Remarks anp_xplor_top.txt Remarks Created by XPLO2D V. 050802/3.3.2 at Thu Feb 28 19:18:17 2008 for A. Nonymous Remarks Auto-generated by XPLO2D from file anp_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 P_1 30.97400 ! assuming P -> 30.97400 + 1.008 * 0 (Hs) MASS O_2 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS O_3 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS O_4 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS P_5 30.97400 ! assuming P -> 30.97400 + 1.008 * 0 (Hs) MASS O_6 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS O_7 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS N_8 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS P_9 30.97400 ! assuming P -> 30.97400 + 1.008 * 0 (Hs) MASS O_10 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS O_11 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (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 C_14 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS C_15 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS O_16 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS C_17 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS O_18 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS C_19 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS O_20 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS C_21 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS N_22 14.00700 ! assuming N -> 14.00700 + 1.008 * 0 (Hs) MASS C_23 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS N_24 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_25 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_26 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS N_27 14.00700 ! assuming N -> 14.00700 + 1.008 * 0 (Hs) MASS N_28 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_29 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS N_30 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_31 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) autogenerate angles=true end RESIdue ANP { 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 PG TYPE P_1 CHARge 0.0 END ! Nr of Hs = 0 ATOM O1G TYPE O_2 CHARge 0.0 END ! Nr of Hs = 1 ATOM O2G TYPE O_3 CHARge 0.0 END ! Nr of Hs = 1 ATOM O3G TYPE O_4 CHARge 0.0 END ! Nr of Hs = 1 ATOM PB TYPE P_5 CHARge 0.0 END ! Nr of Hs = 0 ATOM O1B TYPE O_6 CHARge 0.0 END ! Nr of Hs = 1 ATOM O2B TYPE O_7 CHARge 0.0 END ! Nr of Hs = 1 ATOM N3B TYPE N_8 CHARge 0.0 END ! Nr of Hs = 1 ATOM PA TYPE P_9 CHARge 0.0 END ! Nr of Hs = 0 ATOM O1A TYPE O_10 CHARge 0.0 END ! Nr of Hs = 1 ATOM O2A TYPE O_11 CHARge 0.0 END ! Nr of Hs = 1 ATOM O3A TYPE O_12 CHARge 0.0 END ! Nr of Hs = 0 ATOM O5' TYPE O_13 CHARge 0.0 END ! Nr of Hs = 0 ATOM C5' TYPE C_14 CHARge 0.0 END ! Nr of Hs = 2 ATOM C4' TYPE C_15 CHARge 0.0 END ! Nr of Hs = 1 ATOM O4' TYPE O_16 CHARge 0.0 END ! Nr of Hs = 0 ATOM C3' TYPE C_17 CHARge 0.0 END ! Nr of Hs = 1 ATOM O3' TYPE O_18 CHARge 0.0 END ! Nr of Hs = 1 ATOM C2' TYPE C_19 CHARge 0.0 END ! Nr of Hs = 1 ATOM O2' TYPE O_20 CHARge 0.0 END ! Nr of Hs = 1 ATOM C1' TYPE C_21 CHARge 0.0 END ! Nr of Hs = 1 ATOM N9 TYPE N_22 CHARge 0.0 END ! Nr of Hs = 0 ATOM C8 TYPE C_23 CHARge 0.0 END ! Nr of Hs = 1 ATOM N7 TYPE N_24 CHARge 0.0 END ! Nr of Hs = 1 ATOM C5 TYPE C_25 CHARge 0.0 END ! Nr of Hs = 0 ATOM C6 TYPE C_26 CHARge 0.0 END ! Nr of Hs = 0 ATOM N6 TYPE N_27 CHARge 0.0 END ! Nr of Hs = 0 ATOM N1 TYPE N_28 CHARge 0.0 END ! Nr of Hs = 1 ATOM C2 TYPE C_29 CHARge 0.0 END ! Nr of Hs = 1 ATOM N3 TYPE N_30 CHARge 0.0 END ! Nr of Hs = 1 ATOM C4 TYPE C_31 CHARge 0.0 END ! Nr of Hs = 0 BOND PG O1G BOND PG O2G BOND PG O3G BOND PG N3B BOND PB O1B BOND PB O2B BOND PB N3B BOND PB O3A BOND PA O1A BOND PA O2A BOND PA O3A BOND PA O5' BOND O5' C5' BOND C5' C4' BOND C4' O4' BOND C4' C3' BOND O4' C1' BOND C3' O3' BOND C3' C2' BOND C2' O2' BOND C2' C1' BOND C1' N9 BOND N9 C8 BOND N9 C4 BOND C8 N7 BOND N7 C5 BOND C5 C6 BOND C5 C4 BOND C6 N6 BOND C6 N1 BOND N1 C2 BOND C2 N3 BOND N3 C4 { Note: edit these DIHEdrals if necessary } ! DIHEdral O1G PG N3B PB ! flexible dihedral ??? 59.98 DIHEdral O2G PG N3B PB ! flat ? (180 degrees = trans) 179.98 ! DIHEdral O3G PG N3B PB ! flexible dihedral ??? -60.00 ! DIHEdral O1B PB N3B PG ! flexible dihedral ??? -60.02 ! DIHEdral O2B PB N3B PG ! flexible dihedral ??? 60.01 DIHEdral O3A PB N3B PG ! flat ? (180 degrees = trans) 180.01 ! DIHEdral O1B PB O3A PA ! flexible dihedral ??? 60.01 ! DIHEdral O2B PB O3A PA ! flexible dihedral ??? -60.00 DIHEdral N3B PB O3A PA ! flat ? (180 degrees = trans) 180.01 ! DIHEdral O1A PA O3A PB ! flexible dihedral ??? -60.00 ! DIHEdral O2A PA O3A PB ! flexible dihedral ??? 59.98 DIHEdral O5' PA O3A PB ! flat ? (180 degrees = trans) 179.98 ! DIHEdral O1A PA O5' C5' ! flexible dihedral ??? 59.99 ! DIHEdral O2A PA O5' C5' ! flexible dihedral ??? -59.97 DIHEdral O3A PA O5' C5' ! flat ? (180 degrees = trans) 180.02 DIHEdral PA O5' C5' C4' ! flat ? (180 degrees = trans) 180.02 ! DIHEdral O5' C5' C4' O4' ! flexible dihedral ??? 61.39 DIHEdral O5' C5' C4' C3' ! flat ? (180 degrees = trans) 176.89 ! DIHEdral C5' C4' C3' O3' ! flexible dihedral ??? 98.32 ! DIHEdral C4' C3' C2' O2' ! flexible dihedral ??? -118.79 DIHEdral C4' C3' C2' C1' ! flat ? (0 degrees = cis) 0.13 DIHEdral O3' C3' C2' O2' ! flat ? (0 degrees = cis) -0.08 ! DIHEdral O3' C3' C2' C1' ! flexible dihedral ??? 118.83 ! DIHEdral O2' C2' C1' N9 ! flexible dihedral ??? -98.52 ! DIHEdral C2' C1' N9 C8 ! flexible dihedral ??? -88.46 ! DIHEdral C2' C1' N9 C4 ! flexible dihedral ??? 91.46 DIHEdral C1' N9 C8 N7 ! flat ? (180 degrees = trans) 179.96 DIHEdral C4 N9 C8 N7 ! flat ? (0 degrees = cis) 0.02 DIHEdral C1' N9 C4 C5 ! flat ? (180 degrees = trans) 180.29 DIHEdral C1' N9 C4 N3 ! flat ? (0 degrees = cis) 0.08 DIHEdral C8 N9 C4 C5 ! flat ? (0 degrees = cis) 0.23 DIHEdral C8 N9 C4 N3 ! flat ? (180 degrees = trans) 180.02 DIHEdral N9 C8 N7 C5 ! flat ? (0 degrees = cis) -0.28 DIHEdral C8 N7 C5 C6 ! flat ? (180 degrees = trans) 179.41 DIHEdral C8 N7 C5 C4 ! flat ? (0 degrees = cis) 0.42 DIHEdral N7 C5 C6 N6 ! flat ? (0 degrees = cis) 0.83 DIHEdral N7 C5 C6 N1 ! flat ? (180 degrees = trans) 180.47 DIHEdral C4 C5 C6 N6 ! flat ? (180 degrees = trans) 179.74 DIHEdral C4 C5 C6 N1 ! flat ? (0 degrees = cis) -0.62 DIHEdral N7 C5 C4 N9 ! flat ? (0 degrees = cis) -0.39 DIHEdral N7 C5 C4 N3 ! flat ? (180 degrees = trans) 179.78 DIHEdral C6 C5 C4 N9 ! flat ? (180 degrees = trans) 180.42 DIHEdral C6 C5 C4 N3 ! flat ? (0 degrees = cis) 0.59 DIHEdral C5 C6 N1 C2 ! flat ? (0 degrees = cis) 0.36 DIHEdral N6 C6 N1 C2 ! flat ? (180 degrees = trans) 180.00 DIHEdral C6 N1 C2 N3 ! flat ? (0 degrees = cis) -0.04 DIHEdral N1 C2 N3 C4 ! flat ? (0 degrees = cis) 0.01 DIHEdral C2 N3 C4 N9 ! flat ? (180 degrees = trans) 179.94 DIHEdral C2 N3 C4 C5 ! flat ? (0 degrees = cis) -0.29 { Note: edit these IMPRopers if necessary } IMPRoper PG O1G O2G O3G ! chirality or flatness improper 35.85 IMPRoper PB O1B O2B N3B ! chirality or flatness improper -36.43 IMPRoper PA O1A O2A O3A ! chirality or flatness improper -35.84 IMPRoper C4' C5' O4' C3' ! chirality or flatness improper -38.08 IMPRoper C3' C4' O3' C2' ! chirality or flatness improper -38.49 IMPRoper C2' C3' O2' C1' ! chirality or flatness improper -38.36 IMPRoper C1' O4' C2' N9 ! chirality or flatness improper 34.51 IMPRoper N9 C1' C8 C4 ! chirality or flatness improper -0.04 IMPRoper C5 N7 C6 C4 ! chirality or flatness improper 0.70 IMPRoper C6 C5 N6 N1 ! chirality or flatness improper -0.21 IMPRoper C4 N9 C5 N3 ! chirality or flatness improper -0.09 { Note: edit any DONOrs and ACCEptors if necessary } ACCEptor O1G PG ACCEptor O2G PG ACCEptor O3G PG ACCEptor O1B PB ACCEptor O2B PB ! DONOr H?1 N3B ACCEptor O1A PA ACCEptor O2A PA ACCEptor O3A PB ACCEptor O5' PA ACCEptor O4' C4' ACCEptor O3' C3' ACCEptor O2' C2' ! DONOr H?1 N7 ! DONOr H?1 N1 ! DONOr H?1 N3 END { RESIdue ANP }