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
No comments:
Post a Comment