Remarks hm2_xplor_top.txt Remarks Created by XPLO2D V. 050802/3.3.2 at Sat Mar 1 06:44:28 2008 for A. Nonymous Remarks Auto-generated by XPLO2D from file hm2_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 N_2 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS N_3 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS N_4 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (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 C_7 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_8 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_9 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_10 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_11 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (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 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_17 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_18 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (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 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_22 15.03500 ! assuming C -> 12.01100 + 1.008 * 3 (Hs) MASS CL_2 35.45300 ! assuming CL -> 35.45300 + 1.008 * 0 (Hs) autogenerate angles=true end RESIdue HM2 { 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 = 1 ATOM N2 TYPE N_2 CHARge 0.0 END ! Nr of Hs = 1 ATOM N3 TYPE N_3 CHARge 0.0 END ! Nr of Hs = 1 ATOM N4 TYPE N_4 CHARge 0.0 END ! Nr of Hs = 1 ATOM C1 TYPE C_5 CHARge 0.0 END ! Nr of Hs = 1 ATOM C2 TYPE C_6 CHARge 0.0 END ! Nr of Hs = 1 ATOM C3 TYPE C_7 CHARge 0.0 END ! Nr of Hs = 1 ATOM C4 TYPE C_8 CHARge 0.0 END ! Nr of Hs = 1 ATOM C5 TYPE C_9 CHARge 0.0 END ! Nr of Hs = 0 ATOM C6 TYPE C_10 CHARge 0.0 END ! Nr of Hs = 0 ATOM C7 TYPE C_11 CHARge 0.0 END ! Nr of Hs = 0 ATOM C8 TYPE C_12 CHARge 0.0 END ! Nr of Hs = 0 ATOM C9 TYPE C_13 CHARge 0.0 END ! Nr of Hs = 0 ATOM C10 TYPE C_14 CHARge 0.0 END ! Nr of Hs = 2 ATOM C11 TYPE C_15 CHARge 0.0 END ! Nr of Hs = 2 ATOM C12 TYPE C_16 CHARge 0.0 END ! Nr of Hs = 0 ATOM C13 TYPE C_17 CHARge 0.0 END ! Nr of Hs = 1 ATOM C14 TYPE C_18 CHARge 0.0 END ! Nr of Hs = 1 ATOM C15 TYPE C_19 CHARge 0.0 END ! Nr of Hs = 1 ATOM C16 TYPE C_20 CHARge 0.0 END ! Nr of Hs = 1 ATOM C17 TYPE C_21 CHARge 0.0 END ! Nr of Hs = 1 ATOM C18 TYPE C_22 CHARge 0.0 END ! Nr of Hs = 3 ATOM CL1 TYPE CL_2 CHARge 0.0 END ! Nr of Hs = 0 BOND N1 C1 BOND N1 C5 BOND N2 C6 BOND N2 C7 BOND N3 C6 BOND N3 C8 BOND N4 C7 BOND N4 C10 BOND C1 C2 BOND C2 C3 BOND C3 C4 BOND C4 C5 BOND C5 C6 BOND C7 C9 BOND C8 C9 BOND C8 C18 BOND C9 CL1 BOND C10 C11 BOND C11 C12 BOND C12 C13 BOND C12 C17 BOND C13 C14 BOND C14 C15 BOND C15 C16 BOND C16 C17 { Note: edit these DIHEdrals if necessary } DIHEdral C5 N1 C1 C2 ! flat ? (0 degrees = cis) 0.67 DIHEdral C1 N1 C5 C4 ! flat ? (0 degrees = cis) -0.67 DIHEdral C1 N1 C5 C6 ! flat ? (180 degrees = trans) 179.68 DIHEdral C7 N2 C6 N3 ! flat ? (0 degrees = cis) 0.00 DIHEdral C7 N2 C6 C5 ! flat ? (180 degrees = trans) 180.05 DIHEdral C6 N2 C7 N4 ! flat ? (180 degrees = trans) 180.05 DIHEdral C6 N2 C7 C9 ! flat ? (0 degrees = cis) -0.33 DIHEdral C8 N3 C6 N2 ! flat ? (0 degrees = cis) 0.00 DIHEdral C8 N3 C6 C5 ! flat ? (180 degrees = trans) 179.95 DIHEdral C6 N3 C8 C9 ! flat ? (0 degrees = cis) 0.33 DIHEdral C6 N3 C8 C18 ! flat ? (180 degrees = trans) 179.99 DIHEdral C10 N4 C7 N2 ! flat ? (0 degrees = cis) -0.10 DIHEdral C10 N4 C7 C9 ! flat ? (180 degrees = trans) 180.29 DIHEdral C7 N4 C10 C11 ! flat ? (180 degrees = trans) 180.05 DIHEdral N1 C1 C2 C3 ! flat ? (0 degrees = cis) -0.35 DIHEdral C1 C2 C3 C4 ! flat ? (0 degrees = cis) 0.05 DIHEdral C2 C3 C4 C5 ! flat ? (0 degrees = cis) -0.05 DIHEdral C3 C4 C5 N1 ! flat ? (0 degrees = cis) 0.35 DIHEdral C3 C4 C5 C6 ! flat ? (180 degrees = trans) 180.00 DIHEdral N1 C5 C6 N2 ! flat ? (0 degrees = cis) -0.35 DIHEdral N1 C5 C6 N3 ! flat ? (180 degrees = trans) 179.70 DIHEdral C4 C5 C6 N2 ! flat ? (180 degrees = trans) 180.00 DIHEdral C4 C5 C6 N3 ! flat ? (0 degrees = cis) 0.05 DIHEdral N2 C7 C9 C8 ! flat ? (0 degrees = cis) 0.65 DIHEdral N2 C7 C9 CL1 ! flat ? (180 degrees = trans) 180.04 DIHEdral N4 C7 C9 C8 ! flat ? (180 degrees = trans) 180.27 DIHEdral N4 C7 C9 CL1 ! flat ? (0 degrees = cis) -0.34 DIHEdral N3 C8 C9 C7 ! flat ? (0 degrees = cis) -0.65 DIHEdral N3 C8 C9 CL1 ! flat ? (180 degrees = trans) 179.96 DIHEdral C18 C8 C9 C7 ! flat ? (180 degrees = trans) 179.69 DIHEdral C18 C8 C9 CL1 ! flat ? (0 degrees = cis) 0.30 DIHEdral N4 C10 C11 C12 ! flat ? (180 degrees = trans) 180.00 ! DIHEdral C10 C11 C12 C13 ! flexible dihedral ??? 90.00 ! DIHEdral C10 C11 C12 C17 ! flexible dihedral ??? -90.27 DIHEdral C11 C12 C13 C14 ! flat ? (180 degrees = trans) 179.96 DIHEdral C17 C12 C13 C14 ! flat ? (0 degrees = cis) 0.24 DIHEdral C11 C12 C17 C16 ! flat ? (180 degrees = trans) 179.81 DIHEdral C13 C12 C17 C16 ! flat ? (0 degrees = cis) -0.47 DIHEdral C12 C13 C14 C15 ! flat ? (0 degrees = cis) 0.03 DIHEdral C13 C14 C15 C16 ! flat ? (0 degrees = cis) -0.07 DIHEdral C14 C15 C16 C17 ! flat ? (0 degrees = cis) -0.17 DIHEdral C15 C16 C17 C12 ! flat ? (0 degrees = cis) 0.44 { Note: edit these IMPRopers if necessary } IMPRoper C5 N1 C4 C6 ! chirality or flatness improper 0.21 IMPRoper C6 N2 N3 C5 ! chirality or flatness improper 0.03 IMPRoper C7 N2 N4 C9 ! chirality or flatness improper -0.22 IMPRoper C8 N3 C9 C18 ! chirality or flatness improper -0.20 IMPRoper C9 C7 C8 CL1 ! chirality or flatness improper -0.37 IMPRoper C12 C11 C13 C17 ! chirality or flatness improper -0.16 { Note: edit any DONOrs and ACCEptors if necessary } ! DONOr H?1 N1 ! DONOr H?1 N2 ! DONOr H?1 N3 ! DONOr H?1 N4 END { RESIdue HM2 }