Remarks ads_xplor_top.txt Remarks Created by XPLO2D V. 050802/3.3.2 at Thu Feb 28 16:46:48 2008 for A. Nonymous Remarks Auto-generated by XPLO2D from file ads_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 S_3 33.07400 ! assuming S -> 32.06600 + 1.008 * 1 (Hs) MASS S_4 33.07400 ! assuming S -> 32.06600 + 1.008 * 1 (Hs) MASS O_5 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS C_6 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS C_7 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (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 O_10 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS C_11 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS O_12 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS C_13 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS N_14 14.00700 ! assuming N -> 14.00700 + 1.008 * 0 (Hs) MASS C_15 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS N_16 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_17 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_18 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS N_19 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS N_20 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_21 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS N_22 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_23 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) autogenerate angles=true end RESIdue ADS { 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 P TYPE P_1 CHARge 0.0 END ! Nr of Hs = 0 ATOM O1P TYPE O_2 CHARge 0.0 END ! Nr of Hs = 1 ATOM S2P TYPE S_3 CHARge 0.0 END ! Nr of Hs = 1 ATOM S3P TYPE S_4 CHARge 0.0 END ! Nr of Hs = 1 ATOM O5' TYPE O_5 CHARge 0.0 END ! Nr of Hs = 0 ATOM C5' TYPE C_6 CHARge 0.0 END ! Nr of Hs = 2 ATOM C4' TYPE C_7 CHARge 0.0 END ! Nr of Hs = 1 ATOM O4' TYPE O_8 CHARge 0.0 END ! Nr of Hs = 0 ATOM C3' TYPE C_9 CHARge 0.0 END ! Nr of Hs = 1 ATOM O3' TYPE O_10 CHARge 0.0 END ! Nr of Hs = 1 ATOM C2' TYPE C_11 CHARge 0.0 END ! Nr of Hs = 1 ATOM O2' TYPE O_12 CHARge 0.0 END ! Nr of Hs = 1 ATOM C1' TYPE C_13 CHARge 0.0 END ! Nr of Hs = 1 ATOM N9 TYPE N_14 CHARge 0.0 END ! Nr of Hs = 0 ATOM C8 TYPE C_15 CHARge 0.0 END ! Nr of Hs = 1 ATOM N7 TYPE N_16 CHARge 0.0 END ! Nr of Hs = 1 ATOM C5 TYPE C_17 CHARge 0.0 END ! Nr of Hs = 0 ATOM C6 TYPE C_18 CHARge 0.0 END ! Nr of Hs = 0 ATOM N6 TYPE N_19 CHARge 0.0 END ! Nr of Hs = 1 ATOM N1 TYPE N_20 CHARge 0.0 END ! Nr of Hs = 1 ATOM C2 TYPE C_21 CHARge 0.0 END ! Nr of Hs = 1 ATOM N3 TYPE N_22 CHARge 0.0 END ! Nr of Hs = 1 ATOM C4 TYPE C_23 CHARge 0.0 END ! Nr of Hs = 0 BOND P O1P BOND P S2P BOND P S3P BOND P 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 O1P P O5' C5' ! flat ? (180 degrees = trans) 179.99 ! DIHEdral S2P P O5' C5' ! flexible dihedral ??? -60.18 ! DIHEdral S3P P O5' C5' ! flexible dihedral ??? 60.52 ! DIHEdral O5' C5' C4' O4' ! flexible dihedral ??? 62.15 DIHEdral O5' C5' C4' C3' ! flat ? (180 degrees = trans) 179.52 ! DIHEdral C5' C4' C3' O3' ! flexible dihedral ??? 80.97 DIHEdral C4' O4' C1' C2' ! flat ? (0 degrees = cis) -5.14 ! DIHEdral C4' O4' C1' N9 ! flexible dihedral ??? -129.01 ! DIHEdral C4' C3' C2' O2' ! flexible dihedral ??? -84.00 ! DIHEdral C2' C1' N9 C8 ! flexible dihedral ??? -86.44 ! DIHEdral C2' C1' N9 C4 ! flexible dihedral ??? 93.65 DIHEdral C1' N9 C8 N7 ! flat ? (180 degrees = trans) 180.04 DIHEdral C4 N9 C8 N7 ! flat ? (0 degrees = cis) -0.04 DIHEdral C1' N9 C4 C5 ! flat ? (180 degrees = trans) 179.97 DIHEdral C1' N9 C4 N3 ! flat ? (0 degrees = cis) -0.11 DIHEdral C8 N9 C4 C5 ! flat ? (0 degrees = cis) 0.05 DIHEdral C8 N9 C4 N3 ! flat ? (180 degrees = trans) 179.98 DIHEdral N9 C8 N7 C5 ! flat ? (0 degrees = cis) 0.02 DIHEdral C8 N7 C5 C6 ! flat ? (180 degrees = trans) 179.99 DIHEdral C8 N7 C5 C4 ! flat ? (0 degrees = cis) 0.02 DIHEdral N7 C5 C6 N6 ! flat ? (0 degrees = cis) -0.01 DIHEdral N7 C5 C6 N1 ! flat ? (180 degrees = trans) 179.98 DIHEdral C4 C5 C6 N6 ! flat ? (180 degrees = trans) 179.96 DIHEdral C4 C5 C6 N1 ! flat ? (0 degrees = cis) -0.05 DIHEdral N7 C5 C4 N9 ! flat ? (0 degrees = cis) -0.04 DIHEdral N7 C5 C4 N3 ! flat ? (180 degrees = trans) 180.03 DIHEdral C6 C5 C4 N9 ! flat ? (180 degrees = trans) 179.98 DIHEdral C6 C5 C4 N3 ! flat ? (0 degrees = cis) 0.06 DIHEdral C5 C6 N1 C2 ! flat ? (0 degrees = cis) 0.00 DIHEdral N6 C6 N1 C2 ! flat ? (180 degrees = trans) 179.99 DIHEdral C6 N1 C2 N3 ! flat ? (0 degrees = cis) 0.06 DIHEdral N1 C2 N3 C4 ! flat ? (0 degrees = cis) -0.06 DIHEdral C2 N3 C4 N9 ! flat ? (180 degrees = trans) 180.08 DIHEdral C2 N3 C4 C5 ! flat ? (0 degrees = cis) -0.01 { Note: edit these IMPRopers if necessary } IMPRoper P O1P S2P S3P ! chirality or flatness improper 38.40 IMPRoper C4' C5' O4' C3' ! chirality or flatness improper -35.75 IMPRoper C3' C4' O3' C2' ! chirality or flatness improper -37.30 IMPRoper C2' C3' O2' C1' ! chirality or flatness improper -40.14 IMPRoper C1' O4' C2' N9 ! chirality or flatness improper 32.71 IMPRoper N9 C1' C8 C4 ! chirality or flatness improper 0.05 IMPRoper C5 N7 C6 C4 ! chirality or flatness improper 0.02 IMPRoper C6 C5 N6 N1 ! chirality or flatness improper 0.00 IMPRoper C4 N9 C5 N3 ! chirality or flatness improper -0.04 { Note: edit any DONOrs and ACCEptors if necessary } ACCEptor O1P P ACCEptor O5' P ACCEptor O4' C4' ACCEptor O3' C3' ACCEptor O2' C2' ! DONOr H?1 N7 ! DONOr H?1 N6 ! DONOr H?1 N1 ! DONOr H?1 N3 END { RESIdue ADS }