Remarks originates from ../../tmp/hicup_complex_10177/FON_top.txt Remarks Created by XPLO2D V. 040616/3.2.2 at Mon Aug 16 17:14:57 2004 for A. Nonymous Remarks Auto-generated by XPLO2D from file ../../tmp/hicup_complex_10177/user.pdb Remarks You *MUST* check/edit MASSes and CHARges !!! Remarks Check DONOrs and ACCEptors Remarks Verify IMPRopers yourself Remarks DIHEdrals which are not flat are commented out Remarks edited by John Cort Remarks: Charges are from InsightII. Remarks: This is the final version Remarks: Created 9_24_04 Remarks: Edited 12_3_04 to make equivalent aromatic Remarks: protons wildcardable: C12=C16 & H12=H16 become Remarks: C121,C122 and H121,H122; C13=C15 & H13=H15 become C131,C132 and Remarks: H131,H132 set echo=false end { edit masses if necessary } MASS NX1 14.00700 ! N1, like guanine N3 (type NC) MASS CX2 12.01100 ! C2, like guanine C2 (type CA) MASS HX3 1.00800 ! H21,H22, like guanine amino (type H2) MASS NX3 14.00700 ! NA2, like guanine amino (type N2) MASS HX4 1.00800 ! H3, like guanine imino (type H) MASS NX4 14.00700 ! N3, like guanine imino (type NA) MASS CX5 12.01100 ! C4, like guanine C6 (type C) MASS OX6 15.99900 ! O4, like guanine O6 (type O) MASS CX7 12.01100 ! C4A, like guanine C5 (type CB) MASS NX8 14.00700 ! N5 MASS HX9 1.00800 ! H6 MASS CX9 12.01100 ! C6 MASS HX10 1.00800 ! H71, H72 MASS CX10 12.01100 ! C7 MASS HX11 1.00800 ! H8 MASS NX11 14.00700 ! N8 MASS CX12 12.01100 ! C8A, like guanine C4 (type CB) MASS HX13 1.00800 ! H91, H92 MASS CX13 12.01100 ! C9 MASS HX14 1.00800 ! H10 MASS NX14 14.00700 ! N10 MASS CX15 12.01100 ! C11 MASS HX16 1.00800 ! H121, aryl H, identical to H122 MASS CX16 12.01100 ! C121, aryl C, identical to C122 MASS HX17 1.00800 ! H131, aryl H, identical to H132 MASS CX17 12.01100 ! C131, aryl C, identical to C132 MASS CX18 12.01100 ! C14 MASS HX19 1.00800 ! H132, aryl H, identical to H131 MASS CX19 12.01100 ! C132, aryl C, identical to C131 MASS HX20 1.00800 ! H122, aryl H, identical to H121 MASS CX20 12.01100 ! C122, aryl C, identical to C121 MASS CX21 12.01100 ! C MASS OX22 15.99900 ! O MASS HX23 1.00800 ! H, like Glu (type H) MASS NX23 14.00700 ! N, like Glu (type NH1) MASS HX24 1.00800 ! HA, like Glu (type HA) MASS CX24 12.01100 ! CA, like Glu (type CT) MASS HX25 1.00800 ! HB1,HB2, like Glu (type HA) MASS CX25 12.01100 ! CB, like Glu (type CT) MASS HX26 1.00800 ! HG1,HG2, like Glu (type HA) MASS CX26 12.01100 ! CG, like Glu (type CT MASS CX27 12.01100 ! CD, like Glu (type C) MASS OX28 15.99900 ! OE1 same as OE2, like Glu (type OC) MASS OX29 15.99900 ! OE2 same as OE1, like Glu (type OC) MASS CX30 12.01100 ! CT, like CTER MASS OX31 15.99900 ! O1 same as O2, like CTER MASS OX32 15.99900 ! O2 same as O1, like CTER MASS HX33 1.00800 ! HP1, formyl H MASS CX33 12.01100 ! CP1, formyl C MASS OX34 15.99900 ! O3, formyl O autogenerate angles=true end RESIdue FON GROUP ATOM N1 TYPE NX1 CHARge -0.22 END ! -0.50 topallhdg.dna GUA ATOM C2 TYPE CX2 CHARge 0.33 END ! 0.50 topallhdg.dna GUA ATOM H21 TYPE HX3 CHARge 0.28 END ! 0.21 topallhdg.dna GUA ATOM H22 TYPE HX3 CHARge 0.28 END ! 0.21 topallhdg.dna GUA ATOM NA2 TYPE NX3 CHARge -0.66 END ! -0.42 topallhdg.dna GUA ATOM H3 TYPE HX4 CHARge 0.28 END ! 0.26 topallhdg.dna GUA ATOM N3 TYPE NX4 CHARge -0.39 END ! -0.26 topallhdg.dna GUA ATOM C4 TYPE CX5 CHARge 0.20 END ! 0.30 topallhdg.dna GUA ATOM O4 TYPE OX6 CHARge -0.38 END ! -0.30 topallhdg.dna GUA ATOM C4A TYPE CX7 CHARge 0.29 END ! 0.02 topallhdg.dna GUA ATOM N5 TYPE NX8 CHARge -0.33 END ! ATOM H6 TYPE HX9 CHARge 0.10 END ! ATOM C6 TYPE CX9 CHARge 0.02 END ! ATOM H71 TYPE HX10 CHARge 0.10 END ! ATOM H72 TYPE HX10 CHARge 0.10 END ! ATOM C7 TYPE CX10 CHARge 0.02 END ! ATOM H8 TYPE HX11 CHARge 0.28 END ! ATOM N8 TYPE NX11 CHARge -0.61 END ! ATOM C8A TYPE CX12 CHARge 0.22 END ! 0.19 topallhdg.dna GUA ATOM H91 TYPE HX13 CHARge 0.10 END ! ATOM H92 TYPE HX13 CHARge 0.10 END ! ATOM C9 TYPE CX13 CHARge 0.02 END ! ATOM H10 TYPE HX14 CHARge 0.14 END ! ATOM N10 TYPE NX14 CHARge -0.48 END ! ATOM C11 TYPE CX15 CHARge 0.18 END ! ATOM H121 TYPE HX16 CHARge 0.10 END ! ATOM C121 TYPE CX16 CHARge 0.10 END ! ATOM H131 TYPE HX17 CHARge 0.10 END ! ATOM C131 TYPE CX17 CHARge -0.10 END ! ATOM C14 TYPE CX18 CHARge 0.12 END ! ATOM H132 TYPE HX19 CHARge 0.10 END ! ATOM C132 TYPE CX19 CHARge -0.10 END ! ATOM H122 TYPE HX20 CHARge 0.10 END ! ATOM C122 TYPE CX20 CHARge -0.10 END ! ATOM C TYPE CX21 CHARge 0.20 END ! ATOM O TYPE OX22 CHARge -0.38 END ! ATOM H TYPE HX23 CHARge 0.28 END ! 0.26 topallhdg_new.pro GLU ATOM N TYPE NX23 CHARge -0.38 END ! -0.36 topallhdg_new.pro GLU ATOM HA TYPE HX24 CHARge 0.10 END ! 0.10 topallhdg_new.pro GLU ATOM CA TYPE CX24 CHARge 0.12 END ! 0.00 topallhdg_new.pro GLU ATOM HB1 TYPE HX25 CHARge 0.10 END ! 0.10 topallhdg_new.pro GLU ATOM HB2 TYPE HX25 CHARge 0.10 END ! 0.10 topallhdg_new.pro GLU ATOM CB TYPE CX25 CHARge -0.20 END ! -0.20 topallhdg_new.pro GLU ATOM HG1 TYPE HX26 CHARge 0.10 END ! 0.10 topallhdg_new.pro GLU ATOM HG2 TYPE HX26 CHARge 0.10 END ! 0.10 topallhdg_new.pro GLU ATOM CG TYPE CX26 CHARge -0.20 END ! -0.45 topallhdg_new.pro GLU ATOM CD TYPE CX27 CHARge 0.14 END ! 0.49 topallhdg_new.pro GLU ATOM OE1 TYPE OX28 CHARge -0.57 END ! -0.62 topallhdg_new.pro GLU ATOM OE2 TYPE OX29 CHARge -0.57 END ! -0.62 topallhdg_new.pro GLU ATOM CT TYPE CX30 CHARge 0.14 END ! 0.14 topallhdg_new.pro CTER ATOM O1 TYPE OX31 CHARge -0.57 END ! -0.57 topallhdg_new.pro CTER ATOM O2 TYPE OX32 CHARge -0.57 END ! -0.57 topallhdg_new.pro CTER ATOM HP1 TYPE HX33 CHARge 0.21 END ! ATOM CP1 TYPE CX33 CHARge 0.17 END ! ATOM O3 TYPE OX34 CHARge 0.38 END ! BOND H21 NA2 BOND H22 NA2 BOND H3 N3 BOND H8 N8 BOND H71 C7 BOND H72 C7 BOND H6 C6 BOND H91 C9 BOND H92 C9 BOND H10 N10 BOND H121 C121 BOND H131 C131 BOND H132 C132 BOND H122 C122 BOND HA CA BOND HB1 CB BOND HB2 CB BOND HG1 CG BOND HG2 CG BOND HP1 CP1 BOND N1 C2 BOND N1 C8A BOND C2 NA2 BOND C2 N3 BOND N3 C4 BOND C4 O4 BOND C4 C4A BOND C4A N5 BOND C4A C8A BOND N5 C6 BOND N5 CP1 BOND C6 C7 BOND C6 C9 BOND C7 N8 BOND N8 C8A BOND C9 N10 BOND N10 C14 BOND C11 C121 BOND C11 C122 BOND C11 C BOND C121 C131 BOND C131 C14 BOND C14 C132 BOND C132 C122 BOND C O BOND C N BOND N CA BOND CA CB BOND CA CT BOND CB CG BOND CG CD BOND CD OE1 BOND CD OE2 BOND CT O1 BOND CT O2 BOND CP1 O3 BOND H N { edit these DIHEdrals if necessary } DIHEdral C8A N1 C2 NA2 ! flat ? (180 degrees = trans) 180 DIHEdral C8A N1 C2 N3 ! flat ? (0 degrees = cis) 0 DIHEdral C2 N1 C8A C4A ! flat ? (0 degrees = cis) 0 DIHEdral C2 N1 C8A N8 ! flat ? (180 degrees = trans) 180 DIHEdral N1 C2 N3 C4 ! flat ? (0 degrees = cis) 0 DIHEdral NA2 C2 N3 C4 ! flat ? (180 degrees = trans) 180 DIHEdral C2 N3 C4 O4 ! flat ? (180 degrees = trans) 180 DIHEdral C2 N3 C4 C4A ! flat ? (0 degrees = cis) 0 DIHEdral N3 C4 C4A N5 ! flat ? (180 degrees = trans) 180 DIHEdral N3 C4 C4A C8A ! flat ? (0 degrees = cis) 0 DIHEdral O4 C4 C4A N5 ! flat ? (0 degrees = cis) 0 DIHEdral O4 C4 C4A C8A ! flat ? (180 degrees = trans) 180 DIHEdral C4 C4A C8A N1 ! flat ? (0 degrees = cis) 0 DIHEdral C4 C4A C8A N8 ! flat ? (180 degrees = trans) 180 DIHEdral N5 C4A C8A N1 ! flat ? (180 degrees = trans) 180 DIHEdral N5 C4A C8A N8 ! flat ? (0 degrees = cis) 0 ! DIHEdral C4A N5 C6 C9 ! somewhat flexible dihedral -66.26 ! DIHEdral CP1 N5 C6 C7 ! somewhat flexible dihedral -128.34 ! DIHEdral CP1 N5 C6 C9 ! somewhat flexible same as previous 118.7 ! DIHEdral C4A N5 CP1 O3 ! flat ? need to let it move! 185.90 ! DIHEdral C6 N5 CP1 O3 ! flat ? need to let it move! 1.67 ! DIHEdral N5 C6 C7 N8 ! somewhat flexible dihedral -51.49 ! DIHEdral C9 C6 C7 N8 ! somewhat flexible same as previous 63.67 ! DIHEdral C7 C6 C9 N10 ! flexible dihedral ! DIHEdral C6 C9 N10 C14 ! flexible dihedral DIHEdral C122 C11 C121 C131 ! flat ? (0 degrees = cis) 0 DIHEdral C C11 C121 C131 ! flat ? (180 degrees = trans) 180 DIHEdral C121 C11 C122 C132 ! flat ? (0 degrees = cis) 0 DIHEdral C C11 C122 C132 ! flat ? (180 degrees = trans) 180 ! DIHEdral C121 C11 C O ! flat ? will let this move 180 ! DIHEdral C121 C11 C N ! flat ? will let this move 0 ! DIHEdral C122 C11 C O ! flat ? will let this move 0 ! DIHEdral C122 C11 C N ! flat ? will let this move 180 DIHEdral C121 C131 C14 N10 ! flat ? (180 degrees = trans) 180 DIHEdral N10 C14 C132 C122 ! flat ? (180 degrees = trans) 180 DIHEdral C131 C14 C132 C122 ! flat ? (0 degrees = cis) 0 DIHEdral C14 C132 C122 C11 ! flat ? (0 degrees = cis) 0 ! DIHEdral C N CA CT ! flexible dihedral ??? -87.43 ! DIHEdral CT CA CB CG ! flexible dihedral ??? 69.07 ! DIHEdral N CA CT O1 ! flexible dihedral ??? 121.23 ! DIHEdral N CA CT O2 ! flexible dihedral ??? -60.88 ! DIHEdral CB CA CT O1 ! flexible dihedral ??? -115.50 ! DIHEdral CB CA CT O2 ! flexible dihedral ??? 62.39 DIHEdral O C N CA ! probably flat O DIHEdral H N C O ! probably flat O { edit these IMPRopers if necessary } IMPRoper C2 N1 NA2 N3 ! chirality or flatness improper 0 IMPRoper C4 N3 O4 C4A ! chirality or flatness improper 0 IMPRoper C4A C4 N5 C8A ! chirality or flatness improper 0 IMPRoper N5 C4A C6 CP1 ! chirality or flatness improper 0 IMPRoper C6 N5 C7 C9 ! chirality or flatness improper 38.33 IMPRoper C8A N1 C4A N8 ! chirality or flatness improper 0 IMPRoper C11 C121 C122 C ! chirality or flatness improper 0 IMPRoper C14 N10 C131 C132 ! chirality or flatness improper 0 IMPRoper C C11 O N ! chirality or flatness improper 0 IMPRoper CA N CB CT ! chirality or flatness improper -31.10 IMPRoper CD CG OE1 OE2 ! chirality or flatness improper 0 IMPRoper CT CA O1 O2 ! chirality or flatness improper 0 IMPRoper N H C CA ! chirality or flatness improper 0 IMPRoper HA N CT CB ! Glu Ca chirality 68.89 IMPRoper HB1 HB2 CA CG ! Stereo CB -71.05 IMPRoper HG1 HG2 CB CD ! Stereo CG -68.41 IMPRoper H121 C121 C131 C14 ! aryl ring Hs 180 IMPRoper H131 C131 C14 C132 ! aryl ring Hs 180 IMPRoper H132 C132 C122 C11 ! aryl ring Hs 180 IMPRoper H122 C122 C11 C121 ! aryl ring Hs 180 IMPRoper H91 H92 C6 N10 ! Stereo C9 -69.41 IMPRoper H71 H72 C6 N8 ! Stereo C7 -70.06 IMPRoper CP1 HP1 N5 O3 ! aldehyde H flatness 0.0 IMPRoper H6 N5 C7 C9 ! C6 chirality 69.59 IMPRoper H8 N8 C8A C4A ! H8 flatness 180 IMPRoper H3 N3 C2 N1 ! H3 flatness 180 IMPRoper H3 C2 C4 N3 ! H3 flatness 0.0 ! IMPRoper H10 N10 C14 C132 ! H10 flatness 180 not flat in 1KL2,1PJ7,1QD1,1WOP IMPRoper H21 H22 C2 NA2 ! amino flatness 0.0 IMPRoper H21 NA2 C2 N3 ! amino flatness wrt ring 0.0 { edit any DONOrs and ACCEptors if necessary } DONOr H3 N3 ACCEptor O4 C4 DONOr H8 N8 DONOr H10 N10 ACCEptor O C DONOr H N ACCEptor OE1 CD ACCEptor OE2 CD ACCEptor O1 CT ACCEptor O2 CT ACCEptor O3 CP1 END { RESIdue FON }