Remarks bfa_xplor_top.txt Remarks Created by XPLO2D V. 050802/3.3.2 at Thu Feb 28 23:30:54 2008 for A. Nonymous Remarks Auto-generated by XPLO2D from file bfa_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 C_2 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_3 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_4 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_5 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS N_6 15.01500 ! assuming N -> 14.00700 + 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 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (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 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS N_15 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_16 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS O_17 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS N_18 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_19 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS C_20 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS N_21 14.00700 ! assuming N -> 14.00700 + 1.008 * 0 (Hs) MASS C_22 15.03500 ! assuming C -> 12.01100 + 1.008 * 3 (Hs) MASS C_23 15.03500 ! assuming C -> 12.01100 + 1.008 * 3 (Hs) autogenerate angles=true end RESIdue BFA { 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 BR TYPE BR_1 CHARge 0.0 END ! Nr of Hs = 0 ATOM C4 TYPE C_2 CHARge 0.0 END ! Nr of Hs = 0 ATOM C3 TYPE C_3 CHARge 0.0 END ! Nr of Hs = 1 ATOM C2 TYPE C_4 CHARge 0.0 END ! Nr of Hs = 1 ATOM C1 TYPE C_5 CHARge 0.0 END ! Nr of Hs = 1 ATOM N9 TYPE N_6 CHARge 0.0 END ! Nr of Hs = 1 ATOM C8 TYPE C_7 CHARge 0.0 END ! Nr of Hs = 1 ATOM C7 TYPE C_8 CHARge 0.0 END ! Nr of Hs = 1 ATOM C6 TYPE C_9 CHARge 0.0 END ! Nr of Hs = 1 ATOM C5 TYPE C_10 CHARge 0.0 END ! Nr of Hs = 0 ATOM C12 TYPE C_11 CHARge 0.0 END ! Nr of Hs = 0 ATOM C11 TYPE C_12 CHARge 0.0 END ! Nr of Hs = 0 ATOM C13 TYPE C_13 CHARge 0.0 END ! Nr of Hs = 0 ATOM C14 TYPE C_14 CHARge 0.0 END ! Nr of Hs = 0 ATOM N10 TYPE N_15 CHARge 0.0 END ! Nr of Hs = 1 ATOM CD1 TYPE C_16 CHARge 0.0 END ! Nr of Hs = 0 ATOM OD1 TYPE O_17 CHARge 0.0 END ! Nr of Hs = 0 ATOM ND1 TYPE N_18 CHARge 0.0 END ! Nr of Hs = 1 ATOM CD2 TYPE C_19 CHARge 0.0 END ! Nr of Hs = 2 ATOM CD3 TYPE C_20 CHARge 0.0 END ! Nr of Hs = 2 ATOM ND2 TYPE N_21 CHARge 0.0 END ! Nr of Hs = 0 ATOM CD7 TYPE C_22 CHARge 0.0 END ! Nr of Hs = 3 ATOM CD8 TYPE C_23 CHARge 0.0 END ! Nr of Hs = 3 BOND BR C5 BOND C4 C3 BOND C4 C12 BOND C4 CD1 BOND C3 C2 BOND C2 C1 BOND C1 C11 BOND N9 C11 BOND N9 C13 BOND C8 C7 BOND C8 C13 BOND C7 C6 BOND C6 C5 BOND C5 C14 BOND C12 C11 BOND C12 N10 BOND C13 C14 BOND C14 N10 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 C12 C4 C3 C2 ! flat ? (0 degrees = cis) 0.21 DIHEdral CD1 C4 C3 C2 ! flat ? (180 degrees = trans) 179.95 DIHEdral C3 C4 C12 C11 ! flat ? (0 degrees = cis) -0.50 DIHEdral C3 C4 C12 N10 ! flat ? (180 degrees = trans) 180.37 DIHEdral CD1 C4 C12 C11 ! flat ? (180 degrees = trans) 179.76 DIHEdral CD1 C4 C12 N10 ! flat ? (0 degrees = cis) 0.63 DIHEdral C3 C4 CD1 OD1 ! flat ? (180 degrees = trans) 180.04 DIHEdral C3 C4 CD1 ND1 ! flat ? (0 degrees = cis) -0.02 DIHEdral C12 C4 CD1 OD1 ! flat ? (0 degrees = cis) -0.23 DIHEdral C12 C4 CD1 ND1 ! flat ? (180 degrees = trans) 179.72 DIHEdral C4 C3 C2 C1 ! flat ? (0 degrees = cis) 0.06 DIHEdral C3 C2 C1 C11 ! flat ? (0 degrees = cis) -0.02 DIHEdral C2 C1 C11 N9 ! flat ? (180 degrees = trans) 179.95 DIHEdral C2 C1 C11 C12 ! flat ? (0 degrees = cis) -0.28 DIHEdral C13 N9 C11 C1 ! flat ? (180 degrees = trans) 179.97 DIHEdral C13 N9 C11 C12 ! flat ? (0 degrees = cis) 0.20 DIHEdral C11 N9 C13 C8 ! flat ? (180 degrees = trans) 180.00 DIHEdral C11 N9 C13 C14 ! flat ? (0 degrees = cis) 0.08 DIHEdral C13 C8 C7 C6 ! flat ? (0 degrees = cis) 0.12 DIHEdral C7 C8 C13 N9 ! flat ? (180 degrees = trans) 179.98 DIHEdral C7 C8 C13 C14 ! flat ? (0 degrees = cis) -0.10 DIHEdral C8 C7 C6 C5 ! flat ? (0 degrees = cis) -0.09 DIHEdral C7 C6 C5 BR ! flat ? (180 degrees = trans) 180.01 DIHEdral C7 C6 C5 C14 ! flat ? (0 degrees = cis) 0.04 DIHEdral BR C5 C14 C13 ! flat ? (180 degrees = trans) 180.01 DIHEdral BR C5 C14 N10 ! flat ? (0 degrees = cis) 0.00 DIHEdral C6 C5 C14 C13 ! flat ? (0 degrees = cis) -0.01 DIHEdral C6 C5 C14 N10 ! flat ? (180 degrees = trans) 179.98 DIHEdral C4 C12 C11 C1 ! flat ? (0 degrees = cis) 0.53 DIHEdral C4 C12 C11 N9 ! flat ? (180 degrees = trans) 180.31 DIHEdral N10 C12 C11 C1 ! flat ? (180 degrees = trans) 179.67 DIHEdral N10 C12 C11 N9 ! flat ? (0 degrees = cis) -0.56 DIHEdral C4 C12 N10 C14 ! flat ? (180 degrees = trans) 179.71 DIHEdral C11 C12 N10 C14 ! flat ? (0 degrees = cis) 0.60 DIHEdral N9 C13 C14 C5 ! flat ? (180 degrees = trans) 179.97 DIHEdral N9 C13 C14 N10 ! flat ? (0 degrees = cis) -0.03 DIHEdral C8 C13 C14 C5 ! flat ? (0 degrees = cis) 0.04 DIHEdral C8 C13 C14 N10 ! flat ? (180 degrees = trans) 180.05 DIHEdral C5 C14 N10 C12 ! flat ? (180 degrees = trans) 179.68 DIHEdral C13 C14 N10 C12 ! flat ? (0 degrees = cis) -0.33 DIHEdral C4 CD1 ND1 CD2 ! flat ? (180 degrees = trans) 180.01 DIHEdral OD1 CD1 ND1 CD2 ! flat ? (0 degrees = cis) -0.04 DIHEdral CD1 ND1 CD2 CD3 ! flat ? (180 degrees = trans) 179.99 DIHEdral ND1 CD2 CD3 ND2 ! flat ? (180 degrees = trans) 179.99 DIHEdral CD2 CD3 ND2 CD7 ! flat ? (180 degrees = trans) 180.03 ! DIHEdral CD2 CD3 ND2 CD8 ! flexible dihedral ??? -66.21 { Note: edit these IMPRopers if necessary } IMPRoper C4 C3 C12 CD1 ! chirality or flatness improper -0.15 IMPRoper C5 BR C6 C14 ! chirality or flatness improper -0.01 IMPRoper C12 C4 C11 N10 ! chirality or flatness improper 0.48 IMPRoper C11 C1 N9 C12 ! chirality or flatness improper -0.14 IMPRoper C13 N9 C8 C14 ! chirality or flatness improper 0.05 IMPRoper C14 C5 C13 N10 ! chirality or flatness improper 0.00 IMPRoper CD1 C4 OD1 ND1 ! chirality or flatness improper -0.03 IMPRoper ND2 CD3 CD7 CD8 ! chirality or flatness improper -39.10 { Note: edit any DONOrs and ACCEptors if necessary } ! DONOr H?1 N9 ! DONOr H?1 N10 ACCEptor OD1 CD1 ! DONOr H?1 ND1 END { RESIdue BFA }