Remarks da5_xplor_top.txt Remarks Created by XPLO2D V. 050802/3.3.2 at Fri Feb 29 11:32:53 2008 for A. Nonymous Remarks Auto-generated by XPLO2D from file da5_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 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_2 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_3 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_4 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_5 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (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 N_10 14.00700 ! assuming N -> 14.00700 + 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 C_13 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_14 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_15 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS BR_1 79.90400 ! assuming BR -> 79.90400 + 1.008 * 0 (Hs) MASS C_17 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS O_18 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS N_19 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_20 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS C_21 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS N_22 14.00700 ! assuming N -> 14.00700 + 1.008 * 0 (Hs) MASS C_23 15.03500 ! assuming C -> 12.01100 + 1.008 * 3 (Hs) MASS C_24 15.03500 ! assuming C -> 12.01100 + 1.008 * 3 (Hs) autogenerate angles=true end RESIdue DA5 { 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 = 1 ATOM C2 TYPE C_2 CHARge 0.0 END ! Nr of Hs = 1 ATOM C3 TYPE C_3 CHARge 0.0 END ! Nr of Hs = 1 ATOM C4 TYPE C_4 CHARge 0.0 END ! Nr of Hs = 0 ATOM C5 TYPE C_5 CHARge 0.0 END ! Nr of Hs = 0 ATOM C6 TYPE C_6 CHARge 0.0 END ! Nr of Hs = 1 ATOM C7 TYPE C_7 CHARge 0.0 END ! Nr of Hs = 1 ATOM C8 TYPE C_8 CHARge 0.0 END ! Nr of Hs = 1 ATOM C9 TYPE C_9 CHARge 0.0 END ! Nr of Hs = 0 ATOM N9 TYPE N_10 CHARge 0.0 END ! Nr of Hs = 0 ATOM N10 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 C12 TYPE C_13 CHARge 0.0 END ! Nr of Hs = 0 ATOM C13 TYPE C_14 CHARge 0.0 END ! Nr of Hs = 0 ATOM C14 TYPE C_15 CHARge 0.0 END ! Nr of Hs = 0 ATOM BR TYPE BR_1 CHARge 0.0 END ! Nr of Hs = 0 ATOM CD1 TYPE C_17 CHARge 0.0 END ! Nr of Hs = 0 ATOM OD1 TYPE O_18 CHARge 0.0 END ! Nr of Hs = 0 ATOM ND1 TYPE N_19 CHARge 0.0 END ! Nr of Hs = 1 ATOM CD2 TYPE C_20 CHARge 0.0 END ! Nr of Hs = 2 ATOM CD3 TYPE C_21 CHARge 0.0 END ! Nr of Hs = 2 ATOM ND2 TYPE N_22 CHARge 0.0 END ! Nr of Hs = 0 ATOM CD7 TYPE C_23 CHARge 0.0 END ! Nr of Hs = 3 ATOM CD8 TYPE C_24 CHARge 0.0 END ! Nr of Hs = 3 BOND C1 C2 BOND C1 C11 BOND C2 C3 BOND C3 C4 BOND C4 C12 BOND C4 CD1 BOND C5 C6 BOND C5 C14 BOND C5 BR BOND C6 C7 BOND C7 C8 BOND C8 C13 BOND C9 N9 BOND C9 C11 BOND C9 C13 BOND N10 C12 BOND N10 C14 BOND C11 C12 BOND C13 C14 BOND CD1 OD1 BOND CD1 ND1 BOND ND1 CD2 BOND CD2 CD3 BOND CD3 ND2 BOND ND2 CD7 BOND ND2 CD8 { Note: edit these DIHEdrals if necessary } DIHEdral C11 C1 C2 C3 ! flat ? (0 degrees = cis) 0.04 DIHEdral C2 C1 C11 C9 ! flat ? (180 degrees = trans) 179.98 DIHEdral C2 C1 C11 C12 ! flat ? (0 degrees = cis) -0.31 DIHEdral C1 C2 C3 C4 ! flat ? (0 degrees = cis) -0.04 DIHEdral C2 C3 C4 C12 ! flat ? (0 degrees = cis) 0.30 DIHEdral C2 C3 C4 CD1 ! flat ? (180 degrees = trans) 179.98 DIHEdral C3 C4 C12 N10 ! flat ? (180 degrees = trans) 180.27 DIHEdral C3 C4 C12 C11 ! flat ? (0 degrees = cis) -0.54 DIHEdral CD1 C4 C12 N10 ! flat ? (0 degrees = cis) 0.60 DIHEdral CD1 C4 C12 C11 ! flat ? (180 degrees = trans) 179.78 DIHEdral C3 C4 CD1 OD1 ! flat ? (180 degrees = trans) 174.29 DIHEdral C3 C4 CD1 ND1 ! flat ? (0 degrees = cis) -5.63 DIHEdral C12 C4 CD1 OD1 ! flat ? (0 degrees = cis) -6.04 DIHEdral C12 C4 CD1 ND1 ! flat ? (180 degrees = trans) 174.04 DIHEdral C14 C5 C6 C7 ! flat ? (0 degrees = cis) -0.04 DIHEdral BR C5 C6 C7 ! flat ? (180 degrees = trans) 179.95 DIHEdral C6 C5 C14 N10 ! flat ? (180 degrees = trans) 179.96 DIHEdral C6 C5 C14 C13 ! flat ? (0 degrees = cis) 0.06 DIHEdral BR C5 C14 N10 ! flat ? (0 degrees = cis) -0.03 DIHEdral BR C5 C14 C13 ! flat ? (180 degrees = trans) 180.07 DIHEdral C5 C6 C7 C8 ! flat ? (0 degrees = cis) 0.01 DIHEdral C6 C7 C8 C13 ! flat ? (0 degrees = cis) -0.01 DIHEdral C7 C8 C13 C9 ! flat ? (180 degrees = trans) 180.03 DIHEdral C7 C8 C13 C14 ! flat ? (0 degrees = cis) 0.03 DIHEdral N9 C9 C11 C1 ! flat ? (0 degrees = cis) -0.01 DIHEdral N9 C9 C11 C12 ! flat ? (180 degrees = trans) 180.27 DIHEdral C13 C9 C11 C1 ! flat ? (180 degrees = trans) 179.96 DIHEdral C13 C9 C11 C12 ! flat ? (0 degrees = cis) 0.24 DIHEdral N9 C9 C13 C8 ! flat ? (0 degrees = cis) -0.04 DIHEdral N9 C9 C13 C14 ! flat ? (180 degrees = trans) 179.96 DIHEdral C11 C9 C13 C8 ! flat ? (180 degrees = trans) 179.99 DIHEdral C11 C9 C13 C14 ! flat ? (0 degrees = cis) -0.01 DIHEdral C14 N10 C12 C4 ! flat ? (180 degrees = trans) 179.76 DIHEdral C14 N10 C12 C11 ! flat ? (0 degrees = cis) 0.60 DIHEdral C12 N10 C14 C5 ! flat ? (180 degrees = trans) 179.75 DIHEdral C12 N10 C14 C13 ! flat ? (0 degrees = cis) -0.35 DIHEdral C1 C11 C12 C4 ! flat ? (0 degrees = cis) 0.55 DIHEdral C1 C11 C12 N10 ! flat ? (180 degrees = trans) 179.73 DIHEdral C9 C11 C12 C4 ! flat ? (180 degrees = trans) 180.27 DIHEdral C9 C11 C12 N10 ! flat ? (0 degrees = cis) -0.55 DIHEdral C8 C13 C14 C5 ! flat ? (0 degrees = cis) -0.06 DIHEdral C8 C13 C14 N10 ! flat ? (180 degrees = trans) 180.04 DIHEdral C9 C13 C14 C5 ! flat ? (180 degrees = trans) 179.95 DIHEdral C9 C13 C14 N10 ! flat ? (0 degrees = cis) 0.05 DIHEdral C4 CD1 ND1 CD2 ! flat ? (180 degrees = trans) 180.00 DIHEdral OD1 CD1 ND1 CD2 ! flat ? (0 degrees = cis) 0.09 DIHEdral CD1 ND1 CD2 CD3 ! flat ? (180 degrees = trans) 179.96 DIHEdral ND1 CD2 CD3 ND2 ! flat ? (180 degrees = trans) 179.96 { Note: edit these IMPRopers if necessary } IMPRoper C4 C3 C12 CD1 ! chirality or flatness improper -0.19 IMPRoper C5 C6 C14 BR ! chirality or flatness improper -0.01 IMPRoper C9 N9 C11 C13 ! chirality or flatness improper 0.02 IMPRoper C11 C1 C9 C12 ! chirality or flatness improper -0.17 IMPRoper C12 C4 N10 C11 ! chirality or flatness improper -0.49 IMPRoper C13 C8 C9 C14 ! chirality or flatness improper 0.00 IMPRoper C14 C5 N10 C13 ! chirality or flatness improper 0.06 IMPRoper CD1 C4 OD1 ND1 ! chirality or flatness improper 0.05 IMPRoper ND2 CD3 CD7 CD8 ! chirality or flatness improper -39.10 { Note: edit any DONOrs and ACCEptors if necessary } ! DONOr H?1 N10 ACCEptor OD1 CD1 ! DONOr H?1 ND1 END { RESIdue DA5 }