Remarks 2bl_xplor_top.txt Remarks Created by XPLO2D V. 050802/3.3.2 at Thu Feb 28 03:25:18 2008 for A. Nonymous Remarks Auto-generated by XPLO2D from file 2bl_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 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 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS C_6 15.03500 ! assuming C -> 12.01100 + 1.008 * 3 (Hs) MASS C_7 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (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 13.01900 ! assuming C -> 12.01100 + 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 15.03500 ! assuming C -> 12.01100 + 1.008 * 3 (Hs) MASS O_14 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS O_15 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS O_16 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS O_17 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS O_18 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs) MASS S_19 32.06600 ! assuming S -> 32.06600 + 1.008 * 0 (Hs) MASS N_20 14.00700 ! assuming N -> 14.00700 + 1.008 * 0 (Hs) autogenerate angles=true end RESIdue 2BL { 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 C TYPE C_1 CHARge 0.0 END ! Nr of Hs = 0 ATOM CA TYPE C_2 CHARge 0.0 END ! Nr of Hs = 1 ATOM CB TYPE C_3 CHARge 0.0 END ! Nr of Hs = 1 ATOM CC TYPE C_4 CHARge 0.0 END ! Nr of Hs = 0 ATOM CD TYPE C_5 CHARge 0.0 END ! Nr of Hs = 2 ATOM CE TYPE C_6 CHARge 0.0 END ! Nr of Hs = 3 ATOM CF TYPE C_7 CHARge 0.0 END ! Nr of Hs = 0 ATOM CG1 TYPE C_8 CHARge 0.0 END ! Nr of Hs = 1 ATOM CG2 TYPE C_9 CHARge 0.0 END ! Nr of Hs = 1 ATOM CH1 TYPE C_10 CHARge 0.0 END ! Nr of Hs = 1 ATOM CH2 TYPE C_11 CHARge 0.0 END ! Nr of Hs = 1 ATOM CI TYPE C_12 CHARge 0.0 END ! Nr of Hs = 0 ATOM CJ TYPE C_13 CHARge 0.0 END ! Nr of Hs = 3 ATOM O TYPE O_14 CHARge 0.0 END ! Nr of Hs = 0 ATOM OA TYPE O_15 CHARge 0.0 END ! Nr of Hs = 0 ATOM OB TYPE O_16 CHARge 0.0 END ! Nr of Hs = 1 ATOM OC TYPE O_17 CHARge 0.0 END ! Nr of Hs = 1 ATOM OD TYPE O_18 CHARge 0.0 END ! Nr of Hs = 1 ATOM S TYPE S_19 CHARge 0.0 END ! Nr of Hs = 0 ATOM N TYPE N_20 CHARge 0.0 END ! Nr of Hs = 0 BOND C CA BOND C O BOND C N BOND CA CB BOND CA CD BOND CB CC BOND CB N BOND CC OA BOND CC OB BOND CD CE BOND CF CG1 BOND CF CG2 BOND CF S BOND CG1 CH1 BOND CG2 CH2 BOND CH1 CI BOND CH2 CI BOND CI CJ BOND OC S BOND OD S BOND S N { Note: edit these DIHEdrals if necessary } DIHEdral O C CA CB ! flat ? (180 degrees = trans) 180.04 ! DIHEdral O C CA CD ! flexible dihedral ??? -65.48 DIHEdral N C CA CB ! flat ? (0 degrees = cis) -0.05 ! DIHEdral N C CA CD ! flexible dihedral ??? 114.43 DIHEdral CA C N CB ! flat ? (0 degrees = cis) 0.05 DIHEdral CA C N S ! flat ? (180 degrees = trans) 180.09 DIHEdral O C N CB ! flat ? (180 degrees = trans) 179.96 DIHEdral O C N S ! flat ? (0 degrees = cis) -0.01 ! DIHEdral C CA CB CC ! flexible dihedral ??? -114.46 DIHEdral C CA CB N ! flat ? (0 degrees = cis) 0.04 ! DIHEdral CD CA CB N ! flexible dihedral ??? -114.46 ! DIHEdral C CA CD CE ! flexible dihedral ??? 81.11 DIHEdral CB CA CD CE ! flat ? (180 degrees = trans) 178.26 ! DIHEdral CA CB CC OA ! flexible dihedral ??? 89.99 ! DIHEdral CA CB CC OB ! flexible dihedral ??? -89.99 DIHEdral N CB CC OA ! flat ? (0 degrees = cis) -6.93 DIHEdral N CB CC OB ! flat ? (180 degrees = trans) 173.09 DIHEdral CA CB N C ! flat ? (0 degrees = cis) -0.05 DIHEdral CA CB N S ! flat ? (180 degrees = trans) 179.91 ! DIHEdral CC CB N C ! flexible dihedral ??? 114.37 ! DIHEdral CC CB N S ! flexible dihedral ??? -65.67 DIHEdral CG2 CF CG1 CH1 ! flat ? (0 degrees = cis) 0.30 DIHEdral S CF CG1 CH1 ! flat ? (180 degrees = trans) 180.01 DIHEdral CG1 CF CG2 CH2 ! flat ? (0 degrees = cis) -0.50 DIHEdral S CF CG2 CH2 ! flat ? (180 degrees = trans) 179.79 ! DIHEdral CG1 CF S N ! flexible dihedral ??? 89.98 ! DIHEdral CG2 CF S N ! flexible dihedral ??? -90.31 DIHEdral CF CG1 CH1 CI ! flat ? (0 degrees = cis) -0.08 DIHEdral CF CG2 CH2 CI ! flat ? (0 degrees = cis) 0.47 DIHEdral CG1 CH1 CI CH2 ! flat ? (0 degrees = cis) 0.06 DIHEdral CG1 CH1 CI CJ ! flat ? (180 degrees = trans) 179.99 DIHEdral CG2 CH2 CI CH1 ! flat ? (0 degrees = cis) -0.25 DIHEdral CG2 CH2 CI CJ ! flat ? (180 degrees = trans) 179.81 ! DIHEdral CF S N C ! flexible dihedral ??? -89.98 ! DIHEdral CF S N CB ! flexible dihedral ??? 90.07 { Note: edit these IMPRopers if necessary } IMPRoper C CA O N ! chirality or flatness improper -0.07 IMPRoper CA C CB CD ! chirality or flatness improper -33.11 IMPRoper CB CA CC N ! chirality or flatness improper -45.93 IMPRoper CC CB OA OB ! chirality or flatness improper 0.01 IMPRoper CF CG1 CG2 S ! chirality or flatness improper -0.18 IMPRoper CI CH1 CH2 CJ ! chirality or flatness improper -0.04 IMPRoper S CF OC OD ! chirality or flatness improper 26.28 IMPRoper N C CB S ! chirality or flatness improper 0.02 { Note: edit any DONOrs and ACCEptors if necessary } ACCEptor O C ACCEptor OA CC ACCEptor OB CC ACCEptor OC S ACCEptor OD S END { RESIdue 2BL }