Remarks hmd_xplor_top.txt Remarks Created by XPLO2D V. 050802/3.3.2 at Sat Mar 1 06:52:00 2008 for A. Nonymous Remarks Auto-generated by XPLO2D from file hmd_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 BR_1 79.90400 ! assuming BR -> 79.90400 + 1.008 * 0 (Hs) MASS O_2 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS O_3 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS N_4 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS N_5 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS N_6 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS N_7 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS N_8 14.00700 ! assuming N -> 14.00700 + 1.008 * 0 (Hs) MASS C_9 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_10 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_11 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_12 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_13 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_14 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS C_15 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS C_16 13.01900 ! assuming C -> 12.01100 + 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 C_19 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) autogenerate angles=true end RESIdue HMD { 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 BR1 TYPE BR_1 CHARge 0.0 END ! Nr of Hs = 0 ATOM O1 TYPE O_2 CHARge 0.0 END ! Nr of Hs = 0 ATOM O2 TYPE O_3 CHARge 0.0 END ! Nr of Hs = 0 ATOM N1 TYPE N_4 CHARge 0.0 END ! Nr of Hs = 1 ATOM N2 TYPE N_5 CHARge 0.0 END ! Nr of Hs = 1 ATOM N3 TYPE N_6 CHARge 0.0 END ! Nr of Hs = 1 ATOM N4 TYPE N_7 CHARge 0.0 END ! Nr of Hs = 1 ATOM N5 TYPE N_8 CHARge 0.0 END ! Nr of Hs = 0 ATOM C1 TYPE C_9 CHARge 0.0 END ! Nr of Hs = 0 ATOM C2 TYPE C_10 CHARge 0.0 END ! Nr of Hs = 1 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 = 0 ATOM C5 TYPE C_13 CHARge 0.0 END ! Nr of Hs = 0 ATOM C6 TYPE C_14 CHARge 0.0 END ! Nr of Hs = 2 ATOM C7 TYPE C_15 CHARge 0.0 END ! Nr of Hs = 2 ATOM C8 TYPE C_16 CHARge 0.0 END ! Nr of Hs = 1 ATOM C9 TYPE C_17 CHARge 0.0 END ! Nr of Hs = 0 ATOM C10 TYPE C_18 CHARge 0.0 END ! Nr of Hs = 0 ATOM C11 TYPE C_19 CHARge 0.0 END ! Nr of Hs = 0 BOND BR1 C1 BOND O1 C5 BOND O2 C10 BOND N1 C1 BOND N1 C4 BOND N2 C5 BOND N2 C6 BOND N3 C10 BOND N3 C11 BOND N4 C9 BOND N4 C11 BOND N5 C11 BOND C1 C2 BOND C2 C3 BOND C3 C4 BOND C3 C8 BOND C4 C5 BOND C6 C7 BOND C7 C8 BOND C8 C9 BOND C9 C10 { Note: edit these DIHEdrals if necessary } DIHEdral C4 N1 C1 BR1 ! flat ? (180 degrees = trans) 182.87 DIHEdral C4 N1 C1 C2 ! flat ? (0 degrees = cis) 2.96 DIHEdral C1 N1 C4 C3 ! flat ? (0 degrees = cis) -5.57 DIHEdral C1 N1 C4 C5 ! flat ? (180 degrees = trans) 173.37 DIHEdral C11 N3 C10 O2 ! flat ? (180 degrees = trans) 180.05 DIHEdral C11 N3 C10 C9 ! flat ? (0 degrees = cis) 0.05 DIHEdral C10 N3 C11 N4 ! flat ? (0 degrees = cis) 0.23 DIHEdral C10 N3 C11 N5 ! flat ? (180 degrees = trans) 180.05 DIHEdral C11 N4 C9 C8 ! flat ? (180 degrees = trans) 180.18 DIHEdral C11 N4 C9 C10 ! flat ? (0 degrees = cis) 0.45 DIHEdral C9 N4 C11 N3 ! flat ? (0 degrees = cis) -0.45 DIHEdral C9 N4 C11 N5 ! flat ? (180 degrees = trans) 179.73 DIHEdral BR1 C1 C2 C3 ! flat ? (180 degrees = trans) 181.21 DIHEdral N1 C1 C2 C3 ! flat ? (0 degrees = cis) 1.12 DIHEdral C1 C2 C3 C4 ! flat ? (0 degrees = cis) -4.09 ! DIHEdral C1 C2 C3 C8 ! flexible dihedral ??? -123.02 DIHEdral C2 C3 C4 N1 ! flat ? (0 degrees = cis) 5.80 DIHEdral C2 C3 C4 C5 ! flat ? (180 degrees = trans) 186.81 ! DIHEdral C8 C3 C4 N1 ! flexible dihedral ??? 124.54 ! DIHEdral C8 C3 C4 C5 ! flexible dihedral ??? -54.45 ! DIHEdral C2 C3 C8 C7 ! flexible dihedral ??? 83.41 ! DIHEdral N1 C4 C5 O1 ! flexible dihedral ??? 61.42 ! DIHEdral N1 C4 C5 N2 ! flexible dihedral ??? -118.59 ! DIHEdral C3 C4 C5 O1 ! flexible dihedral ??? -119.82 ! DIHEdral C3 C4 C5 N2 ! flexible dihedral ??? 60.17 ! DIHEdral C6 C7 C8 C3 ! flexible dihedral ??? 82.94 ! DIHEdral C3 C8 C9 N4 ! flexible dihedral ??? 114.94 ! DIHEdral C3 C8 C9 C10 ! flexible dihedral ??? -65.38 DIHEdral C7 C8 C9 N4 ! flat ? (0 degrees = cis) -5.29 DIHEdral C7 C8 C9 C10 ! flat ? (180 degrees = trans) 174.39 DIHEdral N4 C9 C10 O2 ! flat ? (180 degrees = trans) 179.68 DIHEdral N4 C9 C10 N3 ! flat ? (0 degrees = cis) -0.31 DIHEdral C8 C9 C10 O2 ! flat ? (0 degrees = cis) -0.05 DIHEdral C8 C9 C10 N3 ! flat ? (180 degrees = trans) 179.95 { Note: edit these IMPRopers if necessary } IMPRoper C1 BR1 N1 C2 ! chirality or flatness improper -0.05 IMPRoper C3 C2 C4 C8 ! chirality or flatness improper 34.69 IMPRoper C4 N1 C3 C5 ! chirality or flatness improper -0.53 IMPRoper C5 O1 N2 C4 ! chirality or flatness improper -0.01 IMPRoper C8 C3 C7 C9 ! chirality or flatness improper 35.00 IMPRoper C9 N4 C8 C10 ! chirality or flatness improper 0.18 IMPRoper C10 O2 N3 C9 ! chirality or flatness improper 0.00 IMPRoper C11 N3 N4 N5 ! chirality or flatness improper -0.10 { Note: edit any DONOrs and ACCEptors if necessary } ACCEptor O1 C5 ACCEptor O2 C10 ! DONOr H?1 N1 ! DONOr H?1 N2 ! DONOr H?1 N3 ! DONOr H?1 N4 END { RESIdue HMD }