Remarks dmj_xplor_top.txt
Remarks Created by XPLO2D V. 050802/3.3.2 at Fri Feb 29 14:51:07 2008 for A. Nonymous
Remarks Auto-generated by XPLO2D from file dmj_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 O_2    17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs)
 MASS C_3    13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs)
 MASS O_4    17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs)
 MASS C_5    13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs)
 MASS O_6    17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs)
 MASS C_7    14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs)
 MASS N_8    15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs)
 MASS C_9    13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs)
 MASS C_10   14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs)
 MASS O_11   17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs)

 autogenerate angles=true end

RESIdue DMJ

 { 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  C4   TYPE C_1   CHARge  0.0  END ! Nr of Hs =  1
 ATOM  O4   TYPE O_2   CHARge  0.0  END ! Nr of Hs =  1
 ATOM  C3   TYPE C_3   CHARge  0.0  END ! Nr of Hs =  1
 ATOM  O3   TYPE O_4   CHARge  0.0  END ! Nr of Hs =  1
 ATOM  C2   TYPE C_5   CHARge  0.0  END ! Nr of Hs =  1
 ATOM  O2   TYPE O_6   CHARge  0.0  END ! Nr of Hs =  1
 ATOM  C1   TYPE C_7   CHARge  0.0  END ! Nr of Hs =  2
 ATOM  N5   TYPE N_8   CHARge  0.0  END ! Nr of Hs =  1
 ATOM  C5   TYPE C_9   CHARge  0.0  END ! Nr of Hs =  1
 ATOM  C6   TYPE C_10  CHARge  0.0  END ! Nr of Hs =  2
 ATOM  O6   TYPE O_11  CHARge  0.0  END ! Nr of Hs =  1

 BOND  C4   O4       BOND  C4   C3       BOND  C4   C5       BOND  C3   O3
 BOND  C3   C2       BOND  C2   O2       BOND  C2   C1       BOND  C1   N5
 BOND  N5   C5       BOND  C5   C6       BOND  C6   O6

 { Note: edit these DIHEdrals if necessary }
! DIHEdral  O4   C4   C3   O3  ! flexible dihedral ???   -64.45
  DIHEdral  O4   C4   C3   C2  ! flat ? (180 degrees = trans)   175.66
  DIHEdral  C5   C4   C3   O3  ! flat ? (180 degrees = trans)   175.50
! DIHEdral  C5   C4   C3   C2  ! flexible dihedral ???    55.61
  DIHEdral  O4   C4   C5   N5  ! flat ? (180 degrees = trans)   178.63
! DIHEdral  O4   C4   C5   C6  ! flexible dihedral ???    58.46
! DIHEdral  C3   C4   C5   N5  ! flexible dihedral ???   -61.37
  DIHEdral  C3   C4   C5   C6  ! flat ? (180 degrees = trans)   178.46
! DIHEdral  C4   C3   C2   O2  ! flexible dihedral ???    64.34
! DIHEdral  C4   C3   C2   C1  ! flexible dihedral ???   -55.60
! DIHEdral  O3   C3   C2   O2  ! flexible dihedral ???   -55.66
  DIHEdral  O3   C3   C2   C1  ! flat ? (180 degrees = trans)   184.40
! DIHEdral  C3   C2   C1   N5  ! flexible dihedral ???    61.39
! DIHEdral  O2   C2   C1   N5  ! flexible dihedral ???   -58.55
! DIHEdral  C2   C1   N5   C5  ! flexible dihedral ???   -65.68
! DIHEdral  C1   N5   C5   C4  ! flexible dihedral ???    65.67
  DIHEdral  C1   N5   C5   C6  ! flat ? (180 degrees = trans)   185.81
  DIHEdral  C4   C5   C6   O6  ! flat ? (180 degrees = trans)   180.20
! DIHEdral  N5   C5   C6   O6  ! flexible dihedral ???    59.85

 { Note: edit these IMPRopers if necessary }
 IMPRoper  C4   O4   C3   C5  ! chirality or flatness improper   -35.79
 IMPRoper  C3   C4   O3   C2  ! chirality or flatness improper    36.02
 IMPRoper  C2   C3   O2   C1  ! chirality or flatness improper    35.90
 IMPRoper  C5   C4   N5   C6  ! chirality or flatness improper    35.53

 { Note: edit any DONOrs and ACCEptors if necessary }
 ACCEptor  O4   C4
 ACCEptor  O3   C3
 ACCEptor  O2   C2
! DONOr H?1  N5
 ACCEptor  O6   C6

END { RESIdue DMJ }