Remarks dud_xplor_top.txt Remarks Created by XPLO2D V. 050802/3.3.2 at Fri Feb 29 17:08:17 2008 for A. Nonymous Remarks Auto-generated by XPLO2D from file dud_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 N_1 14.00700 ! assuming N -> 14.00700 + 1.008 * 0 (Hs) MASS C_2 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS N_3 15.01500 ! assuming N -> 14.00700 + 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 O_7 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS O_8 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS C_9 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_10 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS C_11 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_12 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (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 C_15 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS O_16 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS P_17 30.97400 ! assuming P -> 30.97400 + 1.008 * 0 (Hs) MASS O_18 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS O_19 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS O_20 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS P_21 30.97400 ! assuming P -> 30.97400 + 1.008 * 0 (Hs) MASS O_22 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS O_23 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS O_24 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) autogenerate angles=true end RESIdue DUD { 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 N1 TYPE N_1 CHARge 0.0 END ! Nr of Hs = 0 ATOM C2 TYPE C_2 CHARge 0.0 END ! Nr of Hs = 0 ATOM N3 TYPE N_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 O2 TYPE O_7 CHARge 0.0 END ! Nr of Hs = 0 ATOM O4 TYPE O_8 CHARge 0.0 END ! Nr of Hs = 0 ATOM C1' TYPE C_9 CHARge 0.0 END ! Nr of Hs = 1 ATOM C2' TYPE C_10 CHARge 0.0 END ! Nr of Hs = 2 ATOM C3' TYPE C_11 CHARge 0.0 END ! Nr of Hs = 1 ATOM C4' TYPE C_12 CHARge 0.0 END ! Nr of Hs = 1 ATOM O4' TYPE O_13 CHARge 0.0 END ! Nr of Hs = 0 ATOM O3' TYPE O_14 CHARge 0.0 END ! Nr of Hs = 1 ATOM C5' TYPE C_15 CHARge 0.0 END ! Nr of Hs = 2 ATOM O5' TYPE O_16 CHARge 0.0 END ! Nr of Hs = 0 ATOM PA TYPE P_17 CHARge 0.0 END ! Nr of Hs = 0 ATOM O1A TYPE O_18 CHARge 0.0 END ! Nr of Hs = 1 ATOM O2A TYPE O_19 CHARge 0.0 END ! Nr of Hs = 1 ATOM O3A TYPE O_20 CHARge 0.0 END ! Nr of Hs = 0 ATOM PB TYPE P_21 CHARge 0.0 END ! Nr of Hs = 0 ATOM O1B TYPE O_22 CHARge 0.0 END ! Nr of Hs = 1 ATOM O2B TYPE O_23 CHARge 0.0 END ! Nr of Hs = 1 ATOM O3B TYPE O_24 CHARge 0.0 END ! Nr of Hs = 1 BOND N1 C2 BOND N1 C6 BOND N1 C1' BOND C2 N3 BOND C2 O2 BOND N3 C4 BOND C4 C5 BOND C4 O4 BOND C5 C6 BOND C1' C2' BOND C1' O4' BOND C2' C3' BOND C3' C4' BOND C3' O3' BOND C4' O4' BOND C4' C5' BOND C5' O5' BOND O5' PA BOND PA O1A BOND PA O2A BOND PA O3A BOND O3A PB BOND PB O1B BOND PB O2B BOND PB O3B { Note: edit these DIHEdrals if necessary } DIHEdral C6 N1 C2 N3 ! flat ? (0 degrees = cis) -0.60 DIHEdral C6 N1 C2 O2 ! flat ? (180 degrees = trans) 180.01 DIHEdral C1' N1 C2 N3 ! flat ? (180 degrees = trans) 179.73 DIHEdral C1' N1 C2 O2 ! flat ? (0 degrees = cis) 0.35 DIHEdral C2 N1 C6 C5 ! flat ? (0 degrees = cis) 0.28 DIHEdral C1' N1 C6 C5 ! flat ? (180 degrees = trans) 179.94 ! DIHEdral C2 N1 C1' C2' ! flexible dihedral ??? -60.35 ! DIHEdral C2 N1 C1' O4' ! flexible dihedral ??? 55.15 ! DIHEdral C6 N1 C1' C2' ! flexible dihedral ??? 119.98 ! DIHEdral C6 N1 C1' O4' ! flexible dihedral ??? -124.51 DIHEdral N1 C2 N3 C4 ! flat ? (0 degrees = cis) 0.62 DIHEdral O2 C2 N3 C4 ! flat ? (180 degrees = trans) 180.00 DIHEdral C2 N3 C4 C5 ! flat ? (0 degrees = cis) -0.31 DIHEdral C2 N3 C4 O4 ! flat ? (180 degrees = trans) 179.70 DIHEdral N3 C4 C5 C6 ! flat ? (0 degrees = cis) 0.00 DIHEdral O4 C4 C5 C6 ! flat ? (180 degrees = trans) 179.99 DIHEdral C4 C5 C6 N1 ! flat ? (0 degrees = cis) 0.02 DIHEdral C1' C2' C3' C4' ! flat ? (0 degrees = cis) -0.09 ! DIHEdral C1' C2' C3' O3' ! flexible dihedral ??? 118.67 ! DIHEdral O3' C3' C4' C5' ! flexible dihedral ??? 98.52 DIHEdral C3' C4' C5' O5' ! flat ? (180 degrees = trans) 176.91 ! DIHEdral O4' C4' C5' O5' ! flexible dihedral ??? 61.43 DIHEdral C4' C5' O5' PA ! flat ? (180 degrees = trans) 179.98 ! DIHEdral C5' O5' PA O1A ! flexible dihedral ??? 60.00 ! DIHEdral C5' O5' PA O2A ! flexible dihedral ??? -60.00 DIHEdral C5' O5' PA O3A ! flat ? (180 degrees = trans) 180.01 DIHEdral O5' PA O3A PB ! flat ? (180 degrees = trans) 180.02 ! DIHEdral O1A PA O3A PB ! flexible dihedral ??? -60.00 ! DIHEdral O2A PA O3A PB ! flexible dihedral ??? 60.01 ! DIHEdral PA O3A PB O1B ! flexible dihedral ??? 60.01 DIHEdral PA O3A PB O2B ! flat ? (180 degrees = trans) 179.98 ! DIHEdral PA O3A PB O3B ! flexible dihedral ??? -60.02 { Note: edit these IMPRopers if necessary } IMPRoper N1 C2 C6 C1' ! chirality or flatness improper 0.20 IMPRoper C2 N1 N3 O2 ! chirality or flatness improper 0.35 IMPRoper C4 N3 C5 O4 ! chirality or flatness improper 0.01 IMPRoper C1' N1 C2' O4' ! chirality or flatness improper -36.91 IMPRoper C3' C2' C4' O3' ! chirality or flatness improper -33.59 IMPRoper C4' C3' O4' C5' ! chirality or flatness improper 34.97 IMPRoper PA O5' O1A O2A ! chirality or flatness improper 35.84 IMPRoper PB O3A O1B O2B ! chirality or flatness improper -35.86 { Note: edit any DONOrs and ACCEptors if necessary } ! DONOr H?1 N3 ACCEptor O2 C2 ACCEptor O4 C4 ACCEptor O4' C1' ACCEptor O3' C3' ACCEptor O5' C5' ACCEptor O1A PA ACCEptor O2A PA ACCEptor O3A PA ACCEptor O1B PB ACCEptor O2B PB ACCEptor O3B PB END { RESIdue DUD }