remarks HEME GROUP, LIGANDS AND HISTIDINE FOR X-PLOR remarks (The histidine is asymmmetric, as in AMBER. The toph19(x).pro remarks histidine should be removed before using this) remarks ===================================== remarks John Kuriyan 19/may/1986 SET ECHO=FALSE END AUTOGENERATE ANGLES=TRUE END {* but see the two omitted angles below *} {*============================ ==================================== *} MASS H 1.00800 ! hydrogen which can h-bond to neutral atom MASS HC 1.00800 ! - " - charged atom MASS HA 1.00800 ! aliphatic hydrogen MASS HT 1.00800 ! TIPS3P WATER HYDROGEN MASS LP 0.0 ! ST2 LONE PAIR MASS CT 12.01100 ! aliphatic carbon MASS C 12.01100 ! carbonyl carbon MASS CH1E 13.01900 ! extended atom carbon w/ one hydrogen MASS CH2E 14.02700 ! - " - two MASS CH3E 15.03500 ! - " - three MASS CR1E 13.01900 ! - " - in aromatic ring w/ one H MASS CM 12.01100 ! carbon in carbonmonoxide MASS N 14.00670 ! peptide nitrogen with no hydrogens attached MASS NR 14.00670 ! nitrogen in 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 -"- MASS NH3 14.00670 ! nitrogen bound to three hydrogens MASS NC2 14.00670 ! charged guanidinuim nitrogen bound to two hydrogens MASS O 15.99940 ! carbonyl oxygen MASS OC 15.99940 ! carboxy oxygen MASS OH1 15.99940 ! hydroxy oxygen MASS OH2 15.99940 ! ST2 water oxygen MASS OM 15.99940 ! oxygen in carbonmonoxide MASS OT 15.99940 ! TIPS3P WATER OXYGEN MASS OS 15.99940 ! ester oxygen MASS S 32.06000 ! sulphur MASS SH1E 33.06800 ! extended atom sulphur with one hydrogen 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 FE 55.84700 ! iroN MASS CPA 12.01100 ! HEME SP2 CARBON MASS CPB 12.01100 ! HEME SP2 CARBON MASS CPM 13.01900 ! HEME MESO CARBON, EXTENDED RESI HIS { SINGLY PROTONATED HISTIDINE} {Rings charges from Del Bene and Cohen} {JACS 100:5285 (1978) Imidazole sto-3g calc.} {This HIS residue has AMBER atom types; the parameters} {make the ring asymmetrical.} GROU ATOM N TYPE NH1 CHARGE -0.35 END ATOM H TYPE H CHARGE 0.25 END ATOM CA TYPE CH1E CHARGE 0.10 END GROU ATOM CB TYPE CH2E CHARGE 0.00 END GROUP ATOM CG TYPE CC CHARGE 0.10 END ATOM ND1 TYPE NA CHARGE -0.40 END ATOM HD1 TYPE H CHARGE 0.30 END GROU ATOM CD2 TYPE CF CHARGE 0.10 END ATOM NE2 TYPE NB CHARGE -0.40 END ATOM CE1 TYPE CP CHARGE 0.30 END GROU 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 H BOND CA CB BOND CB CG BOND CG ND1 BOND CG CD2 BOND ND1 HD1 BOND ND1 CE1 BOND CD2 NE2 BOND CE1 NE2 DIHE N CA CB CG DIHE CA CB CG ND1 IMPR CA N C CB IMPR CG ND1 CD2 CB IMPR ND1 CG CE1 HD1 IMPR CG ND1 CE1 NE2 IMPR ND1 CE1 NE2 CD2 IMPR CE1 NE2 CD2 CG IMPR NE2 CD2 CG ND1 IMPR CD2 CG ND1 CE1 DONOr H N DONOr HD1 ND1 ACCEptor 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 END {HISTIDINE} remark THE HEME GROUP WHICH FOLLOWS IS FOR THE LIGANDED FE(II) STATE remark WITH PERFECT D4H SYMMETRY. THE ATOM TYPES USED ARE FOR remark 19MAY86 AND THE STRUCTURAL PARAMETERS ARE TAKEN FROM remark KITAGAWA, ABE AND OGOSHI J.C.P. 69, (1978) PAGES 4526-4534 remark JOHN KURIYAN 26-OCT-1985/19-MAY-86/19-JULY-86 remark RESI HEME GROU 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 GROU ATOM C1A TYPE CPA CHARGE 0.03 END ATOM CHA TYPE CPM CHARGE 0.04 END ATOM HA TYPE HA CHARGE 0.0 END ATOM C4D TYPE CPA CHARGE 0.02 END GROU ATOM C1B TYPE CPA CHARGE 0.03 END ATOM CHB TYPE CPM CHARGE 0.04 END ATOM HB TYPE HA CHARGE 0.0 END ATOM C4A TYPE CPA CHARGE 0.02 END GROU ATOM C1C TYPE CPA CHARGE 0.03 END ATOM CHC TYPE CPM CHARGE 0.04 END ATOM HC TYPE HA CHARGE 0.0 END ATOM C4B TYPE CPA CHARGE 0.02 END GROU ATOM C1D TYPE CPA CHARGE 0.03 END ATOM CHD TYPE CPM CHARGE 0.04 END ATOM HD TYPE HA CHARGE 0.0 END ATOM C4C TYPE CPA CHARGE 0.02 END GROU ATOM C2A TYPE CPB CHARGE -0.02 END ATOM CAA TYPE CH2E CHARGE 0.04 END GROU ATOM C3A TYPE CPB CHARGE 0.02 END ATOM CMA TYPE CH3E CHARGE -0.04 END GROU 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 GROU ATOM C2B TYPE CPB CHARGE 0.02 END ATOM CMB TYPE CH3E CHARGE -0.04 END GROU ATOM C3B TYPE CPB CHARGE -0.05 END ATOM CAB TYPE CR1E CHARGE 0.03 END ATOM CBB TYPE CH2E CHARGE -0.10 END GROU ATOM C2C TYPE CPB CHARGE 0.02 END ATOM CMC TYPE CH3E CHARGE -0.04 END GROU ATOM C3C TYPE CPB CHARGE -0.05 END ATOM CAC TYPE CR1E CHARGE 0.03 END ATOM CBC TYPE CH2E CHARGE -0.10 END GROU ATOM C2D TYPE CPB CHARGE 0.02 END ATOM CMD TYPE CH3E CHARGE -0.04 END GROU ATOM C3D TYPE CPB CHARGE -0.02 END ATOM CAD TYPE CH2E CHARGE 0.04 END GROU 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 BOND CHA HA BOND CHB HB BOND CHC HC BOND CHD HD {} OMIT ANGLE NA FE NC OMIT ANGLE NB FE ND {} DIHE C1A C2A CAA CBA DIHE C2A CAA CBA CGA DIHE CAA CBA CGA O1A DIHE C2B C3B CAB CBB DIHE C2C C3C CAC CBC DIHE C2D C3D CAD CBD DIHE C3D CAD CBD CGD DIHE CAD CBD CGD O1D {} IMPR C2A C1A C3A CAA IMPR C3A C2A C4A CMA IMPR C2B C1B C3B CMB IMPR C3B C2B C4B CAB IMPR C2C C1C C3C CMC IMPR C3C C2C C4C CAC IMPR C2D C1D C3D CMD IMPR C3D C2D C4D CAD IMPR CBA O1A O2A CGA IMPR CBD O1D O2D CGD {} {} { IMPROPER TORSIONS SELECTED TO MATCH LI AND SPIRO'S TORSIONS AND } { OUT OF PLANE BENDING COORDINATES. ALL DIHEDRALS REMOVED TO MAINTAIN } { QUADRATIC POTENTIAL } {} IMPR C4A NA C1A C2A IMPR C1A NA C4A C3A IMPR C4B NB C1B C2B IMPR C1B NB C4B C3B IMPR C4C NC C1C C2C IMPR C1C NC C4C C3C IMPR C4D ND C1D C2D IMPR C1D ND C4D C3D {} IMPR NA C1A C2A C3A IMPR NA C4A C3A C2A IMPR NB C1B C2B C3B IMPR NB C4B C3B C2B IMPR NC C1C C2C C3C IMPR NC C4C C3C C2C IMPR ND C1D C2D C3D IMPR ND C4D C3D C2D {} IMPR NA C1A CHA C4D IMPR NA C4A CHB C1B IMPR NB C1B CHB C4A IMPR NB C4B CHC C1C IMPR NC C1C CHC C4B IMPR NC C4C CHD C1D IMPR ND C1D CHD C4C IMPR ND C4D CHA C1A {} IMPR CHA C1A C4D HA IMPR CHB C1B C4A HB IMPR CHC C1C C4B HC IMPR CHD C1D C4C HD {} {} IMPR C1A C2A CHA NA IMPR C4A C3A CHB NA IMPR C1B C2B CHB NB IMPR C4B C3B CHC NB IMPR C1C C2C CHC NC IMPR C4C C3C CHD NC IMPR C1D C2D CHD ND IMPR C4D C3D CHA ND {} IMPR NA C1A C4A FE IMPR NB C1B C4B FE IMPR NC C1C C4C FE IMPR ND C1D C4D FE {} 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 C1A *CHA HA 0.0 0.0 180.0 0.0 0.0 IC C4A C1B *CHB HB 0.0 0.0 180.0 0.0 0.0 IC C4B C1C *CHC HC 0.0 0.0 180.0 0.0 0.0 IC C4C C1D *CHD HD 0.0 0.0 180.0 0.0 0.0 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 {HEME} RESIDUE CO GROUP ATOM C TYPE=CM CHARGE= 0.021 END ATOM O TYPE=OM CHARGE= -0.021 END BOND C O END {CO} AUTOGENERATE ANGLES = FALSE END { RESIDUE FEOX IS THE IRON-OXYGEN-IRON LINKAGE IN } { MYOHEMERYTHRIN } RESIDUE FEOX GROUP ATOM FE1 TYPE=FE CHARGE = 0.0 END ATOM FE2 TYPE=FE CHARGE = 0.0 END ATOM OFE TYPE=O CHARGE = 0.0 END BOND FE1 OFE BOND OFE FE2 END {FEOX} { THE AZIDE RESIDUE WHICH FOLLOWS IS A LIGAND FOR THE IRON MOEITY } { IN MYOHEMYRYTHRIN } RESIDUE AZID GROUP ATOM N1 TYPE=N CHARGE = 0.0 END ATOM N2 TYPE=N CHARGE = 0.0 END ATOM N3 TYPE=N CHARGE = 0.0 END BOND N1 N2 BOND N2 N3 ANGLE N1 N2 N3 END { AZIDE } 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 END {* PHEM *} !------------------------------------------------------------------------- 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 END {* PLO2 *} !------------------------------------------------------------------- PRESidue PLIG ! Patch residue for Heme ligand. Residues must be, ! 1-CO , 2-HEME , and 3-HIS BOND 1C 2FE ANGL 1C 2FE 3NE2 ANGLe 1O 1C 2FE ANGLe 1C 2FE 2NA ANGLe 1C 2FE 2NB ANGLe 1C 2FE 2NC ANGle 1C 2FE 2ND END {* PLIG *} SET ECHO=TRUE END