NMR Restraints Grid |
Result table
image | mrblock_id | pdb_id | cing | stage | position | program | type |
10787 | 1qby | cing | 1-original | 2 | XPLOR/CNS | molecular system |
AUTOGENERATE ANGLES=true END {*==============================*} {* DNA/RNA default atomic masses *} MASS H 1.00800 MASS H2 1.00800 MASS HT 1.00800 MASS HO 1.00800 MASS C 12.01100 MASS CH 12.01100 MASS C2 12.01100 MASS CA 12.01100 MASS CP 12.01100 MASS CB 12.01100 MASS CE 12.01100 MASS CF 12.01100 MASS C3 12.01100 MASS CS 12.01100 MASS N2 14.00670 MASS NT 14.00670 MASS NA 14.00670 MASS NB 14.00670 MASS NC 14.00670 MASS NS 14.00670 MASS NH2E 16.02270 MASS NH3 14.02270 MASS O 15.99940 MASS O2 15.99940 MASS OS 15.99940 MASS OH 15.99940 MASS SD 22.98980 MASS P 30.97400 MASS BR 79.90400 MASS MG 24.30500 !======================================================================== ! set H on C to .035 and take up slack on C (Kollman) RESIdue G GROUP ATOM P TYPE=P CHARGE=1.20 END ATOM O1P TYPE=O2 CHARge=-0.40 END ATOM O2P TYPE=O2 CHARge=-0.40 END ATOM O5' TYPE=OS CHARge=-0.36 END GROUP ATOM C5' TYPE=C2 CHARge=-0.07 END! rationalized ATOM H5' TYPE=H CHARge=0.035 END!" ATOM H5'' TYPE=H CHARge=0.035 END!" GROUP ATOM C4' TYPE=CH CHARge=0.065 END!" ATOM H4' TYPE=H CHARge=0.035 END!" ATOM O4' TYPE=OS CHARge=-0.30 END ATOM C1' TYPE=CH CHARge=0.165 END!" ATOM H1' TYPE=H CHARge=0.035 END!" GROUP ATOM N9 TYPE=NS CHARge=-0.19 END ATOM C4 TYPE=CB CHARge=0.19 EXCL=( N1 ) END GROUP ATOM N3 TYPE=NC CHARge=-0.50 EXCL=( C6 ) END ATOM C2 TYPE=CA CHARge=0.50 EXCL=( C5 ) END GROUP ATOM N2 TYPE=N2 CHARge=-0.42 END! ATOM H21 TYPE=H2 CHARge=0.21 END! ATOM H22 TYPE=H2 CHARge=0.21 END! GROUP ATOM N1 TYPE=NA CHARge=-0.26 END ATOM H1 TYPE=H CHARge=0.26 END GROUP ATOM C6 TYPE=C CHARge=0.30 END ATOM O6 TYPE=O CHARge=-0.30 END GROUP ATOM C5 TYPE=CB CHARge=0.02 END ATOM N7 TYPE=NB CHARge=-0.25 END ATOM C8 TYPE=CE CHARge=0.195 END ATOM H8 TYPE=H CHARge=0.035 END!" GROUP ATOM C2' TYPE=CH CHARge=0.115 END!" ATOM H2'' TYPE=H CHARge=0.035 END!" ATOM O2' TYPE=OH CHARge=-0.40 END ATOM H2' TYPE=HO CHARge=0.25 END GROUP ATOM C3' TYPE=CH CHARge=-0.035 END!" ATOM H3' TYPE=H CHARge=0.035 END!" GROUP ATOM O3' TYPE=OS 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 IMPRoper N3 C2 N2 H21 ! 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'' ! 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' 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 ! 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 {* 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' " " END {* GUA *} !======================================================================== ! set H on C to .035 and take up slack on C (Kollman) RESIdue GSR GROUP ATOM P TYPE=P CHARGE=1.20 END ATOM O1P TYPE=O2 CHARge=-0.40 END ATOM O2P TYPE=O2 CHARge=-0.40 END ATOM O5' TYPE=OS CHARge=-0.36 END GROUP ATOM C5' TYPE=C2 CHARge=-0.07 END! rationalized ATOM H5' TYPE=H CHARge=0.035 END!" ATOM H5'' TYPE=H CHARge=0.035 END!" GROUP ATOM C4' TYPE=CH CHARge=0.065 END!" ATOM H4' TYPE=H CHARge=0.035 END!" ATOM O4' TYPE=OS CHARge=-0.30 END ATOM C1' TYPE=CH CHARge=0.165 END!" ATOM H1' TYPE=H CHARge=0.035 END!" GROUP ATOM N9 TYPE=NS CHARge=-0.19 END ATOM C4 TYPE=CB CHARge=0.19 EXCL=( N1 ) END GROUP ATOM N3 TYPE=NC CHARge=-0.50 EXCL=( C6 ) END ATOM C2 TYPE=CA CHARge=0.50 EXCL=( C5 ) END GROUP ATOM N2 TYPE=N2 CHARge=-0.42 END! ATOM H2 TYPE=H2 CHARge=0.21 END! GROUP ATOM CA TYPE=CT CHARge=-0.10 END ATOM HA TYPE=HA CHARge=0.21 END GROUP ATOM CB TYPE=CT CHARge=0.08 END ATOM HB' TYPE=HA CHARge=0.10 END ATOM HB'' TYPE=HA CHARge=0.10 END ATOM OB TYPE=OH CHARge=-0.68 END ATOM HOB TYPE=HO CHARge=0.40 END GROUP ATOM CJ TYPE=CP CHARge=0.03 EXCLUDE=(CP) END ATOM CO TYPE=CP CHARge=-0.16 EXCLUDE=(CM') END ATOM HO TYPE=HA CHARge=0.14 END ATOM CO' TYPE=CP CHARge=-0.16 EXCLUDE=(CM) END ATOM HO' TYPE=HA CHARge=0.14 END ATOM CM TYPE=CP CHARge=-0.15 EXCLUDE=(CO') END ATOM HM TYPE=HA CHARge=0.14 END ATOM CM' TYPE=CP CHARge=-0.15 EXCLUDE=(CO) END ATOM HM' TYPE=HA CHARge=0.14 END ATOM CP TYPE=CP CHARge=-0.15 EXCLUDE=(CJ) END ATOM HP TYPE=HA CHARge=0.14 END GROUP ATOM N1 TYPE=NA CHARge=-0.26 END ATOM H1 TYPE=H CHARge=0.26 END GROUP ATOM C6 TYPE=C CHARge=0.30 END ATOM O6 TYPE=O CHARge=-0.30 END GROUP ATOM C5 TYPE=CB CHARge=0.02 END ATOM N7 TYPE=NB CHARge=-0.25 END ATOM C8 TYPE=CE CHARge=0.195 END ATOM H8 TYPE=H CHARge=0.035 END!" GROUP ATOM C2' TYPE=CH CHARge=0.115 END!" ATOM H2'' TYPE=H CHARge=0.035 END!" ATOM O2' TYPE=OH CHARge=-0.40 END ATOM H2' TYPE=HO CHARge=0.25 END GROUP ATOM C3' TYPE=CH CHARge=-0.035 END!" ATOM H3' TYPE=H CHARge=0.035 END!" GROUP ATOM O3' TYPE=OS 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 CA BOND N2 H2 BOND CA HA BOND CA CB BOND CB HB' BOND CB HB'' BOND CB OB BOND OB HOB BOND CA CJ BOND CJ CO BOND CO HO BOND CO CM BOND CM HM BOND CM CP BOND CP HP BOND CP CM' BOND CM' HM' BOND CM' CO' BOND CO' HO' BOND CO' CJ 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 IMPRoper N3 C2 N2 H2 ! 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'' ! 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' 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 CA H2 C2 N2 ! 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 {* IMPR C2' C3' C1' O2' *} IMPR H8 N7 N9 C8 ! To keep H's in phenyl planar IMPR HO' CO' CM' CP IMPR HM' CM' CP CM IMPR HP CP CM CO IMPR HM CM CO CJ IMPR HO CO CJ CA ! TO Keep carbons in phenyl planar IMPR CJ CO CM CP IMPR CO CM CP CM' IMPR CM CP CM' CO' IMPR CP CM' CO' CJ IMPR CM' CO' CJ CO IMPR CO' CJ CO CM IMPR CA CJ CO CM IMPR HB' HB'' CA OB ! STEREO AT CB IMPR HA N2 CB CJ ! STEREO AT CA DIHE CO CJ CA CB DONO H2 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' " " END {* GUA *} !=========================================================================== RESIdue PDG GROUP ATOM P TYPE=P CHARGE=1.20 END ATOM O1P TYPE=O2 CHARge=-0.40 END ATOM O2P TYPE=O2 CHARge=-0.40 END ATOM O5' TYPE=OS CHARge=-0.36 END GROUP ATOM C5' TYPE=C2 CHARge=-0.07 END! rationalized ATOM H5' TYPE=H CHARge=0.035 END!" ATOM H5'' TYPE=H CHARge=0.035 END!" GROUP ATOM C4' TYPE=CH CHARge=0.065 END!" ATOM H4' TYPE=H CHARge=0.035 END!" ATOM O4' TYPE=OS CHARge=-0.30 END ATOM C1' TYPE=CH CHARge=0.165 END!" ATOM H1' TYPE=H CHARge=0.035 END!" GROUP ATOM N9 TYPE=NS CHARge=-0.0084 END ATOM C4 TYPE=CB CHARge=0.1642 EXCL=( N1 ) END GROUP ATOM N3 TYPE=NC CHARge=-0.3497 EXCL=( C6 ) END ATOM C2 TYPE=CA CHARge=0.3939 EXCL=( C5 ) END GROUP ATOM N2 TYPE=NA CHARge=-0.3609 END! ATOM H2 TYPE=H CHARge=0.2091 END! GROUP ATOM C6A TYPE=C2 CHARge=0.1686 END ATOM H6A1 TYPE=H CHARge=0.0209 END ATOM H6A2 TYPE=H CHARge=-0.0014 END ATOM C7A TYPE=C2 CHARge=-0.0507 END ATOM H7A1 TYPE=H CHARge=0.0299 END ATOM H7A2 TYPE=H CHARge=0.0285 END ATOM C8A TYPE=C2 CHARge=0.1668 END ATOM H8A1 TYPE=H CHARge=0.0376 END ATOM H8A2 TYPE=H CHARge=0.0164 END GROUP ATOM N1 TYPE=NS CHARge=-0.4106 END GROUP ATOM C6 TYPE=C CHARge=0.4602 END ATOM O6 TYPE=O CHARge=-0.3174 END GROUP ATOM C5 TYPE=CB CHARge=-0.2304 END ATOM N7 TYPE=NB CHARge=-0.1403 END ATOM C8 TYPE=CE CHARge=0.0437 END ATOM H8 TYPE=H CHARge=0.1300 END!" GROUP ATOM C2' TYPE=CH CHARge=0.115 END!" ATOM H2'' TYPE=H CHARge=0.035 END!" ATOM O2' TYPE=OH CHARge=-0.40 END ATOM H2' TYPE=HO CHARge=0.25 END GROUP ATOM C3' TYPE=CH CHARge=-0.035 END!" ATOM H3' TYPE=H CHARge=0.035 END!" GROUP ATOM O3' TYPE=OS 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 H2 BOND N2 C6A BOND C6A H6A1 BOND C6A H6A2 BOND C6A C7A BOND C7A H7A1 BOND C7A H7A2 BOND C8A C7A BOND C8A H8A1 BOND C8A H8A2 BOND N1 C8A 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 IMPRoper N3 C2 N2 H2 ! 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'' ! ! DIHE N2 C6A C7A C8A DIHE C6A C7A C8A N1 ! ! 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' 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 N1 C2 N2 C8A 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 N1 C2 N2 H2 IMPR N1 C2 N2 N3 IMPR N2 C2 N1 C8A ! 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 {* IMPR C2' C3' C1' O2' *} IMPR H8 N7 N9 C8 DONO H2 N2 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' " " END {* PDG *} !=========================================================================== RESIdue A GROUP ATOM P TYPE=P CHARge=1.20 END ATOM O1P TYPE=O2 CHARge=-0.40 END ATOM O2P TYPE=O2 CHARge=-0.40 END ATOM O5' TYPE=OS CHARge=-0.36 END GROUP ATOM C5' TYPE=C2 CHARge=-0.070 END!" ATOM H5' TYPE=H CHARge=0.035 END!" ATOM H5'' TYPE=H CHARge=0.035 END!" GROUP ATOM C4' TYPE=CH CHARge=0.065 END! " ATOM H4' TYPE=H CHARge=0.035 END!" ATOM O4' TYPE=OS CHARge=-0.30 END ATOM C1' TYPE=CH CHARge=0.165 END!" ATOM H1' TYPE=H CHARge=0.035 END!" GROUP ATOM N9 TYPE=NS CHARge=-0.19 END ATOM C4 TYPE=CB CHARge=0.19 EXCL=( N1 ) END GROUP ATOM N3 TYPE=NC CHARge=-0.26 EXCL=( C6 ) END ATOM C2 TYPE=CE CHARge=0.225 EXCL=( C5 ) END !" ATOM H2 TYPE=H CHARge=0.035 END!" GROUP ATOM N1 TYPE=NC CHARge=-0.28 END ATOM C6 TYPE=CA CHARge=0.28 END GROUP ATOM N6 TYPE=N2 CHARGE=-0.42 END! ATOM H61 TYPE=H2 CHARge=0.21 END! ATOM H62 TYPE=H2 CHARge=0.21 END! GROUP ATOM C5 TYPE=CB CHARge=0.02 END ATOM N7 TYPE=NB CHARge=-0.25 END ATOM C8 TYPE=CE CHARge=0.195 END!" ATOM H8 TYPE=H CHARge=0.035 END!" GROUP ATOM C2' TYPE=CH CHARge=0.115 END!" ATOM H2'' TYPE=H CHARge=0.035 END!" ATOM O2' TYPE=OH CHARge=-0.40 END ATOM H2' TYPE=HO CHARge=0.25 END GROUP ATOM C3' TYPE=CH CHARge=-0.035 END!" ATOM H3' TYPE=H CHARge=0.035 END!" GROUP ATOM O3' TYPE=OS 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 IMPRoper C5 C6 N6 H61 ! 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'' ! 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' 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' ! 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 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' " " END {* ADE *} !========================================================================= RESIdue ABP GROUP ATOM P TYPE=P CHARge=1.20 END ATOM O1P TYPE=O2 CHARge=-0.40 END ATOM O2P TYPE=O2 CHARge=-0.40 END ATOM O5' TYPE=OS CHARge=-0.36 END GROUP ATOM C5' TYPE=C2 CHARge=-0.070 END!" ATOM H5' TYPE=H CHARge=0.035 END!" ATOM H5'' TYPE=H CHARge=0.035 END!" GROUP ATOM C4' TYPE=CH CHARge=0.065 END! " ATOM H4' TYPE=H CHARge=0.035 END!" ATOM O4' TYPE=OS CHARge=-0.30 END ATOM C1' TYPE=CH CHARge=0.165 END!" ATOM H1' TYPE=H CHARge=0.035 END!" GROUP ATOM N9 TYPE=NS CHARge=-0.19 END ATOM C4 TYPE=CB CHARge=0.19 EXCL=( N1 ) END GROUP ATOM N3 TYPE=NC CHARge=-0.26 EXCL=( C6 ) END ATOM C2 TYPE=CE CHARge=0.225 EXCL=( C5 ) END !" ATOM H2 TYPE=H CHARge=0.035 END!" GROUP ATOM N1 TYPE=NC CHARge=-0.28 END ATOM C6 TYPE=CA CHARge=0.28 END GROUP ATOM N6 TYPE=N2 CHARGE=-0.42 END ATOM H6 TYPE=H2 CHARge=0.21 END GROUP ATOM C10 TYPE=CH CHARge=0.1427 END ATOM H10 TYPE=H CHARge=-0.004 END GROUP ATOM C9 TYPE=CH CHARge=0.1854 END ATOM H9 TYPE=H CHARge=-0.0379 END ATOM O9 TYPE=OH CHARge=-0.2722 END ATOM HO9 TYPE=HO CHARge=0.1558 END GROUP ATOM C8A TYPE=CH CHARge=0.1824 END ATOM H8A TYPE=H CHARge=-0.0481 END ATOM O8A TYPE=OH CHARge=-0.2863 END ATOM HO8A TYPE=HO CHARge=0.1590 END GROUP ATOM C7 TYPE=CH CHARge=0.2036 END ATOM H7 TYPE=H CHARge=-0.0082 END ATOM O7 TYPE=OH CHARge=-0.2975 END ATOM HO7 TYPE=HO CHARge=0.1552 END GROUP ATOM C6A TYPE=CP9 CHARge=0.0135 END GROUP ATOM C6B TYPE=CP8 CHARge=0.0051 END ATOM H6B TYPE=HA CHARge=-0.0271 END GROUP ATOM C5A TYPE=CP7 CHARge=0.0239 END GROUP ATOM C5B TYPE=CP6 CHARge=0.0241 END ATOM H5B TYPE=HA CHARge=-0.0320 END GROUP ATOM C4A TYPE=CP5 CHARge=0.0510 END ATOM H4A TYPE=HA CHARge=-0.0295 END GROUP ATOM C3A TYPE=CP4 CHARge=0.0300 END GROUP ATOM C3 TYPE=CP3 CHARge=0.0076 END ATOM H3 TYPE=HA CHARge=-0.0251 END GROUP ATOM C2A TYPE=CP2 CHARge=0.0253 END ATOM H2A TYPE=HA CHARge=-0.0270 END GROUP ATOM C1 TYPE=CP1 CHARge=0.0095 END ATOM H1 TYPE=HA CHARge=-0.0273 END GROUP ATOM C12A TYPE=CP14 CHARge=0.0295 END ATOM C12B TYPE=CP15 CHARge=0.0111 END ATOM C12C TYPE=CP16 CHARge=0.0008 END ATOM C10A TYPE=CP10 CHARge=-.0153 END ATOM C10B TYPE=CP11 CHARge=0.0298 END GROUP ATOM C11 TYPE=CP12 CHARge=0.0088 END ATOM H11 TYPE=HA CHARge=-0.0288 END GROUP ATOM C12 TYPE=CP13 CHARge=0.0219 END ATOM H12 TYPE=HA CHARge=-0.0329 END GROUP ATOM C5 TYPE=CB CHARge=0.02 END ATOM N7 TYPE=NB CHARge=-0.25 END ATOM C8 TYPE=CE CHARge=0.195 END!" ATOM H8 TYPE=H CHARge=0.035 END!" GROUP ATOM C2' TYPE=CH CHARge=0.115 END!" ATOM H2'' TYPE=H CHARge=0.035 END!" ATOM O2' TYPE=OH CHARge=-0.40 END ATOM H2' TYPE=HO CHARge=0.25 END GROUP ATOM C3' TYPE=CH CHARge=-0.035 END!" ATOM H3' TYPE=H CHARge=0.035 END!" GROUP ATOM O3' TYPE=OS 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 C10 BOND N6 H6 BOND C6 C5 BOND C5 N7 BOND N7 C8 BOND C10 H10 BOND C10 C9 BOND C10 C10A BOND C9 H9 BOND C9 O9 BOND O9 HO9 BOND C9 C8A BOND C8A H8A BOND C8A O8A BOND O8A HO8A BOND C8A C7 BOND C7 H7 BOND C7 O7 BOND O7 HO7 BOND C7 C6A BOND C6A C10A BOND C6A C6B BOND C6B H6B BOND C6B C5A BOND C5A C12C BOND C5A C5B BOND C5B H5B BOND C5B C4A BOND C4A H4A BOND C4A C3A BOND C3A C12B BOND C3A C3 BOND C3 H3 BOND C3 C2A BOND C2A H2A BOND C2A C1 BOND C1 H1 BOND C1 C12A BOND C12A C12 BOND C12A C12B BOND C12B C12C BOND C12C C10B BOND C10B C10A BOND C10B C11 BOND C11 H11 BOND C11 C12 BOND C12 H12 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 IMPRoper C5 C6 N6 H6 ! 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'' !Benzo(a)pyrene DIHE C10 C9 C8A C7 DIHE C9 C8A C7 C6A DIHE C8A C7 C6A C10A ! ! 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' 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 C10 C6 H6 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' ! 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 ! To Keep H's in pyrenyl ring planar IMPR H1 C1 C2A C3 IMPR H2A C2A C3 C3A IMPR H3 C3 C3A C12B IMPR H4A C4A C5B C5A IMPR H5B C5B C5A C12C IMPR H6B C6B C6A C10A IMPR H11 C11 C12 C12A IMPR H12 C12 C12A C12B ! ! To Keep carbons in pyrenyl ring planar IMPR C1 C2A C3 C3A IMPR C2A C3 C3A C12B IMPR C3 C3A C12B C12A IMPR C3A C12B C12A C1 IMPR C12B C12A C1 C2A IMPR C12A C1 C2A C3 ! IMPR C12C C12B C3A C4A IMPR C12B C3A C4A C5B IMPR C3A C4A C5B C5A IMPR C4A C5B C5A C12C IMPR C5B C5A C12C C12B IMPR C5A C12C C12B C3A ! IMPR C11 C12 C12A C12B IMPR C12 C12A C12B C12C IMPR C12A C12B C12C C10B IMPR C12B C12C C10B C11 IMPR C12C C10B C11 C12 IMPR C10B C11 C12 C12A ! IMPR C10A C10B C12C C5A IMPR C10B C12C C5A C6B IMPR C12C C5A C6B C6A IMPR C5A C6B C6A C10A IMPR C6B C6A C10A C10B IMPR C6A C10A C10B C12C ! To Keep pyrene rings planner with respect to each other IMPR C10 C10A C10B C12C IMPR C7 C6A C6B C5A IMPR C12A C12B C3A C4A IMPR C2A C3 C3A C4A IMPR C1 C12A C12B C12C IMPR C12 C12A C12B C3A IMPR C12A C12B C12C C5A IMPR C11 C10B C12C C5A IMPR C11 C10B C10A C6A IMPR C12B C12C C5A C6B IMPR C10B C12C C5A C5B IMPR C3 C3A C4A C5B IMPR C10 C10A C10B C11 IMPR C10 C10A C6A C7 IMPR H10 N6 C9 C10A ! STEREO AT C10 DONO H61 N6 DONO H62 N6 DONO H2' O2' DONO HO7 O7 DONO HO8A O8A DONO HO9 O9 ACCE N3 " " ACCE N1 " " ACCE N7 " " ACCE O1P P ACCE O2P P ACCE O2' " " ACCE O3' " " ACCE O4' " " ACCE O5' " " END {* ABP *} !========================================================================= RESIdue ABA GROUP ATOM P TYPE=P CHARge=1.20 END ATOM O1P TYPE=O2 CHARge=-0.40 END ATOM O2P TYPE=O2 CHARge=-0.40 END ATOM O5' TYPE=OS CHARge=-0.36 END GROUP ATOM C5' TYPE=C2 CHARge=-0.070 END!" ATOM H5' TYPE=H CHARge=0.035 END!" ATOM H5'' TYPE=H CHARge=0.035 END!" GROUP ATOM C4' TYPE=CH CHARge=0.065 END! " ATOM H4' TYPE=H CHARge=0.035 END!" ATOM O4' TYPE=OS CHARge=-0.30 END ATOM C1' TYPE=CH CHARge=0.165 END!" ATOM H1' TYPE=H CHARge=0.035 END!" GROUP ATOM N9 TYPE=NS CHARge=-0.2100 END ATOM C4 TYPE=CB CHARge=0.0783 EXCL=( N1 ) END GROUP ATOM N3 TYPE=NC CHARge=-0.1841 EXCL=( C6 ) END ATOM C2 TYPE=CE CHARge=0.1842 EXCL=( C5 ) END !" ATOM H2 TYPE=H CHARge=0.1194 END!" GROUP ATOM N1 TYPE=NC CHARge=-0.3563 END ATOM C6 TYPE=CA CHARge=0.3065 END GROUP ATOM N6 TYPE=N2 CHARGE=-0.2910 END ATOM H6 TYPE=H2 CHARge=0.2071 END ! GROUP ATOM C4C TYPE=CH CHARge=0.2227 END ATOM H4C TYPE=H CHARge=0.0901 END GROUP ATOM C9C TYPE=CH CHARge=0.0911 END ATOM H9C TYPE=H CHARge=0.0456 END ATOM O3 TYPE=OH CHARge=-0.3361 END ATOM H3 TYPE=HO CHARge=0.1774 END GROUP ATOM C8B TYPE=CH CHARge=0.0833 END ATOM H8B TYPE=H CHARge=0.0390 END ATOM O2 TYPE=OH CHARge=-0.3179 END ATOM HO2 TYPE=HO CHARge=0.1884 END GROUP ATOM C3B TYPE=CH CHARge=0.1440 END ATOM H3B TYPE=H CHARge=0.0532 END ATOM O1 TYPE=OH CHARge=-0.3128 END ATOM H1 TYPE=HO CHARge=0.1866 END GROUP ATOM C3A TYPE=CP23 CHARge=-0.0606 END GROUP ATOM C2A TYPE=CP22 CHARge=-0.0543 END ATOM H2A TYPE=HA CHARge=0.0760 END GROUP ATOM C4A TYPE=CP24 CHARge=-0.0892 END GROUP ATOM C1A TYPE=CP21 CHARge=-0.0224 END ATOM H1A TYPE=HA CHARge=0.0673 END GROUP ATOM C5A TYPE=CP26 CHARge=-0.0376 END ATOM H5A TYPE=HA CHARge=0.0589 END GROUP ATOM C4B TYPE=CP25 CHARge=-0.0322 END GROUP ATOM C6A TYPE=CP27 CHARge=-0.0497 END ATOM H6A TYPE=HA CHARge=0.0635 END GROUP ATOM C7A TYPE=CP28 CHARge=-0.0467 END ATOM H7A TYPE=HA CHARge=0.0643 END GROUP ATOM C8A TYPE=CP29 CHARge=-0.0540 END ATOM H8A TYPE=HA CHARge=0.0652 END GROUP ATOM C5B TYPE=CP30 CHARge=-0.0235 END ATOM C9B TYPE=CP31 CHARge=-0.0327 END ATOM C11 TYPE=CP32 CHARge=-0.0435 END GROUP ATOM C9A TYPE=CP33 CHARge=-0.0444 END ATOM H9A TYPE=HA CHARge=0.0612 END GROUP ATOM C10 TYPE=CP34 CHARge=-0.0124 END ATOM H10 TYPE=HA CHARge=0.0624 END ! ! GROUP ATOM C5 TYPE=CB CHARge=-0.1350 END ATOM N7 TYPE=NB CHARge=-0.1903 END ATOM C8 TYPE=CE CHARge=0.0714 END!" ATOM H8 TYPE=H CHARge=0.1295 END!" GROUP ATOM C2' TYPE=CH CHARge=0.115 END!" ATOM H2'' TYPE=H CHARge=0.035 END!" ATOM O2' TYPE=OH CHARge=-0.40 END ATOM H2' TYPE=HO CHARge=0.25 END GROUP ATOM C3' TYPE=CH CHARge=-0.035 END!" ATOM H3' TYPE=H CHARge=0.035 END!" GROUP ATOM O3' TYPE=OS 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 C4C BOND N6 H6 BOND C6 C5 BOND C5 N7 BOND N7 C8 BOND C4C H4C BOND C4C C9C BOND C4C C4A BOND C9C H9C BOND C9C O3 BOND O3 H3 BOND C9C C8B BOND C8B H8B BOND C8B O2 BOND O2 HO2 BOND C8B C3B BOND C3B H3B BOND C3B O1 BOND O1 H1 BOND C3B C3A BOND C3A C2A BOND C3A C4A BOND C2A H2A BOND C4A C4B BOND C4B C5A BOND C5A C5B BOND C5A H5A BOND C5B C6A BOND C6A H6A BOND C6A C7A BOND C7A H7A BOND C7A C8A BOND C8A H8A BOND C8A C9A BOND C9A H9A BOND C9A C9B BOND C9B C5B BOND C9B C10 BOND C10 C11 BOND C1A C11 BOND C1A C2A BOND C11 C4B BOND C1A H1A BOND C10 H10 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 IMPR C5 C6 N6 H6 ! 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'' !Benz[a]anthracene ! DIHE C4C C9C C8B C3B ! DIHE C9C C8B C3B C3A DIHE C5 C6 N6 H6 ! DIHE C5 C6 N6 C4C ! 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' 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 C4C C6 H6 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' ! 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 ! To Keep H's in pyrenyl ring planar IMPR H1A C1A C2A C3A IMPR H2A C2A C3A C4A IMPR H10 C10 C11 C4B IMPR H5A C5A C5B C9B IMPR H6A C6A C7A C8A IMPR H7A C7A C8A C9A IMPR H8A C8A C9A C9B IMPR H9A C9A C9B C5B ! To Keep carbons in pyrenyl ring planar IMPR C6A C7A C8A C9A IMPR C7A C8A C9A C9B IMPR C8A C9A C9B C5B IMPR C9A C9B C5B C6A IMPR C9B C5B C6A C7A IMPR C5B C6A C7A C8A IMPR C5A C5B C9B C10 IMPR C5B C9B C10 C11 IMPR C9B C10 C11 C4B IMPR C10 C11 C4B C5A IMPR C11 C4B C5A C5B IMPR C4B C5A C5B C9B IMPR C4A C4B C11 C1A IMPR C4B C11 C1A C2A IMPR C11 C1A C2A C3A IMPR C1A C2A C3A C4A IMPR C2A C3A C4A C4B IMPR C3A C4A C4B C11 ! To Keep anthracene rings planner with respect to each other IMPR C4C C4A C4B C11 IMPR C3B C3A C2A C1A IMPR C4C C4A C4B C5A IMPR C4C C4A C3A C3B IMPR C6A C5B C5A C4B IMPR C9A C9B C10 C11 IMPR C5A C4B C4A C3A IMPR C10 C11 C1A C2A IMPR C5A C4B C11 C1A IMPR C10 C11 C4B C4A IMPR H4C N6 C9C C4A ! STEREO AT C4C DONO H61 N6 DONO H62 N6 DONO H2' O2' DONO H1 O1 DONO HO2 O2 DONO H3 O3 ACCE N3 " " ACCE N1 " " ACCE N7 " " ACCE O1P P ACCE O2P P ACCE O2' " " ACCE O3' " " ACCE O4' " " ACCE O5' " " END {* ABA *} !========================================================================= ! RESIdue AST GROUP ATOM P TYPE=P CHARge=1.20 END ATOM O1P TYPE=O2 CHARge=-0.40 END ATOM O2P TYPE=O2 CHARge=-0.40 END ATOM O5' TYPE=OS CHARge=-0.36 END GROUP ATOM C5' TYPE=C2 CHARge=-0.070 END!" ATOM H5' TYPE=H CHARge=0.035 END!" ATOM H5'' TYPE=H CHARge=0.035 END!" GROUP ATOM C4' TYPE=CH CHARge=0.065 END! " ATOM H4' TYPE=H CHARge=0.035 END!" ATOM O4' TYPE=OS CHARge=-0.30 END ATOM C1' TYPE=CH CHARge=0.165 END!" ATOM H1' TYPE=H CHARge=0.035 END!" GROUP ATOM N9 TYPE=NS CHARge=-0.19 END ATOM C4 TYPE=CB CHARge=0.19 EXCL=( N1 ) END GROUP ATOM N3 TYPE=NC CHARge=-0.26 EXCL=( C6 ) END ATOM C2 TYPE=CE CHARge=0.225 EXCL=( C5 ) END !" ATOM H2 TYPE=H CHARge=0.035 END!" GROUP ATOM N1 TYPE=NC CHARge=-0.28 END ATOM C6 TYPE=CA CHARge=0.28 END GROUP ATOM N6 TYPE=N2 CHARGE=-0.42 END! ATOM H6 TYPE=H2 CHARge=0.21 END! GROUP ATOM CA TYPE=CT CHARge=-0.10 END ATOM HA TYPE=HA CHARge=0.21 END GROUP ATOM CB TYPE=CT CHARge=0.08 END ATOM HB' TYPE=HA CHARge=0.10 END ATOM HB'' TYPE=HA CHARge=0.10 END ATOM OB TYPE=OH CHARge=-0.68 END ATOM HOB TYPE=HO CHARge=0.40 END GROUP ATOM CJ TYPE=CP CHARge=0.03 EXCLUDE=(CP) END ATOM CO TYPE=CP CHARge=-0.16 EXCLUDE=(CM') END ATOM HO TYPE=HA CHARge=0.14 END ATOM CO' TYPE=CP CHARge=-0.16 EXCLUDE=(CM) END ATOM HO' TYPE=HA CHARge=0.14 END ATOM CM TYPE=CP CHARge=-0.15 EXCLUDE=(CO') END ATOM HM TYPE=HA CHARge=0.14 END ATOM CM' TYPE=CP CHARge=-0.15 EXCLUDE=(CO) END ATOM HM' TYPE=HA CHARge=0.14 END ATOM CP TYPE=CP CHARge=-0.15 EXCLUDE=(CJ) END ATOM HP TYPE=HA CHARge=0.14 END GROUP ATOM C5 TYPE=CB CHARge=0.02 END ATOM N7 TYPE=NB CHARge=-0.25 END ATOM C8 TYPE=CE CHARge=0.195 END!" ATOM H8 TYPE=H CHARge=0.035 END!" GROUP ATOM C2' TYPE=CH CHARge=0.115 END!" ATOM H2'' TYPE=H CHARge=0.035 END!" ATOM O2' TYPE=OH CHARge=-0.40 END ATOM H2' TYPE=HO CHARge=0.25 END GROUP ATOM C3' TYPE=CH CHARge=-0.035 END!" ATOM H3' TYPE=H CHARge=0.035 END!" GROUP ATOM O3' TYPE=OS 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 CA BOND N6 H6 BOND CA HA BOND CA CB BOND CB HB' BOND CB HB'' BOND CB OB BOND OB HOB BOND CA CJ BOND CJ CO BOND CO HO BOND CO CM BOND CM HM BOND CM CP BOND CP HP BOND CP CM' BOND CM' HM' BOND CM' CO' BOND CO' HO' BOND CO' CJ 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 IMPRoper C5 C6 N6 H6 ! 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'' ! 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' 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 CA C6 H6 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' ! 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 ! To keep H's in phenyl planar IMPR HO' CO' CM' CP IMPR HM' CM' CP CM IMPR HP CP CM CO IMPR HM CM CO CJ IMPR HO CO CJ CA ! TO Keep carbons in phenyl planar IMPR CJ CO CM CP IMPR CO CM CP CM' IMPR CM CP CM' CO' IMPR CP CM' CO' CJ IMPR CM' CO' CJ CO IMPR CO' CJ CO CM IMPR CA CJ CO CM IMPR HB' HB'' CA OB ! STEREO AT CB IMPR HA N6 CB CJ ! STEREO AT CA DIHE CO CJ CA CB DONO H61 N6 DONO H62 N6 DONO H2' O2' DONO HOB OB ACCE N3 " " ACCE N1 " " ACCE N7 " " ACCE O1P P ACCE O2P P ACCE O2' " " ACCE O3' " " ACCE O4' " " ACCE O5' " " END {* AST *} !========================================================================= RESIdue PUR GROUP ATOM P TYPE=P CHARge=1.20 END ATOM O1P TYPE=O2 CHARge=-0.40 END ATOM O2P TYPE=O2 CHARge=-0.40 END ATOM O5' TYPE=OS CHARge=-0.36 END GROUP ATOM C5' TYPE=C2 CHARge=-0.070 END!" ATOM H5' TYPE=H CHARge=0.035 END!" ATOM H5'' TYPE=H CHARge=0.035 END!" GROUP ATOM C4' TYPE=CH CHARge=0.065 END! " ATOM H4' TYPE=H CHARge=0.035 END!" ATOM O4' TYPE=OS CHARge=-0.30 END ATOM C1' TYPE=CH CHARge=0.165 END!" ATOM H1' TYPE=H CHARge=0.035 END!" GROUP ATOM N9 TYPE=NS CHARge=-0.19 END ATOM C4 TYPE=CB CHARge=0.19 EXCL=( N1 ) END GROUP ATOM N3 TYPE=NC CHARge=-0.26 EXCL=( C6 ) END ATOM C2 TYPE=CE CHARge=0.225 EXCL=( C5 ) END !" ATOM H2 TYPE=H CHARge=0.035 END!" GROUP ATOM N1 TYPE=NC CHARge=-0.28 END ATOM C6 TYPE=CE CHARge=0.28 END ATOM H6 TYPE=H CHARge= 0.035 END GROUP ATOM C5 TYPE=CB CHARge=0.02 END ATOM N7 TYPE=NB CHARge=-0.25 END ATOM C8 TYPE=CE CHARge=0.195 END!" ATOM H8 TYPE=H CHARge=0.035 END!" GROUP ATOM C2' TYPE=CH CHARge=0.115 END!" ATOM H2'' TYPE=H CHARge=0.035 END!" ATOM O2' TYPE=OH CHARge=-0.40 END ATOM H2' TYPE=HO CHARge=0.25 END GROUP ATOM C3' TYPE=CH CHARge=-0.035 END!" ATOM H3' TYPE=H CHARge=0.035 END!" GROUP ATOM O3' TYPE=OS 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'' ! 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' 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 {* removed: IMPR C6 C5 C4 N3, ATB *} IMPR C5 C4 N3 C2 IMPR H8 N7 N9 C8 IMPR H2 N1 N3 C2 !IMPR C2' C3' C1' O2' ! 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 DONO H2' O2' ACCE N3 " " ACCE N1 " " ACCE N7 " " ACCE O1P P ACCE O2P P ACCE O2' " " ACCE O3' " " ACCE O4' " " ACCE O5' " " END {* PUR *} !========================================================================= RESIdue C GROUP ATOM P TYPE=P CHARge=1.20 END ATOM O1P TYPE=O2 CHARge=-0.40 END ATOM O2P TYPE=O2 CHARge=-0.40 END ATOM O5' TYPE=OS CHARge=-0.36 END GROUP ATOM C5' TYPE=C2 CHARge=-0.070 END! rationalized ATOM H5' TYPE=H CHARge=0.035 END! " ATOM H5'' TYPE=H CHARge=0.035 END! " GROUP ATOM C4' TYPE=CH CHARge=0.065 END! " ATOM H4' TYPE=H CHARge=0.035 END!" ATOM O4' TYPE=OS CHARge=-0.30 END ATOM C1' TYPE=CH CHARge=0.165 END!" ATOM H1' TYPE=H CHARge=0.035 END!" GROUP ATOM N1 TYPE=NS CHARge=-0.19 EXCL=( C4 ) END ATOM C6 TYPE=CF CHARge=0.155 EXCL=( N3 ) END !" ATOM H6 TYPE=H CHARge=0.035 END!" GROUP ATOM C2 TYPE=C CHARge=0.30 EXCL=( C5 ) END ATOM O2 TYPE=O CHARge=-0.30 END GROUP ATOM N3 TYPE=NC CHARge=-0.28 END ATOM C4 TYPE=CA CHARge=0.28 END GROUP ATOM N4 TYPE=N2 CHARge=-0.42 END! ATOM H41 TYPE=H2 CHARge=0.21 END! ATOM H42 TYPE=H2 CHARge=0.21 END! GROUP ATOM C5 TYPE=CF CHARge=-0.035 END!" ATOM H5 TYPE=H CHARge=0.035 END!" GROUP ATOM C2' TYPE=CH CHARge=0.115 END!" ATOM H2'' TYPE=H CHARge=0.035 END!" ATOM O2' TYPE=OH CHARge=-0.40 END ATOM H2' TYPE=HO CHARge=0.25 END GROUP ATOM C3' TYPE=CH CHARge=-0.035 END!" ATOM H3' TYPE=H CHARge=0.035 END!" GROUP ATOM O3' TYPE=OS 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 IMPRoper C5 C4 N4 H41 ! 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' 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' 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' " " END {* CYT *} !======================================================================== RESIdue C+ GROUP ATOM P TYPE=P CHARge=1.20 END ATOM O1P TYPE=O2 CHARge=-0.40 END ATOM O2P TYPE=O2 CHARge=-0.40 END ATOM O5' TYPE=OS CHARge=-0.36 END GROUP ATOM C5' TYPE=C2 CHARge=-0.070 END! rationalized ATOM H5' TYPE=H CHARge=0.035 END! " ATOM H5'' TYPE=H CHARge=0.035 END! " GROUP ATOM C4' TYPE=CH CHARge=0.065 END! " ATOM H4' TYPE=H CHARge=0.035 END!" ATOM O4' TYPE=OS CHARge=-0.30 END ATOM C1' TYPE=CH CHARge=0.165 END!" ATOM H1' TYPE=H CHARge=0.035 END!" GROUP ATOM N1 TYPE=NS CHARge=-0.057 EXCL=( C4 ) END ATOM C6 TYPE=CF CHARge=0.286 EXCL=( N3 ) END !" ATOM H6 TYPE=H CHARge=0.1364 END!" GROUP ATOM C2 TYPE=C CHARge=0.4729 EXCL=( C5 ) END ATOM O2 TYPE=O CHARge=-0.2359 END GROUP ATOM N3 TYPE=NC CHARge=-0.3401 END ATOM H3 TYPE=H CHARge=0.2509 END ATOM C4 TYPE=CA CHARge=0.4445 END GROUP ATOM N4 TYPE=N2 CHARge=-0.2805 END! ATOM H41 TYPE=H2 CHARge=0.2467 END! ATOM H42 TYPE=H2 CHARge=0.2378 END! GROUP ATOM C5 TYPE=CF CHARge=-0.2929 END!" ATOM H5 TYPE=H CHARge=0.1312 END!" GROUP ATOM C2' TYPE=CH CHARge=0.115 END!" ATOM H2'' TYPE=H CHARge=0.035 END!" ATOM O2' TYPE=OH CHARge=-0.40 END ATOM H2' TYPE=HO CHARge=0.25 END GROUP ATOM C3' TYPE=CH CHARge=-0.035 END!" ATOM H3' TYPE=H CHARge=0.035 END!" GROUP ATOM O3' TYPE=OS 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 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 IMPRoper C5 C4 N4 H41 ! 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' 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' DONO H42 N4 DONO H2' O2' DONO H41 N4 DONO H3 N3 ACCE O2 C2 ACCE O1P P ACCE O2P P ACCE O2' " " ACCE O3' " " ACCE O4' " " ACCE O5' " " END {* C+ *} !======================================================================== RESIdue T GROUP ATOM P TYPE=P CHARge=1.20 END ATOM O1P TYPE=O2 CHARge=-0.40 END ATOM O2P TYPE=O2 CHARge=-0.40 END ATOM O5' TYPE=OS CHARge=-0.36 END GROUP ATOM C5' TYPE=C2 CHARge=-0.070 END! rationalized ATOM H5' TYPE=H CHARge=0.035 END! " ATOM H5'' TYPE=H CHARge=0.035 END! " GROUP ATOM C4' TYPE=CH CHARge=0.065 END! " ATOM H4' TYPE=H CHARge=0.035 END!" ATOM O4' TYPE=OS CHARge=-0.30 END ATOM C1' TYPE=CH CHARge=0.165 END!" ATOM H1' TYPE=H CHARge=0.035 END!" GROUP ATOM N1 TYPE=NS CHARge=-0.19 EXCL=( C4 ) END ATOM C6 TYPE=CF CHARge=0.155 EXCL=( N3 ) END ATOM H6 TYPE=H CHARge=0.035 END GROUP ATOM C2 TYPE=C CHARge=0.35 EXCL=( C5 ) END ATOM O2 TYPE=O CHARge=-0.35 END GROUP ATOM N3 TYPE=NA CHARge=-0.26 END ATOM H3 TYPE=H CHARge=0.26 END GROUP ATOM C4 TYPE=C CHARge=0.30 END ATOM O4 TYPE=O CHARge=-0.30 END GROUP ATOM C5 TYPE=CS CHARge=-0.035 END! THESE CHARGES ? ATOM C5A TYPE=C3 CHARge=-0.070 END!" ATOM H51 TYPE=H CHARge=0.035 END!" ATOM H52 TYPE=H CHARge=0.035 END!" ATOM H53 TYPE=H CHARge=0.035 END!" GROUP ATOM C2' TYPE=CH CHARge=0.115 END!" ATOM H2'' TYPE=H CHARge=0.035 END!" ATOM O2' TYPE=OH CHARge=-0.40 END ATOM H2' TYPE=HO CHARge=0.25 END GROUP ATOM C3' TYPE=CH CHARge=-0.035 END!" ATOM H3' TYPE=H CHARge=0.035 END!" GROUP ATOM O3' TYPE=OS 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 ! 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' 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' " " END {* THY *} !============================================================================ RESIdue URI GROUP ATOM P TYPE=P CHARge=1.20 END ATOM O1P TYPE=O2 CHARge=-0.40 END ATOM O2P TYPE=O2 CHARge=-0.40 END ATOM O5' TYPE=OS CHARge=-0.36 END GROUP ATOM C5' TYPE=C2 CHARge=-0.070 END! rationalized ATOM H5' TYPE=H CHARge=0.035 END! " ATOM H5'' TYPE=H CHARge=0.035 END! " GROUP ATOM C4' TYPE=CH CHARge=0.065 END! " ATOM H4' TYPE=H CHARge=0.035 END!" ATOM O4' TYPE=OS CHARge=-0.30 END ATOM C1' TYPE=CH CHARge=0.165 END!" ATOM H1' TYPE=H CHARge=0.035 END!" GROUP ATOM N1 TYPE=NS CHARge=-0.19 EXCL=( C4 ) END ATOM C6 TYPE=CF CHARge=0.155 EXCL=( N3 ) END ATOM H6 TYPE=H CHARge=0.035 END GROUP ATOM C2 TYPE=C CHARge=0.35 EXCL=( C5 ) END ATOM O2 TYPE=O CHARge=-0.35 END GROUP ATOM N3 TYPE=NA CHARge=-0.26 END ATOM H3 TYPE=H CHARge=0.26 END GROUP ATOM C4 TYPE=C CHARge=0.30 END ATOM O4 TYPE=O CHARge=-0.30 END GROUP ATOM C5 TYPE=CF CHARge=-0.035 END ATOM H5 TYPE=H CHARge=0.035 END GROUP ATOM C2' TYPE=CH CHARge=0.115 END!" ATOM H2'' TYPE=H CHARge=0.035 END!" ATOM O2' TYPE=OH CHARge=-0.40 END ATOM H2' TYPE=HO CHARge=0.25 END GROUP ATOM C3' TYPE=CH CHARge=-0.035 END!" ATOM H3' TYPE=H CHARge=0.035 END!" GROUP ATOM O3' TYPE=OS 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' 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' " " END {* URI *} !============================================================================ !------------------------------------------------------------------ PRESidue DEOX ! Patch to make DEOXYribose of the ribose DELETE ATOM O2' END GROUP MODIFY ATOM C2' TYPE=C2 CHARGE=-0.07 END MODIFY ATOM H2' TYPE=H CHARGE=0.035 END MODIFY ATOM H2'' TYPE=H CHARGE=0.035 END ADD BOND C2' H2' ADD ANGLE C1' C2' H2' ADD ANGLE C3' C2' H2' ADD ANGLE H2' C2' H2'' ADD DIHEDRAL O4' C1' C2' H2' 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=HO CHARGE=0.25 END !H MODIFY ATOM +O5' TYPE=OH CHARGE=-0.40 END !H MODIFY ATOM +C5' TYPE=C2 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' 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=HO CHARGE=0.15 END ADD ATOM +O5T TYPE=OH 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 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=CH CHARGE=0.115 END MODIFY ATOM -H3' TYPE=H CHARGE=0.035 END MODIFY ATOM -O3' TYPE=OH CHARGE=-0.40 END ADD ATOM -H3T TYPE=HO CHARGE=0.25 END ! ADD BOND -O3' -H3T ADD ANGLe -C3' -O3' -H3T ADD DIHEdral -C4' -C3' -O3' -H3T ADD DONOr -H3T -O3' 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 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=SD CHARGE=1.00 END END {NA} !------------------------------------------------------------------ RESIdue MG GROUp ATOM MG TYPE=MG CHARGE=2.0 END END {MG} !------------------------------------------------------------------ !------------------------------------------------------------------ PRESidue RMHB ! removes hbond donor in the backbone DELETE DONOR H2' O2' END PRESidue UNPR ! removes hydrogen bond acceptors and donors in ! unpaired base DELETE DONOR H21 N2 DELETE DONOR H21 N2 DELETE DONOR H22 N2 DELETE DONOR H1 N1 DELETE DONO H61 N6 DELETE DONO H62 N6 DELETE DONO H42 N4 DELETE DONO H41 N4 DELETE DONO H3 N3 DELETE ACCEPTOR O6 C6 DELETE ACCEPTOR N3 " " DELETE ACCEPTOR N7 " " DELETE ACCEPTOR N1 " " DELETE ACCEPTOR O2 C2 DELETE ACCEPTOR O4 C4
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