Remarks r88_xplor_top.txt Remarks Created by XPLO2D V. 050802/3.3.2 at Sun Mar 2 16:03:04 2008 for A. Nonymous Remarks Auto-generated by XPLO2D from file r88_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 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_2 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS O_3 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS C_4 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (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 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_8 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS C_9 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_10 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_11 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS N_12 14.00700 ! assuming N -> 14.00700 + 1.008 * 0 (Hs) MASS C_13 15.03500 ! assuming C -> 12.01100 + 1.008 * 3 (Hs) MASS C_14 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (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 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 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS O_21 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS C_22 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS BR_2 79.90400 ! assuming BR -> 79.90400 + 1.008 * 0 (Hs) MASS C_24 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_25 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) autogenerate angles=true end RESIdue R88 { 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 C1A TYPE C_1 CHARge 0.0 END ! Nr of Hs = 0 ATOM C1 TYPE C_2 CHARge 0.0 END ! Nr of Hs = 0 ATOM O2 TYPE O_3 CHARge 0.0 END ! Nr of Hs = 0 ATOM C1B TYPE C_4 CHARge 0.0 END ! Nr of Hs = 0 ATOM C6B TYPE C_5 CHARge 0.0 END ! Nr of Hs = 1 ATOM C5B TYPE C_6 CHARge 0.0 END ! Nr of Hs = 1 ATOM C4B TYPE C_7 CHARge 0.0 END ! Nr of Hs = 0 ATOM C2C TYPE C_8 CHARge 0.0 END ! Nr of Hs = 2 ATOM C3C TYPE C_9 CHARge 0.0 END ! Nr of Hs = 1 ATOM C4C TYPE C_10 CHARge 0.0 END ! Nr of Hs = 1 ATOM C5C TYPE C_11 CHARge 0.0 END ! Nr of Hs = 2 ATOM N1D TYPE N_12 CHARge 0.0 END ! Nr of Hs = 0 ATOM C1F TYPE C_13 CHARge 0.0 END ! Nr of Hs = 3 ATOM C1E TYPE C_14 CHARge 0.0 END ! Nr of Hs = 1 ATOM C2E TYPE C_15 CHARge 0.0 END ! Nr of Hs = 2 ATOM C3B TYPE C_16 CHARge 0.0 END ! Nr of Hs = 1 ATOM C2B TYPE C_17 CHARge 0.0 END ! Nr of Hs = 1 ATOM C6A TYPE C_18 CHARge 0.0 END ! Nr of Hs = 1 ATOM C5A TYPE C_19 CHARge 0.0 END ! Nr of Hs = 1 ATOM C4A TYPE C_20 CHARge 0.0 END ! Nr of Hs = 0 ATOM O1C TYPE O_21 CHARge 0.0 END ! Nr of Hs = 0 ATOM C3E TYPE C_22 CHARge 0.0 END ! Nr of Hs = 2 ATOM BR23 TYPE BR_2 CHARge 0.0 END ! Nr of Hs = 0 ATOM C3A TYPE C_24 CHARge 0.0 END ! Nr of Hs = 1 ATOM C2A TYPE C_25 CHARge 0.0 END ! Nr of Hs = 1 BOND C1A C1 BOND C1A C6A BOND C1A C2A BOND C1 O2 BOND C1 C1B BOND C1B C6B BOND C1B C2B BOND C6B C5B BOND C5B C4B BOND C4B C3B BOND C4B O1C BOND C2C C3C BOND C2C O1C BOND C3C C4C BOND C4C C5C BOND C5C N1D BOND N1D C1F BOND N1D C1E BOND C1E C2E BOND C1E C3E BOND C2E C3E BOND C3B C2B BOND C6A C5A BOND C5A C4A BOND C4A BR23 BOND C4A C3A BOND C3A C2A { Note: edit these DIHEdrals if necessary } DIHEdral C6A C1A C1 O2 ! flat ? (0 degrees = cis) -7.62 DIHEdral C6A C1A C1 C1B ! flat ? (180 degrees = trans) 172.40 DIHEdral C2A C1A C1 O2 ! flat ? (180 degrees = trans) 172.20 DIHEdral C2A C1A C1 C1B ! flat ? (0 degrees = cis) -7.79 DIHEdral C1 C1A C6A C5A ! flat ? (180 degrees = trans) 180.01 DIHEdral C2A C1A C6A C5A ! flat ? (0 degrees = cis) 0.19 DIHEdral C1 C1A C2A C3A ! flat ? (180 degrees = trans) 179.72 DIHEdral C6A C1A C2A C3A ! flat ? (0 degrees = cis) -0.46 DIHEdral C1 C1B C6B C5B ! flat ? (180 degrees = trans) 179.98 DIHEdral C2B C1B C6B C5B ! flat ? (0 degrees = cis) 0.00 DIHEdral C1 C1B C2B C3B ! flat ? (180 degrees = trans) 179.76 DIHEdral C6B C1B C2B C3B ! flat ? (0 degrees = cis) -0.27 DIHEdral C1B C6B C5B C4B ! flat ? (0 degrees = cis) 0.02 DIHEdral C6B C5B C4B C3B ! flat ? (0 degrees = cis) 0.23 DIHEdral C6B C5B C4B O1C ! flat ? (180 degrees = trans) 179.99 DIHEdral C5B C4B C3B C2B ! flat ? (0 degrees = cis) -0.50 DIHEdral O1C C4B C3B C2B ! flat ? (180 degrees = trans) 179.74 DIHEdral C5B C4B O1C C2C ! flat ? (180 degrees = trans) 179.96 DIHEdral C3B C4B O1C C2C ! flat ? (0 degrees = cis) -0.28 ! DIHEdral O1C C2C C3C C4C ! flexible dihedral ??? 120.04 DIHEdral C3C C2C O1C C4B ! flat ? (180 degrees = trans) 179.97 DIHEdral C2C C3C C4C C5C ! flat ? (180 degrees = trans) 179.97 ! DIHEdral C3C C4C C5C N1D ! flexible dihedral ??? 119.94 ! DIHEdral C4C C5C N1D C1F ! flexible dihedral ??? -66.10 DIHEdral C4C C5C N1D C1E ! flat ? (180 degrees = trans) 180.02 DIHEdral C5C N1D C1E C2E ! flat ? (180 degrees = trans) 180.04 ! DIHEdral C5C N1D C1E C3E ! flexible dihedral ??? -111.31 ! DIHEdral C1F N1D C1E C2E ! flexible dihedral ??? 66.17 DIHEdral C4B C3B C2B C1B ! flat ? (0 degrees = cis) 0.52 DIHEdral C1A C6A C5A C4A ! flat ? (0 degrees = cis) 0.04 DIHEdral C6A C5A C4A BR23 ! flat ? (180 degrees = trans) 179.93 DIHEdral C6A C5A C4A C3A ! flat ? (0 degrees = cis) 0.00 DIHEdral C5A C4A C3A C2A ! flat ? (0 degrees = cis) -0.27 DIHEdral BR23 C4A C3A C2A ! flat ? (180 degrees = trans) 179.80 DIHEdral C4A C3A C2A C1A ! flat ? (0 degrees = cis) 0.50 { Note: edit these IMPRopers if necessary } IMPRoper C1A C1 C6A C2A ! chirality or flatness improper -0.11 IMPRoper C1 C1A O2 C1B ! chirality or flatness improper 0.01 IMPRoper C1B C1 C6B C2B ! chirality or flatness improper -0.02 IMPRoper C4B C5B C3B O1C ! chirality or flatness improper -0.14 IMPRoper N1D C5C C1F C1E ! chirality or flatness improper 39.06 IMPRoper C1E N1D C2E C3E ! chirality or flatness improper -59.90 IMPRoper C4A C5A BR23 C3A ! chirality or flatness improper 0.04 { Note: edit any DONOrs and ACCEptors if necessary } ACCEptor O2 C1 ACCEptor O1C C4B END { RESIdue R88 }