Remarks yol_xplor_top.txt Remarks Created by XPLO2D V. 050802/3.3.2 at Mon Mar 3 11:34:59 2008 for A. Nonymous Remarks Auto-generated by XPLO2D from file yol_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 O_1 17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (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 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (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 N_10 14.00700 ! assuming N -> 14.00700 + 1.008 * 0 (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 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_15 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_16 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_17 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS O_18 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS FE_1 55.84700 ! assuming FE -> 55.84700 + 1.008 * 0 (Hs) MASS O_20 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS C_21 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_22 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_23 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (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) MASS C_26 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_27 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS N_28 14.00700 ! assuming N -> 14.00700 + 1.008 * 0 (Hs) autogenerate angles=true end RESIdue YOL { 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 O2A TYPE O_1 CHARge 0.0 END ! Nr of Hs = 1 ATOM CAA TYPE C_2 CHARge 0.0 END ! Nr of Hs = 0 ATOM O1A TYPE O_3 CHARge 0.0 END ! Nr of Hs = 0 ATOM CC5 TYPE C_4 CHARge 0.0 END ! Nr of Hs = 0 ATOM CC6 TYPE C_5 CHARge 0.0 END ! Nr of Hs = 1 ATOM CC1 TYPE C_6 CHARge 0.0 END ! Nr of Hs = 0 ATOM CC2 TYPE C_7 CHARge 0.0 END ! Nr of Hs = 0 ATOM CC3 TYPE C_8 CHARge 0.0 END ! Nr of Hs = 1 ATOM CC4 TYPE C_9 CHARge 0.0 END ! Nr of Hs = 1 ATOM NA TYPE N_10 CHARge 0.0 END ! Nr of Hs = 0 ATOM CA TYPE C_11 CHARge 0.0 END ! Nr of Hs = 1 ATOM CA1 TYPE C_12 CHARge 0.0 END ! Nr of Hs = 0 ATOM CA6 TYPE C_13 CHARge 0.0 END ! Nr of Hs = 1 ATOM CA5 TYPE C_14 CHARge 0.0 END ! Nr of Hs = 1 ATOM CA4 TYPE C_15 CHARge 0.0 END ! Nr of Hs = 1 ATOM CA3 TYPE C_16 CHARge 0.0 END ! Nr of Hs = 1 ATOM CA2 TYPE C_17 CHARge 0.0 END ! Nr of Hs = 0 ATOM OA TYPE O_18 CHARge 0.0 END ! Nr of Hs = 0 ATOM FE TYPE FE_1 CHARge 0.0 END ! Nr of Hs = 0 ATOM OB TYPE O_20 CHARge 0.0 END ! Nr of Hs = 0 ATOM CB2 TYPE C_21 CHARge 0.0 END ! Nr of Hs = 0 ATOM CB3 TYPE C_22 CHARge 0.0 END ! Nr of Hs = 1 ATOM CB4 TYPE C_23 CHARge 0.0 END ! Nr of Hs = 1 ATOM CB5 TYPE C_24 CHARge 0.0 END ! Nr of Hs = 1 ATOM CB6 TYPE C_25 CHARge 0.0 END ! Nr of Hs = 1 ATOM CB1 TYPE C_26 CHARge 0.0 END ! Nr of Hs = 0 ATOM CB TYPE C_27 CHARge 0.0 END ! Nr of Hs = 1 ATOM NB TYPE N_28 CHARge 0.0 END ! Nr of Hs = 0 BOND O2A CAA BOND CAA O1A BOND CAA CC5 BOND CC5 CC6 BOND CC5 CC4 BOND CC6 CC1 BOND CC1 CC2 BOND CC1 NA BOND CC2 CC3 BOND CC2 NB BOND CC3 CC4 BOND NA CA BOND NA FE BOND CA CA1 BOND CA1 CA6 BOND CA1 CA2 BOND CA6 CA5 BOND CA5 CA4 BOND CA4 CA3 BOND CA3 CA2 BOND CA2 OA BOND OA FE BOND FE OB BOND FE NB BOND OB CB2 BOND CB2 CB3 BOND CB2 CB1 BOND CB3 CB4 BOND CB4 CB5 BOND CB5 CB6 BOND CB6 CB1 BOND CB1 CB BOND CB NB { Note: edit these DIHEdrals if necessary } DIHEdral O2A CAA CC5 CC6 ! flat ? (180 degrees = trans) 180.10 DIHEdral O2A CAA CC5 CC4 ! flat ? (0 degrees = cis) 0.07 DIHEdral O1A CAA CC5 CC6 ! flat ? (0 degrees = cis) 0.03 DIHEdral O1A CAA CC5 CC4 ! flat ? (180 degrees = trans) 180.00 DIHEdral CAA CC5 CC6 CC1 ! flat ? (180 degrees = trans) 180.11 DIHEdral CC4 CC5 CC6 CC1 ! flat ? (0 degrees = cis) 0.14 DIHEdral CAA CC5 CC4 CC3 ! flat ? (180 degrees = trans) 179.81 DIHEdral CC6 CC5 CC4 CC3 ! flat ? (0 degrees = cis) -0.22 DIHEdral CC5 CC6 CC1 CC2 ! flat ? (0 degrees = cis) 0.18 DIHEdral CC5 CC6 CC1 NA ! flat ? (180 degrees = trans) 180.10 DIHEdral CC6 CC1 CC2 CC3 ! flat ? (0 degrees = cis) -0.42 DIHEdral CC6 CC1 CC2 NB ! flat ? (180 degrees = trans) 179.42 DIHEdral NA CC1 CC2 CC3 ! flat ? (180 degrees = trans) 179.66 DIHEdral NA CC1 CC2 NB ! flat ? (0 degrees = cis) -0.51 DIHEdral CC6 CC1 NA CA ! flat ? (0 degrees = cis) 0.21 DIHEdral CC6 CC1 NA FE ! flat ? (180 degrees = trans) 180.19 DIHEdral CC2 CC1 NA CA ! flat ? (180 degrees = trans) 180.13 DIHEdral CC2 CC1 NA FE ! flat ? (0 degrees = cis) 0.11 DIHEdral CC1 CC2 CC3 CC4 ! flat ? (0 degrees = cis) 0.34 DIHEdral NB CC2 CC3 CC4 ! flat ? (180 degrees = trans) 180.52 DIHEdral CC1 CC2 NB FE ! flat ? (0 degrees = cis) 0.64 DIHEdral CC1 CC2 NB CB ! flat ? (180 degrees = trans) 180.78 DIHEdral CC3 CC2 NB FE ! flat ? (180 degrees = trans) 180.46 DIHEdral CC3 CC2 NB CB ! flat ? (0 degrees = cis) 0.61 DIHEdral CC2 CC3 CC4 CC5 ! flat ? (0 degrees = cis) -0.02 DIHEdral CC1 NA CA CA1 ! flat ? (180 degrees = trans) 180.39 DIHEdral FE NA CA CA1 ! flat ? (0 degrees = cis) 0.41 DIHEdral CC1 NA FE OA ! flat ? (180 degrees = trans) 179.63 DIHEdral CC1 NA FE OB ! flat ? (180 degrees = trans) 170.61 DIHEdral CC1 NA FE NB ! flat ? (0 degrees = cis) 0.20 DIHEdral CA NA FE OA ! flat ? (0 degrees = cis) -0.39 DIHEdral CA NA FE OB ! flat ? (0 degrees = cis) -9.41 DIHEdral CA NA FE NB ! flat ? (180 degrees = trans) 180.18 DIHEdral NA CA CA1 CA6 ! flat ? (180 degrees = trans) 179.81 DIHEdral NA CA CA1 CA2 ! flat ? (0 degrees = cis) -0.19 DIHEdral CA CA1 CA6 CA5 ! flat ? (180 degrees = trans) 180.06 DIHEdral CA2 CA1 CA6 CA5 ! flat ? (0 degrees = cis) 0.05 DIHEdral CA CA1 CA2 CA3 ! flat ? (180 degrees = trans) 179.91 DIHEdral CA CA1 CA2 OA ! flat ? (0 degrees = cis) 0.02 DIHEdral CA6 CA1 CA2 CA3 ! flat ? (0 degrees = cis) -0.09 DIHEdral CA6 CA1 CA2 OA ! flat ? (180 degrees = trans) 180.02 DIHEdral CA1 CA6 CA5 CA4 ! flat ? (0 degrees = cis) -0.01 DIHEdral CA6 CA5 CA4 CA3 ! flat ? (0 degrees = cis) 0.00 DIHEdral CA5 CA4 CA3 CA2 ! flat ? (0 degrees = cis) -0.04 DIHEdral CA4 CA3 CA2 CA1 ! flat ? (0 degrees = cis) 0.08 DIHEdral CA4 CA3 CA2 OA ! flat ? (180 degrees = trans) 179.98 DIHEdral CA1 CA2 OA FE ! flat ? (0 degrees = cis) -0.11 DIHEdral CA3 CA2 OA FE ! flat ? (180 degrees = trans) 180.00 DIHEdral CA2 OA FE NA ! flat ? (0 degrees = cis) 0.25 DIHEdral CA2 OA FE OB ! flat ? (180 degrees = trans) 179.60 DIHEdral CA2 OA FE NB ! flat ? (180 degrees = trans) 172.35 DIHEdral NA FE OB CB2 ! flat ? (180 degrees = trans) 189.79 DIHEdral OA FE OB CB2 ! flat ? (180 degrees = trans) 180.67 DIHEdral NB FE OB CB2 ! flat ? (0 degrees = cis) 0.15 DIHEdral NA FE NB CC2 ! flat ? (0 degrees = cis) -0.46 DIHEdral NA FE NB CB ! flat ? (180 degrees = trans) 179.40 DIHEdral OA FE NB CC2 ! flat ? (180 degrees = trans) 187.40 DIHEdral OA FE NB CB ! flat ? (0 degrees = cis) 7.25 DIHEdral OB FE NB CC2 ! flat ? (180 degrees = trans) 180.22 DIHEdral OB FE NB CB ! flat ? (0 degrees = cis) 0.08 DIHEdral FE OB CB2 CB3 ! flat ? (180 degrees = trans) 179.80 DIHEdral FE OB CB2 CB1 ! flat ? (0 degrees = cis) -0.30 DIHEdral OB CB2 CB3 CB4 ! flat ? (180 degrees = trans) 179.97 DIHEdral CB1 CB2 CB3 CB4 ! flat ? (0 degrees = cis) 0.07 DIHEdral OB CB2 CB1 CB6 ! flat ? (180 degrees = trans) 180.10 DIHEdral OB CB2 CB1 CB ! flat ? (0 degrees = cis) 0.20 DIHEdral CB3 CB2 CB1 CB6 ! flat ? (0 degrees = cis) 0.00 DIHEdral CB3 CB2 CB1 CB ! flat ? (180 degrees = trans) 180.10 DIHEdral CB2 CB3 CB4 CB5 ! flat ? (0 degrees = cis) -0.06 DIHEdral CB3 CB4 CB5 CB6 ! flat ? (0 degrees = cis) 0.00 DIHEdral CB4 CB5 CB6 CB1 ! flat ? (0 degrees = cis) 0.06 DIHEdral CB5 CB6 CB1 CB2 ! flat ? (0 degrees = cis) -0.06 DIHEdral CB5 CB6 CB1 CB ! flat ? (180 degrees = trans) 179.84 DIHEdral CB2 CB1 CB NB ! flat ? (0 degrees = cis) 0.03 DIHEdral CB6 CB1 CB NB ! flat ? (180 degrees = trans) 180.14 DIHEdral CB1 CB NB CC2 ! flat ? (180 degrees = trans) 179.67 DIHEdral CB1 CB NB FE ! flat ? (0 degrees = cis) -0.16 { Note: edit these IMPRopers if necessary } IMPRoper CAA O2A O1A CC5 ! chirality or flatness improper -0.04 IMPRoper CC5 CAA CC6 CC4 ! chirality or flatness improper -0.02 IMPRoper CC1 CC6 CC2 NA ! chirality or flatness improper -0.04 IMPRoper CC2 CC1 CC3 NB ! chirality or flatness improper -0.10 IMPRoper NA CC1 CA FE ! chirality or flatness improper -0.01 IMPRoper CA1 CA CA6 CA2 ! chirality or flatness improper 0.00 IMPRoper CA2 CA1 CA3 OA ! chirality or flatness improper 0.06 IMPRoper FE NA OA OB ! chirality or flatness improper 0.50 IMPRoper CB2 OB CB3 CB1 ! chirality or flatness improper -0.06 IMPRoper CB1 CB2 CB6 CB ! chirality or flatness improper 0.06 IMPRoper NB CC2 FE CB ! chirality or flatness improper 0.07 { Note: edit any DONOrs and ACCEptors if necessary } ACCEptor O2A CAA ACCEptor O1A CAA ACCEptor OA CA2 ACCEptor OB FE END { RESIdue YOL }