Remarks 65b_xplor_top.txt Remarks Created by XPLO2D V. 050802/3.3.2 at Thu Feb 28 11:17:01 2008 for A. Nonymous Remarks Auto-generated by XPLO2D from file 65b_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 O_2 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS C_3 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_4 15.03500 ! assuming C -> 12.01100 + 1.008 * 3 (Hs) MASS C_5 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_6 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_7 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_8 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_9 15.03500 ! assuming C -> 12.01100 + 1.008 * 3 (Hs) MASS C_10 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS N_11 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_12 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS N_13 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS N_14 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_15 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS N_16 14.00700 ! assuming N -> 14.00700 + 1.008 * 0 (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 C_19 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_20 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_21 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_22 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_23 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_24 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS N_25 14.00700 ! assuming N -> 14.00700 + 1.008 * 0 (Hs) MASS C_26 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS N_27 14.00700 ! assuming N -> 14.00700 + 1.008 * 0 (Hs) MASS BR_2 79.90400 ! assuming BR -> 79.90400 + 1.008 * 0 (Hs) autogenerate angles=true end RESIdue 65B { 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 O17 TYPE O_2 CHARge 0.0 END ! Nr of Hs = 0 ATOM C2 TYPE C_3 CHARge 0.0 END ! Nr of Hs = 0 ATOM C2' TYPE C_4 CHARge 0.0 END ! Nr of Hs = 3 ATOM C3 TYPE C_5 CHARge 0.0 END ! Nr of Hs = 1 ATOM C4 TYPE C_6 CHARge 0.0 END ! Nr of Hs = 0 ATOM C5 TYPE C_7 CHARge 0.0 END ! Nr of Hs = 1 ATOM C6 TYPE C_8 CHARge 0.0 END ! Nr of Hs = 0 ATOM C6' TYPE C_9 CHARge 0.0 END ! Nr of Hs = 3 ATOM C13 TYPE C_10 CHARge 0.0 END ! Nr of Hs = 0 ATOM N12 TYPE N_11 CHARge 0.0 END ! Nr of Hs = 1 ATOM C11 TYPE C_12 CHARge 0.0 END ! Nr of Hs = 0 ATOM N5 TYPE N_13 CHARge 0.0 END ! Nr of Hs = 1 ATOM N16 TYPE N_14 CHARge 0.0 END ! Nr of Hs = 1 ATOM C15 TYPE C_15 CHARge 0.0 END ! Nr of Hs = 0 ATOM N18 TYPE N_16 CHARge 0.0 END ! Nr of Hs = 0 ATOM C14 TYPE C_17 CHARge 0.0 END ! Nr of Hs = 0 ATOM C21 TYPE C_18 CHARge 0.0 END ! Nr of Hs = 0 ATOM C22 TYPE C_19 CHARge 0.0 END ! Nr of Hs = 1 ATOM C23 TYPE C_20 CHARge 0.0 END ! Nr of Hs = 1 ATOM C24 TYPE C_21 CHARge 0.0 END ! Nr of Hs = 0 ATOM C25 TYPE C_22 CHARge 0.0 END ! Nr of Hs = 1 ATOM C26 TYPE C_23 CHARge 0.0 END ! Nr of Hs = 1 ATOM C27 TYPE C_24 CHARge 0.0 END ! Nr of Hs = 1 ATOM N27 TYPE N_25 CHARge 0.0 END ! Nr of Hs = 0 ATOM C4' TYPE C_26 CHARge 0.0 END ! Nr of Hs = 1 ATOM N4' TYPE N_27 CHARge 0.0 END ! Nr of Hs = 0 ATOM BR TYPE BR_2 CHARge 0.0 END ! Nr of Hs = 0 BOND C1 O17 BOND C1 C2 BOND C1 C6 BOND O17 C13 BOND C2 C2' BOND C2 C3 BOND C3 C4 BOND C4 C5 BOND C4 C4' BOND C5 C6 BOND C6 C6' BOND C13 N12 BOND C13 C14 BOND N12 C11 BOND C11 N5 BOND C11 N16 BOND N5 C21 BOND N16 C15 BOND C15 N18 BOND C15 C14 BOND C14 BR BOND C21 C22 BOND C21 C26 BOND C22 C23 BOND C23 C24 BOND C24 C25 BOND C24 C27 BOND C25 C26 BOND C27 N27 BOND C4' N4' { Note: edit these DIHEdrals if necessary } ! DIHEdral C2 C1 O17 C13 ! flexible dihedral ??? -90.47 ! DIHEdral C6 C1 O17 C13 ! flexible dihedral ??? 90.04 DIHEdral O17 C1 C2 C2' ! flat ? (0 degrees = cis) 0.24 DIHEdral O17 C1 C2 C3 ! flat ? (180 degrees = trans) 179.97 DIHEdral C6 C1 C2 C2' ! flat ? (180 degrees = trans) 179.73 DIHEdral C6 C1 C2 C3 ! flat ? (0 degrees = cis) -0.54 DIHEdral O17 C1 C6 C5 ! flat ? (180 degrees = trans) 180.04 DIHEdral O17 C1 C6 C6' ! flat ? (0 degrees = cis) -0.29 DIHEdral C2 C1 C6 C5 ! flat ? (0 degrees = cis) 0.55 DIHEdral C2 C1 C6 C6' ! flat ? (180 degrees = trans) 180.22 DIHEdral C1 O17 C13 N12 ! flat ? (0 degrees = cis) -0.01 DIHEdral C1 O17 C13 C14 ! flat ? (180 degrees = trans) 179.71 DIHEdral C1 C2 C3 C4 ! flat ? (0 degrees = cis) 0.25 DIHEdral C2' C2 C3 C4 ! flat ? (180 degrees = trans) 179.98 DIHEdral C2 C3 C4 C5 ! flat ? (0 degrees = cis) 0.02 DIHEdral C2 C3 C4 C4' ! flat ? (180 degrees = trans) 180.00 DIHEdral C3 C4 C5 C6 ! flat ? (0 degrees = cis) -0.01 DIHEdral C4' C4 C5 C6 ! flat ? (180 degrees = trans) 180.01 DIHEdral C4 C5 C6 C1 ! flat ? (0 degrees = cis) -0.28 DIHEdral C4 C5 C6 C6' ! flat ? (180 degrees = trans) 180.06 DIHEdral O17 C13 N12 C11 ! flat ? (180 degrees = trans) 179.96 DIHEdral C14 C13 N12 C11 ! flat ? (0 degrees = cis) 0.24 DIHEdral O17 C13 C14 C15 ! flat ? (180 degrees = trans) 179.75 DIHEdral O17 C13 C14 BR ! flat ? (0 degrees = cis) 0.28 DIHEdral N12 C13 C14 C15 ! flat ? (0 degrees = cis) -0.53 DIHEdral N12 C13 C14 BR ! flat ? (180 degrees = trans) 180.00 DIHEdral C13 N12 C11 N5 ! flat ? (180 degrees = trans) 180.03 DIHEdral C13 N12 C11 N16 ! flat ? (0 degrees = cis) 0.05 DIHEdral N12 C11 N5 C21 ! flat ? (180 degrees = trans) 174.51 DIHEdral N16 C11 N5 C21 ! flat ? (0 degrees = cis) -5.51 DIHEdral N12 C11 N16 C15 ! flat ? (0 degrees = cis) -0.03 DIHEdral N5 C11 N16 C15 ! flat ? (180 degrees = trans) 179.99 DIHEdral C11 N16 C15 N18 ! flat ? (180 degrees = trans) 180.03 DIHEdral C11 N16 C15 C14 ! flat ? (0 degrees = cis) -0.28 DIHEdral N16 C15 C14 C13 ! flat ? (0 degrees = cis) 0.55 DIHEdral N16 C15 C14 BR ! flat ? (180 degrees = trans) 180.02 DIHEdral N18 C15 C14 C13 ! flat ? (180 degrees = trans) 180.24 DIHEdral N18 C15 C14 BR ! flat ? (0 degrees = cis) -0.29 DIHEdral N5 C21 C22 C23 ! flat ? (180 degrees = trans) 179.75 DIHEdral C26 C21 C22 C23 ! flat ? (0 degrees = cis) -0.48 DIHEdral N5 C21 C26 C25 ! flat ? (180 degrees = trans) 180.03 DIHEdral C22 C21 C26 C25 ! flat ? (0 degrees = cis) 0.26 DIHEdral C21 C22 C23 C24 ! flat ? (0 degrees = cis) 0.42 DIHEdral C22 C23 C24 C25 ! flat ? (0 degrees = cis) -0.15 DIHEdral C22 C23 C24 C27 ! flat ? (180 degrees = trans) 179.78 DIHEdral C23 C24 C25 C26 ! flat ? (0 degrees = cis) -0.07 DIHEdral C27 C24 C25 C26 ! flat ? (180 degrees = trans) 180.00 DIHEdral C24 C25 C26 C21 ! flat ? (0 degrees = cis) 0.01 { Note: edit these IMPRopers if necessary } IMPRoper C1 O17 C2 C6 ! chirality or flatness improper 0.30 IMPRoper C2 C1 C2' C3 ! chirality or flatness improper -0.15 IMPRoper C4 C3 C5 C4' ! chirality or flatness improper -0.01 IMPRoper C6 C1 C5 C6' ! chirality or flatness improper -0.20 IMPRoper C13 O17 N12 C14 ! chirality or flatness improper -0.16 IMPRoper C11 N12 N5 N16 ! chirality or flatness improper 0.01 IMPRoper C15 N16 N18 C14 ! chirality or flatness improper -0.18 IMPRoper C14 C13 C15 BR ! chirality or flatness improper 0.33 IMPRoper C21 N5 C22 C26 ! chirality or flatness improper 0.13 IMPRoper C24 C23 C25 C27 ! chirality or flatness improper -0.04 { Note: edit any DONOrs and ACCEptors if necessary } ACCEptor O17 C1 ! DONOr H?1 N12 ! DONOr H?1 N5 ! DONOr H?1 N16 END { RESIdue 65B }