Remarks ahx_xplor_top.txt Remarks Created by XPLO2D V. 050802/3.3.2 at Thu Feb 28 17:39:47 2008 for A. Nonymous Remarks Auto-generated by XPLO2D from file ahx_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 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_2 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_3 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS O_4 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS C_5 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS O_6 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS N_7 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS P_8 30.97400 ! assuming P -> 30.97400 + 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 O_11 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS O_12 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS C_13 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS C_14 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS O_15 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS C_16 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS O_17 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS C_18 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS O_19 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS C_20 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS N_21 14.00700 ! assuming N -> 14.00700 + 1.008 * 0 (Hs) MASS C_22 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS N_23 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_24 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_25 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS N_26 14.00700 ! assuming N -> 14.00700 + 1.008 * 0 (Hs) MASS N_27 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_28 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS N_29 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_30 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) autogenerate angles=true end RESIdue AHX { 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 N10 TYPE N_1 CHARge 0.0 END ! Nr of Hs = 1 ATOM CA TYPE C_2 CHARge 0.0 END ! Nr of Hs = 1 ATOM CB TYPE C_3 CHARge 0.0 END ! Nr of Hs = 2 ATOM OG TYPE O_4 CHARge 0.0 END ! Nr of Hs = 1 ATOM C9 TYPE C_5 CHARge 0.0 END ! Nr of Hs = 0 ATOM O9 TYPE O_6 CHARge 0.0 END ! Nr of Hs = 0 ATOM N8 TYPE N_7 CHARge 0.0 END ! Nr of Hs = 1 ATOM PA TYPE P_8 CHARge 0.0 END ! Nr of Hs = 0 ATOM O1A TYPE O_9 CHARge 0.0 END ! Nr of Hs = 1 ATOM O2A TYPE O_10 CHARge 0.0 END ! Nr of Hs = 1 ATOM O3A TYPE O_11 CHARge 0.0 END ! Nr of Hs = 0 ATOM O5' TYPE O_12 CHARge 0.0 END ! Nr of Hs = 0 ATOM C5' TYPE C_13 CHARge 0.0 END ! Nr of Hs = 2 ATOM C4' TYPE C_14 CHARge 0.0 END ! Nr of Hs = 1 ATOM O4' TYPE O_15 CHARge 0.0 END ! Nr of Hs = 0 ATOM C3' TYPE C_16 CHARge 0.0 END ! Nr of Hs = 1 ATOM O3' TYPE O_17 CHARge 0.0 END ! Nr of Hs = 1 ATOM C2' TYPE C_18 CHARge 0.0 END ! Nr of Hs = 1 ATOM O2' TYPE O_19 CHARge 0.0 END ! Nr of Hs = 1 ATOM C1' TYPE C_20 CHARge 0.0 END ! Nr of Hs = 1 ATOM N9 TYPE N_21 CHARge 0.0 END ! Nr of Hs = 0 ATOM C8 TYPE C_22 CHARge 0.0 END ! Nr of Hs = 1 ATOM N7 TYPE N_23 CHARge 0.0 END ! Nr of Hs = 1 ATOM C5 TYPE C_24 CHARge 0.0 END ! Nr of Hs = 0 ATOM C6 TYPE C_25 CHARge 0.0 END ! Nr of Hs = 0 ATOM N6 TYPE N_26 CHARge 0.0 END ! Nr of Hs = 0 ATOM N1 TYPE N_27 CHARge 0.0 END ! Nr of Hs = 1 ATOM C2 TYPE C_28 CHARge 0.0 END ! Nr of Hs = 1 ATOM N3 TYPE N_29 CHARge 0.0 END ! Nr of Hs = 1 ATOM C4 TYPE C_30 CHARge 0.0 END ! Nr of Hs = 0 BOND N10 CA BOND CA CB BOND CA C9 BOND CB OG BOND C9 O9 BOND C9 N8 BOND N8 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 N10 CA CB OG ! flexible dihedral ??? -59.93 DIHEdral C9 CA CB OG ! flat ? (180 degrees = trans) 180.01 ! DIHEdral CB CA C9 O9 ! flexible dihedral ??? 90.02 ! DIHEdral CB CA C9 N8 ! flexible dihedral ??? -89.96 DIHEdral CA C9 N8 O3A ! flat ? (180 degrees = trans) 179.96 DIHEdral O9 C9 N8 O3A ! flat ? (0 degrees = cis) -0.02 DIHEdral C9 N8 O3A PA ! flat ? (180 degrees = trans) 179.99 ! DIHEdral O1A PA O3A N8 ! flexible dihedral ??? -59.98 ! DIHEdral O2A PA O3A N8 ! flexible dihedral ??? 59.99 DIHEdral O5' PA O3A N8 ! flat ? (180 degrees = trans) 180.03 ! DIHEdral O1A PA O5' C5' ! flexible dihedral ??? 60.02 ! DIHEdral O2A PA O5' C5' ! flexible dihedral ??? -59.96 DIHEdral O3A PA O5' C5' ! flat ? (180 degrees = trans) 180.03 DIHEdral PA O5' C5' C4' ! flat ? (180 degrees = trans) 179.97 ! DIHEdral O5' C5' C4' O4' ! flexible dihedral ??? 61.70 DIHEdral O5' C5' C4' C3' ! flat ? (180 degrees = trans) 179.68 ! DIHEdral C5' C4' C3' O3' ! flexible dihedral ??? 119.86 ! DIHEdral C5' C4' C3' C2' ! flexible dihedral ??? -121.38 ! DIHEdral O4' C4' C3' O3' ! flexible dihedral ??? -120.66 DIHEdral O4' C4' C3' C2' ! flat ? (0 degrees = cis) -1.90 ! DIHEdral O3' C3' C2' C1' ! flexible dihedral ??? 98.01 ! DIHEdral O2' C2' C1' N9 ! flexible dihedral ??? -86.17 ! DIHEdral C2' C1' N9 C8 ! flexible dihedral ??? -85.67 ! DIHEdral C2' C1' N9 C4 ! flexible dihedral ??? 94.14 DIHEdral C1' N9 C8 N7 ! flat ? (180 degrees = trans) 180.03 DIHEdral C4 N9 C8 N7 ! flat ? (0 degrees = cis) 0.18 DIHEdral C1' N9 C4 C5 ! flat ? (180 degrees = trans) 179.80 DIHEdral C1' N9 C4 N3 ! flat ? (0 degrees = cis) 0.69 DIHEdral C8 N9 C4 C5 ! flat ? (0 degrees = cis) -0.36 DIHEdral C8 N9 C4 N3 ! flat ? (180 degrees = trans) 180.53 DIHEdral N9 C8 N7 C5 ! flat ? (0 degrees = cis) 0.08 DIHEdral C8 N7 C5 C6 ! flat ? (180 degrees = trans) 180.03 DIHEdral C8 N7 C5 C4 ! flat ? (0 degrees = cis) -0.30 DIHEdral N7 C5 C6 N6 ! flat ? (0 degrees = cis) -0.05 DIHEdral N7 C5 C6 N1 ! flat ? (180 degrees = trans) 179.91 DIHEdral C4 C5 C6 N6 ! flat ? (180 degrees = trans) 180.31 DIHEdral C4 C5 C6 N1 ! flat ? (0 degrees = cis) 0.27 DIHEdral N7 C5 C4 N9 ! flat ? (0 degrees = cis) 0.40 DIHEdral N7 C5 C4 N3 ! flat ? (180 degrees = trans) 179.68 DIHEdral C6 C5 C4 N9 ! flat ? (180 degrees = trans) 180.13 DIHEdral C6 C5 C4 N3 ! flat ? (0 degrees = cis) -0.58 DIHEdral C5 C6 N1 C2 ! flat ? (0 degrees = cis) 0.04 DIHEdral N6 C6 N1 C2 ! flat ? (180 degrees = trans) 179.99 DIHEdral C6 N1 C2 N3 ! flat ? (0 degrees = cis) -0.03 DIHEdral N1 C2 N3 C4 ! flat ? (0 degrees = cis) -0.31 DIHEdral C2 N3 C4 N9 ! flat ? (180 degrees = trans) 179.63 DIHEdral C2 N3 C4 C5 ! flat ? (0 degrees = cis) 0.61 { Note: edit these IMPRopers if necessary } IMPRoper CA N10 CB C9 ! chirality or flatness improper -35.28 IMPRoper C9 CA O9 N8 ! chirality or flatness improper 0.01 IMPRoper PA O1A O2A O3A ! chirality or flatness improper -35.87 IMPRoper C4' C5' O4' C3' ! chirality or flatness improper -36.83 IMPRoper C3' C4' O3' C2' ! chirality or flatness improper -38.58 IMPRoper C2' C3' O2' C1' ! chirality or flatness improper -39.49 IMPRoper C1' O4' C2' N9 ! chirality or flatness improper 34.31 IMPRoper N9 C1' C8 C4 ! chirality or flatness improper -0.10 IMPRoper C5 N7 C6 C4 ! chirality or flatness improper -0.23 IMPRoper C6 C5 N6 N1 ! chirality or flatness improper -0.03 IMPRoper C4 N9 C5 N3 ! chirality or flatness improper 0.39 { Note: edit any DONOrs and ACCEptors if necessary } ! DONOr H?1 N10 ACCEptor OG CB ACCEptor O9 C9 ! DONOr H?1 N8 ACCEptor O1A PA ACCEptor O2A PA ACCEptor O3A N8 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 AHX }