Remarks pnp_xplor_top.txt Remarks Created by XPLO2D V. 050802/3.3.2 at Sun Mar 2 12:14:14 2008 for A. Nonymous Remarks Auto-generated by XPLO2D from file pnp_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 15.03500 ! assuming C -> 12.01100 + 1.008 * 3 (Hs) MASS N_8 14.00700 ! assuming N -> 14.00700 + 1.008 * 0 (Hs) MASS O_9 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS O_10 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS P_11 30.97400 ! assuming P -> 30.97400 + 1.008 * 0 (Hs) MASS O_12 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS O_13 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS O_14 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) autogenerate angles=true end RESIdue PNP { 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 C1 TYPE C_1 CHARge 0.0 END ! Nr of Hs = 0 ATOM C2 TYPE C_2 CHARge 0.0 END ! Nr of Hs = 1 ATOM C3 TYPE C_3 CHARge 0.0 END ! Nr of Hs = 1 ATOM C4 TYPE C_4 CHARge 0.0 END ! Nr of Hs = 0 ATOM C5 TYPE C_5 CHARge 0.0 END ! Nr of Hs = 1 ATOM C6 TYPE C_6 CHARge 0.0 END ! Nr of Hs = 1 ATOM CM TYPE C_7 CHARge 0.0 END ! Nr of Hs = 3 ATOM N TYPE N_8 CHARge 0.0 END ! Nr of Hs = 0 ATOM O1N TYPE O_9 CHARge 0.0 END ! Nr of Hs = 1 ATOM O2N TYPE O_10 CHARge 0.0 END ! Nr of Hs = 1 ATOM P TYPE P_11 CHARge 0.0 END ! Nr of Hs = 0 ATOM O1P TYPE O_12 CHARge 0.0 END ! Nr of Hs = 0 ATOM O2P TYPE O_13 CHARge 0.0 END ! Nr of Hs = 1 ATOM O3P TYPE O_14 CHARge 0.0 END ! Nr of Hs = 1 BOND C1 C2 BOND C1 C6 BOND C1 O1P BOND C2 C3 BOND C3 C4 BOND C4 C5 BOND C4 N BOND C5 C6 BOND CM P BOND N O1N BOND N O2N BOND P O1P BOND P O2P BOND P O3P { Note: edit these DIHEdrals if necessary } DIHEdral C6 C1 C2 C3 ! flat ? (0 degrees = cis) 0.18 DIHEdral O1P C1 C2 C3 ! flat ? (180 degrees = trans) 180.00 DIHEdral C2 C1 C6 C5 ! flat ? (0 degrees = cis) -0.44 DIHEdral O1P C1 C6 C5 ! flat ? (180 degrees = trans) 179.73 ! DIHEdral C2 C1 O1P P ! flexible dihedral ??? 89.95 ! DIHEdral C6 C1 O1P P ! flexible dihedral ??? -90.23 DIHEdral C1 C2 C3 C4 ! flat ? (0 degrees = cis) 0.01 DIHEdral C2 C3 C4 C5 ! flat ? (0 degrees = cis) 0.06 DIHEdral C2 C3 C4 N ! flat ? (180 degrees = trans) 179.97 DIHEdral C3 C4 C5 C6 ! flat ? (0 degrees = cis) -0.32 DIHEdral N C4 C5 C6 ! flat ? (180 degrees = trans) 179.77 DIHEdral C3 C4 N O1N ! flat ? (180 degrees = trans) 180.01 DIHEdral C3 C4 N O2N ! flat ? (0 degrees = cis) 0.07 DIHEdral C5 C4 N O1N ! flat ? (0 degrees = cis) -0.08 DIHEdral C5 C4 N O2N ! flat ? (180 degrees = trans) 179.97 DIHEdral C4 C5 C6 C1 ! flat ? (0 degrees = cis) 0.51 DIHEdral CM P O1P C1 ! flat ? (180 degrees = trans) 180.00 ! DIHEdral O2P P O1P C1 ! flexible dihedral ??? 59.97 ! DIHEdral O3P P O1P C1 ! flexible dihedral ??? -59.95 { Note: edit these IMPRopers if necessary } IMPRoper C1 C2 C6 O1P ! chirality or flatness improper -0.10 IMPRoper C4 C3 C5 N ! chirality or flatness improper -0.05 IMPRoper N C4 O1N O2N ! chirality or flatness improper 0.03 IMPRoper P CM O1P O2P ! chirality or flatness improper -33.32 { Note: edit any DONOrs and ACCEptors if necessary } ACCEptor O1N N ACCEptor O2N N ACCEptor O1P C1 ACCEptor O2P P ACCEptor O3P P END { RESIdue PNP }