Wednesday, March 11, 2015

Toluene Prodgr

The PDB file (all hydrogens)
REMARK  
REMARK  
REMARK  This file was generated by PRODRG version AA100323.0717
REMARK  PRODRG written/copyrighted by Daan van Aalten
REMARK  and Alexander Schuettelkopf
REMARK  
REMARK  Questions/comments to dava@davapc1.bioch.dundee.ac.uk
REMARK  
REMARK  When using this software in a publication, cite:
REMARK  A. W. Schuettelkopf and D. M. F. van Aalten (2004).
REMARK  PRODRG - a tool for high-throughput crystallography
REMARK  of protein-ligand complexes.
REMARK  Acta Crystallogr. D60, 1355--1363.
REMARK  
REMARK  
HETATM    1  CAG DRG     1      -7.620   3.400   8.770  1.00 20.00           C  
HETATM    2  HAG DRG     1      -6.729   2.808   8.977  1.00 20.00           H  
HETATM    3  HAH DRG     1      -7.326   4.380   8.395  1.00 20.00           H  
HETATM    4  HAI DRG     1      -8.244   3.492   9.659  1.00 20.00           H  
HETATM    5  CAC DRG     1      -8.400   2.750   7.810  1.00 20.00           C  
HETATM    6  CAB DRG     1      -7.960   1.520   7.260  1.00 20.00           C  
HETATM    7  HAB DRG     1      -7.030   1.060   7.600  1.00 20.00           H  
HETATM    8  CAA DRG     1      -8.740   0.870   6.280  1.00 20.00           C  
HETATM    9  HAA DRG     1      -8.410  -0.070   5.850  1.00 20.00           H  
HETATM   10  CAD DRG     1      -9.950   1.460   5.860  1.00 20.00           C  
HETATM   11  HAD DRG     1     -10.550   0.960   5.100  1.00 20.00           H  
HETATM   12  CAE DRG     1     -10.400   2.690   6.400  1.00 20.00           C  
HETATM   13  HAE DRG     1     -11.340   3.130   6.070  1.00 20.00           H  
HETATM   14  CAF DRG     1      -9.620   3.340   7.380  1.00 20.00           C  
HETATM   15  HAF DRG     1      -9.960   4.280   7.800  1.00 20.00           H  
CONECT    1    2    3    4    5
CONECT    2    1
CONECT    3    1
CONECT    4    1
CONECT    5    1    6   14
CONECT    6    5    7    8
CONECT    7    6
CONECT    8    6    9   10
CONECT    9    8
CONECT   10    8   11   12
CONECT   11   10
CONECT   12   10   13   14
CONECT   13   12
CONECT   14    5   12   15
CONECT   15   14
END

The PDB file (polar/aromatic hydrogens)
REMARK  
REMARK  
REMARK  This file was generated by PRODRG version AA100323.0717
REMARK  PRODRG written/copyrighted by Daan van Aalten
REMARK  and Alexander Schuettelkopf
REMARK  
REMARK  Questions/comments to dava@davapc1.bioch.dundee.ac.uk
REMARK  
REMARK  When using this software in a publication, cite:
REMARK  A. W. Schuettelkopf and D. M. F. van Aalten (2004).
REMARK  PRODRG - a tool for high-throughput crystallography
REMARK  of protein-ligand complexes.
REMARK  Acta Crystallogr. D60, 1355--1363.
REMARK  
REMARK  
HETATM    1  CAG DRG     1      -7.620   3.400   8.770  1.00 20.00           C  
HETATM    2  CAC DRG     1      -8.400   2.750   7.810  1.00 20.00           C  
HETATM    3  CAB DRG     1      -7.960   1.520   7.260  1.00 20.00           C  
HETATM    4  HAB DRG     1      -7.030   1.060   7.600  1.00 20.00           H  
HETATM    5  CAA DRG     1      -8.740   0.870   6.280  1.00 20.00           C  
HETATM    6  HAA DRG     1      -8.410  -0.070   5.850  1.00 20.00           H  
HETATM    7  CAD DRG     1      -9.950   1.460   5.860  1.00 20.00           C  
HETATM    8  HAD DRG     1     -10.550   0.960   5.100  1.00 20.00           H  
HETATM    9  CAE DRG     1     -10.400   2.690   6.400  1.00 20.00           C  
HETATM   10  HAE DRG     1     -11.340   3.130   6.070  1.00 20.00           H  
HETATM   11  CAF DRG     1      -9.620   3.340   7.380  1.00 20.00           C  
HETATM   12  HAF DRG     1      -9.960   4.280   7.800  1.00 20.00           H  
CONECT    1    2
CONECT    2    1    3   11
CONECT    3    2    4    5
CONECT    4    3
CONECT    5    3    6    7
CONECT    6    5
CONECT    7    5    8    9
CONECT    8    7
CONECT    9    7   10   11
CONECT   10    9
CONECT   11    2    9   12
CONECT   12   11
END


The PDB file (polar hydrogens)
REMARK  
REMARK  
REMARK  This file was generated by PRODRG version AA100323.0717
REMARK  PRODRG written/copyrighted by Daan van Aalten
REMARK  and Alexander Schuettelkopf
REMARK  
REMARK  Questions/comments to dava@davapc1.bioch.dundee.ac.uk
REMARK  
REMARK  When using this software in a publication, cite:
REMARK  A. W. Schuettelkopf and D. M. F. van Aalten (2004).
REMARK  PRODRG - a tool for high-throughput crystallography
REMARK  of protein-ligand complexes.
REMARK  Acta Crystallogr. D60, 1355--1363.
REMARK  
REMARK  
HETATM    1  CAG DRG     1      -7.620   3.400   8.770  1.00 20.00           C  
HETATM    2  CAC DRG     1      -8.400   2.750   7.810  1.00 20.00           C  
HETATM    3  CAB DRG     1      -7.960   1.520   7.260  1.00 20.00           C  
HETATM    4  CAA DRG     1      -8.740   0.870   6.280  1.00 20.00           C  
HETATM    5  CAD DRG     1      -9.950   1.460   5.860  1.00 20.00           C  
HETATM    6  CAE DRG     1     -10.400   2.690   6.400  1.00 20.00           C  
HETATM    7  CAF DRG     1      -9.620   3.340   7.380  1.00 20.00           C  
CONECT    1    2
CONECT    2    1    3    7
CONECT    3    2    4
CONECT    4    3    5
CONECT    5    4    6
CONECT    6    5    7
CONECT    7    2    6
END


The PDB file (no hydrogens)
REMARK  
REMARK  
REMARK  This file was generated by PRODRG version AA100323.0717
REMARK  PRODRG written/copyrighted by Daan van Aalten
REMARK  and Alexander Schuettelkopf
REMARK  
REMARK  Questions/comments to dava@davapc1.bioch.dundee.ac.uk
REMARK  
REMARK  When using this software in a publication, cite:
REMARK  A. W. Schuettelkopf and D. M. F. van Aalten (2004).
REMARK  PRODRG - a tool for high-throughput crystallography
REMARK  of protein-ligand complexes.
REMARK  Acta Crystallogr. D60, 1355--1363.
REMARK  
REMARK  
HETATM    1  CAG DRG     1      -7.620   3.400   8.770  1.00 20.00           C  
HETATM    2  CAC DRG     1      -8.400   2.750   7.810  1.00 20.00           C  
HETATM    3  CAB DRG     1      -7.960   1.520   7.260  1.00 20.00           C  
HETATM    4  CAA DRG     1      -8.740   0.870   6.280  1.00 20.00           C  
HETATM    5  CAD DRG     1      -9.950   1.460   5.860  1.00 20.00           C  
HETATM    6  CAE DRG     1     -10.400   2.690   6.400  1.00 20.00           C  
HETATM    7  CAF DRG     1      -9.620   3.340   7.380  1.00 20.00           C  
CONECT    1    2
CONECT    2    1    3    7
CONECT    3    2    4
CONECT    4    3    5
CONECT    5    4    6
CONECT    6    5    7
CONECT    7    2    6
END

The GROMACS topology
;       
;       
;       This file was generated by PRODRG version AA100323.0717
;       PRODRG written/copyrighted by Daan van Aalten
;       and Alexander Schuettelkopf
;       
;       Questions/comments to dava@davapc1.bioch.dundee.ac.uk
;       
;       When using this software in a publication, cite:
;       A. W. Schuettelkopf and D. M. F. van Aalten (2004).
;       PRODRG - a tool for high-throughput crystallography
;       of protein-ligand complexes.
;       Acta Crystallogr. D60, 1355--1363.
;       
;       

[ moleculetype ]
; Name nrexcl
DRG      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       CH3     1  DRG     CAG     1    0.040  15.0350   
     2         C     1  DRG     CAC     1   -0.020  12.0110   
     3       CR1     1  DRG     CAB     1   -0.012  12.0110   
     4        HC     1  DRG     HAB     1    0.008   1.0080   
     5       CR1     1  DRG     CAA     1   -0.012  12.0110   
     6        HC     1  DRG     HAA     1    0.008   1.0080   
     7       CR1     1  DRG     CAD     1   -0.012  12.0110   
     8        HC     1  DRG     HAD     1    0.008   1.0080   
     9       CR1     1  DRG     CAE     1   -0.012  12.0110   
    10        HC     1  DRG     HAE     1    0.008   1.0080   
    11       CR1     1  DRG     CAF     1   -0.012  12.0110   
    12        HC     1  DRG     HAF     1    0.008   1.0080   

[ bonds ]
; ai  aj  fu    c0, c1, ...
   2   1   2    0.139   8660000.0    0.139   8660000.0 ;   CAC  CAG   
   2   3   2    0.139  10800000.0    0.139  10800000.0 ;   CAC  CAB   
   2  11   2    0.139  10800000.0    0.139  10800000.0 ;   CAC  CAF   
   3   4   2    0.109  12300000.0    0.109  12300000.0 ;   CAB  HAB   
   3   5   2    0.139  10800000.0    0.139  10800000.0 ;   CAB  CAA   
   5   6   2    0.109  12300000.0    0.109  12300000.0 ;   CAA  HAA   
   5   7   2    0.139  10800000.0    0.139  10800000.0 ;   CAA  CAD   
   7   8   2    0.109  12300000.0    0.109  12300000.0 ;   CAD  HAD   
   7   9   2    0.139  10800000.0    0.139  10800000.0 ;   CAD  CAE   
   9  10   2    0.109  12300000.0    0.109  12300000.0 ;   CAE  HAE   
   9  11   2    0.139  10800000.0    0.139  10800000.0 ;   CAE  CAF   
  11  12   2    0.109  12300000.0    0.109  12300000.0 ;   CAF  HAF   

[ pairs ]
; ai  aj  fu    c0, c1, ...
   1   4   1                                           ;   CAG  HAB   
   1   5   1                                           ;   CAG  CAA   
   1   9   1                                           ;   CAG  CAE   
   1  12   1                                           ;   CAG  HAF   
   2   6   1                                           ;   CAC  HAA   
   2   7   1                                           ;   CAC  CAD   
   2  10   1                                           ;   CAC  HAE   
   3   8   1                                           ;   CAB  HAD   
   3   9   1                                           ;   CAB  CAE   
   3  12   1                                           ;   CAB  HAF   
   4   6   1                                           ;   HAB  HAA   
   4   7   1                                           ;   HAB  CAD   
   4  11   1                                           ;   HAB  CAF   
   5  10   1                                           ;   CAA  HAE   
   5  11   1                                           ;   CAA  CAF   
   6   8   1                                           ;   HAA  HAD   
   6   9   1                                           ;   HAA  CAE   
   7  12   1                                           ;   CAD  HAF   
   8  10   1                                           ;   HAD  HAE   
   8  11   1                                           ;   HAD  CAF   
  10  12   1                                           ;   HAE  HAF   

[ angles ]
; ai  aj  ak  fu    c0, c1, ...
   1   2   3   2    120.0       560.0    120.0       560.0 ;   CAG  CAC  CAB   
   1   2  11   2    120.0       560.0    120.0       560.0 ;   CAG  CAC  CAF   
   3   2  11   2    120.0       560.0    120.0       560.0 ;   CAB  CAC  CAF   
   2   3   4   2    120.0       505.0    120.0       505.0 ;   CAC  CAB  HAB   
   2   3   5   2    120.0       505.0    120.0       505.0 ;   CAC  CAB  CAA   
   4   3   5   2    120.0       505.0    120.0       505.0 ;   HAB  CAB  CAA   
   3   5   6   2    120.0       505.0    120.0       505.0 ;   CAB  CAA  HAA   
   3   5   7   2    120.0       505.0    120.0       505.0 ;   CAB  CAA  CAD   
   6   5   7   2    120.0       505.0    120.0       505.0 ;   HAA  CAA  CAD   
   5   7   8   2    120.0       505.0    120.0       505.0 ;   CAA  CAD  HAD   
   5   7   9   2    120.0       505.0    120.0       505.0 ;   CAA  CAD  CAE   
   8   7   9   2    120.0       505.0    120.0       505.0 ;   HAD  CAD  CAE   
   7   9  10   2    120.0       505.0    120.0       505.0 ;   CAD  CAE  HAE   
   7   9  11   2    120.0       505.0    120.0       505.0 ;   CAD  CAE  CAF   
  10   9  11   2    120.0       505.0    120.0       505.0 ;   HAE  CAE  CAF   
   2  11   9   2    120.0       505.0    120.0       505.0 ;   CAC  CAF  CAE   
   2  11  12   2    120.0       505.0    120.0       505.0 ;   CAC  CAF  HAF   
   9  11  12   2    120.0       505.0    120.0       505.0 ;   CAE  CAF  HAF   

[ dihedrals ]
; ai  aj  ak  al  fu    c0, c1, m, ...
   2   1  11   3   2      0.0  167.4        0.0  167.4   ; imp   CAC  CAG  CAF  CAB   
   3   2   5   4   2      0.0  167.4        0.0  167.4   ; imp   CAB  CAC  CAA  HAB   
   5   3   7   6   2      0.0  167.4        0.0  167.4   ; imp   CAA  CAB  CAD  HAA   
   7   5   9   8   2      0.0  167.4        0.0  167.4   ; imp   CAD  CAA  CAE  HAD   
   9   7  11  10   2      0.0  167.4        0.0  167.4   ; imp   CAE  CAD  CAF  HAE   
  11   2   9  12   2      0.0  167.4        0.0  167.4   ; imp   CAF  CAC  CAE  HAF   
   2   3   5   7   2      0.0  209.3        0.0  209.3   ; imp   CAC  CAB  CAA  CAD   
   3   5   7   9   2      0.0  209.3        0.0  209.3   ; imp   CAB  CAA  CAD  CAE   
   5   7   9  11   2      0.0  209.3        0.0  209.3   ; imp   CAA  CAD  CAE  CAF   
   7   9  11   2   2      0.0  209.3        0.0  209.3   ; imp   CAD  CAE  CAF  CAC   
   9  11   2   3   2      0.0  209.3        0.0  209.3   ; imp   CAE  CAF  CAC  CAB   
  11   2   3   5   2      0.0  209.3        0.0  209.3   ; imp   CAF  CAC  CAB  CAA   


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