remarks remarks TOPH19.RCV remarks ========== remarks remarks Topology file for prosthetic groups of the remarks photosynthetic reaction center of Rps. viridis remarks remarks (H. Treutlein et al., in: The photosynthetical bacterial remarks reaction center: Structure and dynamics, J.Breton, A.Vermeglio,Eds. remarks (Plenum Press, London 1987), p. 139 remarks remarks The charge distributions of the groups have been calculated remarks by means of the semi-empirical quantum chemistry program remarks MOPAC (see M.J.S. Dewar, W. Thiel, J.Am.Chem.Soc. 99(1977)4899) remarks Each group has been calculated seperately in vacuum. The remarks Mg-atom was represented by a sparkle with charge 2. remarks remarks The file include all prosthetic groups in their neutral charge remarks state and ionized states of the bacteriochlorophylls BCMP, BCLA remarks and the bacteriopheophytin BPL. However, in reality, the positve remarks charge is distributed among the whole special pair (BCMP and BCLP), remarks see e.g. M. Plato et al., in: "The photosynthetic bacterial remarks reaction center: structure and dynamics, remarks J.Breton and A.Vermeglio, Eds., remarks (Plenum Press, London 1987), p. 379. Patches to protein residues remarks are also provided. remarks remarks The topology and parameters of the heme group which is remarks included in this file are from John Kuriyan (26-Oct-1985). remarks The Heme group is for the liganded FE(II) state remarks with perfect D4H symmetry. The atom types used are for remarks PARAM19 and the structural parameters are taken from remarks Kitagawa, Abe and Ogoshi J.C.P. 69, (1978) pages 4526-4534 remarks remarks H. Treutlein (6-Sept-1989) set echo=false end AUTOGENERATE ANGLES=TRUE END {* but see the two omitted angles below *} {*============================ ==================================== *} {* protein default masses *} MASS H 1.00800! hydrogen which can h-bond to neutral atom MASS HC 1.00800! ="= ="= ="= to charged atom MASS C 12.01100! carbonyl carbon MASS CH1E 13.01900! extended atom carbon with one hydrogen MASS CH2E 14.02700! ="= ="= ="= two hydrogens MASS CH3E 15.03500! ="= ="= ="= three hydrogens MASS CR1E 13.01900! ="= ="= in an aromatic ring with one H MASS N 14.00670! peptide nitrogen with no hydrogens attached MASS NR 14.00670! nitrogen in an aromatic ring with no hydrogens MASS NP 14.00670! pyrole nitrogen MASS NH1 14.00670! peptide nitrogen bound to one hydrogen MASS NH2 14.00670! ="= ="= ="= two hydrogens MASS NH3 14.00670! nitrogen bound to three hydrogens MASS NC2 14.00670! charged guandinium nitrogen bound to two hydrogens MASS O 15.99940! carbonyl oxygen MASS OC 15.99940! carboxy oxygen MASS OH1 15.99940! hydroxy oxygen MASS ON 15.99940! oxygen in LDAO ( bond N-O ) MASS S 32.06000! sulphur MASS SH1E 33.06800! extended atom sulfur with one hydrogen MASS HP 1.00800! ST2 water hydrogen MASS LP 0.00000! ST2 lone pair MASS HT 1.00800! TIPS3P water hydrogen MASS HA 1.00800! aliphatic hydrogen MASS CT 12.01100! aliphatic carbon MASS OH2 15.99940! ST2 water oxygen MASS OT 15.99940 ! TIPS3P water oxygen MASS HT 1.00800 ! TIPS3P WATER HYDROGEN MASS CM 12.01100 ! carbon in carbonmonoxide MASS OM 15.99940 ! oxygen in carbonmonoxide MASS OS 15.99940 ! ester oxygen MASS CP 13.019 ! (AMBER)imidazole carbon for assymm. histidine CE1 MASS CF 13.019 ! IMIDAZOLE CARBON FOR ASSYM. HISTIDINE CE2 MASS NB 14.0067 ! IMIDAZOLE NITROGEN NE2 MASS CC 12.011 ! IMIDAZOLE CARBON CG MASS NA 14.0067 ! IMIDAZOLE PROTONATED NITROGEN MASS CPA 12.01100 ! HEME SP2 CARBON MASS CPB 12.01100 ! HEME SP2 CARBON MASS CPM 13.01900 ! HEME MESO CARBON, EXTENDED MASS FE 55.84700 ! IRON MASS MG 24.30500 ! magnesium MASS EL 0.00054 ! magnesium RESIdue FE1 GROUp ATOM FE TYPE=FE CHARGE=2.0 END END {* FE1 *} RESIdue BCB ! Bacteriochlorophyll b ! Charge 0.0 ! Charge distribution from MOPAC calculations GROUp ATOM MG TYPE=MG CHARGE=2.00 END ATOM NA TYPE=NP CHARGE=-0.54 END ATOM NB TYPE=NP CHARGE=-0.58 END ATOM NC TYPE=NP CHARGE=-0.52 END ATOM ND TYPE=NP CHARGE=-0.60 END GROUp ATOM C1A TYPE=CPA CHARGE=0.13 END ATOM CHA TYPE=C CHARGE=-0.15 END ATOM C4D TYPE=CPA CHARGE=0.11 END GROUp ATOM C1B TYPE=CPA CHARGE=0.00 END ATOM CHB TYPE=CPM CHARGE=0.00 END ATOM C4A TYPE=CPA CHARGE=0.01 END GROUp ATOM C1C TYPE=CPA CHARGE=0.00 END ATOM CHC TYPE=CPM CHARGE=0.00 END ATOM C4B TYPE=CPA CHARGE=0.01 END GROUp ATOM C1D TYPE=CPA CHARGE=0.00 END ATOM CHD TYPE=CPM CHARGE=0.00 END ATOM C4C TYPE=CPA CHARGE=0.10 END GROUp ATOM C2A TYPE=CH1E CHARGE=0.03 END ATOM CAA TYPE=CH2E CHARGE=0.03 END GROUp ATOM C3A TYPE=CH1E CHARGE=-0.01 END ATOM CMA TYPE=CH3E CHARGE=0.08 END GROUp ATOM C2B TYPE=CPB CHARGE=-0.05 END ATOM CMB TYPE=CH3E CHARGE=0.13 END GROUp ATOM C3B TYPE=CPB CHARGE=-0.18 END ATOM CAB TYPE=C CHARGE=0.43 END ATOM CBB TYPE=CH3E CHARGE=0.10 END ATOM OBB TYPE=O CHARGE=-0.51 END GROUp ATOM C2C TYPE=CH1E CHARGE=0.04 END ATOM CMC TYPE=CH3E CHARGE=0.08 END GROUp ATOM C3C TYPE=C CHARGE=-0.19 END ATOM CAC TYPE=CR1E CHARGE=0.02 END ATOM CBC TYPE=CH3E CHARGE=0.10 END GROUp ATOM C2D TYPE=CPB CHARGE=0.02 END ATOM CMD TYPE=CH3E CHARGE=0.15 END GROUp ATOM C3D TYPE=CPB CHARGE=-0.22 END ATOM CAD TYPE=C CHARGE=0.49 END ATOM OBD TYPE=O CHARGE=-0.47 END GROUp ATOM CBD TYPE=CH1E CHARGE=0.07 END ATOM CGD TYPE=C CHARGE=0.54 END ATOM O1D TYPE=OC CHARGE=-0.53 END ATOM O2D TYPE=OS CHARGE=-0.49 END ATOM CED TYPE=CH3E CHARGE=0.42 END GROUp ATOM CBA TYPE=CH2E CHARGE=0.02 END ATOM CGA TYPE=C CHARGE=0.54 END ATOM O1A TYPE=O CHARGE=-0.49 END GROUp ATOM O2A TYPE=OS CHARGE=-0.52 END ATOM CP1 TYPE=CH2E CHARGE=0.45 END ATOM CP2 TYPE=CPM CHARGE=-0.11 END ATOM CP3 TYPE=CPA CHARGE=-0.07 END ATOM CP4 TYPE=CH3E CHARGE=0.07 END ATOM CP5 TYPE=CH2E CHARGE=0.05 END ATOM CP6 TYPE=CH2E CHARGE=0.00 END ATOM CP7 TYPE=CH2E CHARGE=0.06 END ATOM CP8 TYPE=CH1E CHARGE=-0.05 END ATOM CP9 TYPE=CH3E CHARGE=0.02 END ATOM CP10 TYPE=CH2E CHARGE=0.00 END ATOM CP11 TYPE=CH2E CHARGE=0.00 END ATOM CP12 TYPE=CH2E CHARGE=0.00 END ATOM CP13 TYPE=CH1E CHARGE=-0.04 END ATOM CP14 TYPE=CH3E CHARGE=0.02 END ATOM CP15 TYPE=CH2E CHARGE=0.01 END ATOM CP16 TYPE=CH2E CHARGE=0.00 END ATOM CP17 TYPE=CH2E CHARGE=0.01 END ATOM CP18 TYPE=CH1E CHARGE=-0.06 END ATOM CP19 TYPE=CH3E CHARGE=0.02 END ATOM CP20 TYPE=CH3E CHARGE=0.02 END BOND MG NA BOND MG NB BOND MG NC BOND MG ND BOND NA C1A BOND C1A C2A BOND C2A C3A BOND C3A C4A BOND NA C4A BOND C2A CAA BOND CAA CBA BOND CBA CGA BOND CGA O1A BOND CGA O2A BOND C3A CMA BOND CHB C4A BOND CHB C1B BOND NB C1B BOND C1B C2B BOND C2B C3B BOND C3B C4B BOND NB C4B BOND C2B CMB BOND C3B CAB BOND CAB CBB BOND CHC C4B BOND CHC C1C BOND NC C1C BOND C1C C2C BOND C2C C3C BOND C3C C4C BOND NC C4C BOND CAB OBB BOND C2C CMC BOND C3C CAC BOND CAC CBC BOND CHD C4C BOND CHD C1D BOND ND C1D BOND C1D C2D BOND C2D C3D BOND C3D C4D BOND ND C4D BOND C2D CMD BOND C3D CAD BOND CAD CBD BOND CBD CGD BOND CGD O1D BOND CGD O2D BOND O2D CED BOND CAD OBD BOND CBD CHA BOND CHA C4D BOND CHA C1A BOND O2A CP1 BOND CP1 CP2 BOND CP2 CP3 BOND CP3 CP4 BOND CP3 CP5 BOND CP5 CP6 BOND CP6 CP7 BOND CP7 CP8 BOND CP8 CP9 BOND CP8 CP10 BOND CP10 CP11 BOND CP11 CP12 BOND CP12 CP13 BOND CP13 CP14 BOND CP13 CP15 BOND CP15 CP16 BOND CP16 CP17 BOND CP17 CP18 BOND CP18 CP19 BOND CP18 CP20 OMIT ANGLE NA MG NC OMIT ANGLE NB MG ND DIHEdral NA C4A CHB C1B DIHEdral C4A CHB C1B NB DIHEdral NB C4B CHC C1C DIHEdral C4B CHC C1C NC DIHEdral NC C4C CHD C1D DIHEdral C4C CHD C1D ND DIHEdral C4D CHA C1A NA DIHEdral C1A C2A CAA CBA DIHEdral C2A CAA CBA CGA DIHEdral CAA CBA CGA O1A DIHEdral O1A CGA O2A CP1 DIHEdral CGA O2A CP1 CP2 DIHEdral O2A CP1 CP2 CP3 DIHEdral CP1 CP2 CP3 CP4 DIHEdral CP2 CP3 CP5 CP6 DIHEdral CP3 CP5 CP6 CP7 DIHEdral CP5 CP6 CP7 CP8 DIHEdral CP6 CP7 CP8 CP9 DIHEdral CP9 CP8 CP10 CP11 DIHEdral CP8 CP10 CP11 CP12 DIHEdral CP10 CP11 CP12 CP13 DIHEdral CP11 CP12 CP13 CP14 DIHEdral CP14 CP13 CP15 CP16 DIHEdral CP13 CP15 CP16 CP17 DIHEdral CP15 CP16 CP17 CP18 DIHEdral CP16 CP17 CP18 CP19 DIHEdral C2B C3B CAB CBB DIHEdral C2C C3C CAC CBC DIHEdral CAD CBD CGD O1D DIHEdral CBD CGD O2D CED IMPRoper MG C1A C4A NA IMPRoper MG C1B C4B NB IMPRoper MG C1C C4C NC IMPRoper MG C1D C4D ND IMPRoper CHA NA C2A C1A IMPRoper CHB NA C3A C4A IMPRoper CHB NB C2B C1B IMPRoper CHC NB C3B C4B IMPRoper CHC NC C2C C1C IMPRoper CHD NC C3C C4C IMPRoper CHD ND C2D C1D IMPRoper CHA ND C3D C4D IMPRoper C2A C1A C3A CAA IMPRoper C3A C4A C2A CMA IMPRoper C2B C1B C3B CMB IMPRoper C3B C2B C4B CAB IMPRoper C2C C3C C1C CMC IMPRoper C3C C4C C1C C2C IMPRoper C2D C1D C3D CMD IMPRoper C3D C2D C4D CAD IMPRoper O1A O2A CBA CGA IMPRoper O1D O2D CBD CGD IMPRoper NA NB MG NC IMPRoper NB NC MG ND IMPRoper NC ND MG NA IMPRoper ND NA MG NB IMPRoper C4D CHA C3D ND IMPRoper CAD C3D CBD OBD IMPRoper CBD C4D CAD CHA IMPRoper CHA C4D CBD C1A IMPRoper C3D C4D CAD C2D IMPRoper CAB OBB CBB C3B IMPRoper CP3 CP2 CP5 CP4 IMPRoper CBD CHA CAD CGD ACCEptor NA " " ACCEptor NB " " ACCEptor NC " " ACCEptor ND " " ACCEptor O1D CGD ACCEptor O1A CGA ACCEPTOR OBD CAD ACCEPTOR OBB CAB ACCEPTOR O2D " " ACCEPTOR O2A " " END {BCL} !-------------------------------------------------------------------- RESIdue BPB ! Bacteriopheophytin b ! Charge 0 ! Charge distribution from MOPAC calculations GROUp ATOM NA TYPE=NP CHARGE=-0.26 END ATOM NB TYPE=NH1 CHARGE=-0.12 END ATOM HB TYPE=H CHARGE=0.24 END ATOM NC TYPE=NP CHARGE=-0.27 END ATOM ND TYPE=NH1 CHARGE=-0.21 END ATOM HD TYPE=H CHARGE=0.26 END GROUp ATOM C1A TYPE=CPA CHARGE=0.09 END ATOM CHA TYPE=C CHARGE=-0.11 END ATOM C4D TYPE=CPA CHARGE=0.13 END GROUp ATOM C1B TYPE=CPA CHARGE=-0.02 END ATOM CHB TYPE=CPM CHARGE=0.07 END ATOM C4A TYPE=CPA CHARGE=-0.05 END GROUp ATOM C1C TYPE=CPA CHARGE=-0.04 END ATOM CHC TYPE=CPM CHARGE=0.04 END ATOM C4B TYPE=CPA CHARGE=0.05 END GROUp ATOM C1D TYPE=CPA CHARGE=0.08 END ATOM CHD TYPE=CPM CHARGE=-0.01 END ATOM C4C TYPE=CPA CHARGE=0.08 END GROUp ATOM C2A TYPE=CH1E CHARGE=0.03 END ATOM CAA TYPE=CH2E CHARGE=0.03 END GROUp ATOM C3A TYPE=CH1E CHARGE=-0.03 END ATOM CMA TYPE=CH3E CHARGE=0.07 END GROUp ATOM C2B TYPE=CPB CHARGE=-0.05 END ATOM CMB TYPE=CH3E CHARGE=0.13 END GROUp ATOM C3B TYPE=CPB CHARGE=-0.20 END ATOM CAB TYPE=C CHARGE=0.44 END ATOM CBB TYPE=CH3E CHARGE=0.09 END ATOM OBB TYPE=O CHARGE=-0.52 END GROUp ATOM C2C TYPE=CH1E CHARGE=0.05 END ATOM CMC TYPE=CH3E CHARGE=0.08 END GROUp ATOM C3C TYPE=C CHARGE=-0.15 END ATOM CAC TYPE=CR1E CHARGE=0.02 END ATOM CBC TYPE=CH3E CHARGE=0.10 END GROUp ATOM C2D TYPE=CPB CHARGE=0.03 END ATOM CMD TYPE=CH3E CHARGE=0.15 END GROUp ATOM C3D TYPE=CPB CHARGE=-0.19 END ATOM CAD TYPE=C CHARGE=0.50 END ATOM OBD TYPE=O CHARGE=-0.47 END GROUp ATOM CBD TYPE=CH1E CHARGE=0.06 END ATOM CGD TYPE=C CHARGE=0.53 END ATOM O1D TYPE=OC CHARGE=-0.55 END ATOM O2D TYPE=OS CHARGE=-0.48 END ATOM CED TYPE=CH3E CHARGE=0.41 END GROUp ATOM CBA TYPE=CH2E CHARGE=0.06 END ATOM CGA TYPE=C CHARGE=0.54 END ATOM O1A TYPE=O CHARGE=-0.50 END GROUp ATOM O2A TYPE=OS CHARGE=-0.54 END ATOM CP1 TYPE=CH2E CHARGE=0.46 END ATOM CP2 TYPE=CPM CHARGE=-0.06 END ATOM CP3 TYPE=CPA CHARGE=-0.11 END ATOM CP4 TYPE=CH3E CHARGE=0.07 END ATOM CP5 TYPE=CH2E CHARGE=0.05 END ATOM CP6 TYPE=CH2E CHARGE=0.00 END ATOM CP7 TYPE=CH2E CHARGE=0.05 END ATOM CP8 TYPE=CH1E CHARGE=-0.05 END ATOM CP9 TYPE=CH3E CHARGE=0.02 END ATOM CP10 TYPE=CH2E CHARGE=0.00 END ATOM CP11 TYPE=CH2E CHARGE=0.00 END ATOM CP12 TYPE=CH2E CHARGE=0.00 END ATOM CP13 TYPE=CH1E CHARGE=-0.04 END ATOM CP14 TYPE=CH3E CHARGE=0.02 END ATOM CP15 TYPE=CH2E CHARGE=0.01 END ATOM CP16 TYPE=CH2E CHARGE=0.00 END ATOM CP17 TYPE=CH2E CHARGE=0.01 END ATOM CP18 TYPE=CH1E CHARGE=-0.06 END ATOM CP19 TYPE=CH3E CHARGE=0.02 END ATOM CP20 TYPE=CH3E CHARGE=0.02 END BOND NB HB BOND ND HD BOND NA C1A BOND C1A C2A BOND C2A C3A BOND C3A C4A BOND NA C4A BOND C2A CAA BOND CAA CBA BOND CBA CGA BOND CGA O1A BOND CGA O2A BOND C3A CMA BOND CHB C4A BOND CHB C1B BOND NB C1B BOND C1B C2B BOND C2B C3B BOND C3B C4B BOND NB C4B BOND C2B CMB BOND C3B CAB BOND CAB CBB BOND CHC C4B BOND CHC C1C BOND NC C1C BOND C1C C2C BOND C2C C3C BOND C3C C4C BOND NC C4C BOND CAB OBB BOND C2C CMC BOND C3C CAC BOND CAC CBC BOND CHD C4C BOND CHD C1D BOND ND C1D BOND C1D C2D BOND C2D C3D BOND C3D C4D BOND ND C4D BOND C2D CMD BOND C3D CAD BOND CAD CBD BOND CBD CGD BOND CGD O1D BOND CGD O2D BOND O2D CED BOND CAD OBD BOND CBD CHA BOND CHA C4D BOND CHA C1A BOND O2A CP1 BOND CP1 CP2 BOND CP2 CP3 BOND CP3 CP4 BOND CP3 CP5 BOND CP5 CP6 BOND CP6 CP7 BOND CP7 CP8 BOND CP8 CP9 BOND CP8 CP10 BOND CP10 CP11 BOND CP11 CP12 BOND CP12 CP13 BOND CP13 CP14 BOND CP13 CP15 BOND CP15 CP16 BOND CP16 CP17 BOND CP17 CP18 BOND CP18 CP19 BOND CP18 CP20 DIHEdral NA C4A CHB C1B DIHEdral C4A CHB C1B NB DIHEdral NB C4B CHC C1C DIHEdral C4B CHC C1C NC DIHEdral NC C4C CHD C1D DIHEdral C4C CHD C1D ND DIHEdral C4D CHA C1A NA DIHEdral C1A C2A CAA CBA DIHEdral C2A CAA CBA CGA DIHEdral CAA CBA CGA O1A DIHEdral O1A CGA O2A CP1 DIHEdral CGA O2A CP1 CP2 DIHEdral O2A CP1 CP2 CP3 DIHEdral CP1 CP2 CP3 CP4 DIHEdral CP2 CP3 CP5 CP6 DIHEdral CP3 CP5 CP6 CP7 DIHEdral CP5 CP6 CP7 CP8 DIHEdral CP6 CP7 CP8 CP9 DIHEdral CP9 CP8 CP10 CP11 DIHEdral CP8 CP10 CP11 CP12 DIHEdral CP10 CP11 CP12 CP13 DIHEdral CP11 CP12 CP13 CP14 DIHEdral CP14 CP13 CP15 CP16 DIHEdral CP13 CP15 CP16 CP17 DIHEdral CP15 CP16 CP17 CP18 DIHEdral CP16 CP17 CP18 CP19 DIHEdral C2B C3B CAB CBB DIHEdral C2C C3C CAC CBC DIHEdral CAD CBD CGD O1D DIHEdral CBD CGD O2D CED DIHEdral CHA C1A NA C4A DIHEdral C1A NA C4A CHB !! DIHEdral NA C4A CHB C1B DIHEdral C4A CHB C1B NB !! keep DIHEdral CHB C1B NB C4B DIHEdral C1B NB C4B CHC !! DIHEdral NB C4B CHC C1C DIHEdral C4B CHC C1C NC !! N* DIHEdral CHC C1C NC C4C DIHEdral C1C NC C4C CHD !! DIHEdral NC C4C CHD C1D DIHEdral C4C CHD C1D ND !! planar DIHEdral CHD C1D ND C4D DIHEdral C1D ND C4D CHA !! DIHEdral ND C4D CHA C1A DIHEdral C4D CHA C1A NA !! ! DIHEdral C1D C3D C4D CHA DIHEdral C1D C4D C3D CAD IMPRoper HB C1A C4A NB IMPRoper HD C1B C4B ND IMPRoper CHA NA C2A C1A IMPRoper CHB NA C3A C4A IMPRoper CHB NB C2B C1B IMPRoper CHC NB C3B C4B IMPRoper CHC NC C2C C1C IMPRoper CHD NC C3C C4C IMPRoper CHD ND C2D C1D IMPRoper CHA ND C3D C4D IMPRoper C2A C1A C3A CAA IMPRoper C3A C4A C2A CMA IMPRoper C2B C1B C3B CMB IMPRoper C3B C2B C4B CAB IMPRoper C2C C3C C1C CMC IMPRoper C3C C4C C1C C2C IMPRoper C2D C1D C3D CMD IMPRoper C3D C2D C4D CAD IMPRoper O1A O2A CBA CGA IMPRoper O1D O2D CBD CGD IMPRoper C4D CHA C3D ND IMPRoper CAD C3D CBD OBD IMPRoper CBD C4D CAD CHA IMPRoper CHA C4D CBD C1A IMPRoper C3D C4D CAD C2D IMPRoper CAB OBB CBB C3B IMPRoper CP3 CP2 CP5 CP4 IMPRoper CBD CHA CAD CGD DONOR HB NB DONOR HD ND ACCEptor NA " " ACCEptor NC " " ACCEptor O1D CGD ACCEptor O1A CGA ACCEPTOR OBD CAD ACCEPTOR OBB CAB ACCEPTOR O2D " " ACCEPTOR O2A " " END {BPB} !--------------------------------------------------------------------- RESIdue MQ7 ! Menaquinone (includes 8 isoprene groups) ! Charges from MOPAC calculations GROUp ATOM C1 TYPE=CPB CHARGE=-0.1 EXCL=(C4 C3D C3C C3B C3A) END ATOM C1M TYPE=CH3E CHARGE= 0.1 END ATOM C2 TYPE=CPA CHARGE= 0.5 EXCL=(C5 C3D C3C C3B) END ATOM O2 TYPE=O CHARGE=-0.5 END ATOM C3 TYPE=CPB CHARGE=-0.1 EXCL=(C6 C3C) END ATOM C4 TYPE=CPB CHARGE=-0.1 EXCL=(C3B) END ATOM C5 TYPE=CPA CHARGE= 0.5 EXCL=(C3C C3A C3B) END ATOM O5 TYPE=O CHARGE=-0.5 END ATOM C6 TYPE=CPB CHARGE=-0.1 EXCL=(C3D C3C C3B C3A) END GROUp ATOM C3A TYPE=CR1E CHARGE= 0.1 EXCL=(C3D) END ATOM C3B TYPE=CR1E CHARGE= 0.0 END ATOM C3C TYPE=CR1E CHARGE= 0.0 END ATOM C3D TYPE=CR1E CHARGE= 0.1 END GROUp ATOM C7 TYPE=CH2E CHARGE= 0.1 END ATOM C8 TYPE=CPM CHARGE=-.05 END ATOM C9 TYPE=CPA CHARGE=-0.1 END ATOM C10 TYPE=CH3E CHARGE= .05 END ATOM C11 TYPE=CH2E CHARGE= .05 END GROUp ATOM C12 TYPE=CH2E CHARGE= .05 END ATOM C13 TYPE=CPM CHARGE=-.05 END ATOM C14 TYPE=CPA CHARGE=-0.1 END ATOM C15 TYPE=CH3E CHARGE= .05 END ATOM C16 TYPE=CH2E CHARGE= .05 END GROUp ATOM C17 TYPE=CH2E CHARGE= .05 END ATOM C18 TYPE=CPM CHARGE=-.05 END ATOM C19 TYPE=CPA CHARGE=-0.1 END ATOM C20 TYPE=CH3E CHARGE= .05 END ATOM C21 TYPE=CH2E CHARGE= .05 END GROUp ATOM C22 TYPE=CH2E CHARGE= .05 END ATOM C23 TYPE=CPM CHARGE=-.05 END ATOM C24 TYPE=CPA CHARGE=-0.1 END ATOM C25 TYPE=CH3E CHARGE= .05 END ATOM C26 TYPE=CH2E CHARGE= .05 END GROUp ATOM C27 TYPE=CH2E CHARGE= .05 END ATOM C28 TYPE=CPM CHARGE=-.05 END ATOM C29 TYPE=CPA CHARGE=-0.1 END ATOM C30 TYPE=CH3E CHARGE= .05 END ATOM C31 TYPE=CH2E CHARGE= .05 END GROUp ATOM C32 TYPE=CH2E CHARGE= .05 END ATOM C33 TYPE=CPM CHARGE=-.05 END ATOM C34 TYPE=CPA CHARGE=-0.1 END ATOM C35 TYPE=CH3E CHARGE= .05 END ATOM C36 TYPE=CH2E CHARGE= .05 END GROUp ATOM C37 TYPE=CH2E CHARGE= .05 END ATOM C38 TYPE=CPM CHARGE=-.05 END ATOM C39 TYPE=CPA CHARGE=-0.1 END ATOM C40 TYPE=CH3E CHARGE= .05 END ATOM C41 TYPE=CH2E CHARGE= .05 END GROUp ATOM C42 TYPE=CH2E CHARGE= .05 END ATOM C43 TYPE=CPM CHARGE=-.05 END ATOM C44 TYPE=CPA CHARGE=-0.1 END ATOM C45 TYPE=CH3E CHARGE= .075 END ATOM C46 TYPE=CH3E CHARGE= .075 END BOND C1 C1M BOND C1 C2 BOND C2 O2 BOND C2 C3 BOND C3 C4 BOND C3 C3A BOND C3A C3B BOND C3B C3C BOND C3C C3D BOND C3D C4 BOND C4 C5 BOND C5 O5 BOND C5 C6 BOND C6 C1 BOND C6 C7 BOND C7 C8 BOND C8 C9 BOND C9 C10 BOND C9 C11 BOND C11 C12 BOND C12 C13 BOND C13 C14 BOND C14 C15 BOND C14 C16 BOND C16 C17 BOND C17 C18 BOND C18 C19 BOND C19 C20 BOND C19 C21 BOND C21 C22 BOND C22 C23 BOND C23 C24 BOND C24 C25 BOND C24 C26 BOND C26 C27 BOND C27 C28 BOND C28 C29 BOND C29 C30 BOND C29 C31 BOND C31 C32 BOND C32 C33 BOND C33 C34 BOND C34 C35 BOND C34 C36 BOND C36 C37 BOND C37 C38 BOND C38 C39 BOND C39 C40 BOND C39 C41 BOND C41 C42 BOND C42 C43 BOND C43 C44 BOND C44 C45 BOND C44 C46 OMITT ANGLE C2 C3 C3A OMITT ANGLE C5 C4 C3D DIHEdral C7 C6 C1 C1M DIHEdral C1M C1 C2 O2 DIHEdral C1 C2 C3 C4 DIHEdral C2 C3 C4 C5 DIHEdral C3 C4 C5 O5 DIHEdral C4 C5 C6 C7 DIHEdral C2 C3 C3A C3B DIHEdral C3 C3A C3B C3C DIHEdral C3A C3B C3C C3D DIHEdral C3B C3C C3D C4 DIHEdral C3C C3D C4 C5 DIHEdral C5 C6 C7 C8 DIHEdral C6 C7 C8 C9 DIHEdral C8 C9 C11 C12 DIHEdral C7 C8 C9 C11 DIHEdral C11 C12 C13 C14 DIHEdral C9 C11 C12 C13 DIHEdral C12 C13 C14 C16 DIHEdral C13 C14 C16 C17 DIHEdral C14 C16 C17 C18 DIHEdral C16 C17 C18 C19 DIHEdral C17 C18 C19 C21 DIHEdral C18 C19 C21 C22 DIHEdral C19 C21 C22 C23 DIHEdral C21 C22 C23 C24 DIHEdral C23 C24 C26 C27 DIHEdral C22 C23 C24 C26 DIHEdral C24 C26 C27 C28 DIHEdral C26 C27 C28 C29 DIHEdral C27 C28 C29 C31 DIHEdral C28 C29 C31 C32 DIHEdral C29 C31 C32 C33 DIHEdral C31 C32 C33 C34 DIHEdral C32 C33 C34 C36 DIHEdral C33 C34 C36 C37 DIHEdral C34 C36 C37 C38 DIHEdral C36 C37 C38 C39 DIHEdral C37 C38 C39 C41 DIHEdral C38 C39 C41 C42 DIHEdral C39 C41 C42 C43 DIHEdral C41 C42 C43 C44 DIHEdral C42 C43 C44 C45 DIHEdral C1 C3 C4 C3C !! SPAWN RINGS AND KEEP DIHEdral C1 C4 C3 C3B !! PARALLEL IMPRoper C1 C6 C2 C1M IMPRoper C2 C1 C3 O2 IMPRoper C3 C2 C3A C4 IMPRoper C4 C3 C5 C3D IMPRoper C5 C6 C4 O5 IMPRoper C1 C6 C5 C4 IMPRoper C6 C5 C4 C3 IMPRoper C5 C4 C3 C2 IMPRoper C4 C3 C2 C1 IMPRoper C3 C2 C1 C6 IMPRoper C2 C1 C6 C5 IMPRoper C6 C5 C1 C7 IMPRoper C9 C10 C11 C8 IMPRoper C14 C15 C16 C13 IMPRoper C19 C20 C21 C18 IMPRoper C24 C25 C26 C23 IMPRoper C29 C30 C31 C28 IMPRoper C34 C35 C36 C33 IMPRoper C39 C40 C41 C38 IMPRoper C44 C45 C46 C43 IMPRoper C3 C4 C3D C3C IMPRoper C4 C3D C3C C3B IMPRoper C3D C3C C3B C3A IMPRoper C3C C3B C3A C3 IMPRoper C3B C3A C3 C4 IMPRoper C3A C3 C4 C3D ACCEPTOR O2 C2 ACCEPTOR O5 C5 IC C36 C37 C38 C39 0.0000 0.00 -180.00 0.00 0.0000 IC C37 C38 C39 C41 0.0000 0.00 180.00 0.00 0.0000 IC C37 C38 C39 C40 0.0000 0.00 0.00 0.00 0.0000 IC C38 C39 C41 C42 0.0000 0.00 -60.00 0.00 0.0000 IC C39 C41 C42 C43 0.0000 0.00 180.00 0.00 0.0000 IC C41 C42 C43 C44 0.0000 0.00 180.00 0.00 0.0000 IC C42 C43 C44 C45 0.0000 0.00 0.00 0.00 0.0000 IC C42 C43 C44 C46 0.0000 0.00 -180.00 0.00 0.0000 END {MQ7} !--------------------------------------------------------------------- RESIdue UQ1 ! Ubiquinone 1 (includes 8 isoprene groups) ! Charges from MOPAC calculations GROUp ATOM C1 TYPE=CPB CHARGE=-0.1 END ATOM CM1 TYPE=CH3E CHARGE= 0.1 END ATOM C2 TYPE=CPA CHARGE= 0.5 END ATOM O2 TYPE=O CHARGE=-0.5 END ATOM C3 TYPE=CPB CHARGE= 0.1 END ATOM C4 TYPE=CPB CHARGE=-0.05 END ATOM C5 TYPE=CPA CHARGE= 0.5 END ATOM O5 TYPE=O CHARGE=-0.5 END ATOM C6 TYPE=CPB CHARGE=-0.1 END GROUp ATOM O3 TYPE=OS CHARGE=-0.5 END ATOM CM3 TYPE=CH3E CHARGE= 0.5 END ATOM O4 TYPE=OS CHARGE=-0.55 END ATOM CM4 TYPE=CH3E CHARGE= 0.5 END GROUp ATOM C7 TYPE=CH2E CHARGE= 0.12 END ATOM C8 TYPE=CPM CHARGE=-.02 END ATOM C9 TYPE=CPA CHARGE=-0.15 END ATOM C10 TYPE=CH3E CHARGE= .05 END ATOM C11 TYPE=CH2E CHARGE= .05 END GROUp ATOM C12 TYPE=CH2E CHARGE= .05 END ATOM C13 TYPE=CPM CHARGE=-.05 END ATOM C14 TYPE=CPA CHARGE=-0.1 END ATOM C15 TYPE=CH3E CHARGE= .05 END ATOM C16 TYPE=CH2E CHARGE= .05 END GROUp ATOM C17 TYPE=CH2E CHARGE= .05 END ATOM C18 TYPE=CPM CHARGE=-.05 END ATOM C19 TYPE=CPA CHARGE=-0.1 END ATOM C20 TYPE=CH3E CHARGE= .05 END ATOM C21 TYPE=CH2E CHARGE= .05 END GROUp ATOM C22 TYPE=CH2E CHARGE= .05 END ATOM C23 TYPE=CPM CHARGE=-.05 END ATOM C24 TYPE=CPA CHARGE=-0.1 END ATOM C25 TYPE=CH3E CHARGE= .05 END ATOM C26 TYPE=CH2E CHARGE= .05 END GROUp ATOM C27 TYPE=CH2E CHARGE= .05 END ATOM C28 TYPE=CPM CHARGE=-.05 END ATOM C29 TYPE=CPA CHARGE=-0.1 END ATOM C30 TYPE=CH3E CHARGE= .05 END ATOM C31 TYPE=CH2E CHARGE= .05 END GROUp ATOM C32 TYPE=CH2E CHARGE= .05 END ATOM C33 TYPE=CPM CHARGE=-.05 END ATOM C34 TYPE=CPA CHARGE=-0.1 END ATOM C35 TYPE=CH3E CHARGE= .05 END ATOM C36 TYPE=CH2E CHARGE= .05 END GROUp ATOM C37 TYPE=CH2E CHARGE= .05 END ATOM C38 TYPE=CPM CHARGE=-.05 END ATOM C39 TYPE=CPA CHARGE=-0.1 END ATOM C40 TYPE=CH3E CHARGE= .05 END ATOM C41 TYPE=CH2E CHARGE= .05 END GROUp ATOM C42 TYPE=CH2E CHARGE= .05 END ATOM C43 TYPE=CPM CHARGE=-.05 END ATOM C44 TYPE=CPA CHARGE=-0.1 END ATOM C45 TYPE=CH3E CHARGE= .075 END ATOM C46 TYPE=CH3E CHARGE= .075 END BOND C1 CM1 BOND C1 C2 BOND C2 O2 BOND C2 C3 BOND C3 C4 BOND C3 O3 BOND O3 CM3 BOND C4 O4 BOND O4 CM4 BOND C4 C5 BOND C5 O5 BOND C5 C6 BOND C6 C1 BOND C6 C7 BOND C7 C8 BOND C8 C9 BOND C9 C10 BOND C9 C11 BOND C11 C12 BOND C12 C13 BOND C13 C14 BOND C14 C15 BOND C14 C16 BOND C16 C17 BOND C17 C18 BOND C18 C19 BOND C19 C20 BOND C19 C21 BOND C21 C22 BOND C22 C23 BOND C23 C24 BOND C24 C25 BOND C24 C26 BOND C26 C27 BOND C27 C28 BOND C28 C29 BOND C29 C30 BOND C29 C31 BOND C31 C32 BOND C32 C33 BOND C33 C34 BOND C34 C35 BOND C34 C36 BOND C36 C37 BOND C37 C38 BOND C38 C39 BOND C39 C40 BOND C39 C41 BOND C41 C42 BOND C42 C43 BOND C43 C44 BOND C44 C45 BOND C44 C46 DIHEdral C7 C6 C1 CM1 DIHEdral CM1 C1 C2 O2 DIHEdral C1 C2 C3 C4 DIHEdral C2 C3 C4 C5 DIHEdral C3 C4 C5 O5 DIHEdral C4 C5 C6 C7 DIHEdral C2 C3 O3 CM3 DIHEdral C5 C4 O4 CM4 DIHEdral C5 C6 C7 C8 DIHEdral C6 C7 C8 C9 DIHEdral C7 C8 C9 C11 DIHEdral C8 C9 C11 C12 DIHEdral C11 C12 C13 C14 DIHEdral C9 C11 C12 C13 DIHEdral C12 C13 C14 C16 DIHEdral C13 C14 C16 C17 DIHEdral C14 C16 C17 C18 DIHEdral C16 C17 C18 C19 DIHEdral C17 C18 C19 C21 DIHEdral C18 C19 C21 C22 DIHEdral C19 C21 C22 C23 DIHEdral C21 C22 C23 C24 DIHEdral C23 C24 C26 C27 DIHEdral C22 C23 C24 C26 DIHEdral C24 C26 C27 C28 DIHEdral C26 C27 C28 C29 DIHEdral C27 C28 C29 C31 DIHEdral C28 C29 C31 C32 DIHEdral C29 C31 C32 C33 DIHEdral C31 C32 C33 C34 DIHEdral C32 C33 C34 C36 DIHEdral C33 C34 C36 C37 DIHEdral C34 C36 C37 C38 DIHEdral C36 C37 C38 C39 DIHEdral C37 C38 C39 C41 DIHEdral C38 C39 C41 C42 DIHEdral C39 C41 C42 C43 DIHEdral C41 C42 C43 C44 DIHEdral C42 C43 C44 C45 IMPRoper C1 C6 C2 CM1 IMPRoper C2 C1 C3 O2 IMPRoper C3 C2 O3 C4 IMPRoper C4 C3 C5 O4 IMPRoper C5 C6 C4 O5 IMPRoper C1 C6 C5 C4 IMPRoper C6 C5 C4 C3 IMPRoper C5 C4 C3 C2 IMPRoper C4 C3 C2 C1 IMPRoper C3 C2 C1 C6 IMPRoper C2 C1 C6 C5 IMPRoper C6 C5 C1 C7 IMPRoper C9 C10 C11 C8 IMPRoper C14 C15 C16 C13 IMPRoper C19 C20 C21 C18 IMPRoper C24 C25 C26 C23 IMPRoper C29 C30 C31 C28 IMPRoper C34 C35 C36 C33 IMPRoper C39 C40 C41 C38 IMPRoper C44 C45 C46 C43 ACCEPTOR O2 C2 ACCEPTOR O5 C5 ACCEPTOR O3 " " ACCEPTOR O4 " " ! Internal coordinates from MQ7: IC C8 C9 C11 C12 0.0000 0.00 -110.67 0.00 0.0000 IC C7 C8 C9 C11 0.0000 0.00 176.95 0.00 0.0000 IC C9 C11 C12 C13 0.0000 0.00 58.05 0.00 0.0000 IC C11 C12 C13 C14 0.0000 0.00 126.62 0.00 0.0000 IC C12 C13 C14 C16 0.0000 0.00 179.84 0.00 0.0000 IC C12 C13 C14 C15 0.0000 0.00 1.00 0.00 0.0000 IC C13 C14 C16 C17 0.0000 0.00 -111.23 0.00 0.0000 IC C14 C16 C17 C18 0.0000 0.00 77.65 0.00 0.0000 IC C16 C17 C18 C19 0.0000 0.00 -155.17 0.00 0.0000 IC C17 C18 C19 C21 0.0000 0.00 179.55 0.00 0.0000 IC C17 C18 C19 C20 0.0000 0.00 0.45 0.00 0.0000 IC C18 C19 C21 C22 0.0000 0.00 97.74 0.00 0.0000 IC C19 C21 C22 C23 0.0000 0.00 -174.86 0.00 0.0000 IC C21 C22 C23 C24 0.0000 0.00 165.53 0.00 0.0000 IC C23 C24 C26 C27 0.0000 0.00 -125.88 0.00 0.0000 IC C22 C23 C24 C26 0.0000 0.00 -176.92 0.00 0.0000 IC C22 C23 C24 C25 0.0000 0.00 -3.00 0.00 0.0000 IC C24 C26 C27 C28 0.0000 0.00 -176.94 0.00 0.0000 IC C26 C27 C28 C29 0.0000 0.00 134.74 0.00 0.0000 IC C27 C28 C29 C31 0.0000 0.00 -179.70 0.00 0.0000 IC C27 C28 C29 C30 0.0000 0.00 -0.30 0.00 0.0000 IC C28 C29 C31 C32 0.0000 0.00 125.53 0.00 0.0000 IC C29 C31 C32 C33 0.0000 0.00 176.37 0.00 0.0000 IC C31 C32 C33 C34 0.0000 0.00 -168.64 0.00 0.0000 IC C32 C33 C34 C36 0.0000 0.00 178.03 0.00 0.0000 IC C32 C33 C34 C35 0.0000 0.00 2.00 0.00 0.0000 IC C33 C34 C36 C37 0.0000 0.00 -57.22 0.00 0.0000 IC C34 C36 C37 C38 0.0000 0.00 178.32 0.00 0.0000 IC C36 C37 C38 C39 0.0000 0.00 148.80 0.00 0.0000 IC C37 C38 C39 C41 0.0000 0.00 -170.66 0.00 0.0000 IC C37 C38 C39 C40 0.0000 0.00 -9.00 0.00 0.0000 IC C38 C39 C41 C42 0.0000 0.00 -78.70 0.00 0.0000 IC C39 C41 C42 C43 0.0000 0.00 172.51 0.00 0.0000 IC C41 C42 C43 C44 0.0000 0.00 -169.68 0.00 0.0000 IC C42 C43 C44 C45 0.0000 0.00 0.26 0.00 0.0000 IC C42 C43 C44 C46 0.0000 0.00 180.00 0.00 0.0000 END {UQ1} !--------------------------------------------------------------------- RESIdue NS1 ! di-hydro-neurosporene ! Charges from MOPAC calculations GROUp ATOM CM1 TYPE=CH3E CHARGE= 0.075 END ATOM CM2 TYPE=CH3E CHARGE= 0.075 END ATOM C1 TYPE=CPA CHARGE=-0.15 END ATOM C2 TYPE=CPM CHARGE=-0.025 END ATOM C3 TYPE=CH2E CHARGE= 0.05 END GROUp ATOM C4 TYPE=CH2E CHARGE= 0.06 END ATOM C5 TYPE=CPA CHARGE=-0.13 END ATOM CM3 TYPE=CH3E CHARGE= 0.075 END ATOM C6 TYPE=CPM CHARGE=-0.02 END ATOM C7 TYPE=CPM CHARGE=-0.02 END GROUp ATOM C8 TYPE=CPM CHARGE=-0.025 END ATOM C9 TYPE=CPA CHARGE=-0.13 END ATOM CM4 TYPE=CH3E CHARGE= 0.075 END ATOM C10 TYPE=CPM CHARGE= 0.025 END ATOM C11 TYPE=CPM CHARGE= 0.025 END GROUp ATOM C12 TYPE=CPM CHARGE= 0.025 END ATOM C13 TYPE=CPA CHARGE=-0.1 END ATOM CM5 TYPE=CH3E CHARGE= 0.075 END ATOM C14 TYPE=CPM CHARGE= 0.025 END ATOM C15 TYPE=CPM CHARGE= 0.025 END ATOM C16 TYPE=CPM CHARGE= 0.025 END GROUp ATOM C17 TYPE=CPM CHARGE=-0.01 END ATOM C18 TYPE=CPA CHARGE=-0.1 END ATOM CM6 TYPE=CH3E CHARGE= 0.075 END ATOM C19 TYPE=CPM CHARGE= 0.025 END ATOM C20 TYPE=CPM CHARGE= 0.01 END GROUp ATOM C21 TYPE=CPM CHARGE= 0.01 END ATOM C22 TYPE=CPA CHARGE=-0.1 END ATOM CM7 TYPE=CH3E CHARGE= 0.075 END ATOM C23 TYPE=CPM CHARGE= 0.01 END ATOM C24 TYPE=CPM CHARGE=-0.04 END GROUp ATOM C25 TYPE=CPM CHARGE= 0.01 END ATOM C26 TYPE=CPA CHARGE=-0.13 END ATOM CM8 TYPE=CH3E CHARGE= 0.075 END ATOM C27 TYPE=CH2E CHARGE= 0.04 END ATOM C28 TYPE=CH2E CHARGE= 0.0 END GROUp ATOM C29 TYPE=CH2E CHARGE=-0.02 END ATOM C30 TYPE=CH1E CHARGE=-0.015 END ATOM CM9 TYPE=CH3E CHARGE=-0.02 END ATOM CM10 TYPE=CH3E CHARGE= 0.07 END BOND CM1 C1 BOND CM2 C1 BOND C1 C2 BOND C3 C4 BOND C4 C5 BOND C5 CM3 BOND C5 C6 BOND C6 C7 BOND C7 C8 BOND C8 C9 BOND C9 CM4 BOND C9 C10 BOND C10 C11 BOND C11 C12 BOND C12 C13 BOND C13 CM5 BOND C13 C14 BOND C14 C15 BOND C15 C16 BOND C16 C17 BOND C17 C18 BOND C18 CM6 BOND C18 C19 BOND C19 C20 BOND C20 C21 BOND C21 C22 BOND C22 CM7 BOND C22 C23 BOND C23 C24 BOND C24 C25 BOND C25 C26 BOND C26 CM8 BOND C26 C27 BOND C27 C28 BOND C28 C29 BOND C29 C30 BOND C30 CM9 BOND C30 CM10 BOND C2 C3 DIHEdral CM1 C1 C2 C3 DIHEdral C1 C2 C3 C4 DIHEdral C2 C3 C4 C5 DIHEdral C3 C4 C5 C6 DIHEdral C4 C5 C6 C7 DIHEdral C5 C6 C7 C8 DIHEdral C6 C7 C8 C9 DIHEdral C7 C8 C9 C10 DIHEdral C8 C9 C10 C11 DIHEdral C9 C10 C11 C12 DIHEdral C10 C11 C12 C13 DIHEdral C11 C12 C13 C14 DIHEdral C12 C13 C14 C15 DIHEdral C13 C14 C15 C16 DIHEdral C14 C15 C16 C17 DIHEdral C15 C16 C17 C18 DIHEdral C16 C17 C18 C19 DIHEdral C17 C18 C19 C20 DIHEdral C18 C19 C20 C21 DIHEdral C19 C20 C21 C22 DIHEdral C20 C21 C22 C23 DIHEdral C21 C22 C23 C24 DIHEdral C22 C23 C24 C25 DIHEdral C23 C24 C25 C26 DIHEdral C24 C25 C26 C27 DIHEdral C25 C26 C27 C28 DIHEdral C26 C27 C28 C29 DIHEdral C27 C28 C29 C30 DIHEdral C28 C29 C30 CM10 END {NS1} !--------------------------------------------------------------------- RESIdue LDA ! Lauryl-dimethyl-amino-oxid ! Charges ! from MOPAC calculations GROUp ATOM CM1 TYPE=CH3E CHARGE= 0.15 END ATOM CM2 TYPE=CH3E CHARGE= 0.15 END ATOM N1 TYPE=N CHARGE= 0.6 END ATOM O1 TYPE=ON CHARGE=-1.2 END GROUp ATOM C1 TYPE=CH2E CHARGE= 0.1 END ATOM C2 TYPE=CH2E CHARGE= 0.2 END ATOM C3 TYPE=CH2E CHARGE= 0.0 END ATOM C4 TYPE=CH2E CHARGE= 0.0 END ATOM C5 TYPE=CH2E CHARGE= 0.0 END ATOM C6 TYPE=CH2E CHARGE= 0.0 END ATOM C7 TYPE=CH2E CHARGE= 0.0 END ATOM C8 TYPE=CH2E CHARGE= 0.0 END ATOM C9 TYPE=CH2E CHARGE= 0.0 END ATOM C10 TYPE=CH2E CHARGE= 0.0 END ATOM C11 TYPE=CH2E CHARGE=-0.01 END ATOM C12 TYPE=CH3E CHARGE= 0.01 END BOND CM1 N1 BOND CM2 N1 BOND O1 N1 BOND C1 N1 BOND C1 C2 BOND C2 C3 BOND C3 C4 BOND C4 C5 BOND C5 C6 BOND C6 C7 BOND C7 C8 BOND C8 C9 BOND C9 C10 BOND C10 C11 BOND C11 C12 DIHEdral CM1 N1 C1 C2 DIHEdral N1 C1 C2 C3 DIHEdral C1 C2 C3 C4 DIHEdral C2 C3 C4 C5 DIHEdral C3 C4 C5 C6 DIHEdral C4 C5 C6 C7 DIHEdral C5 C6 C7 C8 DIHEdral C6 C7 C8 C9 DIHEdral C7 C8 C9 C10 DIHEdral C8 C9 C10 C11 DIHEdral C9 C10 C11 C12 IMPRoper CM1 N1 O1 CM2 ACCEptor O1 N1 END {LDA} !-------------------------------------------------------------------- ! THE HEME GROUP WHICH FOLLOWS IS FOR THE LIGANDED FE(II) STATE ! WITH PERFECT D4H SYMMETRY. THE ATOM TYPES USED ARE FOR ! P19TEST AND THE STRUCTURAL PARAMETERS ARE TAKEN FROM ! KITAGAWA, ABE AND OGOSHI J.C.P. 69, (1978) PAGES 4526-4534 ! JOHN KURIYAN 26-OCT-1985 RESIdue HEM GROUp ATOM FE TYPE=FE CHARGE=0.24 END ATOM NA TYPE=NP CHARGE=-0.18 END ATOM NB TYPE=NP CHARGE=-0.18 END ATOM NC TYPE=NP CHARGE=-0.18 END ATOM ND TYPE=NP CHARGE=-0.18 END GROUp ATOM C1A TYPE=CPA CHARGE=0.03 END ATOM CHA TYPE=CPM CHARGE=0.04 END ATOM C4D TYPE=CPA CHARGE=0.02 END GROUp ATOM C1B TYPE=CPA CHARGE=0.03 END ATOM CHB TYPE=CPM CHARGE=0.04 END ATOM C4A TYPE=CPA CHARGE=0.02 END GROUp ATOM C1C TYPE=CPA CHARGE=0.03 END ATOM CHC TYPE=CPM CHARGE=0.04 END ATOM C4B TYPE=CPA CHARGE=0.02 END GROUp ATOM C1D TYPE=CPA CHARGE=0.03 END ATOM CHD TYPE=CPM CHARGE=0.04 END ATOM C4C TYPE=CPA CHARGE=0.02 END GROUp ATOM C2A TYPE=CPB CHARGE=-0.02 END ATOM CAA TYPE=CH2E CHARGE=0.04 END GROUp ATOM C3A TYPE=CPB CHARGE=0.02 END ATOM CMA TYPE=CH3E CHARGE=-0.04 END GROUp ATOM CBA TYPE=CH2E CHARGE=-0.10 END ATOM CGA TYPE=C CHARGE=0.30 END ATOM O1A TYPE=OC CHARGE=-0.50 END ATOM O2A TYPE=OC CHARGE=-0.50 END GROUp ATOM C2B TYPE=CPB CHARGE=0.02 END ATOM CMB TYPE=CH3E CHARGE=-0.04 END GROUp ATOM C3B TYPE=CPB CHARGE=-0.05 END ATOM CAB TYPE=CR1E CHARGE=0.03 END ATOM CBB TYPE=CH2E CHARGE=-0.10 END GROUp ATOM C2C TYPE=CPB CHARGE=0.02 END ATOM CMC TYPE=CH3E CHARGE=-0.04 END GROUp ATOM C3C TYPE=CPB CHARGE=-0.05 END ATOM CAC TYPE=CR1E CHARGE=0.03 END ATOM CBC TYPE=CH2E CHARGE=-0.10 END GROUp ATOM C2D TYPE=CPB CHARGE=0.02 END ATOM CMD TYPE=CH3E CHARGE=-0.04 END GROUp ATOM C3D TYPE=CPB CHARGE=-0.02 END ATOM CAD TYPE=CH2E CHARGE=0.04 END GROUp ATOM CBD TYPE=CH2E CHARGE=-0.10 END ATOM CGD TYPE=C CHARGE=0.30 END ATOM O1D TYPE=OC CHARGE=-0.50 END ATOM O2D TYPE=OC CHARGE=-0.50 END BOND FE NA BOND FE NB BOND FE NC BOND FE ND BOND NA C1A BOND C1A C2A BOND C2A C3A BOND C3A C4A BOND NA C4A BOND C2A CAA BOND CAA CBA BOND CBA CGA BOND CGA O1A BOND CGA O2A BOND C3A CMA BOND CHB C4A BOND CHB C1B BOND NB C1B BOND C1B C2B BOND C2B C3B BOND C3B C4B BOND NB C4B BOND C2B CMB BOND C3B CAB BOND CAB CBB BOND CHC C4B BOND CHC C1C BOND NC C1C BOND C1C C2C BOND C2C C3C BOND C3C C4C BOND NC C4C BOND C2C CMC BOND C3C CAC BOND CAC CBC BOND CHD C4C BOND CHD C1D BOND ND C1D BOND C1D C2D BOND C2D C3D BOND C3D C4D BOND ND C4D BOND C2D CMD BOND C3D CAD BOND CAD CBD BOND CBD CGD BOND CGD O1D BOND CGD O2D BOND CHA C4D BOND CHA C1A OMIT ANGLE NA FE NC OMIT ANGLE NB FE ND DIHEdral NA C4A CHB C1B DIHEdral C4A CHB C1B NB DIHEdral NB C4B CHC C1C DIHEdral C4B CHC C1C NC DIHEdral NC C4C CHD C1D DIHEdral C4C CHD C1D ND DIHEdral ND C4D CHA C1A DIHEdral C4D CHA C1A NA DIHEdral C1A C2A CAA CBA DIHEdral C2A CAA CBA CGA DIHEdral CAA CBA CGA O1A DIHEdral C2B C3B CAB CBB DIHEdral C2C C3C CAC CBC DIHEdral C2D C3D CAD CBD DIHEdral C3D CAD CBD CGD DIHEdral CAD CBD CGD O1D IMPRoper FE C1A C4A NA IMPRoper FE C1B C4B NB IMPRoper FE C1C C4C NC IMPRoper FE C1D C4D ND IMPRoper CHA NA C2A C1A IMPRoper CHB NA C3A C4A IMPRoper CHB NB C2B C1B IMPRoper CHC NB C3B C4B IMPRoper CHC NC C2C C1C IMPRoper CHD NC C3C C4C IMPRoper CHD ND C2D C1D IMPRoper CHA ND C3D C4D IMPRoper C2A C1A C3A CAA IMPRoper C3A C2A C4A CMA IMPRoper C2B C1B C3B CMB IMPRoper C3B C2B C4B CAB IMPRoper C2C C1C C3C CMC IMPRoper C3C C2C C4C CAC IMPRoper C2D C1D C3D CMD IMPRoper C3D C2D C4D CAD IMPRoper CBA O1A O2A CGA IMPRoper CBD O1D O2D CGD IMPRoper NA NB FE NC IMPRoper NB NC FE ND IMPRoper NC ND FE NA IMPRoper ND NA FE NB ACCEptor NA " " ACCEptor O1A CGA ACCEptor O2A CGA ACCEptor NB " " ACCEptor NC " " ACCEptor ND " " ACCEptor O1D CGD ACCEptor O2D CGD IC FE NA C4A CHB 0.0000 0.00 0.00 0.00 0.0000 IC NA C4A CHB C1B 0.0000 0.00 0.00 0.00 0.0000 IC NA CHB *C4A C3A 0.0000 0.00 180.00 0.00 0.0000 IC C4A CHB C1B NB 0.0000 0.00 0.00 0.00 0.0000 IC CHB NB *C1B C2B 0.0000 0.00 180.00 0.00 0.0000 IC FE C1B *NB C4B 0.0000 0.00 180.00 0.00 0.0000 IC FE NB C4B CHC 0.0000 0.00 0.00 0.00 0.0000 IC CHC NB *C4B C3B 0.0000 0.00 180.00 0.00 0.0000 IC C3B C1B *C2B CMB 0.0000 0.00 180.00 0.00 0.0000 IC C4B C2B *C3B CAB 0.0000 0.00 180.00 0.00 0.0000 IC C2B C3B CAB CBB 0.0 0.00 -45.00 0.00 0.0 ! PREVENTS VINYL COLLISION IC NB C4B CHC C1C 0.0000 0.00 0.00 0.00 0.0000 IC C4B CHC C1C NC 0.0000 0.00 0.00 0.00 0.0000 IC CHC NC *C1C C2C 0.0000 0.00 180.00 0.00 0.0000 IC FE C1C *NC C4C 0.0000 0.00 180.00 0.00 0.0000 IC FE NC C4C CHD 0.0000 0.00 0.00 0.00 0.0000 IC CHD NC *C4C C3C 0.0000 0.00 180.00 0.00 0.0000 IC CHC C1C C2C CMC 0.0000 0.00 0.00 0.00 0.0000 IC C4C C2C *C3C CAC 0.0000 0.00 180.00 0.00 0.0000 IC C2C C3C CAC CBC 0.0 0.00 -45.0 0.00 0.0 ! PREVENTS VINYL COLLISION IC NC C4C CHD C1D 0.0000 0.00 0.00 0.00 0.0000 IC C4C CHD C1D ND 0.0000 0.00 0.00 0.00 0.0000 IC FE C1D *ND C4D 0.0000 0.00 180.00 0.00 0.0000 IC CHD ND *C1D C2D 0.0000 0.00 180.00 0.00 0.0000 IC FE ND C4D CHA 0.0000 0.00 0.00 0.00 0.0000 IC CHA ND *C4D C3D 0.0000 0.00 180.00 0.00 0.0000 IC C4D C2D *C3D CAD 0.0000 0.00 180.00 0.00 0.0000 IC C3D C1D *C2D CMD 0.0000 0.00 180.00 0.00 0.0000 IC C2D C3D CAD CBD 0.0000 0.00 -120.00 0.00 0.0000 IC C3D CAD CBD CGD 0.0000 0.00 180.00 0.00 0.0000 IC CAD CBD CGD O1D 0.0000 0.00 0.00 0.00 0.0000 IC CAD CBD CGD O2D 0.0000 0.00 180.00 0.00 0.0000 IC ND C4D CHA C1A 0.0000 0.00 0.00 0.00 0.0000 IC CHA NA *C1A C2A 0.0000 0.00 180.00 0.00 0.0000 IC C4A C2A *C3A CMA 0.0000 0.00 180.00 0.00 0.0000 IC C3A C1A *C2A CAA 0.0000 0.00 180.00 0.00 0.0000 IC C1A C2A CAA CBA 0.0000 0.00 120.00 0.00 0.0000 IC C2A CAA CBA CGA 0.0000 0.00 180.00 0.00 0.0000 IC CAA CBA CGA O1A 0.0000 0.00 0.00 0.00 0.0000 IC CAA CBA CGA O2A 0.0000 0.00 180.00 0.00 0.0000 IC C4D CHA C1A NA 0.0000 0.00 0.00 0.00 0.0000 IC C1D ND FE NC 0.0000 0.00 0.00 0.00 0.0000 IC C4A NA FE NB 0.0000 0.00 0.00 0.00 0.0000 IC C4C NC FE ND 0.0000 0.00 0.00 0.00 0.0000 IC C1B NB FE NA 0.0000 0.00 0.00 0.00 0.0000 IC FE C1A *NA C4A 0.0000 0.00 180.00 0.00 0.0000 IC C3C C1C *C2C CMC 0.0000 0.00 180.00 0.00 0.0000 IC CBA O1A *O2A CGA 0.0000 0.00 180.00 0.00 0.0000 IC CBD O1D *O2D CGD 0.0000 0.00 180.00 0.00 0.0000 IC NA NB *NC ND 0.0000 0.00 180.00 0.00 0.0000 IC NB NC *ND NA 0.0000 0.00 180.00 0.00 0.0000 IC NC ND *NA NB 0.0000 0.00 180.00 0.00 0.0000 IC ND NA *NB NC 0.0 0.0 180.0 0.0 0.0 IC NA ND *FE NB 0.0 0.0 180.0 0.0 0.0 IC ND NC *FE NA 0.0 0.0 180.0 0.0 0.0 IC NC NB *FE ND 0.0 0.0 180.0 0.0 0.0 IC NB NA *FE NC 0.0 0.0 180.0 0.0 0.0 END {HEM} !-------------------------------------------------------------------------- PRESidue PHEM ! Patch for HEME. Patch residues must be 1-HIS, and 2-HEME. BOND 1NE2 2FE ANGLe 1CD2 1NE2 2FE ANGLe 1CE1 1NE2 2FE ANGLe 1NE2 2FE 2NA ANGLe 1NE2 2FE 2NB ANGLe 1NE2 2FE 2NC ANGLe 1NE2 2FE 2ND ! DIHEdral 1CD2 1NE2 2FE 2NA IC 1CD2 1NE2 2FE 2NA 0.0 0.0 0.0 0.0 0.0 IC 1CD2 1NE2 2FE 2NB 0.0 0.0 0.0 0.0 0.0 IC 1CD2 1NE2 2FE 2NB 0.0 0.0 0.0 0.0 0.0 IC 1CD2 1NE2 2FE 2NB 0.0 0.0 0.0 0.0 0.0 IC 1CE1 1NE2 2FE 2NA 0.0 0.0 0.0 0.0 0.0 END {* PHEM *} !-------------------------------------------------------------------------- PRESidue PMET ! Patch for HEME. Patch residues must be 1-MET, and 2-HEME. ADD BOND 1SD 2FE ADD ANGLe 1CG 1SD 2FE ADD ANGLe 1CE 1SD 2FE ADD ANGLe 1SD 2FE 2NA ADD ANGLe 1SD 2FE 2NB ADD ANGLe 1SD 2FE 2NC ADD ANGLe 1SD 2FE 2ND ! ADD DIHEdral 1CG 1SD 2FE 2NA END {* PMET *} !------------------------------------------------------------------------- PRESidue PLO2 ! 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 !ANGLe 1O1 2FE 3NE2 ANGLe 1O2 1O1 2FE ANGLe 1O1 2FE 2NA ANGLe 1O1 2FE 2NB ANGLe 1O1 2FE 2NC ANGLe 1O1 2FE 2ND DIHEdral 1O2 1O1 2FE 2NA IC 1O2 1O1 2FE 2NA 0.0 0.0 0.0 0.0 0.0 IC 1O2 1O1 2FE 3NE2 0.0 0.0 0.0 0.0 0.0 END {* PLO2 *} !------------------------------------------------------------------- PRESidue PLIG ! Patch residue for Heme ligand. Residues must be, ! 1-CO , 2-HEME , and 3-HIS BOND 1C 2FE ANGLe 1C 2FE 3NE2 ANGLe 1O 1C 2FE ANGLe 1C 2FE 2NA ANGLe 1C 2FE 2NB ANGLe 1C 2FE 2NC ANGle 1C 2FE 2ND ! DIHEdral 1O 1C 2FE 2NA IC 1O 1C 2FE 2NA 0.0 0.0 0.0 0.0 0.0 IC 1O 1C 2FE 3NE2 0.0 0.0 0.0 0.0 0.0 END {* PLIG *} !-------------------------------------------------------------------------- PRESidue PCYB ! Patch for HEME. Patch residues must be 1-CYS, and 2-HEME. ! Patch to heme CAB atom GROUP MODIfy ATOM 1SG TYPE=S CHARge=-0.19 END GROUP MODIfy ATOM 2CAB TYPE=CH1E CHARGE=0.03 END MODIfy ATOM 2CBB TYPE=CH3E CHARGE=-0.10 END ADD BOND 1SG 2CAB ADD ANGLe 1CB 1SG 2CAB ADD ANGLe 1SG 2CAB 2CBB ADD ANGLe 1SG 2CAB 2C3C ADD DIHEdral 1CB 1SG 2CAB 2C3B ADD IMPRoper 2CAB 1SG 2C3B 2CBB END {* PCYB *} !-------------------------------------------------------------------------- PRESidue PCYC ! Patch for HEME. Patch residues must be 1-CYS, and 2-HEME. ! Patch to heme CAC atom GROUP MODIfy ATOM 1SG TYPE=S CHARge=-0.19 END GROUP MODIfy ATOM 2CAC TYPE=CH1E CHARGE=0.03 END MODIfy ATOM 2CBC TYPE=CH3E CHARGE=-0.10 END ADD BOND 1SG 2CAC ADD ANGLe 1CB 1SG 2CAC ADD ANGLe 1SG 2CAC 2CBB ADD ANGLe 1SG 2CAC 2C3C ADD DIHEdral 1CB 1SG 2CAC 2C3B ADD IMPRoper 2CAC 1SG 2C3C 2CBC END {* PCYC *} !-------------------------------------------------------------------------- PRES GLUA ! Patch to change deprotonated GLU to protonated glutamine ! has to be patched as REFErence=NIL= GROUp MODIFY ATOM CB TYPE=CH2E CHARge= 0.10 END !# GROUp MODIFY ATOM CG TYPE=CH2E CHARge= 0.15 END !# MODIFY ATOM CD TYPE=C CHARge= 0.40 END !# MODIFY ATOM OE1 TYPE=OC CHARge=-0.40 END !# MODIFY ATOM OE2 TYPE=OH1 CHARge=-0.50 END !# ADD ATOM HE TYPE=H CHARge= 0.25 END !# ADD BOND OE2 HE ADD ANGLe CD OE2 HE ADD DIHEdral OE1 CD OE2 HE DELETE ACCEptor OE2 CD ADD DONOr HE OE2 END {GLUA} !-------------------------------------------------------------------------- PRES HISD ! Patch to change doubly protonated HIS to singly ! protonated histidine (HD1) ! has to be patched as REFErence=NIL= GROUP MODIFY ATOM CB TYPE=CH2E CHARge= 0.00 END GROUP MODIFY ATOM CG TYPE=C CHARge= 0.10 END !# MODIFY ATOM ND1 TYPE=NH1 CHARge=-0.40 END !# MODIFY ATOM HD1 TYPE=H CHARge= 0.30 END !# GROUP MODIFY ATOM CD2 TYPE=CR1E CHARge= 0.10 END !# MODIFY ATOM NE2 TYPE=NR CHARge=-0.40 END !# MODIFY ATOM CE1 TYPE=CR1E CHARge= 0.30 END !# DELETE ATOM HE2 END ADD ACCEPTOR NE2 " " END {HISD} !-------------------------------------------------------------------- PRES HIBD ! Patch to change doubly protonated HIS to singly ! protonated histidine (HD1) (MOPAC calculation for ! patch to Mg(2+) in Bchl b (BCL) ! has to be patched as REFErence=NIL= GROUP MODIFY ATOM CB TYPE=CH2E CHARge= 0.15 END GROUP MODIFY ATOM CG TYPE=C CHARge= 0.04 END !# MODIFY ATOM ND1 TYPE=NH1 CHARge=-0.17 END !# MODIFY ATOM HD1 TYPE=H CHARge= 0.27 END !# GROUP MODIFY ATOM CD2 TYPE=CR1E CHARge= 0.01 END !# MODIFY ATOM NE2 TYPE=NR CHARge=-0.67 END !# MODIFY ATOM CE1 TYPE=CR1E CHARge= 0.37 END !# DELETE ATOM HE2 END ADD ACCEPTOR NE2 " " END {HISD} !-------------------------------------------------------------------------- PRESidue PBCL ! Patch for BCL. Patch residues must be 1-HIS, and 2-BCL. BOND 1NE2 2MG ANGLe 1CD2 1NE2 2MG ANGLe 1CE1 1NE2 2MG ANGLe 1NE2 2MG 2NA ANGLe 1NE2 2MG 2NB ANGLe 1NE2 2MG 2NC ANGLe 1NE2 2MG 2ND ! DIHEdral 1CD2 1NE2 2MG 2NA IC 1CD2 1NE2 2MG 2NA 0.0 0.0 0.0 0.0 0.0 IC 1CD2 1NE2 2MG 2NB 0.0 0.0 0.0 0.0 0.0 IC 1CD2 1NE2 2MG 2NB 0.0 0.0 0.0 0.0 0.0 IC 1CD2 1NE2 2MG 2NB 0.0 0.0 0.0 0.0 0.0 IC 1CE1 1NE2 2MG 2NA 0.0 0.0 0.0 0.0 0.0 END {* PBCL *} !-------------------------------------------------------------------------- PRESidue PFE ! Patch for FE 2+ . Patch residues must be 1-HIS, and 2-FE1. ADD BOND 1NE2 2FE ADD ANGLe 1CD2 1NE2 2FE ADD ANGLe 1CE1 1NE2 2FE MODIFY ATOM 1NE2 TYPE=NR CHARge=-0.65 END !# END {* PFE *} !-------------------------------------------------------------------------- PRESidue FEGL ! Patch for FE 2+ . Patch residues must be 1-GLU, and 2-FE1. ADD BOND 1OE1 2FE ADD BOND 1OE2 2FE ADD ANGLe 1CD 1OE1 2FE ADD ANGLe 1CD 1OE2 2FE GROUp MODIFY ATOM CB TYPE=CH2E CHARge= 0.06 END !# GROUp MODIFY ATOM CG TYPE=CH2E CHARge= 0.08 END !# MODIFY ATOM CD TYPE=C CHARge= 0.36 END !# MODIFY ATOM OE1 TYPE=OC CHARge=-0.75 END !# MODIFY ATOM OE2 TYPE=OC CHARge=-0.75 END !# END {* PFE *} ! --------------------------------------------------------------------- ! ! Following: ! special protein residues used in the reaction center ! ! --------------------------------------------------------------------- RESIdue FME ! Formylmethionine ! use in connection with TFME to repair NTER patch GROUp ATOM OF TYPE=O CHARGE=-0.55 END ATOM CF TYPE=CR1E CHARGE= 0.58 END GROUp ATOM N TYPE=NH1 CHARge=-0.38 END ATOM H TYPE=H CHARge= 0.25 END ATOM CA TYPE=CH1E CHARge= 0.10 END ! different MOPAC charges: GROUp ATOM CB TYPE=CH2E CHARge= 0.00 END !-0.02 GROUp ATOM CG TYPE=CH2E CHARge= 0.06 END ! 0.07 ATOM SD TYPE=S CHARge=-0.12 END !-0.15 ATOM CE TYPE=CH3E CHARge= 0.06 END ! 0.09 GROUp ATOM C TYPE=C CHARge= 0.55 END !# ATOM O TYPE=O CHARge=-0.55 END !# BOND OF CF BOND CF N BOND N CA BOND CA C BOND C O BOND N H BOND CA CB BOND CB CG BOND CG SD BOND SD CE DIHEdral OF CF N CA DIHEdral N CA CB CG DIHEdral CA CB CG SD DIHEdral CB CG SD CE IMPRoper CA N C CB !tetrahedral CA DONOr H N ACCEptor O C ACCEptor OF CF END {FME} !------------------------------------------------------------------ PRESidue TFME { UNDO THE PATCH TO NTER-FME } GROUp DELETE ATOM HT1 TYPE=HC END DELETE ATOM HT2 TYPE=HC END MODIfy ATOM N TYPE=NH1 CHARge=-0.38 END DELETE ATOM HT3 TYPE=HC END ADD ATOM H TYPE=H CHARge= 0.25 END MODIfy ATOM CA TYPE=CH1E CHARge= 0.10 END ADD BOND H N ADD ANGLE H N CA ADD DIHEdral H N CA C ADD DONOr H N END {TFME} !------------------------------------------------------------------ RESIdue CPR GROUp ATOM N TYPE=N CHARge=-0.20 END ATOM CD TYPE=CH2E CHARge= 0.10 END ATOM CA TYPE=CH1E CHARge= 0.10 END GROUp ATOM CB TYPE=CH2E CHARge= 0.00 END ATOM CG TYPE=CH2E CHARge= 0.00 END GROUp ATOM C TYPE=C CHARge= 0.55 END ATOM O TYPE=O CHARge=-0.55 END BOND N CA BOND CA C BOND C O BOND N CD BOND CA CB BOND CB CG BOND CG CD DIHEdral N CA CB CG !! DIHEdral CA CB CG CD !! DIHEdral CB CG CD N !! the PROline ring is represented by dihedrals DIHEdral CG CD N CA !! IMPRoper CA N C CB !tetrahedral CA ACCEptor O C IC N C *CA CB 0.0000 0.00 -120.00 0.00 0.0000 IC N CA CB CG 0.0000 0.00 0.00 0.00 0.0000 END {CPR} !-------------------------------------------------------------------- ! !Following patches are used for charge transfer ! ! BCMP --------> BPL ! e- ! !-------------------------------------------------------------------- PRESidue BMPP ! Patch from residue BCL to ! Bacteriochlorophyll b BCMP in the SPECIAL PAIR of ! the reaction-center ! Charge 1.0 ! Charge distribution from MOPAC calculations ! NO planar C4B, OBB, CBB, C3B !!!!! GROUp MODIFY ATOM MG TYPE=MG CHARGE=2.00 END MODIFY ATOM NA TYPE=NP CHARGE=-0.60 END MODIFY ATOM NB TYPE=NP CHARGE=-0.61 END MODIFY ATOM NC TYPE=NP CHARGE=-0.66 END MODIFY ATOM ND TYPE=NP CHARGE=-0.66 END GROUp MODIFY ATOM C1A TYPE=CPA CHARGE=0.25 END MODIFY ATOM CHA TYPE=C CHARGE=-0.14 END MODIFY ATOM C4D TYPE=CPA CHARGE=0.22 END GROUp MODIFY ATOM C1B TYPE=CPA CHARGE=0.07 END MODIFY ATOM CHB TYPE=CPM CHARGE=0.00 END MODIFY ATOM C4A TYPE=CPA CHARGE=0.16 END GROUp MODIFY ATOM C1C TYPE=CPA CHARGE=0.18 END MODIFY ATOM CHC TYPE=CPM CHARGE=-0.08 END MODIFY ATOM C4B TYPE=CPA CHARGE=0.20 END GROUp MODIFY ATOM C1D TYPE=CPA CHARGE=0.20 END MODIFY ATOM CHD TYPE=CPM CHARGE=-0.04 END MODIFY ATOM C4C TYPE=CPA CHARGE=0.28 END GROUp MODIFY ATOM C2A TYPE=CH1E CHARGE=0.04 END MODIFY ATOM CAA TYPE=CH2E CHARGE=0.05 END GROUp MODIFY ATOM C3A TYPE=CH1E CHARGE=0.00 END MODIFY ATOM CMA TYPE=CH3E CHARGE=0.11 END GROUp MODIFY ATOM C2B TYPE=CPB CHARGE=0.01 END MODIFY ATOM CMB TYPE=CH3E CHARGE=0.13 END GROUp MODIFY ATOM C3B TYPE=CPB CHARGE=-0.29 END !! MODIFY ATOM CAB TYPE=C CHARGE=0.47 END !! not MODIFY ATOM CBB TYPE=CH3E CHARGE=0.17 END !! planar !!!! MODIFY ATOM OBB TYPE=O CHARGE=-0.85 END !! GROUp MODIFY ATOM C2C TYPE=CH1E CHARGE=0.07 END MODIFY ATOM CMC TYPE=CH3E CHARGE=0.10 END GROUp MODIFY ATOM C3C TYPE=C CHARGE=-0.22 END MODIFY ATOM CAC TYPE=CR1E CHARGE=0.22 END MODIFY ATOM CBC TYPE=CH3E CHARGE=0.11 END GROUp MODIFY ATOM C2D TYPE=CPB CHARGE=0.05 END MODIFY ATOM CMD TYPE=CH3E CHARGE=0.17 END GROUp MODIFY ATOM C3D TYPE=CPB CHARGE=-0.15 END MODIFY ATOM CAD TYPE=C CHARGE=0.47 END MODIFY ATOM OBD TYPE=O CHARGE=-0.40 END GROUp MODIFY ATOM CBD TYPE=CH1E CHARGE=0.06 END MODIFY ATOM CGD TYPE=C CHARGE=0.53 END MODIFY ATOM O1D TYPE=OC CHARGE=-0.51 END MODIFY ATOM O2D TYPE=OS CHARGE=-0.52 END MODIFY ATOM CED TYPE=CH3E CHARGE=0.44 END GROUp MODIFY ATOM CBA TYPE=CH2E CHARGE=0.02 END MODIFY ATOM CGA TYPE=C CHARGE=0.54 END MODIFY ATOM O1A TYPE=O CHARGE=-0.48 END GROUp ! Phytol residue MODIFY ATOM O2A TYPE=OS CHARGE=-0.51 END MODIFY ATOM CP1 TYPE=CH2E CHARGE=0.45 END MODIFY ATOM CP2 TYPE=CPM CHARGE=-0.11 END MODIFY ATOM CP3 TYPE=CPA CHARGE=-0.07 END MODIFY ATOM CP4 TYPE=CH3E CHARGE=0.07 END MODIFY ATOM CP5 TYPE=CH2E CHARGE=0.05 END MODIFY ATOM CP6 TYPE=CH2E CHARGE=0.00 END MODIFY ATOM CP7 TYPE=CH2E CHARGE=0.06 END MODIFY ATOM CP8 TYPE=CH1E CHARGE=-0.05 END MODIFY ATOM CP9 TYPE=CH3E CHARGE=0.02 END MODIFY ATOM CP10 TYPE=CH2E CHARGE=0.00 END MODIFY ATOM CP11 TYPE=CH2E CHARGE=0.00 END MODIFY ATOM CP12 TYPE=CH2E CHARGE=0.00 END MODIFY ATOM CP13 TYPE=CH1E CHARGE=-0.04 END MODIFY ATOM CP14 TYPE=CH3E CHARGE=0.02 END MODIFY ATOM CP15 TYPE=CH2E CHARGE=0.01 END MODIFY ATOM CP16 TYPE=CH2E CHARGE=0.00 END MODIFY ATOM CP17 TYPE=CH2E CHARGE=0.01 END MODIFY ATOM CP18 TYPE=CH1E CHARGE=-0.06 END MODIFY ATOM CP19 TYPE=CH3E CHARGE=0.02 END MODIFY ATOM CP20 TYPE=CH3E CHARGE=0.02 END END {BMPP} !-------------------------------------------------------------------- PRESidue BPHC ! Patch to charged Bacteriopheophytin b BPL ! Charge -1.0 ! Charge distribution from MOPAC calculations GROUp MODIFY ATOM NA TYPE=NP CHARGE=-0.33 END MODIFY ATOM NB TYPE=NH1 CHARGE=-0.15 END MODIFY ATOM HB TYPE=H CHARGE=0.25 END MODIFY ATOM NC TYPE=NP CHARGE=-0.34 END MODIFY ATOM ND TYPE=NH1 CHARGE=-0.14 END MODIFY ATOM HD TYPE=H CHARGE=0.26 END GROUp MODIFY ATOM C1A TYPE=CPA CHARGE=0.12 END MODIFY ATOM CHA TYPE=C CHARGE=-0.21 END MODIFY ATOM C4D TYPE=CPA CHARGE=0.14 END GROUp MODIFY ATOM C1B TYPE=CPA CHARGE=0.01 END MODIFY ATOM CHB TYPE=CPM CHARGE=-0.06 END MODIFY ATOM C4A TYPE=CPA CHARGE=0.02 END GROUp MODIFY ATOM C1C TYPE=CPA CHARGE=0.06 END MODIFY ATOM CHC TYPE=CPM CHARGE=-0.11 END MODIFY ATOM C4B TYPE=CPA CHARGE=0.13 END GROUp MODIFY ATOM C1D TYPE=CPA CHARGE=0.00 END MODIFY ATOM CHD TYPE=CPM CHARGE=-0.04 END MODIFY ATOM C4C TYPE=CPA CHARGE=0.03 END GROUp MODIFY ATOM C2A TYPE=CH1E CHARGE=0.02 END MODIFY ATOM CAA TYPE=CH2E CHARGE=0.00 END GROUp MODIFY ATOM C3A TYPE=CH1E CHARGE=0.00 END MODIFY ATOM CMA TYPE=CH3E CHARGE=0.01 END GROUp MODIFY ATOM C2B TYPE=CPB CHARGE=-0.04 END MODIFY ATOM CMB TYPE=CH3E CHARGE=0.06 END GROUp MODIFY ATOM C3B TYPE=CPB CHARGE=-0.22 END MODIFY ATOM CAB TYPE=C CHARGE=0.44 END MODIFY ATOM CBB TYPE=CH3E CHARGE=-0.08 END MODIFY ATOM OBB TYPE=O CHARGE=-0.52 END GROUp MODIFY ATOM C2C TYPE=CH1E CHARGE=0.09 END MODIFY ATOM CMC TYPE=CH3E CHARGE=-0.01 END GROUp MODIFY ATOM C3C TYPE=C CHARGE=-0.11 END MODIFY ATOM CAC TYPE=CR1E CHARGE=0.02 END MODIFY ATOM CBC TYPE=CH3E CHARGE=-0.04 END GROUp MODIFY ATOM C2D TYPE=CPB CHARGE=-0.01 END MODIFY ATOM CMD TYPE=CH3E CHARGE=0.09 END GROUp MODIFY ATOM C3D TYPE=CPB CHARGE=-0.27 END MODIFY ATOM CAD TYPE=C CHARGE=0.53 END MODIFY ATOM OBD TYPE=O CHARGE=-0.55 END GROUp MODIFY ATOM CBD TYPE=CH1E CHARGE=0.06 END MODIFY ATOM CGD TYPE=C CHARGE=0.53 END MODIFY ATOM O1D TYPE=OC CHARGE=-0.54 END MODIFY ATOM O2D TYPE=OS CHARGE=-0.48 END MODIFY ATOM CED TYPE=CH3E CHARGE=0.41 END GROUp MODIFY ATOM CBA TYPE=CH2E CHARGE=0.06 END MODIFY ATOM CGA TYPE=C CHARGE=0.54 END MODIFY ATOM O1A TYPE=O CHARGE=-0.50 END GROUp ! Phytol residue MODIFY ATOM O2A TYPE=OS CHARGE=-0.54 END MODIFY ATOM CP1 TYPE=CH2E CHARGE=0.46 END MODIFY ATOM CP2 TYPE=CPM CHARGE=-0.06 END MODIFY ATOM CP3 TYPE=CPA CHARGE=-0.11 END MODIFY ATOM CP4 TYPE=CH3E CHARGE=0.07 END MODIFY ATOM CP5 TYPE=CH2E CHARGE=0.05 END MODIFY ATOM CP6 TYPE=CH2E CHARGE=0.00 END MODIFY ATOM CP7 TYPE=CH2E CHARGE=0.05 END MODIFY ATOM CP8 TYPE=CH1E CHARGE=-0.05 END MODIFY ATOM CP9 TYPE=CH3E CHARGE=0.02 END MODIFY ATOM CP10 TYPE=CH2E CHARGE=0.00 END MODIFY ATOM CP11 TYPE=CH2E CHARGE=0.00 END MODIFY ATOM CP12 TYPE=CH2E CHARGE=0.00 END MODIFY ATOM CP13 TYPE=CH1E CHARGE=-0.04 END MODIFY ATOM CP14 TYPE=CH3E CHARGE=0.02 END MODIFY ATOM CP15 TYPE=CH2E CHARGE=0.01 END MODIFY ATOM CP16 TYPE=CH2E CHARGE=0.00 END MODIFY ATOM CP17 TYPE=CH2E CHARGE=0.01 END MODIFY ATOM CP18 TYPE=CH1E CHARGE=-0.06 END MODIFY ATOM CP19 TYPE=CH3E CHARGE=0.02 END MODIFY ATOM CP20 TYPE=CH3E CHARGE=0.02 END END {BPHC} !-------------------------------------------------------------------- PRESidue BCHC ! Patch to charged Bacteriochlorophyll b BCLA ! Charge -1.0 ! Charge distribution from MOPAC calculations GROUp MODIFY ATOM MG TYPE=MG CHARGE=2.00 END MODIFY ATOM NA TYPE=NP CHARGE=-0.60 END MODIFY ATOM NB TYPE=NP CHARGE=-0.55 END MODIFY ATOM NC TYPE=NP CHARGE=-0.60 END MODIFY ATOM ND TYPE=NP CHARGE=-0.55 END GROUp MODIFY ATOM C1A TYPE=CPA CHARGE=0.14 END MODIFY ATOM CHA TYPE=C CHARGE=-0.20 END MODIFY ATOM C4D TYPE=CPA CHARGE=0.10 END GROUp MODIFY ATOM C1B TYPE=CPA CHARGE=-0.04 END MODIFY ATOM CHB TYPE=CPM CHARGE=-0.10 END MODIFY ATOM C4A TYPE=CPA CHARGE=0.01 END GROUp MODIFY ATOM C1C TYPE=CPA CHARGE=0.06 END MODIFY ATOM CHC TYPE=CPM CHARGE=-0.11 END MODIFY ATOM C4B TYPE=CPA CHARGE=0.10 END GROUp MODIFY ATOM C1D TYPE=CPA CHARGE=0.0 END MODIFY ATOM CHD TYPE=CPM CHARGE=-0.07 END MODIFY ATOM C4C TYPE=CPA CHARGE=0.05 END GROUp MODIFY ATOM C2A TYPE=CH1E CHARGE=0.02 END MODIFY ATOM CAA TYPE=CH2E CHARGE=0.00 END GROUp MODIFY ATOM C3A TYPE=CH1E CHARGE=0.00 END MODIFY ATOM CMA TYPE=CH3E CHARGE=0.01 END GROUp MODIFY ATOM C2B TYPE=CPB CHARGE=-0.06 END MODIFY ATOM CMB TYPE=CH3E CHARGE=0.07 END GROUp MODIFY ATOM C3B TYPE=CPB CHARGE=-0.22 END MODIFY ATOM CAB TYPE=C CHARGE=0.44 END MODIFY ATOM CBB TYPE=CH3E CHARGE=-0.08 END MODIFY ATOM OBB TYPE=O CHARGE=-0.52 END GROUp MODIFY ATOM C2C TYPE=CH1E CHARGE=0.09 END MODIFY ATOM CMC TYPE=CH3E CHARGE=0.00 END GROUp MODIFY ATOM C3C TYPE=C CHARGE=-0.11 END MODIFY ATOM CAC TYPE=CR1E CHARGE=0.02 END MODIFY ATOM CBC TYPE=CH3E CHARGE=-0.04 END GROUp MODIFY ATOM C2D TYPE=CPB CHARGE=-0.01 END MODIFY ATOM CMD TYPE=CH3E CHARGE=0.09 END GROUp MODIFY ATOM C3D TYPE=CPB CHARGE=-0.27 END MODIFY ATOM CAD TYPE=C CHARGE=0.53 END MODIFY ATOM OBD TYPE=O CHARGE=-0.55 END GROUp MODIFY ATOM CBD TYPE=CH1E CHARGE=0.06 END MODIFY ATOM CGD TYPE=C CHARGE=0.53 END MODIFY ATOM O1D TYPE=OC CHARGE=-0.54 END MODIFY ATOM O2D TYPE=OS CHARGE=-0.48 END MODIFY ATOM CED TYPE=CH3E CHARGE=0.41 END GROUp MODIFY ATOM CBA TYPE=CH2E CHARGE=0.06 END MODIFY ATOM CGA TYPE=C CHARGE=0.54 END MODIFY ATOM O1A TYPE=O CHARGE=-0.50 END GROUp ! Phytol residue MODIFY ATOM O2A TYPE=OS CHARGE=-0.54 END MODIFY ATOM CP1 TYPE=CH2E CHARGE=0.46 END MODIFY ATOM CP2 TYPE=CPM CHARGE=-0.06 END MODIFY ATOM CP3 TYPE=CPA CHARGE=-0.11 END MODIFY ATOM CP4 TYPE=CH3E CHARGE=0.07 END MODIFY ATOM CP5 TYPE=CH2E CHARGE=0.05 END MODIFY ATOM CP6 TYPE=CH2E CHARGE=0.00 END MODIFY ATOM CP7 TYPE=CH2E CHARGE=0.05 END MODIFY ATOM CP8 TYPE=CH1E CHARGE=-0.05 END MODIFY ATOM CP9 TYPE=CH3E CHARGE=0.02 END MODIFY ATOM CP10 TYPE=CH2E CHARGE=0.00 END MODIFY ATOM CP11 TYPE=CH2E CHARGE=0.00 END MODIFY ATOM CP12 TYPE=CH2E CHARGE=0.00 END MODIFY ATOM CP13 TYPE=CH1E CHARGE=-0.04 END MODIFY ATOM CP14 TYPE=CH3E CHARGE=0.02 END MODIFY ATOM CP15 TYPE=CH2E CHARGE=0.01 END MODIFY ATOM CP16 TYPE=CH2E CHARGE=0.00 END MODIFY ATOM CP17 TYPE=CH2E CHARGE=0.01 END MODIFY ATOM CP18 TYPE=CH1E CHARGE=-0.06 END MODIFY ATOM CP19 TYPE=CH3E CHARGE=0.02 END MODIFY ATOM CP20 TYPE=CH3E CHARGE=0.02 END END {BCHC} !-------------------------------------------------------------------- set echo=true end