Remarks 2cm_xplor_top.txt
Remarks Created by XPLO2D V. 050802/3.3.2 at Thu Feb 28 03:34:30 2008 for A. Nonymous
Remarks Auto-generated by XPLO2D from file 2cm_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 C_3    12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs)
 MASS N_4    14.00700 ! assuming N -> 14.00700 + 1.008 * 0 (Hs)
 MASS C_5    13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs)
 MASS C_6    15.03500 ! assuming C -> 12.01100 + 1.008 * 3 (Hs)
 MASS C_7    13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs)
 MASS CL_8   35.45300 ! assuming CL -> 35.45300 + 1.008 * 0 (Hs)
 MASS C_9    13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs)

 autogenerate angles=true end

RESIdue 2CM

 { 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  C3   TYPE C_3   CHARge  0.0  END ! Nr of Hs =  0
 ATOM  N4   TYPE N_4   CHARge  0.0  END ! Nr of Hs =  0
 ATOM  C5   TYPE C_5   CHARge  0.0  END ! Nr of Hs =  1
 ATOM  C6   TYPE C_6   CHARge  0.0  END ! Nr of Hs =  3
 ATOM  C7   TYPE C_7   CHARge  0.0  END ! Nr of Hs =  1
 ATOM CL8   TYPE CL_8  CHARge  0.0  END ! Nr of Hs =  0
 ATOM  C9   TYPE C_9   CHARge  0.0  END ! Nr of Hs =  1

 BOND  C1   C2       BOND  C1   C3       BOND  C1   N4       BOND  C2   C5
 BOND  C2   C6       BOND  C3   C7       BOND  C3  CL8       BOND  C5   C9
 BOND  C7   C9

 { Note: edit these DIHEdrals if necessary }
  DIHEdral  C3   C1   C2   C5  ! flat ? (0 degrees = cis)    -0.52
  DIHEdral  C3   C1   C2   C6  ! flat ? (180 degrees = trans)   179.68
  DIHEdral  N4   C1   C2   C5  ! flat ? (180 degrees = trans)   180.00
  DIHEdral  N4   C1   C2   C6  ! flat ? (0 degrees = cis)     0.20
  DIHEdral  C2   C1   C3   C7  ! flat ? (0 degrees = cis)     0.52
  DIHEdral  C2   C1   C3  CL8  ! flat ? (180 degrees = trans)   180.24
  DIHEdral  N4   C1   C3   C7  ! flat ? (180 degrees = trans)   180.00
  DIHEdral  N4   C1   C3  CL8  ! flat ? (0 degrees = cis)    -0.29
  DIHEdral  C1   C2   C5   C9  ! flat ? (0 degrees = cis)     0.24
  DIHEdral  C6   C2   C5   C9  ! flat ? (180 degrees = trans)   180.04
  DIHEdral  C1   C3   C7   C9  ! flat ? (0 degrees = cis)    -0.24
  DIHEdral CL8   C3   C7   C9  ! flat ? (180 degrees = trans)   180.05
  DIHEdral  C2   C5   C9   C7  ! flat ? (0 degrees = cis)     0.05
  DIHEdral  C3   C7   C9   C5  ! flat ? (0 degrees = cis)    -0.05

 { Note: edit these IMPRopers if necessary }
 IMPRoper  C1   C2   C3   N4  ! chirality or flatness improper     0.30
 IMPRoper  C2   C1   C5   C6  ! chirality or flatness improper     0.12
 IMPRoper  C3   C1   C7  CL8  ! chirality or flatness improper    -0.18

 { Note: edit any DONOrs and ACCEptors if necessary }

END { RESIdue 2CM }