Remarks ph9_xplor_top.txt Remarks Created by XPLO2D V. 050802/3.3.2 at Sun Mar 2 10:37:08 2008 for A. Nonymous Remarks Auto-generated by XPLO2D from file ph9_msd.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 set echo=false end { Note: edit masses if necessary } MASS C_1 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_2 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_3 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_4 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_5 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_6 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_7 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_8 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS N_9 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_10 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_11 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS O_12 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS O_13 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS O_14 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS O_15 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS C_16 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_17 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_18 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_19 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_20 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_21 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS BR_2 79.90400 ! assuming BR -> 79.90400 + 1.008 * 0 (Hs) MASS C_23 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS C_24 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_25 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_26 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS C_27 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS C_28 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_29 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS C_30 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_31 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS C_32 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) autogenerate angles=true end RESIdue PH9 { Note: electrostatics should normally not be used in } { crystallographic refinement since it can produce } { artefacts. For this reason, all charges are set to } { zero by default. Edit them if necessary } GROUp ATOM CB2 TYPE C_1 CHARge 0.0 END ! Nr of Hs = 0 ATOM CB3 TYPE C_2 CHARge 0.0 END ! Nr of Hs = 1 ATOM CB4 TYPE C_3 CHARge 0.0 END ! Nr of Hs = 1 ATOM CB6 TYPE C_4 CHARge 0.0 END ! Nr of Hs = 0 ATOM CB5 TYPE C_5 CHARge 0.0 END ! Nr of Hs = 1 ATOM CB1 TYPE C_6 CHARge 0.0 END ! Nr of Hs = 1 ATOM C2 TYPE C_7 CHARge 0.0 END ! Nr of Hs = 1 ATOM C1 TYPE C_8 CHARge 0.0 END ! Nr of Hs = 2 ATOM N TYPE N_9 CHARge 0.0 END ! Nr of Hs = 1 ATOM C TYPE C_10 CHARge 0.0 END ! Nr of Hs = 0 ATOM CO2 TYPE C_11 CHARge 0.0 END ! Nr of Hs = 0 ATOM O TYPE O_12 CHARge 0.0 END ! Nr of Hs = 0 ATOM OC1 TYPE O_13 CHARge 0.0 END ! Nr of Hs = 0 ATOM OC2 TYPE O_14 CHARge 0.0 END ! Nr of Hs = 1 ATOM OAB TYPE O_15 CHARge 0.0 END ! Nr of Hs = 0 ATOM CA1 TYPE C_16 CHARge 0.0 END ! Nr of Hs = 0 ATOM CA2 TYPE C_17 CHARge 0.0 END ! Nr of Hs = 0 ATOM CA3 TYPE C_18 CHARge 0.0 END ! Nr of Hs = 1 ATOM CA4 TYPE C_19 CHARge 0.0 END ! Nr of Hs = 1 ATOM CA5 TYPE C_20 CHARge 0.0 END ! Nr of Hs = 1 ATOM CA6 TYPE C_21 CHARge 0.0 END ! Nr of Hs = 1 ATOM BRA2 TYPE BR_2 CHARge 0.0 END ! Nr of Hs = 0 ATOM CC4 TYPE C_23 CHARge 0.0 END ! Nr of Hs = 2 ATOM CC3 TYPE C_24 CHARge 0.0 END ! Nr of Hs = 1 ATOM CC5 TYPE C_25 CHARge 0.0 END ! Nr of Hs = 1 ATOM CC2 TYPE C_26 CHARge 0.0 END ! Nr of Hs = 2 ATOM CC6 TYPE C_27 CHARge 0.0 END ! Nr of Hs = 2 ATOM CC1 TYPE C_28 CHARge 0.0 END ! Nr of Hs = 0 ATOM C10 TYPE C_29 CHARge 0.0 END ! Nr of Hs = 2 ATOM CC8 TYPE C_30 CHARge 0.0 END ! Nr of Hs = 1 ATOM CC9 TYPE C_31 CHARge 0.0 END ! Nr of Hs = 2 ATOM CC7 TYPE C_32 CHARge 0.0 END ! Nr of Hs = 2 BOND CB2 CB3 BOND CB2 CB1 BOND CB2 C1 BOND CB3 CB4 BOND CB4 CB6 BOND CB6 CB5 BOND CB6 OAB BOND CB5 CB1 BOND C2 C1 BOND C2 N BOND C2 CO2 BOND N C BOND C O BOND C CC1 BOND CO2 OC1 BOND CO2 OC2 BOND OAB CA1 BOND CA1 CA2 BOND CA1 CA6 BOND CA2 CA3 BOND CA2 BRA2 BOND CA3 CA4 BOND CA4 CA5 BOND CA5 CA6 BOND CC4 CC3 BOND CC4 CC5 BOND CC3 CC6 BOND CC3 CC9 BOND CC5 CC2 BOND CC5 C10 BOND CC2 CC1 BOND CC6 CC1 BOND CC1 CC7 BOND C10 CC8 BOND CC8 CC9 BOND CC8 CC7 { Note: edit these DIHEdrals if necessary } DIHEdral CB1 CB2 CB3 CB4 ! flat ? (0 degrees = cis) 0.31 DIHEdral C1 CB2 CB3 CB4 ! flat ? (180 degrees = trans) 179.99 DIHEdral CB3 CB2 CB1 CB5 ! flat ? (0 degrees = cis) -0.55 DIHEdral C1 CB2 CB1 CB5 ! flat ? (180 degrees = trans) 179.77 ! DIHEdral CB3 CB2 C1 C2 ! flexible dihedral ??? 90.04 ! DIHEdral CB1 CB2 C1 C2 ! flexible dihedral ??? -90.28 DIHEdral CB2 CB3 CB4 CB6 ! flat ? (0 degrees = cis) -0.06 DIHEdral CB3 CB4 CB6 CB5 ! flat ? (0 degrees = cis) 0.05 DIHEdral CB3 CB4 CB6 OAB ! flat ? (180 degrees = trans) 180.04 DIHEdral CB4 CB6 CB5 CB1 ! flat ? (0 degrees = cis) -0.29 DIHEdral OAB CB6 CB5 CB1 ! flat ? (180 degrees = trans) 179.72 ! DIHEdral CB4 CB6 OAB CA1 ! flexible dihedral ??? 89.38 ! DIHEdral CB5 CB6 OAB CA1 ! flexible dihedral ??? -90.63 DIHEdral CB6 CB5 CB1 CB2 ! flat ? (0 degrees = cis) 0.54 ! DIHEdral N C2 C1 CB2 ! flexible dihedral ??? 64.95 DIHEdral CO2 C2 C1 CB2 ! flat ? (180 degrees = trans) 184.96 ! DIHEdral CO2 C2 N C ! flexible dihedral ??? 85.01 ! DIHEdral C1 C2 CO2 OC1 ! flexible dihedral ??? -120.02 ! DIHEdral C1 C2 CO2 OC2 ! flexible dihedral ??? 60.00 DIHEdral N C2 CO2 OC1 ! flat ? (0 degrees = cis) -0.03 DIHEdral N C2 CO2 OC2 ! flat ? (180 degrees = trans) 179.99 DIHEdral C2 N C O ! flat ? (0 degrees = cis) 0.00 DIHEdral C2 N C CC1 ! flat ? (180 degrees = trans) 180.00 DIHEdral N C CC1 CC2 ! flat ? (180 degrees = trans) 179.99 ! DIHEdral N C CC1 CC6 ! flexible dihedral ??? -60.02 ! DIHEdral N C CC1 CC7 ! flexible dihedral ??? 60.02 DIHEdral O C CC1 CC2 ! flat ? (0 degrees = cis) -0.01 ! DIHEdral O C CC1 CC6 ! flexible dihedral ??? 119.98 ! DIHEdral O C CC1 CC7 ! flexible dihedral ??? -119.98 DIHEdral CB6 OAB CA1 CA2 ! flat ? (180 degrees = trans) 181.26 DIHEdral CB6 OAB CA1 CA6 ! flat ? (0 degrees = cis) 1.55 DIHEdral OAB CA1 CA2 CA3 ! flat ? (180 degrees = trans) 179.74 DIHEdral OAB CA1 CA2 BRA2 ! flat ? (0 degrees = cis) 0.31 DIHEdral CA6 CA1 CA2 CA3 ! flat ? (0 degrees = cis) -0.55 DIHEdral CA6 CA1 CA2 BRA2 ! flat ? (180 degrees = trans) 180.02 DIHEdral OAB CA1 CA6 CA5 ! flat ? (180 degrees = trans) 179.99 DIHEdral CA2 CA1 CA6 CA5 ! flat ? (0 degrees = cis) 0.28 DIHEdral CA1 CA2 CA3 CA4 ! flat ? (0 degrees = cis) 0.58 DIHEdral BRA2 CA2 CA3 CA4 ! flat ? (180 degrees = trans) 180.00 DIHEdral CA2 CA3 CA4 CA5 ! flat ? (0 degrees = cis) -0.33 DIHEdral CA3 CA4 CA5 CA6 ! flat ? (0 degrees = cis) 0.06 DIHEdral CA4 CA5 CA6 CA1 ! flat ? (0 degrees = cis) -0.03 ! DIHEdral CC5 CC4 CC3 CC6 ! flexible dihedral ??? -59.97 ! DIHEdral CC5 CC4 CC3 CC9 ! flexible dihedral ??? 60.01 ! DIHEdral CC3 CC4 CC5 CC2 ! flexible dihedral ??? 59.97 ! DIHEdral CC3 CC4 CC5 C10 ! flexible dihedral ??? -59.97 ! DIHEdral CC4 CC3 CC6 CC1 ! flexible dihedral ??? 60.00 ! DIHEdral CC9 CC3 CC6 CC1 ! flexible dihedral ??? -59.96 ! DIHEdral CC4 CC3 CC9 CC8 ! flexible dihedral ??? -59.99 ! DIHEdral CC6 CC3 CC9 CC8 ! flexible dihedral ??? 59.96 ! DIHEdral CC4 CC5 CC2 CC1 ! flexible dihedral ??? -59.97 ! DIHEdral C10 CC5 CC2 CC1 ! flexible dihedral ??? 59.99 ! DIHEdral CC4 CC5 C10 CC8 ! flexible dihedral ??? 59.95 ! DIHEdral CC2 CC5 C10 CC8 ! flexible dihedral ??? -60.01 DIHEdral CC5 CC2 CC1 C ! flat ? (180 degrees = trans) 180.01 ! DIHEdral CC5 CC2 CC1 CC6 ! flexible dihedral ??? 60.00 ! DIHEdral CC5 CC2 CC1 CC7 ! flexible dihedral ??? -60.00 DIHEdral CC3 CC6 CC1 C ! flat ? (180 degrees = trans) 180.01 ! DIHEdral CC3 CC6 CC1 CC2 ! flexible dihedral ??? -60.02 ! DIHEdral CC3 CC6 CC1 CC7 ! flexible dihedral ??? 59.96 DIHEdral C CC1 CC7 CC8 ! flat ? (180 degrees = trans) 179.95 ! DIHEdral CC2 CC1 CC7 CC8 ! flexible dihedral ??? 59.99 ! DIHEdral CC6 CC1 CC7 CC8 ! flexible dihedral ??? -59.99 ! DIHEdral CC5 C10 CC8 CC9 ! flexible dihedral ??? -59.99 ! DIHEdral CC5 C10 CC8 CC7 ! flexible dihedral ??? 60.03 ! DIHEdral C10 CC8 CC9 CC3 ! flexible dihedral ??? 60.02 ! DIHEdral CC7 CC8 CC9 CC3 ! flexible dihedral ??? -60.01 ! DIHEdral C10 CC8 CC7 CC1 ! flexible dihedral ??? -60.04 ! DIHEdral CC9 CC8 CC7 CC1 ! flexible dihedral ??? 60.02 { Note: edit these IMPRopers if necessary } IMPRoper CB2 CB3 CB1 C1 ! chirality or flatness improper -0.19 IMPRoper CB6 CB4 CB5 OAB ! chirality or flatness improper 0.00 IMPRoper C2 C1 N CO2 ! chirality or flatness improper -35.34 IMPRoper C N O CC1 ! chirality or flatness improper 0.00 IMPRoper CO2 C2 OC1 OC2 ! chirality or flatness improper 0.01 IMPRoper CA1 OAB CA2 CA6 ! chirality or flatness improper 0.17 IMPRoper CA2 CA1 CA3 BRA2 ! chirality or flatness improper 0.36 IMPRoper CC3 CC4 CC6 CC9 ! chirality or flatness improper -35.27 IMPRoper CC5 CC4 CC2 C10 ! chirality or flatness improper 35.30 IMPRoper CC1 C CC2 CC6 ! chirality or flatness improper -35.35 IMPRoper CC8 C10 CC9 CC7 ! chirality or flatness improper -35.26 { Note: edit any DONOrs and ACCEptors if necessary } ! DONOr H?1 N ACCEptor O C ACCEptor OC1 CO2 ACCEptor OC2 CO2 ACCEptor OAB CB6 END { RESIdue PH9 }