! ! xplor-nih nucleic acid topology file, version 2.0 ! ! This file is intended to work with the parameter file nucleic-2.0.par ! ! This is a re-named and fixed copy of the file topnah1er1_mod_new.inp ! ! We've created this new filename in order to eliminate confusion ! between the various parameter/topology combinations that ship ! with xplor-nih. It has version numbers, and will be updated ! along with the rest of the xplor-nih package. ! ! chemical types have been named such that mixed protein/nucleic acid ! refinements are possible. ! ! If you find errors, PLEASE let us know. ! remark Nucleic Acid A L L HYDROGEN TOPOLOGY FILE CREATION RUN remark This file is the fault of MP and LN (1984). remark Includes topology for purine (GMC; 1987) remark RESIDUE TOPOLOGY FILE FOR RNA/DNA USING ALL HYDROGENS. remark CHARGES DERIVED FROM toprna10/ H charges set to 0.035 and slack taken on C remark SOME HINTS TAKEN FROM GELIN AND ROSSKY KARPLUS RAHMAN PAPER. remark GROUPING REMOVED. (ONE GROUP/RESIDUE PUT BACK). remark H-BOND CHARGES FOR R_DIEL & EPS=1.0 remark REDUCED PHOSPHATE CHARGES. CH-stretches and bends from remark uracil normal mode fit. Sugar dihedrals adapted from W.Olson JACS (1982) remark planarity of hydrogens on bases is now maintained by impropers remark instead of dihedrals, and all impropers governing the planes remark have their force constants increased to 80 (G.M. CLORE remark 16/5/85) remark included impropers for chirality from topallhdg.dna (CDS 2005/11/03) set echo=false mess off end AUTOGENERATE ANGLES=true END {*==============================*} {* DNA/RNA default atomic masses *} MASS XH 1.00800 MASS YH 1.00800 MASS XH2 1.00800 MASS XHO 1.00800 MASS XC 12.01100 MASS XCH 12.01100 MASS XC2 12.01100 MASS YC2 12.01100 MASS XCA 12.01100 MASS XCB 12.01100 MASS XCE 12.01100 MASS XCF 12.01100 MASS XC3 12.01100 MASS XCS 12.01100 MASS XN2 14.00670 MASS XNA 14.00670 MASS XNB 14.00670 MASS XNC 14.00670 MASS XNS 14.00670 MASS XNH2E 16.02270 MASS XNH3 14.02270 MASS XO 15.99940 MASS XO2 15.99940 MASS XOS 15.99940 MASS XOH 15.99940 MASS XSD 22.98980 MASS XP 30.97400 MASS XBR 79.90400 MASS XMG 24.30500 !======================================================================== ! set H on C to .035 and take up slack on C (Kollman) RESIdue GUA GROUP ATOM P TYPE=XP CHARGE=1.20 END ATOM O1P TYPE=XO2 CHARge=-0.40 END ATOM O2P TYPE=XO2 CHARge=-0.40 END ATOM O5' TYPE=XOS CHARge=-0.36 END GROUP ATOM C5' TYPE=XC2 CHARge=-0.07 END! rationalized ATOM H5' TYPE=XH CHARge=0.035 END!" ATOM H5'' TYPE=XH CHARge=0.035 END!" GROUP ATOM C4' TYPE=XCH CHARge=0.065 END!" ATOM H4' TYPE=XH CHARge=0.035 END!" ATOM O4' TYPE=XOS CHARge=-0.30 END ATOM C1' TYPE=XCH CHARge=0.165 END!" ATOM H1' TYPE=XH CHARge=0.035 END!" GROUP ATOM N9 TYPE=XNS CHARge=-0.19 END ATOM C4 TYPE=XCB CHARge=0.19 EXCL=( N1 ) END GROUP ATOM N3 TYPE=XNC CHARge=-0.50 EXCL=( C6 ) END ATOM C2 TYPE=XCA CHARge=0.50 EXCL=( C5 ) END GROUP ATOM N2 TYPE=XN2 CHARge=-0.42 END! ATOM H21 TYPE=XH2 CHARge=0.21 END! ATOM H22 TYPE=XH2 CHARge=0.21 END! GROUP ATOM N1 TYPE=XNA CHARge=-0.26 END ATOM H1 TYPE=XH CHARge=0.26 END GROUP ATOM C6 TYPE=XC CHARge=0.30 END ATOM O6 TYPE=XO CHARge=-0.30 END GROUP ATOM C5 TYPE=XCB CHARge=0.02 END ATOM N7 TYPE=XNB CHARge=-0.25 END ATOM C8 TYPE=XCE CHARge=0.195 END ATOM H8 TYPE=XH CHARge=0.035 END!" GROUP ATOM C2' TYPE=XCH CHARge=0.115 END!" ATOM H2' TYPE=XH CHARge=0.035 END!" ATOM O2' TYPE=XOH CHARge=-0.40 END ATOM H2'' TYPE=XHO CHARge=0.25 END GROUP ATOM C3' TYPE=XCH CHARge=-0.035 END!" ATOM H3' TYPE=XH CHARge=0.035 END!" GROUP ATOM O3' TYPE=XOS CHARge=-0.36 END BOND P O1P BOND P O2P BOND P O5' BOND O5' C5' BOND C5' C4' BOND C4' O4' BOND C4' C3' BOND O4' C1' BOND C1' N9 BOND C1' C2' BOND N9 C4 BOND N9 C8 BOND C4 N3 BOND C4 C5 BOND N3 C2 BOND C2 N2 BOND C2 N1 BOND N2 H21 BOND N2 H22 BOND N1 H1 BOND N1 C6 BOND C6 O6 BOND C6 C5 BOND C5 N7 BOND N7 C8 BOND C2' C3' BOND C3' O3' {* BOND O3' +P *} BOND C2' O2' BOND O2' H2'' BOND C1' H1' BOND C2' H2' BOND C3' H3' BOND C4' H4' BOND C5' H5' BOND C5' H5'' BOND C8 H8 {* DIHE -O3' P O5' C5' DIHE -O3' P O5' C5' *} DIHE P O5' C5' C4' DIHE O5' C5' C4' O4' DIHE O5' C5' C4' C3' {* DIHE C4' C3' O3' +P DIHE C3' O3' +P +O5' DIHE C3' O3' +P +O5' *} DIHE O4' C1' N9 C4 ! N O T E: SUGAR RING TERMS SET UP AS W. OLSON DOES IT DIHE O4' C1' C2' C3' ! O-C-C-C, twofold term DIHE O4' C1' C2' C3' DIHE C1' C2' C3' C4' DIHE C2' C3' C4' O4' ! O-C-C-C, twofold term DIHE C2' C3' C4' O4' DIHE C3' C4' O4' C1' DIHE C4' O4' C1' C2' ! AND THE SPECIAL GAUCHE TERMS DIHE C5' C4' C3' O3' DIHE O4' C4' C3' O3' DIHE O4' C1' C2' O2' DIHE C1' C2' C3' O3' DIHE C4' C3' C2' O2' DIHE O3' C3' C2' O2' DIHE C3' C2' O2' H2'' ! SO THE ALLHYDROGEN TERMS DIHE O4' C4' C3' H3' DIHE O4' C1' C2' H2' DIHE C4' O4' C1' H1' DIHE C1' O4' C4' H4' DIHE C3' C4' C5' H5' DIHE C3' C4' C5' H5'' ! Dihedrals to keep the two purine rings parallel: impr C8 C4 C5 N1 impr C8 C5 C4 C2 impr N3 C4 C5 N7 impr C6 C5 C4 N9 ! this first improper is insufficient to keep the N2 group coplanar, ! so I'm adding more. JJK 3/10/04 IMPRoper N3 C2 N2 H21 IMPRoper N1 C2 N2 H22 IMPRoper N3 C2 H21 H22 IMPRoper N1 C2 H22 H21 ! The ring-spanning impropers have been left out. ! And the chiral impropers are not needed with all hydrogens present {* IMPR C5' O4' C3' C4' IMPR O3' C2' C4' C3' IMPR N9 C2' O4' C1' *} {* chiral impropers included for DG and SA *} improper H1' C2' O4' N9 improper H2' C3' C1' O2' improper H3' C4' C2' O3' improper H4' C5' C3' O4' {* chiral improper included for H5'/H5'' definition, according to *} {* Wijmenga, Mooren and Hilbers in NMR of nucl. acids, (Ed. Roberts) *} improper H5' O5' H5'' C4' !C5' IMPR C1' C4 C8 N9 ! THIS IS AN SP2 IMPROPER ABOUT N9 IMPR N9 C4 C5 N7 IMPR C4 C5 N7 C8 IMPR C5 N7 C8 N9 IMPR N7 C8 N9 C4 IMPR C8 N9 C4 C5 IMPR N2 N3 N1 C2 IMPR H1 C2 C6 N1 IMPR O6 N1 C5 C6 IMPR C4 N3 C2 N1 IMPR N3 C2 N1 C6 IMPR C2 N1 C6 C5 IMPR N1 C6 C5 C4 IMPR C6 C5 C4 N3 IMPR C5 C4 N3 C2 IMPR H22 H21 C2 N2 {* IMPR C2' C3' C1' O2' *} IMPR H8 N7 N9 C8 DONO H21 N2 DONO H22 N2 DONO H1 N1 DONO H2'' O2' ACCE O6 C6 ACCE N3 " " ACCE N7 " " !added ACCE O1P P ACCE O2P P ACCE O2' " " ACCE O3' " " ACCE O4' " " ACCE O5' " " {* IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 *} {* IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 *} {* IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 *} IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 {* IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 *} {* IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 *} IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 -96.0 125.59 1.3783 IC C1' C4 *N9 C8 1.4896 125.59 -179.99 105.19 1.3777 IC C4 N9 C8 N7 1.3783 105.19 0.02 114.02 1.3107 IC C8 N9 C4 C5 1.3777 105.19 -0.01 106.45 1.3749 IC N9 C5 *C4 N3 1.3783 106.45 179.96 128.52 1.3591 IC C5 C4 N3 C2 1.3749 128.52 0.04 112.23 1.3310 IC C4 N3 C2 N1 1.3591 112.23 0.00 123.30 1.3813 IC N1 N3 *C2 N2 1.3813 123.30 179.93 120.68 1.3350 IC N3 C2 N2 H21 1.3310 120.68 179.25 127.00 1.0100 IC H21 C2 *N2 H22 1.0100 127.00 -178.62 116.53 1.0100 IC N3 C2 N1 C6 1.3310 123.30 -0.04 125.24 1.4021 IC C6 C2 *N1 H1 1.4021 125.24 180.00 117.40 1.0000 IC C5 N1 *C6 O6 1.4188 111.38 179.92 119.80 1.2276 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 !INFERENCE IC H2'' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 !GUESS ! the all hydrogen part (NOT TOO CAREFULLY DONE /LN) IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 ! THE BASE: IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 END {* GUA *} !=========================================================================== RESIdue ADE GROUP ATOM P TYPE=XP CHARge=1.20 END ATOM O1P TYPE=XO2 CHARge=-0.40 END ATOM O2P TYPE=XO2 CHARge=-0.40 END ATOM O5' TYPE=XOS CHARge=-0.36 END GROUP ATOM C5' TYPE=XC2 CHARge=-0.070 END!" ATOM H5' TYPE=XH CHARge=0.035 END!" ATOM H5'' TYPE=XH CHARge=0.035 END!" GROUP ATOM C4' TYPE=XCH CHARge=0.065 END! " ATOM H4' TYPE=XH CHARge=0.035 END!" ATOM O4' TYPE=XOS CHARge=-0.30 END ATOM C1' TYPE=XCH CHARge=0.165 END!" ATOM H1' TYPE=XH CHARge=0.035 END!" GROUP ATOM N9 TYPE=XNS CHARge=-0.19 END ATOM C4 TYPE=XCB CHARge=0.19 EXCL=( N1 ) END GROUP ATOM N3 TYPE=XNC CHARge=-0.26 EXCL=( C6 ) END ATOM C2 TYPE=XCE CHARge=0.225 EXCL=( C5 ) END !" ATOM H2 TYPE=XH CHARge=0.035 END!" GROUP ATOM N1 TYPE=XNC CHARge=-0.28 END ATOM C6 TYPE=XCA CHARge=0.28 END GROUP ATOM N6 TYPE=XN2 CHARGE=-0.42 END! ATOM H61 TYPE=XH2 CHARge=0.21 END! ATOM H62 TYPE=XH2 CHARge=0.21 END! GROUP ATOM C5 TYPE=XCB CHARge=0.02 END ATOM N7 TYPE=XNB CHARge=-0.25 END ATOM C8 TYPE=XCE CHARge=0.195 END!" ATOM H8 TYPE=XH CHARge=0.035 END!" GROUP ATOM C2' TYPE=XCH CHARge=0.115 END!" ATOM H2' TYPE=XH CHARge=0.035 END!" ATOM O2' TYPE=XOH CHARge=-0.40 END ATOM H2'' TYPE=XHO CHARge=0.25 END GROUP ATOM C3' TYPE=XCH CHARge=-0.035 END!" ATOM H3' TYPE=XH CHARge=0.035 END!" GROUP ATOM O3' TYPE=XOS CHARge=-0.36 END BOND P O1P BOND P O2P BOND P O5' BOND O5' C5' BOND C5' C4' BOND C4' O4' BOND C4' C3' BOND O4' C1' BOND C1' N9 BOND C1' C2' BOND N9 C4 BOND N9 C8 BOND C4 N3 BOND C4 C5 BOND N3 C2 BOND C2 N1 BOND N1 C6 BOND C6 N6 BOND N6 H61 BOND N6 H62 BOND C6 C5 BOND C5 N7 BOND N7 C8 BOND C2' C3' BOND C2' O2' BOND O2' H2'' BOND C3' O3' {* BOND O3'+P *} BOND C1' H1' BOND C2' H2' BOND C3' H3' BOND C4' H4' BOND C5' H5' BOND C5' H5'' BOND C8 H8 BOND C2 H2 {* DIHE -O3' P O5' C5' DIHE -O3' P O5' C5' *} DIHE P O5' C5' C4' DIHE O5' C5' C4' O4' DIHE O5' C5' C4' C3' {* DIHE C4' C3' O3' +P DIHE C3' O3' +P +O5' DIHE C3' O3' +P +O5' *} DIHE O4' C1' N9 C4 ! N O T E: SUGAR RING TERMS SET UP AS W. OLSON DOES IT DIHE O4' C1' C2' C3' ! O-C-C-C, twofold term DIHE O4' C1' C2' C3' DIHE C1' C2' C3' C4' DIHE C2' C3' C4' O4' ! O-C-C-C, twofold term DIHE C2' C3' C4' O4' DIHE C3' C4' O4' C1' DIHE C4' O4' C1' C2' ! AND THE SPECIAL GAUCHE TERMS DIHE C5' C4' C3' O3' DIHE O4' C4' C3' O3' DIHE O4' C1' C2' O2' DIHE C1' C2' C3' O3' DIHE C4' C3' C2' O2' DIHE O3' C3' C2' O2' DIHE C3' C2' O2' H2'' ! SO THE ALLHYDROGEN TERMS DIHE O4' C4' C3' H3' DIHE O4' C1' C2' H2' DIHE C4' O4' C1' H1' DIHE C1' O4' C4' H4' DIHE C3' C4' C5' H5' DIHE C3' C4' C5' H5'' ! Dihedrals to keep the two purine rings parallel: impr C8 C4 C5 N1 impr C8 C5 C4 C2 impr N3 C4 C5 N7 impr C6 C5 C4 N9 ! The ring-spanning impropers have been left out. !IMPR C5' O4' C3' C4' IMPR O3' C2' C4' C3' IMPR N9 C2' O4' C1' {* chiral impropers included for DG and SA *} improper H1' C2' O4' N9 improper H2' C3' C1' O2' improper H3' C4' C2' O3' improper H4' C5' C3' O4' {* chiral improper included for H5'/H5'' definition, according to *} {* Wijmenga, Mooren and Hilbers in NMR of nucl. acids, (Ed. Roberts) *} improper H5' O5' H5'' C4' !C5' IMPR C1' C4 C8 N9 IMPR N9 C4 C5 N7 IMPR C4 C5 N7 C8 IMPR C5 N7 C8 N9 IMPR N7 C8 N9 C4 IMPR C8 N9 C4 C5 IMPR N6 N1 C5 C6 IMPR H62 C6 H61 N6 IMPR C4 N3 C2 N1 IMPR N3 C2 N1 C6 IMPR C2 N1 C6 C5 IMPR N1 C6 C5 C4 IMPR C6 C5 C4 N3 IMPR C5 C4 N3 C2 IMPR H8 N7 N9 C8 IMPR H2 N1 N3 C2 !IMPR C2' C3' C1' O2' ! this first improper is insufficient to keep the N2 group coplanar, ! so I'm adding more. JJK 3/10/04 ! Changed signs to match Discover? params, JJK 3/16/04 ! Changed them back to match IUPAC (Eur J Biochem 131,9, fig 2) JJK 7/19/04 IMPRoper C5 C6 N6 H61 IMPRoper N1 C6 N6 H62 IMPRoper C5 C6 H61 H62 IMPRoper N1 C6 H62 H61 DONO H61 N6 DONO H62 N6 DONO H2'' O2' ACCE N3 " " ACCE N1 " " ACCE N7 " " ACCE O1P P ACCE O2P P ACCE O2' " " ACCE O3' " " ACCE O4' " " ACCE O5' " " {* IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 *} {* IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 *} {* IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 *} IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 {* IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 *} {* IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 *} IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 IC C1' C4 *N9 C8 1.4896 125.97 -179.94 105.00 1.3768 IC C4 N9 C8 N7 1.3703 105.00 -0.07 113.93 1.2970 IC C8 N9 C4 C5 1.3768 105.00 0.06 106.60 1.3650 IC N9 C5 *C4 N3 1.3703 106.60 -179.93 126.69 1.3486 IC C5 C4 N3 C2 1.3650 126.69 -0.04 111.18 1.3130 IC C4 N3 C2 N1 1.3486 111.18 -0.02 128.64 1.3399 IC N3 C2 N1 C6 1.3130 128.64 0.06 118.95 1.3456 IC C5 N1 *C6 N6 1.4034 117.43 -179.96 119.06 1.3410 IC N1 C6 N6 H61 1.3456 119.06 179.96 120.00 1.0100 IC H61 C6 *N6 H62 1.0100 120.00 180.00 120.00 1.0100 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 !INFERENCE IC H2'' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 !GUESS ! the all hydrogen part (NOT TOO CAREFULLY DONE /LN) IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 ! THE BASE: IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 END {* ADE *} !========================================================================= RESIdue PUR GROUP ATOM P TYPE=XP CHARge=1.20 END ATOM O1P TYPE=XO2 CHARge=-0.40 END ATOM O2P TYPE=XO2 CHARge=-0.40 END ATOM O5' TYPE=XOS CHARge=-0.36 END GROUP ATOM C5' TYPE=XC2 CHARge=-0.070 END!" ATOM H5' TYPE=XH CHARge=0.035 END!" ATOM H5'' TYPE=XH CHARge=0.035 END!" GROUP ATOM C4' TYPE=XCH CHARge=0.065 END! " ATOM H4' TYPE=XH CHARge=0.035 END!" ATOM O4' TYPE=XOS CHARge=-0.30 END ATOM C1' TYPE=XCH CHARge=0.165 END!" ATOM H1' TYPE=XH CHARge=0.035 END!" GROUP ATOM N9 TYPE=XNS CHARge=-0.19 END ATOM C4 TYPE=XCB CHARge=0.19 EXCL=( N1 ) END GROUP ATOM N3 TYPE=XNC CHARge=-0.26 EXCL=( C6 ) END ATOM C2 TYPE=XCE CHARge=0.225 EXCL=( C5 ) END !" ATOM H2 TYPE=XH CHARge=0.035 END!" GROUP ATOM N1 TYPE=XNC CHARge=-0.28 END ATOM C6 TYPE=XCE CHARge=0.28 END ATOM H6 TYPE=XH CHARge= 0.035 END GROUP ATOM C5 TYPE=XCB CHARge=0.02 END ATOM N7 TYPE=XNB CHARge=-0.25 END ATOM C8 TYPE=XCE CHARge=0.195 END!" ATOM H8 TYPE=XH CHARge=0.035 END!" GROUP ATOM C2' TYPE=XCH CHARge=0.115 END!" ATOM H2' TYPE=XH CHARge=0.035 END!" ATOM O2' TYPE=XOH CHARge=-0.40 END ATOM H2'' TYPE=XHO CHARge=0.25 END GROUP ATOM C3' TYPE=XCH CHARge=-0.035 END!" ATOM H3' TYPE=XH CHARge=0.035 END!" GROUP ATOM O3' TYPE=XOS CHARge=-0.36 END BOND P O1P BOND P O2P BOND P O5' BOND O5' C5' BOND C5' C4' BOND C4' O4' BOND C4' C3' BOND O4' C1' BOND C1' N9 BOND C1' C2' BOND N9 C4 BOND N9 C8 BOND C4 N3 BOND C4 C5 BOND N3 C2 BOND C2 N1 BOND N1 C6 BOND C6 H6 BOND C6 C5 BOND C5 N7 BOND N7 C8 BOND C2' C3' BOND C2' O2' BOND O2' H2'' BOND C3' O3' {* BOND O3'+P *} BOND C1' H1' BOND C2' H2' BOND C3' H3' BOND C4' H4' BOND C5' H5' BOND C5' H5'' BOND C8 H8 BOND C2 H2 {* DIHE -O3' P O5' C5' DIHE -O3' P O5' C5' *} DIHE P O5' C5' C4' DIHE O5' C5' C4' O4' DIHE O5' C5' C4' C3' {* DIHE C4' C3' O3' +P DIHE C3' O3' +P +O5' DIHE C3' O3' +P +O5' *} DIHE O4' C1' N9 C4 ! N O T E: SUGAR RING TERMS SET UP AS W. OLSON DOES IT DIHE O4' C1' C2' C3' ! O-C-C-C, twofold term DIHE O4' C1' C2' C3' DIHE C1' C2' C3' C4' DIHE C2' C3' C4' O4' ! O-C-C-C, twofold term DIHE C2' C3' C4' O4' DIHE C3' C4' O4' C1' DIHE C4' O4' C1' C2' ! AND THE SPECIAL GAUCHE TERMS DIHE C5' C4' C3' O3' DIHE O4' C4' C3' O3' DIHE O4' C1' C2' O2' DIHE C1' C2' C3' O3' DIHE C4' C3' C2' O2' DIHE O3' C3' C2' O2' DIHE C3' C2' O2' H2'' ! SO THE ALLHYDROGEN TERMS DIHE O4' C4' C3' H3' DIHE O4' C1' C2' H2' DIHE C4' O4' C1' H1' DIHE C1' O4' C4' H4' DIHE C3' C4' C5' H5' DIHE C3' C4' C5' H5'' ! Dihedrals to keep the two purine rings parallel: impr C8 C4 C5 N1 impr C8 C5 C4 C2 impr N3 C4 C5 N7 impr C6 C5 C4 N9 ! The ring-spanning impropers have been left out. !IMPR C5' O4' C3' C4' IMPR O3' C2' C4' C3' IMPR N9 C2' O4' C1' {* chiral impropers included for DG and SA *} improper H1' C2' O4' N9 improper H2' C3' C1' O2' improper H3' C4' C2' O3' improper H4' C5' C3' O4' {* chiral improper included for H5'/H5'' definition, according to *} {* Wijmenga, Mooren and Hilbers in NMR of nucl. acids, (Ed. Roberts) *} improper H5' O5' H5'' C4' !C5' IMPR C1' C4 C8 N9 IMPR N9 C4 C5 N7 IMPR C4 C5 N7 C8 IMPR C5 N7 C8 N9 IMPR N7 C8 N9 C4 IMPR C8 N9 C4 C5 IMPR H6 N1 C5 C6 IMPR C4 N3 C2 N1 IMPR N3 C2 N1 C6 IMPR C2 N1 C6 C5 IMPR N1 C6 C5 C4 IMPR C6 C5 C4 N3 IMPR C5 C4 N3 C2 IMPR H8 N7 N9 C8 IMPR H2 N1 N3 C2 !IMPR C2' C3' C1' O2' DONO H2'' O2' ACCE N3 " " ACCE N1 " " ACCE N7 " " ACCE O1P P ACCE O2P P ACCE O2' " " ACCE O3' " " ACCE O4' " " ACCE O5' " " {* IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 *} {* IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 *} {* IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 *} IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 {* IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 *} {* IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 *} IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 IC C1' C4 *N9 C8 1.4896 125.97 -179.94 105.00 1.3768 IC C4 N9 C8 N7 1.3703 105.00 -0.07 113.93 1.2970 IC C8 N9 C4 C5 1.3768 105.00 0.06 106.60 1.3650 IC N9 C5 *C4 N3 1.3703 106.60 -179.93 126.69 1.3486 IC C5 C4 N3 C2 1.3650 126.69 -0.04 111.18 1.3130 IC C4 N3 C2 N1 1.3486 111.18 -0.02 128.64 1.3399 IC N3 C2 N1 C6 1.3130 128.64 0.06 118.95 1.3456 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 !INFERENCE IC H2'' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 !GUESS ! the all hydrogen part (NOT TOO CAREFULLY DONE /LN) IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 ! THE BASE: IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 IC C5 N1 *C6 H6 0.0 0.0 180.0 0.0 0.0 END {* PUR *} !========================================================================= RESIdue CYT GROUP ATOM P TYPE=XP CHARge=1.20 END ATOM O1P TYPE=XO2 CHARge=-0.40 END ATOM O2P TYPE=XO2 CHARge=-0.40 END ATOM O5' TYPE=XOS CHARge=-0.36 END GROUP ATOM C5' TYPE=XC2 CHARge=-0.070 END! rationalized ATOM H5' TYPE=XH CHARge=0.035 END! " ATOM H5'' TYPE=XH CHARge=0.035 END! " GROUP ATOM C4' TYPE=XCH CHARge=0.065 END! " ATOM H4' TYPE=XH CHARge=0.035 END!" ATOM O4' TYPE=XOS CHARge=-0.30 END ATOM C1' TYPE=XCH CHARge=0.165 END!" ATOM H1' TYPE=XH CHARge=0.035 END!" GROUP ATOM N1 TYPE=XNS CHARge=-0.19 EXCL=( C4 ) END ATOM C6 TYPE=XCF CHARge=0.155 EXCL=( N3 ) END !" ATOM H6 TYPE=XH CHARge=0.035 END!" GROUP ATOM C2 TYPE=XC CHARge=0.30 EXCL=( C5 ) END ATOM O2 TYPE=XO CHARge=-0.30 END GROUP ATOM N3 TYPE=XNC CHARge=-0.28 END ATOM C4 TYPE=XCA CHARge=0.28 END GROUP ATOM N4 TYPE=XN2 CHARge=-0.42 END! ATOM H41 TYPE=XH2 CHARge=0.21 END! ATOM H42 TYPE=XH2 CHARge=0.21 END! GROUP ATOM C5 TYPE=XCF CHARge=-0.035 END!" ATOM H5 TYPE=XH CHARge=0.035 END!" GROUP ATOM C2' TYPE=XCH CHARge=0.115 END!" ATOM H2' TYPE=XH CHARge=0.035 END!" ATOM O2' TYPE=XOH CHARge=-0.40 END ATOM H2'' TYPE=XHO CHARge=0.25 END GROUP ATOM C3' TYPE=XCH CHARge=-0.035 END!" ATOM H3' TYPE=XH CHARge=0.035 END!" GROUP ATOM O3' TYPE=XOS CHARge=-0.36 END BOND P O1P BOND P O2P BOND P O5' BOND O5' C5' BOND C5' C4' BOND C4' O4' BOND C4' C3' BOND O4' C1' BOND C1' N1 BOND C1' C2' BOND N1 C2 BOND N1 C6 BOND C2 O2 BOND C2 N3 BOND N3 C4 BOND C4 N4 BOND N4 H41 BOND N4 H42 BOND C4 C5 BOND C5 C6 BOND C2' C3' BOND C3' O3' {* BOND O3' +P *} BOND C2' O2' BOND O2' H2'' BOND C1' H1' BOND C2' H2' BOND C3' H3' BOND C4' H4' BOND C5' H5' BOND C5' H5'' BOND C5 H5 BOND C6 H6 {* DIHE -O3' P O5' C5' DIHE -O3' P O5' C5' *} DIHE P O5' C5' C4' DIHE O5' C5' C4' O4' DIHE O5' C5' C4' C3' {* DIHE C4' C3' O3' +P DIHE C3' O3' +P +O5' DIHE C3' O3' +P +O5' *} DIHE O4' C1' N1 C2 ! N O T E: SUGAR RING TERMS SET UP AS W. OLSON DOES IT DIHE O4' C1' C2' C3' ! O-C-C-C, twofold term DIHE O4' C1' C2' C3' DIHE C1' C2' C3' C4' DIHE C2' C3' C4' O4' ! O-C-C-C, twofold term DIHE C2' C3' C4' O4' DIHE C3' C4' O4' C1' DIHE C4' O4' C1' C2' ! AND THE SPECIAL GAUCHE TERMS DIHE C5' C4' C3' O3' DIHE O4' C4' C3' O3' DIHE O4' C1' C2' O2' DIHE C1' C2' C3' O3' DIHE C4' C3' C2' O2' DIHE O3' C3' C2' O2' DIHE C3' C2' O2' H2'' ! SO THE ALLHYDROGEN TERMS DIHE O4' C4' C3' H3' DIHE O4' C1' C2' H2' DIHE C4' O4' C1' H1' DIHE C1' O4' C4' H4' DIHE C3' C4' C5' H5' DIHE C3' C4' C5' H5'' !IMPR C5' O4' C3' C4' IMPR O3' C2' C4' C3' IMPR N1 C2' O4' C1' {* chiral impropers included for DG and SA *} improper H1' C2' O4' N1 improper H2' C3' C1' O2' improper H3' C4' C2' O3' improper H4' C5' C3' O4' {* chiral improper included for H5'/H5'' definition, according to *} {* Wijmenga, Mooren and Hilbers in NMR of nucl. acids, (Ed. Roberts) *} improper H5' O5' H5'' C4' !C5' IMPR C1' C2 C6 N1 IMPR O2 N1 N3 C2 IMPR N4 N3 C5 C4 IMPR N1 C2 N3 C4 IMPR C2 N3 C4 C5 IMPR N3 C4 C5 C6 IMPR C4 C5 C6 N1 IMPR C5 C6 N1 C2 IMPR C6 N1 C2 N3 IMPR H42 C4 H41 N4 IMPR H6 N1 C5 C6 IMPR H5 C4 C6 C5 !IMPR C2' C3' C1' O2' ! this first improper is insufficient to keep the N2 group coplanar, ! so I'm adding more. JJK 3/10/04 ! Changed the order to match Discover? params JJK 3/16/04 ! Changed them back to match IUPAC (Eur J Biochem 131,9, fig 2) JJK 7/19/04 IMPRoper C5 C4 N4 H41 IMPRoper N3 C4 N4 H42 IMPRoper C5 C4 H41 H42 IMPRoper N3 C4 H42 H41 DONO H42 N4 DONO H2'' O2' DONO H41 N4 ACCE O2 C2 ACCE N3 " " ACCE O1P P ACCE O2P P ACCE O2' " " ACCE O3' " " ACCE O4' " " ACCE O5' " " {* IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 *} {* IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 *} {* IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 *} IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 {* IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 *} {* IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 *} IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 IC C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 -96.0 117.79 1.3923 IC C1' C2 *N1 C6 1.4896 117.79 -179.99 121.13 1.3595 IC C2 N1 C6 C5 1.3923 121.13 0.02 121.13 1.3570 IC C6 N1 C2 N3 1.3595 121.13 0.01 118.71 1.3578 IC N1 N3 *C2 O2 1.3923 118.71 179.98 122.46 1.2378 IC N1 C2 N3 C4 1.3923 118.71 -0.03 120.61 1.3386 IC C5 N3 *C4 N4 1.4331 121.58 180.00 118.32 1.3246 IC N3 C4 N4 H41 1.3386 118.32 180.00 117.70 1.0100 IC H41 C4 *N4 H42 1.0100 117.70 180.00 120.27 1.0100 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 !INFERENCE IC H2'' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 !GUESS ! the all hydrogen part (NOT TOO CAREFULLY DONE /LN) IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 ! THE BASE: IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 END {* CYT *} !======================================================================== RESIdue THY GROUP ATOM P TYPE=XP CHARge=1.20 END ATOM O1P TYPE=XO2 CHARge=-0.40 END ATOM O2P TYPE=XO2 CHARge=-0.40 END ATOM O5' TYPE=XOS CHARge=-0.36 END GROUP ATOM C5' TYPE=XC2 CHARge=-0.070 END! rationalized ATOM H5' TYPE=XH CHARge=0.035 END! " ATOM H5'' TYPE=XH CHARge=0.035 END! " GROUP ATOM C4' TYPE=XCH CHARge=0.065 END! " ATOM H4' TYPE=XH CHARge=0.035 END!" ATOM O4' TYPE=XOS CHARge=-0.30 END ATOM C1' TYPE=XCH CHARge=0.165 END!" ATOM H1' TYPE=XH CHARge=0.035 END!" GROUP ATOM N1 TYPE=XNS CHARge=-0.19 EXCL=( C4 ) END ATOM C6 TYPE=XCF CHARge=0.155 EXCL=( N3 ) END ATOM H6 TYPE=XH CHARge=0.035 END GROUP ATOM C2 TYPE=XC CHARge=0.35 EXCL=( C5 ) END ATOM O2 TYPE=XO CHARge=-0.35 END GROUP ATOM N3 TYPE=XNA CHARge=-0.26 END ATOM H3 TYPE=XH CHARge=0.26 END GROUP ATOM C4 TYPE=XC CHARge=0.30 END ATOM O4 TYPE=XO CHARge=-0.30 END GROUP ATOM C5 TYPE=XCS CHARge=-0.035 END! THESE CHARGES ? ATOM C5A TYPE=XC3 CHARge=-0.070 END!" ATOM H51 TYPE=XH CHARge=0.035 END!" ATOM H52 TYPE=XH CHARge=0.035 END!" ATOM H53 TYPE=XH CHARge=0.035 END!" GROUP ATOM C2' TYPE=XCH CHARge=0.115 END!" ATOM H2' TYPE=XH CHARge=0.035 END!" ATOM O2' TYPE=XOH CHARge=-0.40 END ATOM H2'' TYPE=XHO CHARge=0.25 END GROUP ATOM C3' TYPE=XCH CHARge=-0.035 END!" ATOM H3' TYPE=XH CHARge=0.035 END!" GROUP ATOM O3' TYPE=XOS CHARge=-0.36 END BOND P O1P BOND P O2P BOND P O5' BOND O5' C5' BOND C5' C4' BOND C4' O4' BOND C4' C3' BOND O4' C1' BOND C1' N1 BOND C1' C2' BOND N1 C2 BOND N1 C6 BOND C2 O2 BOND C2 N3 BOND N3 H3 BOND N3 C4 BOND C4 O4 BOND C4 C5 BOND C5 C5A BOND C5 C6 BOND C2' C3' BOND C3' O3' {* BOND O3' +P *} BOND C2' O2' BOND O2' H2'' BOND C1' H1' BOND C2' H2' BOND C3' H3' BOND C4' H4' BOND C5' H5' BOND C5' H5'' BOND C6 H6 BOND C5A H51 BOND C5A H52 BOND C5A H53 DIHE C6 C5 C5A H51 DIHE C6 C5 C5A H52 DIHE C6 C5 C5A H53 {* DIHE -O3' P O5' C5' DIHE -O3' P O5' C5' *} DIHE P O5' C5' C4' DIHE O5' C5' C4' O4' DIHE O5' C5' C4' C3' {* DIHE C4' C3' O3' +P DIHE C3' O3' +P +O5' DIHE C3' O3' +P +O5' *} DIHE O4' C1' N1 C2 IMPRoper H51 H53 C5 H52 ! thy methyl chirality JJK 3/9/04 JFD mod for IUPAC order kind of. ! N O T E: SUGAR RING TERMS SET UP AS W. OLSON DOES IT DIHE O4' C1' C2' C3' ! O-C-C-C, twofold term DIHE O4' C1' C2' C3' DIHE C1' C2' C3' C4' DIHE C2' C3' C4' O4' ! O-C-C-C, twofold term DIHE C2' C3' C4' O4' DIHE C3' C4' O4' C1' DIHE C4' O4' C1' C2' ! AND THE SPECIAL GAUCHE TERMS DIHE C5' C4' C3' O3' DIHE O4' C4' C3' O3' DIHE O4' C1' C2' O2' DIHE C1' C2' C3' O3' DIHE C4' C3' C2' O2' DIHE O3' C3' C2' O2' DIHE C3' C2' O2' H2'' ! SO THE ALLHYDROGEN TERMS DIHE O4' C4' C3' H3' DIHE O4' C1' C2' H2' DIHE C4' O4' C1' H1' DIHE C1' O4' C4' H4' DIHE C3' C4' C5' H5' DIHE C3' C4' C5' H5'' !IMPR C5' O4' C3' C4' IMPR O3' C2' C4' C3' IMPR N1 C2' O4' C1' {* chiral impropers included for DG and SA *} improper H1' C2' O4' N1 improper H2' C3' C1' O2' improper H3' C4' C2' O3' improper H4' C5' C3' O4' {* chiral improper included for H5'/H5'' definition, according to *} {* Wijmenga, Mooren and Hilbers in NMR of nucl. acids, (Ed. Roberts) *} improper H5' O5' H5'' C4' !C5' IMPR C1' C2 C6 N1 IMPR O2 N1 N3 C2 IMPR H3 C2 C4 N3 IMPR O4 N3 C5 C4 IMPR C5A C4 C6 C5 IMPR N1 C2 N3 C4 IMPR C2 N3 C4 C5 IMPR N3 C4 C5 C6 IMPR C4 C5 C6 N1 IMPR C5 C6 N1 C2 IMPR C6 N1 C2 N3 IMPR H6 N1 C5 C6 !IMPR C2' C3' C1' O2' DONO H3 N3 DONO H2'' O2' ACCE O2 C2 ACCE O4 C4 ACCE O1P P ACCE O2P P ACCE O2' " " ACCE O3' " " ACCE O4' " " ACCE O5' " " {* IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 *} {* IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 *} {* IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 *} IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 {* IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 *} {* IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 *} IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 IC C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 IC C4 C6 *C5 C5A 1.4439 120.78 -179.94 121.63 1.5000 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 !INFERENCE IC H2'' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 !GUESS ! the all hydrogen part (NOT TOO CAREFULLY DONE /LN) IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 ! THE BASE: IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C6 C5 C5A H51 0.0 0.0 90.0 0.0 0.0 IC C6 C5 C5A H52 0.0 0.0 -30.0 0.0 0.0 IC C6 C5 C5A H53 0.0 0.0 -150.0 0.0 0.0 END {* THY *} !============================================================================ RESIdue URI GROUP ATOM P TYPE=XP CHARge=1.20 END ATOM O1P TYPE=XO2 CHARge=-0.40 END ATOM O2P TYPE=XO2 CHARge=-0.40 END ATOM O5' TYPE=XOS CHARge=-0.36 END GROUP ATOM C5' TYPE=XC2 CHARge=-0.070 END! rationalized ATOM H5' TYPE=XH CHARge=0.035 END! " ATOM H5'' TYPE=XH CHARge=0.035 END! " GROUP ATOM C4' TYPE=XCH CHARge=0.065 END! " ATOM H4' TYPE=XH CHARge=0.035 END!" ATOM O4' TYPE=XOS CHARge=-0.30 END ATOM C1' TYPE=XCH CHARge=0.165 END!" ATOM H1' TYPE=XH CHARge=0.035 END!" GROUP ATOM N1 TYPE=XNS CHARge=-0.19 EXCL=( C4 ) END ATOM C6 TYPE=XCF CHARge=0.155 EXCL=( N3 ) END ATOM H6 TYPE=XH CHARge=0.035 END GROUP ATOM C2 TYPE=XC CHARge=0.35 EXCL=( C5 ) END ATOM O2 TYPE=XO CHARge=-0.35 END GROUP ATOM N3 TYPE=XNA CHARge=-0.26 END ATOM H3 TYPE=XH CHARge=0.26 END GROUP ATOM C4 TYPE=XC CHARge=0.30 END ATOM O4 TYPE=XO CHARge=-0.30 END GROUP ATOM C5 TYPE=XCF CHARge=-0.035 END ATOM H5 TYPE=XH CHARge=0.035 END GROUP ATOM C2' TYPE=XCH CHARge=0.115 END!" ATOM H2' TYPE=XH CHARge=0.035 END!" ATOM O2' TYPE=XOH CHARge=-0.40 END ATOM H2'' TYPE=XHO CHARge=0.25 END GROUP ATOM C3' TYPE=XCH CHARge=-0.035 END!" ATOM H3' TYPE=XH CHARge=0.035 END!" GROUP ATOM O3' TYPE=XOS CHARge=-0.36 END BOND P O1P BOND P O2P BOND P O5' BOND O5' C5' BOND C5' C4' BOND C4' O4' BOND C4' C3' BOND O4' C1' BOND C1' N1 BOND C1' C2' BOND N1 C2 BOND N1 C6 BOND C2 O2 BOND C2 N3 BOND N3 H3 BOND N3 C4 BOND C4 O4 BOND C4 C5 BOND C5 C6 BOND C2' C3' BOND C3' O3' {* BOND O3' +P *} BOND C2' O2' BOND O2' H2'' BOND C1' H1' BOND C2' H2' BOND C3' H3' BOND C4' H4' BOND C5' H5' BOND C5' H5'' BOND C5 H5 BOND C6 H6 {* DIHE -O3' P O5' C5' DIHE -O3' P O5' C5' *} DIHE P O5' C5' C4' DIHE O5' C5' C4' O4' DIHE O5' C5' C4' C3' {* DIHE C4' C3' O3' +P DIHE C3' O3' +P +O5' DIHE C3' O3' +P +O5' *} DIHE O4' C1' N1 C2 ! N O T E: SUGAR RING TERMS SET UP AS W. OLSON DOES IT DIHE O4' C1' C2' C3' ! O-C-C-C, twofold term DIHE O4' C1' C2' C3' DIHE C1' C2' C3' C4' DIHE C2' C3' C4' O4' ! O-C-C-C, twofold term DIHE C2' C3' C4' O4' DIHE C3' C4' O4' C1' DIHE C4' O4' C1' C2' ! AND THE SPECIAL GAUCHE TERMS DIHE C5' C4' C3' O3' DIHE O4' C4' C3' O3' DIHE O4' C1' C2' O2' DIHE C1' C2' C3' O3' DIHE C4' C3' C2' O2' DIHE O3' C3' C2' O2' DIHE C3' C2' O2' H2'' ! SO THE ALLHYDROGEN TERMS DIHE O4' C4' C3' H3' DIHE O4' C1' C2' H2' DIHE C4' O4' C1' H1' DIHE C1' O4' C4' H4' DIHE C3' C4' C5' H5' DIHE C3' C4' C5' H5'' !IMPR C5' O4' C3' C4' IMPR O3' C2' C4' C3' IMPR N1 C2' O4' C1' {* chiral impropers included for DG and SA *} improper H1' C2' O4' N1 improper H2' C3' C1' O2' improper H3' C4' C2' O3' improper H4' C5' C3' O4' {* chiral improper included for H5'/H5'' definition, according to *} {* Wijmenga, Mooren and Hilbers in NMR of nucl. acids, (Ed. Roberts) *} improper H5' O5' H5'' C4' !C5' IMPR C1' C2 C6 N1 IMPR O2 N1 N3 C2 IMPR H3 C2 C4 N3 IMPR O4 N3 C5 C4 IMPR N1 C2 N3 C4 IMPR C2 N3 C4 C5 IMPR N3 C4 C5 C6 IMPR C4 C5 C6 N1 IMPR C5 C6 N1 C2 IMPR C6 N1 C2 N3 IMPR H6 N1 C5 C6 IMPR H5 C4 C6 C5 !IMPR C2' C3' C1' O2' DONO H3 N3 DONO H2'' O2' ACCE O2 C2 ACCE O4 C4 ACCE O1P P ACCE O2P P ACCE O2' " " ACCE O3' " " ACCE O4' " " ACCE O5' " " {* IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 *} {* IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 *} {* IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 *} IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 {* IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 *} {* IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 *} IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 IC C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 !INFERENCE IC H2'' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 !GUESS ! the all hydrogen part (NOT TOO CAREFULLY DONE /LN) IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 ! THE BASE: IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 END {* URI *} !============================================================================ PRESIdue 2END ! Patch to put ribose in 2'endo conformation MODIfy IC C5' C4' C3' O3' 1.5160 116.10 150.88 115.12 1.4212 MODIfy IC O4' C3' *C4' C5' 1.4572 104.06 -121.24 116.10 1.5160 MODIfy IC C2' C4' *C3' O3' 1.5284 101.91 -114.59 110.88 1.4212 MODIfy IC C4' C3' C2' C1' 1.5284 101.78 -39.92 101.97 1.5251 MODIfy IC C1' C3' *C2' O2' 1.5284 100.04 -124.67 115.81 1.4212 !INFERENCE END {2END} !------------------------------------------------------------------ PRESidue DEOX ! Patch to make DEOXYribose of the ribose DELETE ATOM O2' END GROUP MODIFY ATOM C2' TYPE=YC2 CHARGE=-0.07 END MODIFY ATOM H2' TYPE=YH CHARGE=0.035 END MODIFY ATOM H2'' TYPE=YH CHARGE=0.035 END ADD BOND C2' H2' DELETE BOND C2' H2' ADD BOND C2' H2'' DELETE BOND C2' C3' ADD BOND C2' C3' DELET BOND C1' C2' ADD BOND C1' C2' ADD ANGLE C1' C2' H2' ADD ANGLE C3' C2' H2' ADD ANGLE H2' C2' H2'' ADD DIHEDRAL O4' C1' C2' H2' DELETE DIHEDRAL C2' C3' C4' O4' ADD DIHEDRAL C2' C3' C4' O4' DELETE DIHEDRAL O4' C1' C2' C3' ADD DIHEDRAL O4' C1' C2' C3' DELETE DIHEDRAL C1' C2' C3' C4' ADD DIHEDRAL C1' C2' C3' C4' DELETE DIHEDRAL C1' C2' C3' O3' ADD DIHEDRAL C1' C2' C3' O3' {* chiral improper included for H2'/H2'' definition, according to *} {* Wijmenga, Mooren and Hilbers in NMR of nucl. acids, (Ed. Roberts) *} ADD IMPROPER H2'' C3' C1' H2' ! JJK 3/9/04 Changed from H2' C3' C1' H2'' to ! conform to RNA version of this improper, ! which is H2'' C3' C1' O2' ADD IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 ! the all hydrogen part (NOT TOO CAREFULLY DONE /LN) ADD IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 ADD IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 ADD IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 END {DEOX} !--------------------------------------------------------------------- PRESidue 5TER ! 5-terminus (without phosphate) ! ! should be used as "FIRST 5TER TAIL + * END" GROUp ! i.e. to be patched to the first RNA residue ADD ATOM +H5T TYPE=XHO CHARGE=0.25 END !H MODIFY ATOM +O5' TYPE=XOH CHARGE=-0.40 END !H MODIFY ATOM +C5' TYPE=XC2 CHARGE=0.08 END !H DELETE ATOM +P END DELETE ATOM +O1P END DELETE ATOM +O2P END ! ADD BOND +H5T +O5' ADD ANGLe +H5T +O5' +C5' ADD DIHEdral +H5T +O5' +C5' +C4' ADD DONOr +H5T +O5' ADD IC +H5T +O5' +C5' +C4' 1.0000 110.00 180.00 110.04 1.5160 END {5TER} !------------------------------------------------------------------ PRESidue 5PHO ! 5-terminus (with phosphate) ! ! should be used as "FIRST 5PHO TAIL + * END" GROUp ! i.e. to be patched to the first RNA residue ADD ATOM +H5T TYPE=XHO CHARGE=0.15 END ADD ATOM +O5T TYPE=XOH CHARGE=-0.15 END !PERHAPS ONE SHOULD CHANGE THE P CHARGE AS WELL???? ADD BOND +H5T +O5T ADD BOND +O5T +P ADD ANGLe +H5T +O5T +P ADD ANGLe +O5' +P +O5T ADD ANGLe +O5T +P +O1P ADD ANGLe +O5T +P +O2P ADD DIHEdral +O5' +P +O5T +H5T ADD DIHEdral +C5' +O5' +P +O5T ADD DONOr +H5T +O5T ADD IC +H5T +O5T +P +O5' 1.0000 115.00 180.00 101.45 1.6001 !GUESS ADD IC +C5' +O5' +P +O5T 1.4461 119.00 -39.52 101.45 1.6001 !GUESS ADD IC +O5T +O5' *+P +O1P 1.6001 101.45 -115.82 109.74 1.4802 !INFEREN. ADD IC +O5T +O5' *+P +O2P 1.6001 101.45 115.90 109.80 1.4801 !INFEREN. END {5PHO} !------------------------------------------------------------------ PRESidue 3TER ! 3-terminus (without phosphate) ! should be used as "LAST 3TER HEAD - * END" GROUp ! i.e. to be patched to the last RNA residue MODIFY ATOM -C3' TYPE=XCH CHARGE=0.115 END MODIFY ATOM -H3' TYPE=XH CHARGE=0.035 END MODIFY ATOM -O3' TYPE=XOH CHARGE=-0.40 END ADD ATOM -H3T TYPE=XHO CHARGE=0.25 END ! ADD BOND -O3' -H3T ADD ANGLe -C3' -O3' -H3T ADD DIHEdral -C4' -C3' -O3' -H3T ADD DONOr -H3T -O3' ADD IC -H3T -O3' -C3' -C4' 0.9600 114.97 148.63 111.92 1.5284 END {3TER} !------------------------------------------------------------------ PRESidue NUC ! patch for nucleic acid backbone ! should be used as "LINK NUC HEAD - * TAIL + * END" ! i.e. it links the previous RNA residue (-) with ! the current one (+) GROUp MODIFY ATOM -O3' END ! MODIFY ATOM +P END ! MODIFY ATOM +O1P END ! this should correctly define the electrostatic MODIFY ATOM +O2P END ! group boundary MODIFY ATOM +O5' END ! ADD BOND -O3' +P ADD ANGLE -C3' -O3' +P ADD ANGLE -O3' +P +O1P ADD ANGLE -O3' +P +O2P ADD ANGLE -O3' +P +O5' ADD DIHEdral -O3' +P +O5' +C5' !\ double ADD DIHEdral -O3' +P +O5' +C5' !/ dihedral ADD DIHEdral -C4' -C3' -O3' +P ADD DIHEdral -C3' -O3' +P +O5' !\ double ADD DIHEdral -C3' -O3' +P +O5' !/ dihedral ! line below fixes the stereochemistry according to IUPAC ! J. L. Markley, A. Bax, Y. Arata, C. W. Hilbers, R. Kaptein, ! B. D. Sykes, P. E. Wright, and K. Wuthrich. ! Recommendations for the presentation of NMR structures of proteins ! and nucleic acids. J.Mol.Biol. 280 (5):933-952, 1998. ! Note it leaves terminal phosphates unrestrained ADD IMPROPER -O3' +O5' +O1P +O2P IC -O3' +P +O5' +C5' 1.6001 101.45 -39.25 119.00 1.4401 IC -O3' +O5' *+P +O1P 1.6001 101.45 -115.82 109.74 1.4802 IC -O3' +O5' *+P +O2P 1.6001 101.45 115.90 109.80 1.4801 IC -C4' -C3' -O3' +P 1.5284 111.92 159.13 119.05 1.6001 IC -C3' -O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 END {NUC} !------------------------------------------------------------------ PRESidue FC ! patch for fully charged phosphate group GROUP MODIFY ATOM O3' CHARGE=-0.46 END MODIFY ATOM P CHARGE=1.36 END MODIFY ATOM O1P CHARGE=-0.72 END MODIFY ATOM O2P CHARGE=-0.72 END MODIFY ATOM O5' CHARGE=-0.46 END END {FC} !------------------------------------------------------------------ RESIdue NA ! Fully charged Na GROUP ATOM NA TYPE=XSD CHARGE=1.00 END END {NA} !------------------------------------------------------------------ RESIdue MG GROUp ATOM MG TYPE=XMG CHARGE=2.0 END END {MG} !------------------------------------------------------------------ set echo=$prev_echo mess=$prev_messages end