Toluene

TOLUENE
MBN is found in 16 entries 
108-88-3 [RN]
218-009-5 [EINECS]
Benzene, methyl
Benzene, methyl- [ACD/Index Name]
CH3C6H5 [Formula]
MeC6H5 [Formula]
Methane, phenyl-
Methyl benzene
methylbenzene [Wiki]
methyl-benzene
phenyl methane
phenylmethane
MBN
  •   Chemical Component Summary  Hide
    NameTOLUENE
    Identifiersmethylbenzene
    FormulaC7 H8
    Molecular Weight92.14 g/mol
    Typenon-polymer
    Isomeric SMILES
    InChI
    InChI keyYXFVVABEGXRONW-UHFFFAOYSA-N


DB01900.pdb
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
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    6    2                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END


GAFF Gas structure 108-88-3-gas.pdb
CRYST1  100.000  100.000  100.000  90.00  90.00  90.00 P 1           1
ATOM      1  C1  MOL X   1       2.020   0.079   0.955  1.00  0.00            
ATOM      2  H1  MOL X   1       2.262  -0.945   1.278  1.00  0.00            
ATOM      3  H2  MOL X   1       2.750   0.457   0.239  1.00  0.00            
ATOM      4  H3  MOL X   1       1.931   0.766   1.789  1.00  0.00            
ATOM      5  C2  MOL X   1       0.637   0.034   0.334  1.00  0.00            
ATOM      6  C3  MOL X   1       0.498   0.340  -1.010  1.00  0.00            
ATOM      7  H4  MOL X   1       1.390   0.510  -1.598  1.00  0.00            
ATOM      8  C4  MOL X   1      -0.733   0.267  -1.657  1.00  0.00            
ATOM      9  H5  MOL X   1      -0.893   0.623  -2.664  1.00  0.00            
ATOM     10  C5  MOL X   1      -1.859  -0.133  -0.947  1.00  0.00            
ATOM     11  H6  MOL X   1      -2.831  -0.223  -1.418  1.00  0.00            
ATOM     12  C6  MOL X   1      -1.683  -0.376   0.406  1.00  0.00            
ATOM     13  H7  MOL X   1      -2.530  -0.558   1.068  1.00  0.00            
ATOM     14  C7  MOL X   1      -0.480  -0.301   1.083  1.00  0.00            
ATOM     15  H8  MOL X   1      -0.478  -0.540   2.141  1.00  0.00            
END

The GlycoBioChem PRODRG2 Server

The GROMACS pdb file

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  C1  MOL     1       1.940   0.100   0.950  1.00 20.00           C  
HETATM    2  C2  MOL     1       0.690   0.040   0.330  1.00 20.00           C  
HETATM    3  C3  MOL     1       0.580   0.340  -1.050  1.00 20.00           C  
HETATM    4  H3  MOL     1       1.450   0.630  -1.630  1.00 20.00           H  
HETATM    5  C4  MOL     1      -0.690   0.260  -1.670  1.00 20.00           C  
HETATM    6  H4  MOL     1      -0.790   0.490  -2.730  1.00 20.00           H  
HETATM    7  C5  MOL     1      -1.820  -0.110  -0.910  1.00 20.00           C  
HETATM    8  H5  MOL     1      -2.790  -0.180  -1.400  1.00 20.00           H  
HETATM    9  C6  MOL     1      -1.710  -0.400   0.460  1.00 20.00           C  
HETATM   10  H6  MOL     1      -2.590  -0.680   1.040  1.00 20.00           H  
HETATM   11  C7  MOL     1      -0.450  -0.320   1.090  1.00 20.00           C  
HETATM   12  H7  MOL     1      -0.360  -0.540   2.160  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 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
MOL      3

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       CH3     1  MOL      C1     1    0.040  15.0350   
     2         C     1  MOL      C2     1   -0.020  12.0110   
     3       CR1     1  MOL      C3     1   -0.012  12.0110   
     4        HC     1  MOL      H3     1    0.008   1.0080   
     5       CR1     1  MOL      C4     1   -0.012  12.0110   
     6        HC     1  MOL      H4     1    0.008   1.0080   
     7       CR1     1  MOL      C5     1   -0.012  12.0110   
     8        HC     1  MOL      H5     1    0.008   1.0080   
     9       CR1     1  MOL      C6     1   -0.012  12.0110   
    10        HC     1  MOL      H6     1    0.008   1.0080   
    11       CR1     1  MOL      C7     1   -0.012  12.0110   
    12        HC     1  MOL      H7     1    0.008   1.0080   

[ bonds ]
; ai  aj  fu    c0, c1, ...
   2   1   2    0.139   8660000.0    0.139   8660000.0 ;    C2   C1   
   2   3   2    0.139  10800000.0    0.139  10800000.0 ;    C2   C3   
   2  11   2    0.139  10800000.0    0.139  10800000.0 ;    C2   C7   
   3   4   2    0.109  12300000.0    0.109  12300000.0 ;    C3   H3   
   3   5   2    0.139  10800000.0    0.139  10800000.0 ;    C3   C4   
   5   6   2    0.109  12300000.0    0.109  12300000.0 ;    C4   H4   
   5   7   2    0.139  10800000.0    0.139  10800000.0 ;    C4   C5   
   7   8   2    0.109  12300000.0    0.109  12300000.0 ;    C5   H5   
   7   9   2    0.139  10800000.0    0.139  10800000.0 ;    C5   C6   
   9  10   2    0.109  12300000.0    0.109  12300000.0 ;    C6   H6   
   9  11   2    0.139  10800000.0    0.139  10800000.0 ;    C6   C7   
  11  12   2    0.109  12300000.0    0.109  12300000.0 ;    C7   H7   

[ pairs ]
; ai  aj  fu    c0, c1, ...
   1   4   1                                           ;    C1   H3   
   1   5   1                                           ;    C1   C4   
   1   9   1                                           ;    C1   C6   
   1  12   1                                           ;    C1   H7   
   2   6   1                                           ;    C2   H4   
   2   7   1                                           ;    C2   C5   
   2  10   1                                           ;    C2   H6   
   3   8   1                                           ;    C3   H5   
   3   9   1                                           ;    C3   C6   
   3  12   1                                           ;    C3   H7   
   4   6   1                                           ;    H3   H4   
   4   7   1                                           ;    H3   C5   
   4  11   1                                           ;    H3   C7   
   5  10   1                                           ;    C4   H6   
   5  11   1                                           ;    C4   C7   
   6   8   1                                           ;    H4   H5   
   6   9   1                                           ;    H4   C6   
   7  12   1                                           ;    C5   H7   
   8  10   1                                           ;    H5   H6   
   8  11   1                                           ;    H5   C7   
  10  12   1                                           ;    H6   H7   

[ angles ]
; ai  aj  ak  fu    c0, c1, ...
   1   2   3   2    120.0       560.0    120.0       560.0 ;    C1   C2   C3   
   1   2  11   2    120.0       560.0    120.0       560.0 ;    C1   C2   C7   
   3   2  11   2    120.0       560.0    120.0       560.0 ;    C3   C2   C7   
   2   3   4   2    120.0       505.0    120.0       505.0 ;    C2   C3   H3   
   2   3   5   2    120.0       505.0    120.0       505.0 ;    C2   C3   C4   
   4   3   5   2    120.0       505.0    120.0       505.0 ;    H3   C3   C4   
   3   5   6   2    120.0       505.0    120.0       505.0 ;    C3   C4   H4   
   3   5   7   2    120.0       505.0    120.0       505.0 ;    C3   C4   C5   
   6   5   7   2    120.0       505.0    120.0       505.0 ;    H4   C4   C5   
   5   7   8   2    120.0       505.0    120.0       505.0 ;    C4   C5   H5   
   5   7   9   2    120.0       505.0    120.0       505.0 ;    C4   C5   C6   
   8   7   9   2    120.0       505.0    120.0       505.0 ;    H5   C5   C6   
   7   9  10   2    120.0       505.0    120.0       505.0 ;    C5   C6   H6   
   7   9  11   2    120.0       505.0    120.0       505.0 ;    C5   C6   C7   
  10   9  11   2    120.0       505.0    120.0       505.0 ;    H6   C6   C7   
   2  11   9   2    120.0       505.0    120.0       505.0 ;    C2   C7   C6   
   2  11  12   2    120.0       505.0    120.0       505.0 ;    C2   C7   H7   
   9  11  12   2    120.0       505.0    120.0       505.0 ;    C6   C7   H7   

[ dihedrals ]
; ai  aj  ak  al  fu    c0, c1, m, ...
   2   1  11   3   2      0.0  167.4        0.0  167.4   ; imp    C2   C1   C7   C3   
   3   2   5   4   2      0.0  167.4        0.0  167.4   ; imp    C3   C2   C4   H3   
   5   3   7   6   2      0.0  167.4        0.0  167.4   ; imp    C4   C3   C5   H4   
   7   5   9   8   2      0.0  167.4        0.0  167.4   ; imp    C5   C4   C6   H5   
   9   7  11  10   2      0.0  167.4        0.0  167.4   ; imp    C6   C5   C7   H6   
  11   2   9  12   2      0.0  167.4        0.0  167.4   ; imp    C7   C2   C6   H7   
   2   3   5   7   2      0.0  209.3        0.0  209.3   ; imp    C2   C3   C4   C5   
   3   5   7   9   2      0.0  209.3        0.0  209.3   ; imp    C3   C4   C5   C6   
   5   7   9  11   2      0.0  209.3        0.0  209.3   ; imp    C4   C5   C6   C7   
   7   9  11   2   2      0.0  209.3        0.0  209.3   ; imp    C5   C6   C7   C2   
   9  11   2   3   2      0.0  209.3        0.0  209.3   ; imp    C6   C7   C2   C3   
  11   2   3   5   2      0.0  209.3        0.0  209.3   ; imp    C7   C2   C3   C4   

Automated Topology Builder (ATB) and Repository

United-Atom PDB (optimised geometry)

TITLE FRAME_00001.pdb
MODEL
ATOM      1  CM  TOL A   1     -15.416  11.637  12.878  1.00  0.00
ATOM      2  C1  TOL A   1     -16.038  11.544  11.483  1.00  0.00
ATOM      3  C2  TOL A   1     -17.088  10.680  11.197  1.00  0.00
ATOM      4  H2  TOL A   1     -17.495  10.030  11.972  1.00  0.00
ATOM      5  C3  TOL A   1     -17.631  10.644   9.918  1.00  0.00
ATOM      6  H3  TOL A   1     -18.559  10.091   9.768  1.00  0.00
ATOM      7  C6  TOL A   1     -15.536  12.343  10.462  1.00  0.00
ATOM      8  H6  TOL A   1     -14.703  13.028  10.620  1.00  0.00
ATOM      9  C5  TOL A   1     -16.086  12.322   9.185  1.00  0.00
ATOM     10  H5  TOL A   1     -15.704  12.957   8.385  1.00  0.00
ATOM     11  C4  TOL A   1     -17.093  11.411   8.891  1.00  0.00
ATOM     12  H4  TOL A   1     -17.595  11.339   7.926  1.00  0.00
TER
CONECT    1    2
CONECT    2    3
CONECT    2    7
CONECT    3    4
CONECT    3    5
CONECT    5    6
CONECT    5   11
CONECT    7    8
CONECT    7    9
CONECT    9   10
CONECT    9   11
CONECT   11   12
ENDMDL

GROMACS G53A5FF United-Atom (ITP file)

[ moleculetype ]
; Name   nrexcl
TOL      3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  charge    mass    total_charge
    1   CH3    1     TOL     CM    1    0.292  15.0350 
    2     C    1     TOL     C1    1   -0.292  12.0110      ;  0.000
    3     C    1     TOL     C2    2   -0.146  12.0110 
    4    HC    1     TOL     H2    2    0.146   1.0080      ;  0.000
    5     C    1     TOL     C3    3   -0.146  12.0110 
    6    HC    1     TOL     H3    3    0.146   1.0080      ;  0.000
    7     C    1     TOL     C6    4   -0.146  12.0110 
    8    HC    1     TOL     H6    4    0.146   1.0080      ;  0.000
    9     C    1     TOL     C5    5   -0.146  12.0110 
   10    HC    1     TOL     H5    5    0.146   1.0080      ;  0.000
   11     C    1     TOL     C4    6   -0.146  12.0110 
   12    HC    1     TOL     H4    6    0.146   1.0080      ;  0.000
; total charge of the molecule:   0.000
[ bonds ]
;  ai   aj  funct   c0         c1
    1    2    2   0.1530   7.1500e+06
    2    3    2   0.1390   1.0800e+07
    2    7    2   0.1390   1.0800e+07
    3    4    2   0.1090   1.2300e+07
    3    5    2   0.1390   1.0800e+07
    5    6    2   0.1090   1.2300e+07
    5   11    2   0.1390   1.0800e+07
    7    8    2   0.1090   1.2300e+07
    7    9    2   0.1390   1.0800e+07
    9   10    2   0.1090   1.2300e+07
    9   11    2   0.1390   1.0800e+07
   11   12    2   0.1090   1.2300e+07
[ pairs ]
;  ai   aj  funct  ;  all 1-4 pairs but the ones excluded in GROMOS itp
[ angles ]
;  ai   aj   ak  funct   angle     fc
    1    2    3    2    120.00   560.00
    1    2    7    2    120.00   560.00
    3    2    7    2    120.00   560.00
    2    3    4    2    120.00   505.00
    2    3    5    2    120.00   560.00
    4    3    5    2    120.00   505.00
    3    5    6    2    120.00   505.00
    3    5   11    2    120.00   560.00
    6    5   11    2    120.00   505.00
    2    7    8    2    120.00   505.00
    2    7    9    2    120.00   560.00
    8    7    9    2    120.00   505.00
    7    9   10    2    120.00   505.00
    7    9   11    2    120.00   560.00
   10    9   11    2    120.00   505.00
    5   11    9    2    120.00   560.00
    5   11   12    2    120.00   505.00
    9   11   12    2    120.00   505.00
[ dihedrals ]
; GROMOS improper dihedrals
;  ai   aj   ak   al  funct   angle     fc
    2    1    3    7    2      0.00   167.36
    2    3    5   11    2      0.00   167.36
    2    7    9   11    2      0.00   167.36
    3    2    4    5    2      0.00   167.36
    3    2    7    9    2      0.00   167.36
    3    5   11    9    2      0.00   167.36
    5    3    6   11    2      0.00   167.36
    7    2    3    5    2      0.00   167.36
    7    2    8    9    2      0.00   167.36
    7    9   11    5    2      0.00   167.36
    9    7   10   11    2      0.00   167.36
   11    5    9   12    2      0.00   167.36
[ dihedrals ]
;  ai   aj   ak   al  funct    ph0      cp     mult

343 toluene Pre-Equilibrated System Information

Picture343 toluene
Name343 toluene
DescriptionRectangular box; 343 molecules
Temperature (K)298.15
Pressure (Bar)1.013
Equilibration time (ns)0.5
Time Step (ps)0.002
Programgromos96
AuthorOostenbrink, Villa, Mark and Van Gunsteren
Literature ReferenceLink
Molecule box ID17

Affiliated molecules:

Molecule IDIUPACCommon Name/DescriptionLink
583toluenemethylbenzeneLink

Links:

gromos96 Input File (INP format)
343 toluene PDB
343 toluene G96
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