Remarks bde_xplor_top.txt Remarks Created by XPLO2D V. 050802/3.3.2 at Thu Feb 28 22:59:14 2008 for A. Nonymous Remarks Auto-generated by XPLO2D from file bde_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 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 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_7 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS O_8 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS N_9 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS N_10 15.01500 ! assuming N -> 14.00700 + 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 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_14 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_16 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS O_17 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS C_18 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS BR_A 79.90400 ! assuming BR -> 79.90400 + 1.008 * 0 (Hs) MASS C_20 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS O_21 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) autogenerate angles=true end RESIdue BDE { 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 CAE TYPE C_1 CHARge 0.0 END ! Nr of Hs = 1 ATOM CAF TYPE C_2 CHARge 0.0 END ! Nr of Hs = 1 ATOM CAA TYPE C_3 CHARge 0.0 END ! Nr of Hs = 1 ATOM NAB TYPE N_4 CHARge 0.0 END ! Nr of Hs = 1 ATOM CAC TYPE C_5 CHARge 0.0 END ! Nr of Hs = 1 ATOM CAD TYPE C_6 CHARge 0.0 END ! Nr of Hs = 0 ATOM CAG TYPE C_7 CHARge 0.0 END ! Nr of Hs = 0 ATOM OAU TYPE O_8 CHARge 0.0 END ! Nr of Hs = 0 ATOM NAH TYPE N_9 CHARge 0.0 END ! Nr of Hs = 1 ATOM NAI TYPE N_10 CHARge 0.0 END ! Nr of Hs = 1 ATOM CAJ TYPE C_11 CHARge 0.0 END ! Nr of Hs = 1 ATOM CAK TYPE C_12 CHARge 0.0 END ! Nr of Hs = 0 ATOM CAL TYPE C_13 CHARge 0.0 END ! Nr of Hs = 1 ATOM CAM TYPE C_14 CHARge 0.0 END ! Nr of Hs = 0 ATOM BRAT TYPE BR_1 CHARge 0.0 END ! Nr of Hs = 0 ATOM CAN TYPE C_16 CHARge 0.0 END ! Nr of Hs = 0 ATOM OAS TYPE O_17 CHARge 0.0 END ! Nr of Hs = 1 ATOM CAO TYPE C_18 CHARge 0.0 END ! Nr of Hs = 0 ATOM BRAR TYPE BR_A CHARge 0.0 END ! Nr of Hs = 0 ATOM CAP TYPE C_20 CHARge 0.0 END ! Nr of Hs = 0 ATOM OAQ TYPE O_21 CHARge 0.0 END ! Nr of Hs = 1 BOND CAE CAF BOND CAE CAD BOND CAF CAA BOND CAA NAB BOND NAB CAC BOND CAC CAD BOND CAD CAG BOND CAG OAU BOND CAG NAH BOND NAH NAI BOND NAI CAJ BOND CAJ CAK BOND CAK CAL BOND CAK CAP BOND CAL CAM BOND CAM BRAT BOND CAM CAN BOND CAN OAS BOND CAN CAO BOND CAO BRAR BOND CAO CAP BOND CAP OAQ { Note: edit these DIHEdrals if necessary } DIHEdral CAD CAE CAF CAA ! flat ? (0 degrees = cis) -0.04 DIHEdral CAF CAE CAD CAC ! flat ? (0 degrees = cis) 0.32 DIHEdral CAF CAE CAD CAG ! flat ? (180 degrees = trans) 180.00 DIHEdral CAE CAF CAA NAB ! flat ? (0 degrees = cis) 0.00 DIHEdral CAF CAA NAB CAC ! flat ? (0 degrees = cis) -0.27 DIHEdral CAA NAB CAC CAD ! flat ? (0 degrees = cis) 0.56 DIHEdral NAB CAC CAD CAE ! flat ? (0 degrees = cis) -0.58 DIHEdral NAB CAC CAD CAG ! flat ? (180 degrees = trans) 179.74 DIHEdral CAE CAD CAG OAU ! flat ? (0 degrees = cis) 0.08 DIHEdral CAE CAD CAG NAH ! flat ? (180 degrees = trans) 180.04 DIHEdral CAC CAD CAG OAU ! flat ? (180 degrees = trans) 179.75 DIHEdral CAC CAD CAG NAH ! flat ? (0 degrees = cis) -0.29 DIHEdral CAD CAG NAH NAI ! flat ? (180 degrees = trans) 180.04 DIHEdral OAU CAG NAH NAI ! flat ? (0 degrees = cis) 0.01 DIHEdral CAG NAH NAI CAJ ! flat ? (180 degrees = trans) 180.00 DIHEdral NAH NAI CAJ CAK ! flat ? (180 degrees = trans) 180.00 DIHEdral NAI CAJ CAK CAL ! flat ? (180 degrees = trans) 180.01 DIHEdral NAI CAJ CAK CAP ! flat ? (0 degrees = cis) 0.01 DIHEdral CAJ CAK CAL CAM ! flat ? (180 degrees = trans) 180.00 DIHEdral CAP CAK CAL CAM ! flat ? (0 degrees = cis) 0.00 DIHEdral CAJ CAK CAP CAO ! flat ? (180 degrees = trans) 179.76 DIHEdral CAJ CAK CAP OAQ ! flat ? (0 degrees = cis) 0.00 DIHEdral CAL CAK CAP CAO ! flat ? (0 degrees = cis) -0.24 DIHEdral CAL CAK CAP OAQ ! flat ? (180 degrees = trans) 180.00 DIHEdral CAK CAL CAM BRAT ! flat ? (180 degrees = trans) 179.99 DIHEdral CAK CAL CAM CAN ! flat ? (0 degrees = cis) 0.00 DIHEdral CAL CAM CAN OAS ! flat ? (180 degrees = trans) 179.95 DIHEdral CAL CAM CAN CAO ! flat ? (0 degrees = cis) 0.24 DIHEdral BRAT CAM CAN OAS ! flat ? (0 degrees = cis) -0.04 DIHEdral BRAT CAM CAN CAO ! flat ? (180 degrees = trans) 180.25 DIHEdral CAM CAN CAO BRAR ! flat ? (180 degrees = trans) 179.97 DIHEdral CAM CAN CAO CAP ! flat ? (0 degrees = cis) -0.48 DIHEdral OAS CAN CAO BRAR ! flat ? (0 degrees = cis) 0.26 DIHEdral OAS CAN CAO CAP ! flat ? (180 degrees = trans) 179.81 DIHEdral CAN CAO CAP CAK ! flat ? (0 degrees = cis) 0.48 DIHEdral CAN CAO CAP OAQ ! flat ? (180 degrees = trans) 180.24 DIHEdral BRAR CAO CAP CAK ! flat ? (180 degrees = trans) 180.02 DIHEdral BRAR CAO CAP OAQ ! flat ? (0 degrees = cis) -0.21 { Note: edit these IMPRopers if necessary } IMPRoper CAD CAE CAC CAG ! chirality or flatness improper -0.19 IMPRoper CAG CAD OAU NAH ! chirality or flatness improper -0.02 IMPRoper CAK CAJ CAL CAP ! chirality or flatness improper 0.00 IMPRoper CAM CAL BRAT CAN ! chirality or flatness improper 0.01 IMPRoper CAN CAM OAS CAO ! chirality or flatness improper 0.17 IMPRoper CAO CAN BRAR CAP ! chirality or flatness improper -0.25 IMPRoper CAP CAK CAO OAQ ! chirality or flatness improper 0.13 { Note: edit any DONOrs and ACCEptors if necessary } ! DONOr H?1 NAB ACCEptor OAU CAG ! DONOr H?1 NAH ! DONOr H?1 NAI ACCEptor OAS CAN ACCEptor OAQ CAP END { RESIdue BDE }