Remarks li8_xplor_top.txt Remarks Created by XPLO2D V. 050802/3.3.2 at Sat Mar 1 15:26:43 2008 for A. Nonymous Remarks Auto-generated by XPLO2D from file li8_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 N_3 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_4 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS N_5 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_6 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS BR_7 79.90400 ! assuming BR -> 79.90400 + 1.008 * 0 (Hs) MASS N_8 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_9 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_10 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_11 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_12 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_13 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_14 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (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 14.00700 ! assuming N -> 14.00700 + 1.008 * 0 (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 C_21 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS C_22 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS N_23 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_24 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS C_25 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS N_26 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_27 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS O_28 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS C_29 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS C_30 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_31 15.03500 ! assuming C -> 12.01100 + 1.008 * 3 (Hs) MASS C_32 15.03500 ! assuming C -> 12.01100 + 1.008 * 3 (Hs) MASS C_33 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS O_34 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS N_35 14.00700 ! assuming N -> 14.00700 + 1.008 * 0 (Hs) autogenerate angles=true end RESIdue LI8 { 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 = 0 ATOM C2 TYPE C_2 CHARge 0.0 END ! Nr of Hs = 0 ATOM N3 TYPE N_3 CHARge 0.0 END ! Nr of Hs = 1 ATOM C4 TYPE C_4 CHARge 0.0 END ! Nr of Hs = 0 ATOM N5 TYPE N_5 CHARge 0.0 END ! Nr of Hs = 1 ATOM C6 TYPE C_6 CHARge 0.0 END ! Nr of Hs = 1 ATOM BR7 TYPE BR_7 CHARge 0.0 END ! Nr of Hs = 0 ATOM N8 TYPE N_8 CHARge 0.0 END ! Nr of Hs = 1 ATOM C10 TYPE C_9 CHARge 0.0 END ! Nr of Hs = 0 ATOM C11 TYPE C_10 CHARge 0.0 END ! Nr of Hs = 1 ATOM C12 TYPE C_11 CHARge 0.0 END ! Nr of Hs = 0 ATOM C13 TYPE C_12 CHARge 0.0 END ! Nr of Hs = 1 ATOM C14 TYPE C_13 CHARge 0.0 END ! Nr of Hs = 1 ATOM C15 TYPE C_14 CHARge 0.0 END ! Nr of Hs = 1 ATOM N16 TYPE N_15 CHARge 0.0 END ! Nr of Hs = 1 ATOM C18 TYPE C_16 CHARge 0.0 END ! Nr of Hs = 0 ATOM O19 TYPE O_17 CHARge 0.0 END ! Nr of Hs = 0 ATOM N20 TYPE N_18 CHARge 0.0 END ! Nr of Hs = 0 ATOM C21 TYPE C_19 CHARge 0.0 END ! Nr of Hs = 2 ATOM C22 TYPE C_20 CHARge 0.0 END ! Nr of Hs = 2 ATOM C23 TYPE C_21 CHARge 0.0 END ! Nr of Hs = 2 ATOM C24 TYPE C_22 CHARge 0.0 END ! Nr of Hs = 2 ATOM N25 TYPE N_23 CHARge 0.0 END ! Nr of Hs = 1 ATOM C27 TYPE C_24 CHARge 0.0 END ! Nr of Hs = 2 ATOM C28 TYPE C_25 CHARge 0.0 END ! Nr of Hs = 2 ATOM N29 TYPE N_26 CHARge 0.0 END ! Nr of Hs = 1 ATOM C31 TYPE C_27 CHARge 0.0 END ! Nr of Hs = 0 ATOM O32 TYPE O_28 CHARge 0.0 END ! Nr of Hs = 0 ATOM C33 TYPE C_29 CHARge 0.0 END ! Nr of Hs = 2 ATOM C34 TYPE C_30 CHARge 0.0 END ! Nr of Hs = 0 ATOM C35 TYPE C_31 CHARge 0.0 END ! Nr of Hs = 3 ATOM C36 TYPE C_32 CHARge 0.0 END ! Nr of Hs = 3 ATOM C37 TYPE C_33 CHARge 0.0 END ! Nr of Hs = 0 ATOM O38 TYPE O_34 CHARge 0.0 END ! Nr of Hs = 0 ATOM N39 TYPE N_35 CHARge 0.0 END ! Nr of Hs = 0 BOND C1 C2 BOND C1 C6 BOND C1 BR7 BOND C2 N3 BOND C2 N25 BOND N3 C4 BOND C4 N5 BOND C4 N8 BOND N5 C6 BOND N8 C10 BOND C10 C11 BOND C10 C15 BOND C11 C12 BOND C12 C13 BOND C12 N16 BOND C13 C14 BOND C14 C15 BOND N16 C18 BOND C18 O19 BOND C18 N20 BOND N20 C21 BOND N20 C24 BOND C21 C22 BOND C22 C23 BOND C23 C24 BOND N25 C27 BOND C27 C28 BOND C28 C33 BOND N29 C31 BOND N29 C33 BOND C31 O32 BOND C31 C34 BOND C34 C35 BOND C34 C36 BOND C34 C37 BOND C37 O38 BOND C37 N39 { Note: edit these DIHEdrals if necessary } DIHEdral C6 C1 C2 N3 ! flat ? (0 degrees = cis) -0.45 DIHEdral C6 C1 C2 N25 ! flat ? (180 degrees = trans) 179.76 DIHEdral BR7 C1 C2 N3 ! flat ? (180 degrees = trans) 179.96 DIHEdral BR7 C1 C2 N25 ! flat ? (0 degrees = cis) 0.17 DIHEdral C2 C1 C6 N5 ! flat ? (0 degrees = cis) 0.44 DIHEdral BR7 C1 C6 N5 ! flat ? (180 degrees = trans) 180.02 DIHEdral C1 C2 N3 C4 ! flat ? (0 degrees = cis) 0.23 DIHEdral N25 C2 N3 C4 ! flat ? (180 degrees = trans) 180.02 DIHEdral C1 C2 N25 C27 ! flat ? (180 degrees = trans) 179.77 DIHEdral N3 C2 N25 C27 ! flat ? (0 degrees = cis) -0.02 DIHEdral C2 N3 C4 N5 ! flat ? (0 degrees = cis) 0.02 DIHEdral C2 N3 C4 N8 ! flat ? (180 degrees = trans) 180.03 DIHEdral N3 C4 N5 C6 ! flat ? (0 degrees = cis) -0.03 DIHEdral N8 C4 N5 C6 ! flat ? (180 degrees = trans) 179.96 DIHEdral N3 C4 N8 C10 ! flat ? (180 degrees = trans) 185.83 DIHEdral N5 C4 N8 C10 ! flat ? (0 degrees = cis) 5.84 DIHEdral C4 N5 C6 C1 ! flat ? (0 degrees = cis) -0.20 DIHEdral N8 C10 C11 C12 ! flat ? (180 degrees = trans) 179.69 DIHEdral C15 C10 C11 C12 ! flat ? (0 degrees = cis) -0.53 DIHEdral N8 C10 C15 C14 ! flat ? (180 degrees = trans) 180.01 DIHEdral C11 C10 C15 C14 ! flat ? (0 degrees = cis) 0.23 DIHEdral C10 C11 C12 C13 ! flat ? (0 degrees = cis) 0.53 DIHEdral C10 C11 C12 N16 ! flat ? (180 degrees = trans) 180.28 DIHEdral C11 C12 C13 C14 ! flat ? (0 degrees = cis) -0.24 DIHEdral N16 C12 C13 C14 ! flat ? (180 degrees = trans) 180.01 DIHEdral C12 C13 C14 C15 ! flat ? (0 degrees = cis) -0.07 DIHEdral C13 C14 C15 C10 ! flat ? (0 degrees = cis) 0.07 DIHEdral C12 N16 C18 O19 ! flat ? (0 degrees = cis) 4.07 DIHEdral C12 N16 C18 N20 ! flat ? (180 degrees = trans) 183.98 DIHEdral N16 C18 N20 C21 ! flat ? (180 degrees = trans) 179.99 DIHEdral N16 C18 N20 C24 ! flat ? (0 degrees = cis) -0.23 DIHEdral O19 C18 N20 C21 ! flat ? (0 degrees = cis) -0.11 DIHEdral O19 C18 N20 C24 ! flat ? (180 degrees = trans) 179.68 DIHEdral C18 N20 C21 C22 ! flat ? (180 degrees = trans) 181.08 DIHEdral C24 N20 C21 C22 ! flat ? (0 degrees = cis) 1.26 DIHEdral C2 N25 C27 C28 ! flat ? (180 degrees = trans) 180.02 DIHEdral N25 C27 C28 C33 ! flat ? (180 degrees = trans) 180.02 DIHEdral C27 C28 C33 N29 ! flat ? (180 degrees = trans) 180.01 DIHEdral C33 N29 C31 O32 ! flat ? (0 degrees = cis) -0.05 DIHEdral C33 N29 C31 C34 ! flat ? (180 degrees = trans) 179.99 DIHEdral C31 N29 C33 C28 ! flat ? (180 degrees = trans) 180.00 ! DIHEdral N29 C31 C34 C35 ! flexible dihedral ??? 59.94 ! DIHEdral N29 C31 C34 C36 ! flexible dihedral ??? -60.01 DIHEdral N29 C31 C34 C37 ! flat ? (180 degrees = trans) 180.00 ! DIHEdral O32 C31 C34 C35 ! flexible dihedral ??? -120.02 ! DIHEdral O32 C31 C34 C36 ! flexible dihedral ??? 120.03 DIHEdral O32 C31 C34 C37 ! flat ? (0 degrees = cis) 0.04 DIHEdral C31 C34 C37 O38 ! flat ? (0 degrees = cis) -0.06 DIHEdral C31 C34 C37 N39 ! flat ? (180 degrees = trans) 180.02 ! DIHEdral C35 C34 C37 O38 ! flexible dihedral ??? 119.98 ! DIHEdral C35 C34 C37 N39 ! flexible dihedral ??? -59.94 ! DIHEdral C36 C34 C37 O38 ! flexible dihedral ??? -120.05 ! DIHEdral C36 C34 C37 N39 ! flexible dihedral ??? 60.03 { Note: edit these IMPRopers if necessary } IMPRoper C1 C2 C6 BR7 ! chirality or flatness improper 0.26 IMPRoper C2 C1 N3 N25 ! chirality or flatness improper 0.12 IMPRoper C4 N3 N5 N8 ! chirality or flatness improper 0.00 IMPRoper C10 N8 C11 C15 ! chirality or flatness improper 0.13 IMPRoper C12 C11 C13 N16 ! chirality or flatness improper -0.15 IMPRoper C18 N16 O19 N20 ! chirality or flatness improper -0.06 IMPRoper N20 C18 C21 C24 ! chirality or flatness improper -0.12 IMPRoper C31 N29 O32 C34 ! chirality or flatness improper 0.02 IMPRoper C34 C31 C35 C36 ! chirality or flatness improper 35.40 IMPRoper C37 C34 O38 N39 ! chirality or flatness improper 0.05 { Note: edit any DONOrs and ACCEptors if necessary } ! DONOr H?1 N3 ! DONOr H?1 N5 ! DONOr H?1 N8 ! DONOr H?1 N16 ACCEptor O19 C18 ! DONOr H?1 N25 ! DONOr H?1 N29 ACCEptor O32 C31 ACCEptor O38 C37 END { RESIdue LI8 }