.00 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate X CT3 CA X 0.0000 6 0.00 ! ALLOW ALI ARO ! toluene, adm jr., 3/7/92 X CT3 CC X 0.0500 6 180.00 ! ALLOW POL PEP ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) X CT3 CD X 0.0000 6 180.00 ! ALLOW POL PEP ! adm jr. 3/19/92, from lipid methyl acetate X CT3 CT3 X 0.1550 3 0.00 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 X CT3 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL ! methylguanidinium, adm jr., 3/26/92 X CT3 NH2 X 0.1100 3 0.00 ! ALLOW POL ! methylamine geom/freq, adm jr., 6/2/92 X CT3 NH3 X 0.0900 3 0.00 ! ALLOW ALI POL ! fine-tuned to ab initio; METHYLAMMONIUM, KK 03/10/92 X CT3 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO ! EMB 11/21/89 methanol vib fit X CT3 OS X -0.1000 3 0.00 ! ALLOW PEP POL ! adm jr. 3/19/92, from lipid methyl acetate X FE CM X 0.0500 4 0.00 ! ALLOW HEM ! Heme (6-liganded): ligands (KK 05/13/91) X FE NPH X 0.0000 2 0.00 ! ALLOW HEM ! Heme (6-liganded): for "ic para" only (KK 05/13/91) X FE OM X 0.0000 4 0.00 ! ALLOW HEM ! Heme (6-liganded): ligands (KK 05/13/91) X NPH CPA X 0.0000 2 0.00 ! ALLOW HEM ! Heme (6-liganded): dummy for "auto dihe" (KK 05/13/91) ! nucleic acids section ! PHOSPHATE ON2 P ON2 CN6 0.95 2 0.0 !DMP, ADM Jr. ON2 P ON2 CN6 0.50 3 0.0 !DMP, ADM Jr. (X P ON2 CN6 ON2) ON2 P ON2 CN8 0.95 2 0.0 !DMP, ADM Jr. (X P ON2 CN6 ON2) ON2 P ON2 CN8 0.50 3 0.0 !DMP, ADM Jr. ON2 P ON2 CN9 0.95 2 0.0 !DMP, ADM Jr. (X P ON2 CN6 ON2) ON2 P ON2 CN9 0.50 3 0.0 !DMP, ADM Jr. ON3 P ON2 CN6 0.10 3 0.0 !DMP, ADM Jr. ON3 P ON2 CN8 0.10 3 0.0 !DMP, ADM Jr. (X P ON2 CN6 ON2) ON3 P ON2 CN9 0.10 3 0.0 !DMP, ADM Jr. (X P ON2 CN6 ON2) ON4 P ON2 CN6 0.95 2 0.0 !MP_1, ADM Jr. ON4 P ON2 CN6 0.50 3 0.0 !MP_1, ADM Jr. ON4 P ON2 CN8 0.95 2 0.0 !MP_1, ADM Jr. ON4 P ON2 CN8 0.50 3 0.0 !MP_1, ADM Jr. ON4 P ON2 CN9 0.95 2 0.0 !MP_1, ADM Jr. ON4 P ON2 CN9 0.50 3 0.0 !MP_1, ADM Jr. X ON4 P X 0.30 3 0.0 !MP_1, ADM Jr. ! phosphate ester related terms X CN8 ON2 X -0.10 3 0.0 !DMP, ADM Jr. (P ON2 CN7 HN7) X CN9 ON2 X -0.10 3 0.0 !DMP, ADM Jr. (P ON2 CN7 HN7) X CN6 ON2 X -0.10 3 0.0 !from (P ON2 CN7 HN7) X CN6 CN6 X 0.15 3 0.0 ! Alkanes (0.2 to 0.15) X CN6 CN6B X 0.15 3 0.0 ! Alkanes (0.2 to 0.15) X CN6 CN6C X 0.15 3 0.0 ! Alkanes (0.2 to 0.15) X CN6B CN6C X 0.15 3 0.0 ! Alkanes (0.2 to 0.15) ! RIBOSE ON5 CN6 CN6 ON2 0.50 3 0.0 ON5 CN6 CN6 ON5 0.50 3 0.0 X CN6 ON6 X 0.10 3 0.0 X CN6B ON6 X 0.10 3 0.0 CN5 NN2 CN6B CN6 0.5 3 0.0 CN3 NN2 CN6B CN6 0.5 3 0.0 HN1 NN1 CN6B CN6 0.5 3 0.0 X CN6B NN2 X 0.0 3 0.0 X CN6B NN1 X 0.0 3 0.0 X CN8 NN2 X 0.0 3 0.0 X CN9 NN2 X 0.0 3 0.0 ! SUGAR GAUCHE TERMS CN6B CN6 CN6 ON2 0.2 2 0.0 ! ADM Jr. (ribo) CN6B CN6C CN6 ON2 0.45 2 0.0 ! ADM Jr. (deo) CN6B CN6 CN6 ON5 0.2 2 0.0 ! ADM Jr. (ribo) CN6B CN6C CN6 ON5 0.45 2 0.0 ! ADM Jr. (deo) ! ! WILDCARDS X CN6 CN8 X 0.200 3 0.0 ! Alkanes X CN6 CN9 X 0.200 3 0.0 ! Alkanes X CN6 ON5 X 0.140 3 0.0 ! MeOH X CN7 CN7 X 0.200 3 0.0 ! Alkanes X CN7 CN8 X 0.200 3 0.0 ! Alkanes X CN7 CN9 X 0.200 3 0.0 ! Alkanes X CN8 CN8 X 0.195 3 0.0 ! Alkanes X CN8 CN9 X 0.160 3 0.0 ! Alkanes X CN8 ON5 X 0.140 3 0.0 ! MeOH ! butane gauche terms CN9 CN8 CN8 CN9 0.15 1 0.0 CN9 CN8 CN8 CN8 0.15 1 0.0 CN8 CN8 CN8 CN8 0.15 1 0.0 ! BASES ! Uracil NN2 CN3 CN3 CN1 4.0 2 180.0 ! par_31 CN3 CN3 CN1 NN2U 3.0 2 180.0 ! par_a1 JWK 9/30/91 CN3 CN1 NN2 CN1 3.5 2 180.0 ! PAR_32 CN1 NN2U CN1 NN2 3.5 2 180.0 ! PAR_32 CN1 NN2 CN3 CN3 3.5 2 180.0 ! PAR_32 NN2U CN1 NN2 CN3 3.0 2 180.0 ! par_a1 JWK 9/30/91 HN3 CN3 CN3 HN3 3.0 2 180.0 ! par_34 HN3 CN3 CN1 ON1 4.0 2 180.0 ! par_a1 JWK 9/30/91 ON1 CN1 NN2 HN2 3.0 2 180.0 ! par_a1 JWK 9/30/91 ON1 CN1 NN2G HN2 3.0 2 180.0 ! PAR_36, adm jr., 7/24/91 ON1 CN1 NN2U HN2 2.5 2 180.0 ! par_a2 JWK 9/30/91 HN2 NN2 CN3 HN3 1.8 2 180.0 ! PAR_36 NN2 CN1 NN2U HN2 1.8 2 180.0 ! par_a2 JWK 9/30/91 CN3 CN1 NN2U HN2 1.8 2 180.0 ! par_a2 JWK 9/30/91 !Thymine NN2 CN1 CN3 CN9 3.00 3 0.0 ! par_51 NN2 CN3 CN3 CN9 3.00 3 0.0 ! par_51 CN1 CN3 CN9 HN7 0.00 3 0.0 ! par_51, adm jr. 8/1/91 CN3 CN3 CN9 HN7 0.00 3 0.0 ! par_51, adm jr. 8/1/91 ! Cytosine NN2 CN3 CN3 CN2 4.0 2 180.0 ! par_7 CN3 CN3 CN2 NN3 4.0 2 180.0 ! par_39 CN3 CN2 NN3 CN1 4.5 2 180.0 ! par_13 CN2 NN3 CN1 NN2 4.5 2 180.0 ! par_13 NN3 CN1 NN2 CN3 3.5 2 180.0 ! par_39 NN3 CN2 NN1 HN1 2.0 2 180.0 ! par_40 CN3 CN2 NN1 HN1 2.0 2 180.0 ! par_40 NN1 CN2 CN3 HN3 2.0 2 180.0 ! par_39 ON1C CN1 NN2 HN2 3.0 2 180.0 ! par_a1 adm jr., 10/2/91 X CN2 NN3 X 1.0 2 180.0 ! par_41 ! 5-methylcytosine NN2 CN3 CN3D CN2 3.0 2 180.0 !5mc, adm jr., 9/9/93 CN3 CN3D CN2 NN3 1.0 2 180.0 !5mc, adm jr., 9/9/93 CN3D CN2 NN3 CN1 10.0 2 180.0 !5mc, adm jr., 9/9/93 CN3D CN3 NN2 CN1 1.0 2 180.0 !5mc, adm jr., 9/9/93 CN3D CN2 NN1 HN1 2.0 2 180.0 !5mc, adm jr., 9/9/93 NN1 CN2 CN3D CN3 0.0 2 180.0 !5mc, adm jr., 9/9/93 NN1 CN2 CN3D CN9 0.0 2 180.0 !5mc, adm jr., 9/9/93 NN2 CN3 CN3D CN9 4.0 2 180.0 !5mc, adm jr., 9/9/93 NN3 CN2 CN3D CN9 0.0 2 180.0 !5mc, adm jr., 9/9/93 CN3 CN3D CN9 HN7 0.0 3 0.0 !5mc, adm jr., 9/9/93 CN2 CN3D CN9 HN7 0.35 3 0.0 !5mc, adm jr., 9/9/93 CN2 CN3D CN3 HN3 4.0 2 180.0 !5mc, adm jr., 9/9/93 CN9 CN3D CN3 HN3 4.0 2 180.0 !5mc, adm jr., 9/9/93 ! Adenine NN3A CN2 CN5 CN5 6.0 2 180.0 ! par_24 par_a7 9/30/91 CN5 CN2 NN3A CN4 6.0 2 180.0 ! par_24 par_a7 9/30/91 NN4 CN4 NN2 CN5 10.0 2 180.0 ! par_47 par_a7 9/30/91 NN3A CN4 NN3A CN5 6.0 2 180.0 ! par_24 par_a7 9/30/91 NN3A CN4 NN3A CN2 8.0 2 180.0 ! par_43 par_a7 9/30/91 NN2 CN4 NN4 CN5 8.0 2 180.0 ! par_25 par_a7 9/30/91 CN2 CN5 CN5 NN3A 6.0 2 180.0 ! par_24 par_a7 9/30/91 NN4 CN5 CN5 NN2 8.0 2 180.0 ! par_25 par_a7 9/30/91 CN5 CN5 NN2 CN4 10.0 2 180.0 ! par_47 par_a7 9/30/91 CN5 CN5 NN3A CN4 6.0 2 180.0 ! par_24 par_a7 9/30/91 CN5 CN5 NN4 CN4 8.0 2 180.0 ! par_25 par_a7 9/30/91 CN5 CN2 NN1 HN1 2.5 2 180.0 ! par_26 par_a10 9/30/91 HN2 NN2 CN4 HN3 1.5 2 180.0 ! par_44 par_a7 9/30/91 NN3A CN2 NN1 HN1 2.5 2 180.0 ! par_40 par_a10 9/30/91 ! Butterfly motion NN3A CN5 CN5 NN4 20.0 2 180.0 !A, par_24 par_a7 9/30/91 CN2 CN5 CN5 NN2 20.0 2 180.0 !A, par_24 ! Guanine NN2G CN1 CN5 CN5 6.0 2 180.0 ! par_49 CN5 CN1 NN2G CN2 6.0 2 180.0 ! par_49 CN1 NN2G CN2 NN3A 6.0 2 180.0 ! par_49 NN2G CN2 NN3A CN5 6.0 2 180.0 ! par_49 CN2 NN3A CN5 CN5 6.0 2 180.0 ! par_49 CN1 CN5 CN5 NN3A 6.0 2 180.0 ! par_49 NN2G CN2 NN1 HN1 2.0 2 180.0 ! par_49 ! Butterfly motion CN1 CN5 CN5 NN2 20.0 2 180.0 ! par_49 ! inosine, adm jr., 2/94 CN5 CN5 NN3I CN4 6.0 2 180.0 NN2G CN4 NN3I CN5 6.0 2 180.0 NN3I CN4 NN2G HN2 1.5 2 180.0 NN3I CN4 NN2G CN1 1.5 2 180.0 HN3 CN4 NN2G HN2 1.5 2 180.0 HN3 CN4 NN2G CN1 1.5 2 180.0 ! Wild cards for inosine X CN4 NN3I X 3.5 2 180.0 X CN5 NN3I X 1.0 2 180.0 ! Wild cards for uracil, thymine and cytosine X CN1 NN3 X 1.0 2 180.0 ! par_39 X CN1 NN2 X 0.9 2 180.0 ! par_36 X CN1 NN2G X 0.9 2 180.0 ! par_36 X CN1 NN2U X 0.9 2 180.0 ! par_36 X CN3 NN2 X 1.0 2 180.0 ! par_36 X CN3 CN3 X 1.0 2 180.0 ! par_36 X CN1 CN3 X 1.0 2 180.0 ! par_36 X CN2 CN3 X 0.8 2 180.0 ! par_39 ! Wild cards for adenine and guanine X CN1 CN5 X 1.0 2 180.0 ! par_49 X CN2 NN2G X 1.0 2 180.0 ! par_49 X CN2 CN5 X 1.0 2 180.0 ! par_41 X CN4 NN2 X 1.5 2 180.0 ! par_44 X CN4 NN3A X 3.5 2 180.0 ! par_47 par_a7 9/30/91 X CN4 NN4 X 1.0 2 180.0 ! par_41 X CN5 CN5 X 0.0 2 180.0 ! par_20 X CN5 NN2 X 1.5 2 180.0 ! par_44 X CN5 NN3A X 1.0 2 180.0 ! par_41 par_a7 9/30/91 X CN5 NN4 X 1.0 2 180.0 ! par_41 X CN2 NN3A X 1.0 2 180.0 ! par_41 par_a7 9/30/91 ! MISC. CN1 NN2 CN9 HN7 0.19 3 0.0 ! 1-M-THY CN3 NN2 CN9 HN7 0.00 3 0.0 ! 1-M-THY CN4 NN2 CN9 HN7 0.00 3 0.0 ! 9-M-ADE CN5 NN2 CN9 HN7 0.19 3 0.0 ! 9-M-ADE ! sp2 amine parameters, adm jr. X CN6B NN5 X 0.110 3 0.0 NN5 CN6B CN6 ON5 0.0501 3 0.0 NN5 CN6B CN6 HN6 0.0501 3 0.0 NN5 CN6B CN6 CN6 0.0501 3 0.0 NN5 CN6B CN6C ON5 0.0501 3 0.0 NN5 CN6B CN6C HN6 0.0501 3 0.0 NN5 CN6B CN6C CN6 0.0501 3 0.0 CN6 ON6 CN6B NN5 0.10 3 0.0 ! nicotinamide adenine dinucleotide CN3 NN2 CN3B HN3B 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 HN2 NN2 CN3B HN3B 3.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 HN3B CN3 CN3A HN3B 2.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 HN3B CN3 CN3B HN3B 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 NN2 CN3B CN3 HN3B 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN1A CN3 HN3B 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN1A CN3 CN3B HN3B 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN1A CN3 CN3A HN3B 5.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN1A CN3 HN3 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN1A CN3 CN3 HN3 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3A CN3 CN1A ON1 2.38 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3B CN3 CN1A ON1 2.38 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3A CN3 CN1A NN1 0.35 1 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3A CN3 CN1A NN1 0.62 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 CN3B CN3 CN1A NN1 0.35 1 0.0 !nad/ppi, jjp1/adm jr. 7/95 CN3B CN3 CN1A NN1 0.62 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3A CN3 CN1A 3.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 CN3A CN3 CN3B 6.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 NN2 CN3B CN3 CN3A 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3B NN2 CN3B CN3 4.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 X CN3 CN3A X 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 X CN3 CN3B X 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 X CN3 CN8 X 1.0 3 180.0 !nad/ppi, jjp1/adm jr. 7/95 X NN1 CN1A X 2.5 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 X NN2 CN3B X 1.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 ! nicotinamide adenine dinucleotide hydride, nadh CN8 CN3 CN1A ON1 1.00 2 180.0 !nadh, jjp1,adm jr. 4/95 CN8 CN3 CN1A ON1 1.00 3 0.0 !nadh, jjp1,adm jr. 4/95 CN8 CN3 CN1A ON1 0.40 6 0.0 !nadh, jjp1,adm jr. 4/95 CN8 CN3 CN1A NN1 0.50 2 180.0 !nadh, jjp1,adm jr. 4/95 CN8 CN3 CN1A NN1 0.35 3 180.0 !nadh, jjp1,adm jr. 4/95 CN8 CN3 CN1A NN1 0.40 6 0.0 !nadh, jjp1,adm jr. 4/95 CN3C CN3 CN1A ON1 0.30 1 0.0 !nadh, jjp1,adm jr. 4/95 CN3C CN3 CN1A ON1 1.95 2 180.0 !nadh, jjp1,adm jr. 4/95 CN3C CN3 CN1A NN1 1.10 1 180.0 !nadh, jjp1,adm jr. 4/95 CN3C CN3 CN1A NN1 1.95 2 180.0 !nadh, jjp1,adm jr. 4/95 HN2 NN2 CN3C HN3 4.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3 NN2 CN3C HN3 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 NN2 CN3C CN3 HN3 7.0 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN8 CN3 CN3C NN2 0.1 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3C CN3 CN8 CN3 4.0 3 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN1A CN3 CN3C NN2 2.5 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 X CN3 CN3C X 0.1 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 X NN2 CN3C X 0.1 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 CN3C NN2 CN3C CN3 0.1 2 180.0 !nad/ppi, jjp1/adm jr. 7/95 ! pyrophosphate (ppi) P2 ON2 P ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 P2 ON2 P ON2 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 P ON2 P2 ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 P ON2 P2 ON2 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 P2 ON2 P2 ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 P2 ON2 P2 ON2 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 P ON2 P ON2 0.03 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 P ON2 P ON2 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 P ON2 P ON3 0.10 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 P ON2 P ON3 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 P ON2 P2 ON3 0.10 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 P ON2 P2 ON3 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 P2 ON2 P ON3 0.10 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 P2 ON2 P ON3 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 P2 ON2 P2 ON3 0.10 2 0.0 !nad/ppi, jjp1/adm jr. 7/95 P2 ON2 P2 ON3 0.03 3 0.0 !nad/ppi, jjp1/adm jr. 7/95 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. IMPROPER CT1 NH1 C CT3 55.0 0 35.26439 ! Andrej Sali; for peptides but PRO & GLY; from param19.inp CT1 NH3 C CT3 55.0 0 35.26439 ! Andrej Sali; for peptides but PRO & GLY (N-term); from param19.inp CT1 NH1 CC CT3 55.0 0 35.26439 ! Andrej Sali; for peptides but PRO & GLY (C-term); from param19.inp CT1 NH3 CC CT3 55.0 0 35.26439 ! Andrej Sali; for peptides but PRO & GLY (N-term and C-term); from param19.inp CT1 NH1 C CT2 55.0 0 35.26439 ! Andrej Sali; for peptides but PRO & GLY; from param19.inp CT1 NH3 C CT2 55.0 0 35.26439 ! Andrej Sali; for peptides but PRO & GLY (N-term); from param19.inp CT1 NH1 CC CT2 55.0 0 35.26439 ! Andrej Sali; for peptides but PRO & GLY (C-term); from param19.inp CT1 NH3 CC CT2 55.0 0 35.26439 ! Andrej Sali; for peptides but PRO & GLY (N-term and C-term); from param19.inp CT1 NH1 C CT1 55.0 0 35.26439 ! Andrej Sali; for peptides but PRO & GLY; from param19.inp CT1 NH3 C CT1 55.0 0 35.26439 ! Andrej Sali; for peptides but PRO & GLY (N-term); from param19.inp CT1 NH1 CC CT1 55.0 0 35.26439 ! Andrej Sali; for peptides but PRO & GLY (C-term); from param19.inp CT1 NH3 CC CT1 55.0 0 35.26439 ! Andrej Sali; for peptides but PRO & GLY (N-term and C-term); from param19.inp CP1 N C CP2 55.0 0 35.26439 ! Andrej Sali; for PRO peptide; from param19.inp CP1 N CC CP2 55.0 0 35.26439 ! Andrej Sali; for PRO peptide (C-term); from param19.inp CP1 NP C CP2 55.0 0 35.26439 ! Andrej Sali; for PRO peptide (N-term); from param19.inp CP1 NP CC CP2 55.0 0 35.26439 ! Andrej Sali; for PRO peptide (N-term and C-term); from param19.inp NC2 CT2 C HC 45.0 0 0.00000 ! Andrej Sali; for ARG sidechain; from param19.inp CT1 CT2 CT3 CT1 55.0 0 35.26439 ! Andrej Sali; for ILE sidechain; from param19.inp CT1 CT3 CT3 CT2 55.0 0 35.26439 ! Andrej Sali; for LEU sidechain; from param19.inp CT1 OH1 CT3 CT1 55.0 0 35.26439 ! Andrej Sali; for THR sidechain; from param19.inp CT1 CT3 CT3 CT1 55.0 0 35.26439 ! Andrej Sali; for VAL sidechain; from param19.inp CA CA CA CT2 90.0 0 180.0 ! Andrej Sali; for PHE/TYR ring; CA CA CA CA 90.0 0 0.0 ! Andrej Sali; for PHE/TYR ring; CA CA CA OH1 150.0 0 180.0 ! Andrej Sali; for TYR ring; CY CA CPT CT2 90.0 0 0.0 ! Andrej Sali; for Trp CG; from param19.inp CY CA NY CPT 25.0 0 0.0 ! Andrej Sali; for Trp CY CPT CPT NY 100.0 0 0.0 ! Andrej Sali; for Trp CA CPT CPT CA 100.0 0 0.0 ! Andrej Sali; for Trp NY CPT CA CA 100.0 0 180.0 ! Andrej Sali; for Trp CY CPT CA CA 100.0 0 180.0 ! Andrej Sali; for Trp CPT X X CA 25.0 0 0.0 ! Andrej Sali; for Trp CG; from param19.inp CPH1 NR1 CPH1 CT2 90.0 0 0.0 ! Andrej Sali; for His CPH1 NR1 CPH2 NR2 100.0 0 0.0 ! Andrej Sali; for His NR1 X X CPH1 25.0 0 0.0 ! Andrej Sali; for His; from param19.inp CPH2 X X CPH1 25.0 0 0.0 ! Andrej Sali; for His; from param19.inp NR1 X X NR2 25.0 0 0.0 ! Andrej Sali; for His; from param19.inp CPH1 NR2 CPH1 CT2 90.0 0 0.0 ! Andrej Sali; for HSE CPH1 NR3 CPH1 CT2 90.0 0 0.0 ! Andrej Sali; for HSP; from param19.inp CPH1 NR3 CPH2 NR3 100.0 0 0.0 ! Andrej Sali; for HSP NR3 CPH1 CPH1 NR3 25.0 0 0.0 ! Andrej Sali; for HSP CPB CPA NPH CPA 20.8000 0 0.0000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPB X X C 90.0000 0 0.0000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT2 X X CPB 90.0000 0 0.0000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) CT3 X X CPB 90.0000 0 0.0000 ! ALLOW HEM ! Heme (6-liganded): substituents (KK 05/13/91) HA C C HA 20.0000 0 0.0000 ! ALLOW PEP POL ARO ! Heme vinyl substituent (KK, from propene (JCS)) HA CPA CPA CPM 29.4000 0 0.0000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) HA CPB C C 20.0000 0 0.0000 ! ALLOW HEM ARO ! Heme (6-liganded): substituents (KK 05/13/91) HA HA C C 20.0000 0 180.0000 ! ALLOW PEP POL ARO ! Heme vinyl substituent (KK, from propene (JCS)) HA2 HA2 CE2 CE2 3.0 0 0.00 ! ! for ethene, yin/adm jr., 12/95 HR1 NR1 NR2 CPH2 0.5000 0 0.0000 ! ALLOW ARO ! his, adm jr., 7/05/90 HR1 NR2 NR1 CPH2 0.5000 0 0.0000 ! ALLOW ARO ! his, adm jr., 7/05/90 HR3 CPH1 NR1 CPH1 0.5000 0 0.0000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 CPH1 NR2 CPH1 0.5000 0 0.0000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 CPH1 NR3 CPH1 1.0000 0 0.0000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 NR1 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HR3 NR2 CPH1 CPH1 0.5000 0 0.0000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params N C CP1 CP3 0.0000 0 0.0000 ! ALLOW PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 NC2 X X C 40.0000 0 0.0000 ! ALLOW PEP POL ARO ! 5.75->40.0 GUANIDINIUM (KK) NH1 X X H 20.0000 0 0.0000 ! ALLOW PEP POL ARO ! NMA Vibrational Modes (LK) NH2 X X H 4.0000 0 0.0000 ! ALLOW POL ! adm jr., 8/13/90 acetamide geometry and vibrations NPH CPA CPA FE 137.4000 0 0.0000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NPH CPA CPB CPB 40.6000 0 0.0000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NPH CPA CPM CPA 18.3000 0 0.0000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NPH CPM CPB CPA 32.7000 0 0.0000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NR1 CPH1 CPH2 H 0.4500 0 0.0000 ! ALLOW ARO ! his, adm jr., 7/05/90 NR1 CPH2 CPH1 H 0.4500 0 0.0000 ! ALLOW ARO ! his, adm jr., 7/05/90 NR3 CPH1 CPH2 H 1.2000 0 0.0000 ! ALLOW ARO ! his, adm jr., 6/27/90 NR3 CPH2 CPH1 H 1.2000 0 0.0000 ! ALLOW ARO ! his, adm jr., 6/27/90 NY CA CY CPT 100.0000 0 0.0000 ! ALLOW ARO !adm jr., 5/15/91, indole 3-21G HE1 out-of-plane surf. O CP1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 O CT1 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL ! adm jr., 8/13/90 acetamide geometry and vibrations O CT2 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL ! adm jr., 8/13/90 acetamide geometry and vibrations O CT3 NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL ! adm jr., 8/13/90 acetamide geometry and vibrations O HA NH2 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO ! adm jr., 5/13/91, formamide geometry and vibrations O N CT2 CC 120.0000 0 0.0000 ! ALLOW PEP POL PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 O NH2 CP1 CC 45.0000 0 0.0000 ! ALLOW PEP POL PRO ! 6-31g* AcProNH2 and ProNH2 RLD 5/19/92 O NH2 CT1 CC 45.0000 0 0.0000 ! ALLOW PEP POL ! adm jr., 8/13/90 acetamide geometry and vibrations O NH2 CT2 CC 45.0000 0 0.0000 ! ALLOW PEP POL ! adm jr., 8/13/90 acetamide geometry and vibrations O NH2 CT3 CC 45.0000 0 0.0000 ! ALLOW PEP POL ! adm jr., 8/13/90 acetamide geometry and vibrations O NH2 HA CC 45.0000 0 0.0000 ! ALLOW PEP POL ! adm jr., 5/13/91, formamide geometry and vibrations O X X C 120.0000 0 0.0000 ! ALLOW PEP POL ARO ! NMA Vibrational Modes (LK) OB X X CD 100.0000 0 0.0000 ! ALLOW ALC ARO POL ! adm jr., 10/17/90, acetic acid vibrations OC X X CC 96.0000 0 0.0000 ! ALLOW PEP POL ARO ION ! 90.0->96.0 acetate, single impr (KK) X FE NP1 X 0.0000 2 0.00 ! ALLOW HEM correct for N-Fe-N angles MJS X NP1 CPA X 0.0000 2 0.00 ! ALLOW HEM correct for N-Fe-N angles MJS CPB CPA NP1 CPA 20.8000 0 0.0000 ! ALLOW HEM correct for N-Fe-N angles MJS NP1 CPA CPA FE 137.4000 0 0.0000 ! ALLOW HEM correct for N-Fe-N angles MJS NP1 CPA CPB CPB 40.6000 0 0.0000 ! ALLOW HEM correct for N-Fe-N angles MJS NP1 CPA CPM CPA 18.3000 0 0.0000 ! ALLOW HEM correct for N-Fe-N angles MJS NP1 CPM CPB CPA 32.7000 0 0.0000 ! ALLOW HEM correct for N-Fe-N angles MJS ! nucleic acids section HN2 CN4 CN5 NN2 7.0 0 0.0 !A, JWK par_42 HN2 CN1 CN1 NN2U 4.0 0 0.0 !U, JWK par_35 HN2 X X NN2 0.3 0 0.0 !C,U, JWK par_15 HN2 X X NN2G 0.3 0 0.0 !G, JWK par_15 HN2 CN4 CN1 NN2G 0.8 0 0.0 !Inosine, adm jr., 2/94 HN1 X X NN1 2.0 0 0.0 !C, JWK par_40 HN3 CN1 CN3 CN3 18.0 0 0.0 ! JWK par_37 HN3 X X CN3 15.0 0 0.0 ! JWK par_37 CN1 X X ON1 70.0 0 0.0 !U, JWK par_32 CN1 X X ON1C 70.0 0 0.0 !C, par_32, adm jr., 10/2/91 CN2 X X NN1 90.0 0 0.0 !C, JWK par_15 HN3 NN2G NN3I CN4 39.0 0 0.0 !Inosine, adm jr., 2/94 HN3 X X CN4 20.0 0 0.0 !A, JWK par_42 CN9 X X CN3 20.0 0 0.0 !T par_51 ! nicotinamide adenine dinucleotide HN3B X X CN3 15.0 0 0.0 !nad/ppi, jjp1/adm jr. HN3B X X CN3A 13.0 0 0.0 !nad/ppi, jjp1/adm jr. HN3B X X CN3B 13.0 0 0.0 !nad/ppi, jjp1/adm jr. HN2 CN3 CN3B NN2 50.0 0 0.0 !nad/ppi, jjp1/adm jr. HN1 HN1 CN1A NN1 -5.0 0 0.0 !nad/ppi, jjp1/adm jr. ON1 X X CN1A 40.0 0 0.0 !nad/ppi, jjp1/adm jr. HN3 X X CN3C 53.0 0 0.0 !nad/ppi, jjp1/adm jr. HN7 CN3 CN3 CN8 18.0 0 0.0 !nad/ppi, jjp1/adm jr. NONBONDED NBXMOD 5 ATOM CDIEL SHIFT VATOM VDISTANCE VSWITCH - CUTNB 13.0 CTOFNB 12.0 CTONNB 10.0 EPS 1.0 E14FAC 1.0 WMIN 1.5 !adm jr., 5/08/91, suggested cutoff scheme UNDF 0.000000 -0.110000 1.700000 ! Assume atoms in Modeller BLK ! residues have a typical heavy-atom radius by default C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO ! NMA pure solvent, adm jr., 3/3/93 CA 0.000000 -0.070000 1.992400 ! ALLOW ARO ! benzene (JES) CAL 0.000000 -0.120000 1.710000 ! ALLOW ION ! optimized before july 89, and need polarization term (BP) CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO ! adm jr. 3/3/92, acetic acid heat of solvation CD 0.000000 -0.070000 2.000000 ! ALLOW POL ! adm jr. 3/19/92, acetate a.i. and dH of solvation CE1 0.000000 -0.068000 2.090000 ! ! ! for propene, yin/adm jr., 12/95 CE2 0.000000 -0.064000 2.080000 ! ! ! for ethene, yin/adm jr., 12/95 CM 0.000000 -0.110000 2.100000 ! ALLOW HEM ! Heme (6-liganded): CO ligand carbon (KK 05/13/91) CP1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CP2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CP3 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! alkane update, adm jr., 3/2/92 CPA 0.000000 -0.090000 1.800000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPB 0.000000 -0.090000 1.800000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPH1 0.000000 -0.050000 1.800000 ! ALLOW ARO ! adm jr., 10/23/91, imidazole solvation and sublimation CPH2 0.000000 -0.050000 1.800000 ! ALLOW ARO ! adm jr., 10/23/91, imidazole solvation and sublimation CPM 0.000000 -0.090000 1.800000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) CPT 0.000000 -0.090000 1.800000 0.000000 -0.090000 1.900000 ! ALLOW ARO ! benzene (JES) CS 0.000000 -0.110000 2.200000 ! ALLOW SUL ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 CT1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! isobutane pure solvent properties, adm jr, 2/3/92 CT2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! propane pure solvent properties, adm jr, 2/3/92 CT3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 ! ALLOW ALI ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 CY 0.000000 -0.070000 1.992400 ! ALLOW ARO ! TRP, JWK 08/29/89 ! carbon wildcards, following atom order is essential for accurate results !C* 0.000000 -0.070000 2.000000 !CP% 0.000000 -0.090000 1.800000 !C%1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 !C%2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 !C%3 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 !CPH+ 0.000000 -0.050000 1.800000 !C 0.000000 -0.110000 2.000000 !CA 0.000000 -0.070000 1.992400 !CE1 0.000000 -0.068000 2.090000 !CE2 0.000000 -0.064000 2.080000 !CM 0.000000 -0.110000 2.100000 !CP3 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI !CPT 0.000000 -0.090000 1.800000 0.000000 -0.090000 1.900000 !CS 0.000000 -0.110000 2.200000 !CY 0.000000 -0.070000 1.992400 FE 0.010000 0.000000 0.650000 ! ALLOW HEM ! Heme (6-liganded): Iron atom (KK 05/13/91) H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC ! same as TIP3P hydrogen, adm jr., 7/20/89 HA 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 HA1 0.000000 -0.031000 1.250000 ! ! ! for propene, yin/adm jr., 12/95 HA2 0.000000 -0.026000 1.260000 ! ! ! for ethene, yin/adm jr., 12/95 HB 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 HC 0.000000 -0.046000 0.224500 ! ALLOW POL ! new, small polar Hydrogen, see also adm jr. JG 8/27/89 HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 ! ALLOW ARO ! JES 8/25/89 values from Jorgensen fit to hydration energy HR1 0.000000 -0.046000 0.900000 ! ALLOW ARO ! adm jr., 6/27/90, his HR2 0.000000 -0.046000 0.700000 ! ALLOW ARO ! adm jr., 6/27/90, his HR3 0.000000 -0.007800 1.468000 ! ALLOW ARO ! adm jr., 3/24/92, maintain old aliphatic H VDW params HS 0.000000 -0.100000 0.450000 ! ALLOW SUL ! methanethiol pure solvent, adm jr., 6/22/92 HT 0.000000 -0.046000 0.224500 ! ALLOW WAT !TIP3P HYDROGEN PARAMETERS, adm jr., NBFIX obsolete ! hydrogen wildcards !H* 0.000000 -0.046000 0.224500 !HA 0.000000 -0.022000 1.320000 !HA1 0.000000 -0.031000 1.250000 !HA2 0.000000 -0.026000 1.260000 !HB 0.000000 -0.022000 1.320000 !HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 !HR1 0.000000 -0.046000 0.900000 !HR2 0.000000 -0.046000 0.700000 !HR3 0.000000 -0.007800 1.468000 !HS 0.000000 -0.100000 0.450000 ! N 0.000000 -0.200000 1.850000 0.000000 -0.000100 1.850000 ! ALLOW PRO ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 NC2 0.000000 -0.200000 1.850000 ! ALLOW POL ! JG 8/27/89; note: NH1 in ARG was changed to NC2. NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! ALLOW PEP POL ARO ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) NH2 0.000000 -0.200000 1.850000 ! ALLOW POL ! adm jr. NH3 0.000000 -0.200000 1.850000 ! ALLOW POL ! adm jr. NP 0.000000 -0.200000 1.850000 ! ALLOW PRO ! N-terminal proline; from 6-31g* +ProNH2 RLD 9/28/90 NPH 0.000000 -0.200000 1.850000 ! ALLOW HEM ! Heme (6-liganded): porphyrin macrocycle (KK 05/13/91) NR1 0.000000 -0.200000 1.850000 ! ALLOW ARO ! His, adm jr., 9/4/89 NR2 0.000000 -0.200000 1.850000 ! ALLOW ARO ! His, adm jr., 9/4/89 NR3 0.000000 -0.200000 1.850000 ! ALLOW ARO ! His, adm jr., 9/4/89 NY 0.000000 -0.200000 1.850000 ! ALLOW ARO ! trp, JWK ! nitrogen wildcards !N* 0.000000 -0.200000 1.850000 !N 0.000000 -0.200000 1.850000 0.000000 -0.000100 1.850000 !NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) OB 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ARO ! adm jr., 10/17/90, acetic acid carbonyl O OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION ! JG 8/27/89 OH1 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P) OM 0.000000 -0.120000 1.700000 ! ALLOW HEM ! Heme (6-liganded): CO ligand oxygen (KK 05/13/91) OS 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO ! adm jr. 9/17/90, avoid O* wildcard OT 0.000000 -0.152100 1.768200 ! ALLOW WAT !TIP3P OXYGEN PARAMETERS, adm jr., NBFIX obsolete ! oxygen wildcards !O* 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 !OC 0.000000 -0.120000 1.700000 !OH1 0.000000 -0.152100 1.770000 !OM 0.000000 -0.120000 1.700000 !OS 0.000000 -0.152100 1.770000 !OT 0.000000 -0.152100 1.768200 S 0.000000 -0.450000 2.000000 ! ALLOW SUL ION ! adm jr., 3/3/92, methanethiol/ethylmethylsulfide pure solvent SM 0.000000 -0.380000 1.975000 ! ALLOW SUL ION ! adm jr., 3/3/92, dimethyldisulphide pure solvent SS 0.000000 -0.470000 2.200000 ! ALLOW SUL ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 ZN 0.000000 -0.250000 1.090000 ! ALLOW ION ! RHS March 18, 1990 DUM 0.000000 -0.000000 0.000000 ! ! dummy atom HE 0.000000 -0.021270 1.4800 ! ! helium, experimental pot. energy surface, adm jr., 12/95 NE 0.000000 -0.086000 1.5300 ! neon, semiempirical pot. energy surface, adm jr., 12/95 ! nucleic acid section ! Emin Rmin/2 ! (kcal/mol) (A) HN1 0.0 -0.0460 0.2245 HN2 0.0 -0.0460 0.2245 HN3 0.0 -0.0220 1.3200 HN3B 0.0 -0.046 0.9000 ! nad/ppi, jjp1/adm jr. HN4 0.0 -0.0460 0.2245 HN5 0.0 -0.0460 0.2245 HN6 0.0 -0.0220 1.3200 HN7 0.0 -0.0220 1.3200 !HT 0.0 -0.0460 0.2245 ! TIP3P ! ! hydrogen wildcards !HN* 0.0 -0.0460 0.2245 ! HN1, HN2, HN4, HN5 !HN3 0.0 -0.0220 1.3200 !HN3B 0.0 -0.046 0.9000 ! nad/ppi, jjp1/adm jr. !HN6 0.0 -0.0220 1.3200 !HN7 0.0 -0.0220 1.3200 !HT 0.0 -0.0460 0.2245 ! TIP3P ! NN1 0.0 -0.20 1.85 NN2 0.0 -0.20 1.85 NN2G 0.0 -0.20 1.85 NN2U 0.0 -0.20 1.85 NN3 0.0 -0.20 1.85 NN3A 0.0 -0.20 1.85 NN3I 0.0 -0.20 1.85 NN4 0.0 -0.20 1.85 NN5 0.0 -0.20 1.85 ! ! nitrogen wildcards !NN* 0.0 -0.20 1.85 ! all nitrogens ! ON1 0.0 -0.1200 1.70 ON1C 0.0 -0.1200 1.70 ON2 0.0 -0.1521 1.77 ON3 0.0 -0.1200 1.70 ON4 0.0 -0.1521 1.77 ON5 0.0 -0.1521 1.77 ON6 0.0 -0.1521 1.77 ON2B 0.0 -0.1521 1.77 ! ! oxygen wildcards !ON* 0.0 -0.1521 1.77 ! types ON2, ON4, ON5, and ON6 !ON1* 0.0 -0.1200 1.70 ! types ON1 and ON1C !ON3 0.0 -0.1200 1.70 !OT 0.0 -0.1521 1.7682 ! TIP3P ! CN1 0.0 -0.14 1.8000 CN1A 0.0 -0.07 2.0000 ! nad/ppi, jjp1/adm jr. (protein CC) CN2 0.0 -0.14 1.8000 CN3 0.0 -0.18 1.8000 CN3A 0.0 -0.18 1.8000 ! nad/ppi, jjp1/adm jr. CN3B 0.0 -0.18 1.8000 ! nad/ppi, jjp1/adm jr. CN3C 0.0 -0.18 1.8000 ! nad/ppi, jjp1/adm jr. CN3D 0.0 -0.18 1.8000 ! 5mc, adm jr. CN4 0.0 -0.12 1.8000 CN5 0.0 -0.12 1.8000 CN6 0.0 -0.02 2.2750 0.0 -0.01 1.90 !equivalent to protein CT1 CN6B 0.0 -0.02 2.2750 0.0 -0.01 1.90 !equivalent to protein CT1 CN6C 0.0 -0.055 2.1750 0.0 -0.01 1.90 !equivalent to protein CT2 CN7 0.0 -0.02 2.2750 0.0 -0.01 1.90 !equivalent to protein CT1 CN8 0.0 -0.055 2.1750 0.0 -0.01 1.90 !equivalent to protein CT2 CN9 0.0 -0.08 2.0600 0.0 -0.01 1.90 !equivalent to protein CT3 ! ! carbon wildcards !CN* 0.0 -0.14 1.8000 ! CN1, CN2, !CN1A 0.0 -0.07 2.0000 ! nad/ppi, jjp1/adm jr. (protein CC) !CN3* 0.0 -0.18 1.8000 ! CN3, CN3A, CN3B, CN3C, CN3D !CN4 0.0 -0.12 1.8000 !CN5 0.0 -0.12 1.8000 !CN6* 0.0 -0.02 2.2750 0.0 -0.01 1.90 ! CN6,CN6B (same as CT1) !CN6C 0.0 -0.055 2.1750 0.0 -0.01 1.90 !equivalent to protein CT2 !CN7 0.0 -0.02 2.2750 0.0 -0.01 1.90 !equivalent to protein CT1 !CN8 0.0 -0.055 2.1750 0.0 -0.01 1.90 !equivalent to protein CT2 !CN9 0.0 -0.08 2.0600 0.0 -0.01 1.90 !equivalent to protein CT3 ! P 0.0 -0.585 2.15 P2 0.0 -0.585 2.15 ! nad/ppi, jjp1/adm jr. ! phosphate wildcards !P* 0.0 -0.585 2.15 ! P and P2 ! SOD 0.0 -0.1000 1.532 ! from Benoit Roux MG 0.0 -0.001 1.65 ! from Blaise Prodhom !DUM 0.0 -0.000 1.00 ! dummy atom NBFIX ! Emin Rmin ! (kcal/mol) (A) ! SOD OT -0.5831 2.6880 ! from Benoit Roux SOD ON1 -0.1000 2.5570 ! from Benoit Roux SOD ON1C -0.1000 2.5570 ! from Benoit Roux MG OT -7.79 2.17 ! From Blaise Prodhom MG ON1 -40.00 1.8 ! From Blaise Prodhom MG ON1C -40.00 1.8 ! From Blaise Prodhom MG ON2 -7.79 2.17 ! From Blaise Prodhom MG ON3 -5.00 2.10 ! From Blaise Prodhom MG ON4 -7.79 2.17 ! From Blaise Prodhom MG ON5 -7.79 2.17 ! From Blaise Prodhom MG ON6 -7.79 2.17 ! From Blaise Prodhom HBOND AEXP 4 REXP 6 HAEX 0 AAEX 0 NOACCEPTORS HBNOEXCLUSIONS ALL - CUTHB 0.5 CTOFHB 5.0 CTONHB 4.0 CUTHA 5.0 CTOFHA 90.0 CTONHA 90.0 N*+* N% 0.000 3.0000 O* N*+* 0.000 2.9000 OH* N% 0.000 2.8500 OH* O* 0.000 2.7500 S N% 0.000 3.0000 ! ALLOW SUL ION S O* 0.000 2.9000 ! ALLOW SUL ION END