TOLUENE
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
|
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
| Picture |  |
| Name | 343 toluene |
| Description | Rectangular box; 343 molecules |
| Temperature (K) | 298.15 |
| Pressure (Bar) | 1.013 |
| Equilibration time (ns) | 0.5 |
| Time Step (ps) | 0.002 |
| Program | gromos96 |
| Author | Oostenbrink, Villa, Mark and Van Gunsteren |
| Literature Reference | Link |
| Molecule box ID | 17 |
Affiliated molecules:
| Molecule ID | IUPAC | Common Name/Description | Link |
|---|---|---|---|
| 583 | toluene | methylbenzene | Link |
Links:
| gromos96 Input File (INP format) |
| 343 toluene PDB |
| 343 toluene G96 |
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