* TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19 * 20 1 ! Version number !references !Reiher, III., W.E. Theoretical Studies of Hydrogen Bonding, Ph.D. !Thesis, Department of Chemistry, Harvard University, Cambridge, MA, !USA, 1985 ! !and ! !Neria, E., Fischer, S., and Karplus, M. Simulation of Activation Free !Energies in Molecular Systems, Journal of Chemical Physics, 1996, 105: !1902-21. MASS 1 H 1.00800 ! hydrogen which can h-bond to neutral atom MASS 2 HC 1.00800 ! - " - charged atom MASS 3 HA 1.00800 ! aliphatic hydrogen MASS 4 HT 1.00800 ! TIPS3P WATER HYDROGEN MASS 5 LP 0.0 ! ST2 LONE PAIR MASS 10 CT 12.01100 ! aliphatic carbon MASS 11 C 12.01100 ! carbonyl carbon MASS 12 CH1E 13.01900 ! extended atom carbon w/ one hydrogen MASS 13 CH2E 14.02700 ! - " - two MASS 14 CH3E 15.03500 ! - " - three MASS 15 CR1E 13.01900 ! - " - in aromatic ring w/ one H MASS 16 CM 12.01100 ! carbon in carbonmonoxide MASS 31 N 14.00670 ! peptide nitrogen with no hydrogens attached MASS 32 NR 14.00670 ! nitrogen in aromatic ring with no hydrogens MASS 33 NP 14.00670 ! pyrole nitrogen !MASS 34 NH1E 15.01470 ! extended atom peptide nitrogen with one hydrogen !MASS 35 NH2E 16.02270 ! - " - two -"- !MASS 36 NH3E 17.03070 ! - " - three -"- !MASS 37 NC2E 16.02270 ! extended atom charged guanidinium nitrogen w/ 2 H MASS 38 NH1 14.00670 ! peptide nitrogen bound to one hydrogen MASS 39 NH2 14.00670 ! - " - two -"- MASS 40 NH3 14.00670 ! nitrogen bound to three hydrogens MASS 41 NC2 14.00670 ! charged guanidinuim nitrogen bound to two hydrogens MASS 51 O 15.99940 ! carbonyl oxygen MASS 52 OC 15.99940 ! carboxy oxygen !MASS 53 OH1E 17.00740 ! extended atom hydroxy oxygen !MASS 54 OH2E 18.01540 ! extended atom water MASS 55 OH1 15.99940 ! hydroxy oxygen MASS 56 OH2 15.99940 ! ST2 water oxygen MASS 57 OM 15.99940 ! oxygen in carbonmonoxide MASS 58 OT 15.99940 ! TIPS3P WATER OXYGEN MASS 59 OS 15.99940 ! ester oxygen MASS 81 S 32.06000 ! sulphur MASS 82 SH1E 33.06800 ! extended atom sulphur with one hydrogen MASS 91 FE 55.84700 ! iron DECL -C DECL -O DECL +N DECL +H DECL +CA AUTOGENERATE ANGLES DEFA FIRS NTER LAST CTER RESI ALA 0.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH3E 0.00 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB DIHE -C N CA C N CA C +N CA C +N +CA IMPH N -C CA H C CA +N O CA N C CB DONO H N ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 RESI ARG 1.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH2E 0.00 ATOM CG CH2E 0.00 GROU ATOM CD CH2E 0.10 ATOM NE NH1 -0.40 ATOM HE H 0.30 ATOM CZ C 0.50 GROU ATOM NH1 NC2 -0.45 ATOM HH11 HC 0.35 ATOM HH12 HC 0.35 GROU ATOM NH2 NC2 -0.45 ATOM HH21 HC 0.35 ATOM HH22 HC 0.35 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB CB CG CG CD CD NE NE HE BOND NE CZ CZ NH1 CZ NH2 NH1 HH11 NH1 HH12 BOND NH2 HH21 NH2 HH22 DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB CG CA CB CG CD CB CG CD NE DIHE CG CD NE CZ CD NE CZ NH1 NE CZ NH1 HH11 DIHE NE CZ NH2 HH21 NE CZ NH1 HH12 NE CZ NH2 HH22 IMPH N -C CA H C CA +N O CA N C CB IMPH NE CD CZ HE CZ NH1 NH2 NE DONO H N DONO HE NE DONO HH11 NH1 DONO HH12 NH1 DONO HH21 NH2 DONO HH22 NH2 ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 IC CA CB CG CD 0.0000 0.00 180.00 0.00 0.0000 IC CB CG CD NE 0.0000 0.00 180.00 0.00 0.0000 IC CG CD NE CZ 0.0000 0.00 180.00 0.00 0.0000 IC CD NE CZ NH1 0.0000 0.00 180.00 0.00 0.0000 IC NH1 NE *CZ NH2 0.0000 0.00 180.00 0.00 0.0000 IC CD CZ *NE HE 0.0000 0.00 180.00 0.00 0.0000 IC NE CZ NH1 HH11 0.0000 0.00 180.00 0.00 0.0000 IC HH11 CZ *NH1 HH12 0.0000 0.00 180.00 0.00 0.0000 IC NE CZ NH2 HH21 0.0000 0.00 180.00 0.00 0.0000 IC HH21 CZ *NH2 HH22 0.0000 0.00 180.00 0.00 0.0000 RESI ASN 0.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH2E 0.00 GROU ATOM CG C 0.55 ATOM OD1 O -0.55 GROU ATOM ND2 NH2 -0.60 ATOM HD21 H 0.30 ATOM HD22 H 0.30 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB CB CG CG OD1 CG ND2 ND2 HD21 BOND ND2 HD22 DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB CG CA CB CG OD1 CB CG ND2 HD21 IMPH N -C CA H C CA +N O CA N C CB IMPH CG OD1 ND2 CB ND2 HD21 HD22 CG DONO H N DONO HD21 ND2 DONO HD22 ND2 ACCE OD1 CG ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 IC CA CB CG OD1 0.0000 0.00 180.00 0.00 0.0000 IC OD1 CB *CG ND2 0.0000 0.00 180.00 0.00 0.0000 IC OD1 CG ND2 HD21 0.0000 0.00 180.00 0.00 0.0000 IC HD21 CG *ND2 HD22 0.0000 0.00 180.00 0.00 0.0000 RESI ASP -1.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH2E -0.16 ATOM CG C 0.36 ATOM OD1 OC -0.60 ATOM OD2 OC -0.60 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB CB CG CG OD1 CG OD2 DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB CG CA CB CG OD1 IMPH N -C CA H C CA +N O CA N C CB IMPH CG OD1 OD2 CB DONO H N ACCE OD1 CG ACCE OD2 CG ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 IC CA CB CG OD1 0.0000 0.00 180.00 0.00 0.0000 IC OD1 CB *CG OD2 0.0000 0.00 180.00 0.00 0.0000 RESI CYS 0.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH2E 0.19 ATOM SG SH1E -0.19 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB CB SG DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB SG IMPH N -C CA H C CA +N O CA N C CB DONO H N ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB SG 0.0000 0.00 180.00 0.00 0.0000 RESI GLN 0.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH2E 0.00 ATOM CG CH2E 0.00 GROU ATOM CD C 0.55 ATOM OE1 O -0.55 GROU ATOM NE2 NH2 -0.60 ATOM HE21 H 0.30 ATOM HE22 H 0.30 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB CB CG CG CD CD OE1 CD NE2 BOND NE2 HE21 NE2 HE22 DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB CG CA CB CG CD CB CG CD OE1 DIHE CG CD NE2 HE21 IMPH N -C CA H C CA +N O CA N C CB IMPH CD OE1 NE2 CG NE2 HE21 HE22 CD DONO H N DONO HE21 NE2 DONO HE22 NE2 ACCE OE1 CD ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 IC CA CB CG CD 0.0000 0.00 180.00 0.00 0.0000 IC CB CG CD OE1 0.0000 0.00 180.00 0.00 0.0000 IC OE1 CG *CD NE2 0.0000 0.00 180.00 0.00 0.0000 IC OE1 CD NE2 HE21 0.0000 0.00 180.00 0.00 0.0000 IC HE21 CD *NE2 HE22 0.0000 0.00 180.00 0.00 0.0000 RESI GLU -1.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH2E 0.00 GROU ATOM CG CH2E -0.16 ATOM CD C 0.36 ATOM OE1 OC -0.60 ATOM OE2 OC -0.60 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB CB CG CG CD CD OE1 CD OE2 DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB CG CA CB CG CD CB CG CD OE1 IMPH N -C CA H C CA +N O CA N C CB IMPH CD OE1 OE2 CG DONO H N ACCE OE1 CD ACCE OE2 CD ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 IC CA CB CG CD 0.0000 0.00 180.00 0.00 0.0000 IC CB CG CD OE1 0.0000 0.00 180.00 0.00 0.0000 IC OE1 CG *CD OE2 0.0000 0.00 180.00 0.00 0.0000 RESI GLY 0.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH2E 0.10 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H DIHE -C N CA C N CA C +N CA C +N +CA IMPH N -C CA H C CA +N O DONO H N ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 PATC FIRS GLYP RESI HIS 0.00000 ! Rings charges from Del Bene and Cohen GROU ! JACS 100:5285 (1978) Imidazole sto-3g calc. ATOM N NH1 -0.35 ! Note that this residue has non-neutral groups. ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH2E 0.00 GROUP ATOM CG C 0.10 ATOM ND1 NH1 -0.40 ATOM HD1 H 0.30 GROU ATOM CD2 CR1E 0.10 ATOM NE2 NR -0.40 ATOM CE1 CR1E 0.30 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB CB CG CG ND1 CG CD2 ND1 HD1 BOND ND1 CE1 CD2 NE2 CE1 NE2 DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB CG CA CB CG ND1 IMPH N -C CA H C CA +N O CA N C CB IMPH CG ND1 CD2 CB ND1 CG CE1 HD1 CG ND1 CE1 NE2 IMPH ND1 CE1 NE2 CD2 CE1 NE2 CD2 CG NE2 CD2 CG ND1 IMPH CD2 CG ND1 CE1 DONO H N DONO HD1 ND1 ACCE NE2 ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 IC CA CB CG CD2 0.0000 0.00 90.00 0.00 0.0000 IC CD2 CB *CG ND1 0.0000 0.00 180.00 0.00 0.0000 IC CD2 CG ND1 CE1 0.0000 0.00 0.00 0.00 0.0000 IC ND1 CG CD2 NE2 0.0000 0.00 0.00 0.00 0.0000 IC CE1 CG *ND1 HD1 0.0000 0.00 180.00 0.00 0.0000 RESI HSD 0.00000 ! see HIS above. GROUP ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH2E 0.00 GROUP ATOM CG C 0.10 ATOM ND1 NR -0.40 ATOM CE1 CR1E 0.30 GROU ATOM CD2 CR1E 0.10 ATOM NE2 NH1 -0.40 ATOM HE2 H 0.30 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB CB CG CG ND1 CG CD2 ND1 CE1 BOND CD2 NE2 CE1 NE2 NE2 HE2 DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB CG CA CB CG ND1 IMPH N -C CA H C CA +N O CA N C CB IMPH CG ND1 CD2 CB NE2 CE1 CD2 HE2 CG ND1 CE1 NE2 IMPH ND1 CE1 NE2 CD2 CE1 NE2 CD2 CG NE2 CD2 CG ND1 IMPH CD2 CG ND1 CE1 DONO H N DONO HE2 NE2 ACCE ND1 ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 IC CA CB CG CD2 0.0000 0.00 90.00 0.00 0.0000 IC CD2 CB *CG ND1 0.0000 0.00 180.00 0.00 0.0000 IC CD2 CG ND1 CE1 0.0000 0.00 0.00 0.00 0.0000 IC ND1 CG CD2 NE2 0.0000 0.00 0.00 0.00 0.0000 IC CE1 CD2 *NE2 HE2 0.0000 0.00 180.00 0.00 0.0000 RESI HSC 1.00000 ! Doubly protonated histidine. Ring charges GROU ATOM N NH1 -0.35 ! Hayes and Kollman jacs 98:3335 (1976). ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH2E 0.10 ATOM CG C 0.15 ATOM CD2 CR1E 0.20 GROU ATOM ND1 NH1 -0.30 ATOM HD1 H 0.35 GROU ATOM CE1 CR1E 0.45 GROU ATOM NE2 NH1 -0.30 ATOM HE2 H 0.35 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB CB CG CG ND1 CG CD2 ND1 HD1 BOND ND1 CE1 CD2 NE2 CE1 NE2 NE2 HE2 DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB CG CA CB CG ND1 IMPH N -C CA H C CA +N O CA N C CB IMPH CG ND1 CD2 CB ND1 CG CE1 HD1 CG ND1 CE1 NE2 IMPH ND1 CE1 NE2 CD2 CE1 NE2 CD2 CG NE2 CD2 CG ND1 IMPH CD2 CG ND1 CE1 NE2 CD2 CE1 HE2 DONO H N DONO HD1 ND1 DONO HE2 NE2 ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 IC CA CB CG CD2 0.0000 0.00 90.00 0.00 0.0000 IC CD2 CB *CG ND1 0.0000 0.00 180.00 0.00 0.0000 IC CD2 CG ND1 CE1 0.0000 0.00 0.00 0.00 0.0000 IC ND1 CG CD2 NE2 0.0000 0.00 0.00 0.00 0.0000 IC CE1 CG *ND1 HD1 0.0000 0.00 180.00 0.00 0.0000 IC CE1 CD2 *NE2 HE2 0.0000 0.00 180.00 0.00 0.0000 RESI ILE 0.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH1E 0.00 ATOM CG2 CH3E 0.00 GROU ATOM CG1 CH2E 0.00 ATOM CD CH3E 0.00 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB CB CG1 CB CG2 CG1 CD DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB CG1 CA CB CG1 CD IMPH N -C CA H C CA +N O CA N C CB IMPH CB CG1 CG2 CA DONO H N ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB CG1 0.0000 0.00 180.00 0.00 0.0000 IC CA CB CG1 CD 0.0000 0.00 180.00 0.00 0.0000 IC CG1 CA *CB CG2 0.0000 0.00 -120.00 0.00 0.0000 RESI LEU 0.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH2E 0.00 ATOM CG CH1E 0.00 ATOM CD1 CH3E 0.00 ATOM CD2 CH3E 0.00 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB CB CG CG CD1 CG CD2 DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB CG CA CB CG CD2 IMPH N -C CA H C CA +N O CA N C CB IMPH CG CD2 CD1 CB DONO H N ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 IC CA CB CG CD1 0.0000 0.00 180.00 0.00 0.0000 IC CD1 CB *CG CD2 0.0000 0.00 120.00 0.00 0.0000 RESI LYS 1.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH2E 0.00 ATOM CG CH2E 0.00 ATOM CD CH2E 0.00 GROU ATOM CE CH2E 0.25 ATOM NZ NH3 -0.30 ATOM HZ1 HC 0.35 ATOM HZ2 HC 0.35 ATOM HZ3 HC 0.35 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB CB CG CG CD CD CE CE NZ BOND NZ HZ1 NZ HZ2 NZ HZ3 DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB CG CA CB CG CD CB CG CD CE DIHE CG CD CE NZ CD CE NZ HZ1 CD CE NZ HZ2 DIHE CD CE NZ HZ3 IMPH N -C CA H C CA +N O CA N C CB DONO H N DONO HZ1 NZ DONO HZ2 NZ DONO HZ3 NZ ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 IC CA CB CG CD 0.0000 0.00 180.00 0.00 0.0000 IC CB CG CD CE 0.0000 0.00 180.00 0.00 0.0000 IC CG CD CE NZ 0.0000 0.00 180.00 0.00 0.0000 IC CD CE NZ HZ1 0.0000 0.00 180.00 0.00 0.0000 IC HZ1 CE *NZ HZ2 0.0000 0.00 120.00 0.00 0.0000 IC HZ2 CE *NZ HZ3 0.0000 0.00 120.00 0.00 0.0000 RESI MET 0.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH2E 0.00 GROU ATOM CG CH2E 0.06 ATOM SD S -0.12 ATOM CE CH3E 0.06 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB CB CG CG SD SD CE DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB CG CA CB CG SD CB CG SD CE IMPH N -C CA H C CA +N O CA N C CB DONO H N ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 IC CA CB CG SD 0.0000 0.00 180.00 0.00 0.0000 IC CB CG SD CE 0.0000 0.00 180.00 0.00 0.0000 ! Penicillamine RESI PEN 0.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CT 0.19 ATOM CG1 CH3E 0.0 ATOM CG2 CH3E 0.0 ATOM SG SH1E -0.19 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB CB SG CB CG1 CB CG2 DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB SG IMPH N -C CA H C CA +N O CA N C CB DONO H N ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB SG 0.0000 0.00 180.00 0.00 0.0000 IC SG CA *CB CG1 0.0000 0.00 120.00 0.00 0.0000 IC SG CA *CB CG2 0.0000 0.00 -120.00 0.00 0.0000 RESI PHE 0.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH2E 0.00 ATOM CG C 0.00 CZ ATOM CD1 CR1E 0.00 CE2 ATOM CD2 CR1E 0.00 CE1 GROU ATOM CE1 CR1E 0.00 ATOM CE2 CR1E 0.00 ATOM CZ CR1E 0.00 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB CB CG CG CD1 CG CD2 CD1 CE1 BOND CD2 CE2 CE1 CZ CE2 CZ DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB CG CA CB CG CD1 IMPH N -C CA H C CA +N O CA N C CB IMPH CG CD1 CE1 CZ CD1 CE1 CZ CE2 CE1 CZ CE2 CD2 IMPH CZ CE2 CD2 CG CE2 CD2 CG CD1 CD2 CG CD1 CE1 IMPH CG CD1 CD2 CB DONO H N ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 IC CA CB CG CD1 0.0000 0.00 90.00 0.00 0.0000 IC CD1 CB *CG CD2 0.0000 120.00 180.00 120.00 0.0000 IC CD1 CG CD2 CE2 0.0000 120.00 0.00 120.00 0.0000 IC CD2 CG CD1 CE1 0.0000 120.00 0.00 120.00 0.0000 IC CG CD1 CE1 CZ 0.0000 120.00 0.00 120.00 0.0000 RESI PRO 0.00000 GROU ATOM N N -0.20 ATOM CD CH2E 0.10 ATOM CA CH1E 0.10 GROU ATOM CB CH2E 0.00 ATOM CG CH2E 0.00 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N CD BOND CA CB CB CG CG CD DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB CG CA CB CG CD CB CG CD N DIHE CG CD N CA IMPH N CA CD -C C CA +N O CA N C CB ACCE O C IC -C CA *N CD 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 -60.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC C N *CA CB 0.0000 0.00 -120.00 0.00 0.0000 IC N CA CB CG 0.0000 0.00 0.00 108.00 0.0000 PATC FIRS PROP RESI SER 0.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH2E 0.25 ATOM OG OH1 -0.65 ATOM HG H 0.40 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB CB OG OG HG DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB OG CA CB OG HG IMPH N -C CA H C CA +N O CA N C CB DONO H N DONO HG OG ACCE OG ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB OG 0.0000 0.00 180.00 0.00 0.0000 IC CA CB OG HG 0.0000 0.00 180.00 0.00 0.0000 RESI THR 0.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH1E 0.25 ATOM OG1 OH1 -0.65 ATOM HG1 H 0.40 GROU ATOM CG2 CH3E 0.00 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB CB OG1 CB CG2 OG1 HG1 DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB OG1 CA CB OG1 HG1 IMPH N -C CA H C CA +N O CA N C CB IMPH CB OG1 CG2 CA DONO H N DONO HG1 OG1 ACCE OG1 ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB OG1 0.0000 0.00 180.00 0.00 0.0000 IC OG1 CA *CB CG2 0.0000 0.00 -120.00 0.00 0.0000 IC CA CB OG1 HG1 0.0000 0.00 180.00 0.00 0.0000 RESI TRP 0.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH2E 0.00 GROU ATOM CG C -0.03 CD1 CD2 NE1 CE2 CE3 CZ2 CZ3 CH2 ATOM CD2 C 0.10 NE1 CE2 CE3 CZ2 CZ3 CH2 ATOM CE2 C -0.04 CE3 CZ2 CZ3 CH2 ATOM CE3 CR1E -0.03 CZ2 CZ3 CH2 GROU ATOM CD1 CR1E 0.06 CD2 NE1 CE2 CE3 CZ2 CZ3 CH2 ATOM NE1 NH1 -0.36 CE2 CE3 CZ2 CZ3 CH2 ATOM HE1 H 0.30 GROU ATOM CZ2 CR1E 0.00 CZ3 CH2 ATOM CZ3 CR1E 0.00 CH2 ATOM CH2 CR1E 0.00 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB CB CG CG CD1 CG CD2 CD1 NE1 BOND CD2 CE2 NE1 HE1 NE1 CE2 CD2 CE3 CE2 CZ2 BOND CE3 CZ3 CZ2 CH2 CZ3 CH2 ! The ring angles are only assigned for the five and six member rings. ! The angles CG CD2 CE3 and NE1 CE2 CZ2 are left out to avoid conflicts ! with the histidine angle parameters and to preserve symmetry. DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB CG CA CB CG CD1 ! The following dihedrals span the rings and keep them parallel. DIHE CD1 CE2 CD2 CZ3 CD1 CD2 CE2 CH2 DIHE CZ2 CE2 CD2 CG CE3 CD2 CE2 NE1 IMPH N -C CA H C CA +N O CA N C CB IMPH CG CD1 CD2 CB NE1 CD1 CE2 HE1 CD2 CE2 CZ2 CH2 IMPH CE2 CZ2 CH2 CZ3 CZ2 CH2 CZ3 CE3 CH2 CZ3 CE3 CD2 IMPH CZ3 CE3 CD2 CE2 CE3 CD2 CE2 CZ2 CG CD1 NE1 CE2 IMPH CD1 NE1 CE2 CD2 NE1 CE2 CD2 CG CE2 CD2 CG CD1 IMPH CD2 CG CD1 NE1 ! These impropers are skipped IMPH CD2 CG CE3 CE2 CE2 CZ2 NE1 CD2 ! because the rings are kept flat by the proper dihedrals noted above. DONO H N DONO HE1 NE1 ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 IC CA CB CG CD2 0.0000 0.00 90.00 127.45 1.3673 IC CD2 CB *CG CD1 1.3673 127.45 180.00 121.78 1.3815 IC CD1 CG CD2 CE2 1.3815 110.77 0.00 102.51 1.3551 IC CD2 CG CD1 NE1 1.3673 110.77 0.00 106.30 1.3203 IC CE2 CD1 *NE1 HE1 1.3374 108.05 180.00 125.46 0.9802 IC CE2 CG *CD2 CE3 1.3551 102.51 180.00 134.73 1.3728 IC CE2 CD2 CE3 CZ3 1.3551 122.76 0.00 115.22 1.3882 IC CE3 CD2 CE2 CZ2 1.3728 122.76 0.00 123.56 1.3712 IC CD2 CE2 CZ2 CH2 1.3551 123.56 0.00 114.96 1.3877 RESI TYR 0.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH2E 0.00 ATOM CG C 0.00 CZ GROU ATOM CD1 CR1E 0.00 CE2 ATOM CE1 CR1E 0.00 CD2 GROU ATOM CD2 CR1E 0.00 ATOM CE2 CR1E 0.00 GROU ATOM CZ C 0.25 ATOM OH OH1 -0.65 ATOM HH H 0.40 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB CB CG CG CD1 CG CD2 CD1 CE1 BOND CD2 CE2 CE1 CZ CE2 CZ CZ OH OH HH DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB CG CA CB CG CD1 CE2 CZ OH HH IMPH N -C CA H C CA +N O CA N C CB IMPH CG CD1 CD2 CB CZ CE1 CE2 OH CG CD1 CE1 CZ IMPH CD1 CE1 CZ CE2 CE1 CZ CE2 CD2 CZ CE2 CD2 CG IMPH CE2 CD2 CG CD1 CD2 CG CD1 CE1 DONO H N DONO HH OH ACCE OH ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB CG 0.0000 0.00 180.00 0.00 0.0000 IC CA CB CG CD1 0.0000 0.00 90.00 0.00 0.0000 IC CD1 CB *CG CD2 0.0000 120.00 180.00 120.00 0.0000 IC CD2 CG CD1 CE1 0.0000 120.00 0.00 120.00 0.0000 IC CD1 CG CD2 CE2 0.0000 120.00 0.00 120.00 0.0000 IC CG CD1 CE1 CZ 0.0000 120.00 0.00 120.00 0.0000 IC CE2 CE1 *CZ OH 0.0000 120.00 180.00 120.00 0.0000 IC CE1 CZ OH HH 0.0000 120.00 180.00 0.00 0.0000 RESI VAL 0.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH1E 0.10 GROU ATOM CB CH1E 0.00 ATOM CG1 CH3E 0.00 ATOM CG2 CH3E 0.00 GROU ATOM C C 0.55 ATOM O O -0.55 BOND N CA CA C C +N C O N H BOND CA CB CB CG1 CB CG2 DIHE -C N CA C N CA C +N CA C +N +CA DIHE N CA CB CG1 IMPH N -C CA H C CA +N O CA N C CB IMPH CB CG2 CG1 CA DONO H N ACCE O C IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 IC -C N CA C 0.0000 0.00 180.00 0.00 0.0000 IC N CA C +N 0.0000 0.00 180.00 0.00 0.0000 IC +N CA *C O 0.0000 0.00 180.00 0.00 0.0000 IC CA C +N +CA 0.0000 0.00 180.00 0.00 0.0000 IC N C *CA CB 0.0000 0.00 120.00 0.00 0.0000 IC N CA CB CG1 0.0000 0.00 180.00 0.00 0.0000 IC CG1 CA *CB CG2 0.0000 0.00 120.00 0.00 0.0000 RESI HEME -2.00000 GROU ATOM FE FE 0.24 ATOM NA NP -0.18 ATOM NB NP -0.18 ATOM NC NP -0.18 ATOM ND NP -0.18 GROU ATOM C1A C 0.03 ATOM CHA CR1E 0.04 ATOM C4D C 0.02 GROU ATOM C1B C 0.03 ATOM CHB CR1E 0.04 ATOM C4A C 0.02 GROU ATOM C1C C 0.03 ATOM CHC CR1E 0.04 ATOM C4B C 0.02 GROU ATOM C1D C 0.03 ATOM CHD CR1E 0.04 ATOM C4C C 0.02 GROU ATOM C2A C -0.02 ATOM CAA CH2E 0.04 GROU ATOM C3A C 0.02 ATOM CMA CH3E -0.04 GROU ATOM CBA CH2E -0.10 ATOM CGA C 0.30 ATOM O1A OC -0.50 ATOM O2A OC -0.50 GROU ATOM C2B C 0.02 ATOM CMB CH3E -0.04 GROU ATOM C3B C -0.05 ATOM CAB CR1E 0.03 ATOM CBB CH2E -0.10 GROU ATOM C2C C 0.02 ATOM CMC CH3E -0.04 GROU ATOM C3C C -0.05 ATOM CAC CR1E 0.03 ATOM CBC CH2E -0.10 GROU ATOM C2D C 0.02 ATOM CMD CH3E -0.04 GROU ATOM C3D C -0.02 ATOM CAD CH2E 0.04 GROU ATOM CBD CH2E -0.10 ATOM CGD C 0.30 ATOM O1D OC -0.50 ATOM O2D OC -0.50 BOND FE NA FE NB FE NC FE ND NA C1A BOND C1A C2A C2A C3A C3A C4A NA C4A C2A CAA BOND CAA CBA CBA CGA CGA O1A CGA O2A C3A CMA BOND CHB C4A CHB C1B NB C1B C1B C2B C2B C3B BOND C3B C4B NB C4B C2B CMB C3B CAB CAB CBB BOND CHC C4B CHC C1C NC C1C C1C C2C C2C C3C BOND C3C C4C NC C4C C2C CMC C3C CAC CAC CBC BOND CHD C4C CHD C1D ND C1D C1D C2D C2D C3D BOND C3D C4D ND C4D C2D CMD C3D CAD CAD CBD BOND CBD CGD CGD O1D CGD O2D CHA C4D CHA C1A DIHE NA C4A CHB C1B C4A CHB C1B NB NB C4B CHC C1C DIHE C4B CHC C1C NC NC C4C CHD C1D C4C CHD C1D ND DIHE ND C4D CHA C1A C4D CHA C1A NA C1A C2A CAA CBA DIHE C2A CAA CBA CGA CAA CBA CGA O1A C2B C3B CAB CBB DIHE C2C C3C CAC CBC C2D C3D CAD CBD C3D CAD CBD CGD DIHE CAD CBD CGD O1D IMPH FE C1A C4A NA FE C1B C4B NB FE C1C C4C NC IMPH FE C1D C4D ND CHA NA C2A C1A CHB NA C3A C4A IMPH CHB NB C2B C1B CHC NB C3B C4B CHC NC C2C C1C IMPH CHD NC C3C C4C CHD ND C2D C1D CHA ND C3D C4D IMPH C2A C1A C3A CAA C3A C2A C4A CMA C2B C1B C3B CMB IMPH C3B C2B C4B CAB C2C C1C C3C CMC C3C C2C C4C CAC IMPH C2D C1D C3D CMD C3D C2D C4D CAD CBA O1A O2A CGA IMPH CBD O1D O2D CGD ACCE NA ACCE O1A CGA ACCE O2A CGA ACCE NB ACCE NC ACCE ND ACCE O1D CGD ACCE O2D CGD PATC FIRS NONE LAST NONE RESI ACE 0.00000 ! Acetyl blocking group with standard naming. GROU ATOM CH3 CH3E 0.00 GROU ATOM C C 0.55 ATOM O O -0.55 BOND CH3 C C +N C O DIHE CH3 C +N +CA IMPH C CH3 +N O ACCE O C IC +N CH3 *C O 0.0000 0.00 180.00 0.00 0.0000 IC CH3 C +N +CA 0.0000 0.00 180.00 0.00 0.0000 PATC FIRS NONE LAST NONE ! ! formamide. Charges according to Reiher (from States?) RESI FORM 0.00000 GROU ATOM HA HA 0.00 GROU ATOM C C 0.55 ATOM O O -0.55 GROU ATOM N NH2 -0.60 ATOM H1 H 0.30 ATOM H2 H 0.30 BOND HA C C N C O BOND N H2 N H1 DIHE HA C N H2 IMPH C HA N O IMPH N C H2 H1 ACCE O C DONO H1 N IC N HA *C O 0.0000 0.00 180.00 0.00 0.0000 IC HA C N H2 0.0000 0.00 180.00 0.00 0.0000 IC C H2 *N H1 0.0000 0.00 180.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI AMN 0.00000 GROU ATOM CL CH3E 0.00 GROU ATOM C C 0.55 ATOM O O -0.55 BOND CL C C +N C O DIHE CL C +N +CA IMPH C CL +N O ACCE O C IC +N CL *C O 0.0000 0.00 180.00 0.00 0.0000 IC CL C +N +CA 0.0000 0.00 180.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI CBX 0.00000 GROU ATOM N NH1 -0.35 ATOM H H 0.25 ATOM CA CH3E 0.10 BOND N CA N H IMPH N -C CA H DONO H N IC -C CA *N H 0.0000 0.00 180.00 0.00 0.0000 PATC FIRS NONE LAST NONE PRES CT2 0.00 ! amidated C-terminus GROUP ! use in generate statement ATOM C C 0.55 ! ATOM O O -0.55 ! | GROUP ! O=C ATOM NT NH2 -0.62 ! | ATOM HT1 H 0.32 ! NT ATOM HT2 H 0.30 ! / \ BOND C NT ! HT1 HT2 BOND NT HT1 NT HT2 ! DIHE CA C NT HT2 ! (HT1 is cis to O) IMPR C NT CA O C CA NT O IMPR NT C HT1 HT2 NT C HT2 HT1 DONOR HT1 NT DONOR HT2 NT IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA C NT HT1 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT1 C *NT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 PRES NTER 1.00000 GROU ATOM HT1 HC 0.35 ATOM HT2 HC 0.35 ATOM N NH3 -0.30 ATOM HT3 HC 0.35 DELETE ATOM H ATOM CA CH1E 0.25 BOND HT1 N HT2 N HT3 N DIHE HT2 N CA C HT1 N CA C HT3 N CA C DONO HT1 N DONO HT2 N DONO HT3 N IC HT1 N CA C 0.0000 0.00 180.00 0.00 0.0000 IC HT2 CA *N HT1 0.0000 0.00 120.00 0.00 0.0000 IC HT3 CA *N HT2 0.0000 0.00 120.00 0.00 0.0000 PRES GLYP 1.00000 GROUP ATOM HT1 HC 0.35 ATOM HT2 HC 0.35 ATOM N NH3 -0.30 ATOM HT3 HC 0.35 DELETE ATOM H ATOM CA CH2E 0.25 BOND HT1 N HT2 N HT3 N DIHE HT2 N CA C HT1 N CA C HT3 N CA C DONO HT1 N DONO HT2 N DONO HT3 N IC HT1 N CA C 0.0000 0.00 180.00 0.00 0.0000 IC HT2 CA *N HT1 0.0000 0.00 120.00 0.00 0.0000 IC HT3 CA *N HT2 0.0000 0.00 120.00 0.00 0.0000 PRES PROP 1.00000 GROUP ATOM HT1 HC 0.35 ATOM HT2 HC 0.35 ATOM N NH3 -0.20 ATOM CD CH2E 0.25 ATOM CA CH1E 0.25 BOND HT1 N HT2 N DIHE HT2 N CA C HT1 N CA C DONO HT1 N DONO HT2 N IC HT1 CA *N CD 0.0000 0.00 120.00 0.00 0.0000 IC HT2 CA *N HT1 0.0000 0.00 120.00 0.00 0.0000 PRES CTER -1.00000 GROU ATOM C C 0.14 ATOM OT1 OC -0.57 ATOM OT2 OC -0.57 DELETE ATOM O BOND C OT1 C OT2 DIHE N CA C OT2 IMPH C CA OT2 OT1 ACCE OT1 C ACCE OT2 C IC N CA C OT2 0.0 0.0 180.0 0.0 0.0 IC OT2 CA *C OT1 0.0 0.0 180.0 0.0 0.0 PRES LINK 0.0 ! linkage for IMAGES or for joining segments ! 1 refers to previous (N terminal), 2 refers to next (C terminal) BOND 1C 2N THET 1C 2N 2CA 1CA 1C 2N THET 1O 1C 2N 1C 2N 2H DIHE 1C 2N 2CA 2C 1N 1CA 1C 2N 1CA 1C 2N 2CA IMPH 2N 1C 2CA 2H 1C 1CA 2N 1O IC 1N 1CA 1C 2N 0.0000 0.00 180.00 0.00 0.0000 IC 2N 1CA *1C 1O 0.0000 0.00 180.00 0.00 0.0000 IC 1CA 1C 2N 2CA 0.0000 0.00 180.00 0.00 0.0000 IC 1C 2N 2CA 2C 0.0000 0.00 180.00 0.00 0.0000 IC 1C 2CA *2N 2H 0.0000 0.00 180.00 0.00 0.0000 RESI O2 0.00000 GROUP ATOM O1 OM 0.021 ATOM O2 OM -0.021 BOND O1 O2 PATC FIRS NONE LAST NONE RESI CO2P 0.00000 GROUP ATOM C CM 0.021 ATOM O OM -0.021 BOND C O PATC FIRS NONE LAST NONE RESI CO 0.00000 GROUP ATOM C CM 0.021 ATOM O OM -0.021 BOND C O PATC FIRS NONE LAST NONE RESI ETH 0.00000 GROU ATOM C2 CH3E 0.00 GROU ATOM C1 CH2E 0.25 ATOM O OH1 -0.65 ATOM H H 0.40 BOND C2 C1 C1 O O H DIHE C2 C1 O H DONO H O ACCE O IC C2 C1 O H 0.0000 0.00 180.00 0.00 0.0000 IC C1 O H BLNK 0.0000 0.00 0.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI ST2 .000 ! NOW INCLUDES THE LONE PAIRS GIVING 5 ATOMS FOR ST2 GROUP ATOM OX2 OH2 .00 ATOM HX1 H .24 ATOM HX2 H .24 ATOM LX1 LP -.24 ATOM LX2 LP -.24 BOND OX2 HX1 OX2 HX2 BOND OX2 LX1 OX2 LX2 ! NOTE: NO DONORS OR ACCEPTORS FOR ST2 PATC FIRS NONE LAST NONE RESI TIP3 .000 ! TIPS3P WATER MODEL GROUP ATOM OH2 OT -0.834 ATOM H1 HT 0.417 ATOM H2 HT 0.417 BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE ANGLE H1 OH2 H2 ACCE OH2 PATC FIRS NONE LAST NONE RESI OH2 .000 ! TIPS3P WATER MODEL GROUP ATOM OH2 OT -0.834 ATOM H1 HT 0.417 ATOM H2 HT 0.417 BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE ANGLE H1 OH2 H2 ACCE OH2 PATC FIRS NONE LAST NONE RESI SO4 -2.0 GROUP ATOM S S 0.0 ATOM O1 OC -0.5 ATOM O2 OC -0.5 ATOM O3 OC -0.5 ATOM O4 OC -0.5 BOND S O1 S O2 S O3 S O4 ACCE O1 S ACCE O2 S ACCE O3 S ACCE O4 S PATC FIRS NONE LAST NONE RESI COH 0.00000 GROU ATOM C CH3E 0.25 ATOM O OH1 -0.65 ATOM H H 0.40 BOND C O O H DONO H O ACCE O IC C O H BLNK 0.0000 0.00 0.00 0.00 0.0000 PATC FIRS NONE LAST NONE PRES DISU 0.000 ! PATCH FOR DISULFIDES. Patch must be 1-CYS and 2-CYS. GROUP ATOM 1CB CH2E 0.19 ATOM 1SG S -0.19 GROUP ATOM 2SG S -0.19 ATOM 2CB CH2E 0.19 BOND 1SG 2SG ANGLE 1CB 1SG 2SG 1SG 2SG 2CB DIHE 1CA 1CB 1SG 2SG 1CB 1SG 2SG 2CB 1SG 2SG 2CB 2CA IC 1CA 1CB 1SG 2SG 0.0 0.0 180.0 0.0 0.0 IC 1CB 1SG 2SG 2CB 0.0 0.0 180.0 0.0 0.0 IC 1SG 2SG 2CB 2CA 0.0 0.0 180.0 0.0 0.0 PRES CYCL 0.000 BOND 1N 2C ANGLE 2CA 2C 1N 2O 2C 1N 2CA 2C 2O ANGLE 2C 1N 1H 2C 1N 1CA 1H 1N 1CA DIHE 2N 2CA 2C 1N 2CA 2C 1N 1CA 2C 1N 1CA 1C IMPH 1N 2C 1CA 1H 2C 2CA 1N 2O PRES FHEM 0.0 ! FIX UP THE HEME BY DELETING UNWANTED ANGLES DELETE ANGLE 2NA 2FE 2NC 2NB 2FE 2ND PRES PHEM 0.0 ! Patch for HEME. Patch residues must be 1-HIS, and 2-HEME. BOND 1NE2 2FE ANGL 1CD2 1NE2 2FE 1CE1 1NE2 2FE 1NE2 2FE 2NA 1NE2 2FE 2NB ANGL 1NE2 2FE 2NC 1NE2 2FE 2ND DELETE ANGLE 2NA 2FE 2NC 2NB 2FE 2ND DIHE 1CD2 1NE2 2FE 2NA PRES PLO2 0.0 ! Patch residue for Heme ligand. Residues must be ! 1-O2 , 2-HEME , and 3-HIS ! O1 of the oxygen is bonded to the iron. BOND 1O1 2FE !ANGL 1O1 2FE 3NE2 ANGL 1O2 1O1 2FE 1O1 2FE 2NA 1O1 2FE 2NB ANGL 1O1 2FE 2NC 1O1 2FE 2ND DIHE 1O2 1O1 2FE 2NA PRES PLIG 0.0 ! Patch residue for Heme ligand. Residues must be, ! 1-CO , 2-HEME , and 3-HIS BOND 1C 2FE !ANGL 1C 2FE 3NE2 ANGL 1O 1C 2FE 1C 2FE 2NA 1C 2FE 2NB ANGL 1C 2FE 2NC 1C 2FE 2ND DIHE 1O 1C 2FE 2NA PRES LTOD 0.0 DELE IMPR 1CA 1N 1C 1CB IMPR 1CA 1C 1N 1CB PRES HS2 0.00 ! Patch for neutral His, move proton from ND1 to NE2 ! ! ! ND1--CE1 ! / | ! -CB--CG | ! \ | ! CD2--NE2 ! \ ! HE2 GROUP ATOM CG C 0.10 ATOM ND1 NR -0.40 ATOM CE1 CR1E 0.30 GROU ATOM CD2 CR1E 0.10 ATOM NE2 NH1 -0.40 ATOM HE2 H 0.30 DELETE ATOM HD1 DELETE ACCE NE2 BOND NE2 HE2 ANGLE CE1 NE2 HE2 CD2 NE2 HE2 IMPR NE2 CE1 CD2 HE2 DONOR HE2 NE2 ACCEPTOR ND1 IC CE1 CD2 *NE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 END