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小分子pdb格式用prodrg转化为top和gro格式求助 已有2人参与
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我在chem3D里面获得丙酮的PDB格式，之后把文本复制到prodrg中，运行得到下面的页面，我再之后怎么做，这种方法得到的top和gro还需要注意什么？金币不多，跪求这方面指教，谢谢 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 CAA UNK 1 -3.050 2.220 1.930 1.00 20.00 C HETATM 2 HAA UNK 1 -2.759 3.041 2.585 1.00 20.00 H HETATM 3 HAB UNK 1 -2.623 1.289 2.303 1.00 20.00 H HETATM 4 HAC UNK 1 -4.133 2.152 1.828 1.00 20.00 H HETATM 5 CAC UNK 1 -2.530 2.490 0.510 1.00 20.00 C HETATM 6 OAD UNK 1 -1.740 1.730 -0.050 1.00 20.00 O HETATM 7 CAB UNK 1 -3.040 3.770 -0.160 1.00 20.00 C HETATM 8 HAE UNK 1 -3.725 4.285 0.513 1.00 20.00 H HETATM 9 HAF UNK 1 -3.562 3.514 -1.082 1.00 20.00 H HETATM 10 HAD UNK 1 -2.148 4.364 -0.356 1.00 20.00 H CONECT 1 2 3 4 5 CONECT 2 1 CONECT 3 1 CONECT 4 1 CONECT 5 1 6 7 CONECT 6 5 CONECT 7 5 8 9 10 CONECT 8 7 CONECT 9 7 CONECT 10 7 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 CAA UNK 1 -3.050 2.220 1.930 1.00 20.00 C HETATM 2 CAC UNK 1 -2.530 2.490 0.510 1.00 20.00 C HETATM 3 OAD UNK 1 -1.740 1.730 -0.050 1.00 20.00 O HETATM 4 CAB UNK 1 -3.040 3.770 -0.160 1.00 20.00 C CONECT 1 2 CONECT 2 1 3 4 CONECT 3 2 CONECT 4 2 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 CAA UNK 1 -3.050 2.220 1.930 1.00 20.00 C HETATM 2 CAC UNK 1 -2.530 2.490 0.510 1.00 20.00 C HETATM 3 OAD UNK 1 -1.740 1.730 -0.050 1.00 20.00 O HETATM 4 CAB UNK 1 -3.040 3.770 -0.160 1.00 20.00 C CONECT 1 2 CONECT 2 1 3 4 CONECT 3 2 CONECT 4 2 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 CAA UNK 1 -3.050 2.220 1.930 1.00 20.00 C HETATM 2 CAC UNK 1 -2.530 2.490 0.510 1.00 20.00 C HETATM 3 OAD UNK 1 -1.740 1.730 -0.050 1.00 20.00 O HETATM 4 CAB UNK 1 -3.040 3.770 -0.160 1.00 20.00 C CONECT 1 2 CONECT 2 1 3 4 CONECT 3 2 CONECT 4 2 END -------------------------------------------------------------------------------- The MDL Molfile (all hydrogens) UNK PRODRG 10 9 0 0 0 0 0 0 0 0999 V2000 -3.0500 2.2200 1.9300 C 0 0 0 0 0 4 0 0 0 0 0 0 -2.7593 3.0410 2.5853 H 0 0 0 0 0 1 0 0 0 0 0 0 -2.6230 1.2891 2.3030 H 0 0 0 0 0 1 0 0 0 0 0 0 -4.1331 2.1521 1.8284 H 0 0 0 0 0 1 0 0 0 0 0 0 -2.5300 2.4900 0.5100 C 0 0 0 0 0 3 0 0 0 0 0 0 -1.7400 1.7300 -0.0500 O 0 0 0 0 0 1 0 0 0 0 0 0 -3.0400 3.7700 -0.1600 C 0 0 0 0 0 4 0 0 0 0 0 0 -3.7250 4.2851 0.5135 H 0 0 0 0 0 1 0 0 0 0 0 0 -3.5615 3.5140 -1.0823 H 0 0 0 0 0 1 0 0 0 0 0 0 -2.1476 4.3644 -0.3558 H 0 0 0 0 0 1 0 0 0 0 0 0 1 2 1 0 0 0 0 1 3 1 0 0 0 0 1 4 1 0 0 0 0 5 1 1 0 0 0 0 5 6 2 0 0 0 0 5 7 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 7 10 1 0 0 0 0 M END -------------------------------------------------------------------------------- The MDL Molfile (polar hydrogens) UNK PRODRG 4 3 0 0 0 0 0 0 0 0999 V2000 -3.0500 2.2200 1.9300 C 0 0 0 0 0 4 0 0 0 0 0 0 -2.5300 2.4900 0.5100 C 0 0 0 0 0 3 0 0 0 0 0 0 -1.7400 1.7300 -0.0500 O 0 0 0 0 0 1 0 0 0 0 0 0 -3.0400 3.7700 -0.1600 C 0 0 0 0 0 4 0 0 0 0 0 0 2 1 1 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 M END -------------------------------------------------------------------------------- The MDL Molfile (no hydrogens) UNK PRODRG 4 3 0 0 0 0 0 0 0 0999 V2000 -3.0500 2.2200 1.9300 C 0 0 0 0 0 4 0 0 0 0 0 0 -2.5300 2.4900 0.5100 C 0 0 0 0 0 3 0 0 0 0 0 0 -1.7400 1.7300 -0.0500 O 0 0 0 0 0 1 0 0 0 0 0 0 -3.0400 3.7700 -0.1600 C 0 0 0 0 0 4 0 0 0 0 0 0 2 1 1 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 M END -------------------------------------------------------------------------------- The GROMOS87/GROMACS coordinate file (all hydrogens) PRODRG COORDS 10 1UNK CAA 1 -0.305 0.222 0.193 1UNK HAA 2 -0.276 0.304 0.259 1UNK HAB 3 -0.262 0.129 0.230 1UNK HAC 4 -0.413 0.215 0.183 1UNK CAC 5 -0.253 0.249 0.051 1UNK OAD 6 -0.174 0.173 -0.005 1UNK CAB 7 -0.304 0.377 -0.016 1UNK HAE 8 -0.372 0.429 0.051 1UNK HAF 9 -0.356 0.351 -0.108 1UNK HAD 10 -0.215 0.436 -0.036 0.51676 0.51676 0.51676 -------------------------------------------------------------------------------- The GROMOS87/GROMACS coordinate file (polar/aromatic hydrogens) PRODRG COORDS 4 1UNK CAA 1 -0.305 0.222 0.193 1UNK CAC 2 -0.253 0.249 0.051 1UNK OAD 3 -0.174 0.173 -0.005 1UNK CAB 4 -0.304 0.377 -0.016 0.35900 0.35900 0.35900 -------------------------------------------------------------------------------- The GROMOS87/GROMACS coordinate file (polar hydrogens) PRODRG COORDS 4 1UNK CAA 1 -0.305 0.222 0.193 1UNK CAC 2 -0.253 0.249 0.051 1UNK OAD 3 -0.174 0.173 -0.005 1UNK CAB 4 -0.304 0.377 -0.016 0.35900 0.35900 0.35900 -------------------------------------------------------------------------------- The CNS topology (parameters) ! ! ! 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. ! ! ! *** NOTE *** IF YOU USE MORE THAN ONE PRODRG-GENERATED TOPOLOGY IN CNS, ! PLEASE CAREFULLY READ THE FAQ AS THIS MAY CAUSE PROBLEMS ! ! set echo=off message=on end evaluate ($pd_x = 1.0) eval ($pd_v=$pd_x* 13971.0) BOND CIAA HIAA $pd_v 1.090 eval ($pd_v=$pd_x* 13971.0) BOND CIAA HIAB $pd_v 1.090 eval ($pd_v=$pd_x* 13971.0) BOND CIAA HIAC $pd_v 1.090 eval ($pd_v=$pd_x* 16001.4) BOND CIAC CIAA $pd_v 1.530 eval ($pd_v=$pd_x* 24009.7) BOND CIAC OIAD $pd_v 1.230 eval ($pd_v=$pd_x* 16001.4) BOND CIAC CIAB $pd_v 1.530 eval ($pd_v=$pd_x* 13971.0) BOND CIAB HIAE $pd_v 1.090 eval ($pd_v=$pd_x* 13971.0) BOND CIAB HIAF $pd_v 1.090 eval ($pd_v=$pd_x* 13971.0) BOND CIAB HIAD $pd_v 1.090 eval ($pd_v=$pd_x* 720.0) ANGLE HIAA CIAA HIAB $pd_v 109.500 eval ($pd_v=$pd_x* 720.0) ANGLE HIAA CIAA HIAC $pd_v 109.500 eval ($pd_v=$pd_x* 720.0) ANGLE HIAA CIAA CIAC $pd_v 109.500 eval ($pd_v=$pd_x* 720.0) ANGLE HIAB CIAA HIAC $pd_v 109.500 eval ($pd_v=$pd_x* 720.0) ANGLE HIAB CIAA CIAC $pd_v 109.500 eval ($pd_v=$pd_x* 720.0) ANGLE HIAC CIAA CIAC $pd_v 109.500 eval ($pd_v=$pd_x* 962.3) ANGLE CIAA CIAC OIAD $pd_v 121.000 eval ($pd_v=$pd_x* 958.0) ANGLE CIAA CIAC CIAB $pd_v 115.000 eval ($pd_v=$pd_x* 962.3) ANGLE OIAD CIAC CIAB $pd_v 121.000 eval ($pd_v=$pd_x* 720.0) ANGLE CIAC CIAB HIAE $pd_v 109.500 eval ($pd_v=$pd_x* 720.0) ANGLE CIAC CIAB HIAF $pd_v 109.500 eval ($pd_v=$pd_x* 720.0) ANGLE CIAC CIAB HIAD $pd_v 109.500 eval ($pd_v=$pd_x* 720.0) ANGLE HIAE CIAB HIAF $pd_v 109.500 eval ($pd_v=$pd_x* 720.0) ANGLE HIAE CIAB HIAD $pd_v 109.500 eval ($pd_v=$pd_x* 720.0) ANGLE HIAF CIAB HIAD $pd_v 109.500 eval ($pd_v=$pd_x* 160.1) IMPR CIAA HIAA HIAC HIAB $pd_v 0 35.264 eval ($pd_v=$pd_x* 80.0) IMPR CIAC CIAA OIAD CIAB $pd_v 0 0.000 eval ($pd_v=$pd_x* 160.1) IMPR CIAB CIAC HIAE HIAF $pd_v 0 35.264 eval ($pd_v=$pd_x* 0.6) DIHE HIAA CIAA CIAC CIAB $pd_v 6 0.000 eval ($pd_v=$pd_x* 0.6) DIHE HIAD CIAB CIAC CIAA $pd_v 6 0.000 NBONds TOLERANCE=0.5 NBXMOD=5 WMIN=1.5 REPEL=1.0 REXPONENT=4 IREXPONENT=1 RCONST=16.0 CTONNB=5.5 CTOFNB=6.0 CUTNB=7.0 END NONBONDED CIAA 0.10000 3.29633 0.10000 3.02906 NONBONDED HIAA 0.10000 2.13816 0.10000 1.87089 NONBONDED HIAB 0.10000 2.13816 0.10000 1.87089 NONBONDED HIAC 0.10000 2.13816 0.10000 1.87089 NONBONDED CIAC 0.10000 3.29633 0.10000 3.02906 NONBONDED OIAD 0.10000 2.58361 0.10000 2.31634 NONBONDED CIAB 0.10000 3.29633 0.10000 3.02906 NONBONDED HIAE 0.10000 2.13816 0.10000 1.87089 NONBONDED HIAF 0.10000 2.13816 0.10000 1.87089 NONBONDED HIAD 0.10000 2.13816 0.10000 1.87089 set echo=on message=on end -------------------------------------------------------------------------------- The CNS 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. ! ! ! *** NOTE *** IF YOU USE MORE THAN ONE PRODRG-GENERATED TOPOLOGY IN CNS, ! PLEASE CAREFULLY READ THE FAQ AS THIS MAY CAUSE PROBLEMS ! ! set echo=false end AUTOGENERATE ANGLES=FALSE END MASS CIAA 12.0110 ! equivalent to CH3 MASS HIAA 1.0080 ! equivalent to HC MASS HIAB 1.0080 ! equivalent to HC MASS HIAC 1.0080 ! equivalent to HC MASS CIAC 12.0110 ! equivalent to C MASS OIAD 15.9994 ! equivalent to O MASS CIAB 12.0110 ! equivalent to CH3 MASS HIAE 1.0080 ! equivalent to HC MASS HIAF 1.0080 ! equivalent to HC MASS HIAD 1.0080 ! equivalent to HC Residue UNK GROUP ATOM CAA TYPE=CIAA CHARGE= 0.084 END ATOM HAA TYPE=HIAA CHARGE= 0.004 END ATOM HAB TYPE=HIAB CHARGE= 0.004 END ATOM HAC TYPE=HIAC CHARGE= 0.004 END ATOM CAC TYPE=CIAC CHARGE= 0.224 END ATOM OAD TYPE=OIAD CHARGE=-0.416 END ATOM CAB TYPE=CIAB CHARGE= 0.084 END ATOM HAE TYPE=HIAE CHARGE= 0.004 END ATOM HAF TYPE=HIAF CHARGE= 0.004 END ATOM HAD TYPE=HIAD CHARGE= 0.004 END BOND CAA HAA BOND CAA HAB BOND CAA HAC BOND CAC CAA BOND CAC OAD BOND CAC CAB BOND CAB HAE BOND CAB HAF BOND CAB HAD ANGLE HAA CAA HAB ANGLE HAA CAA HAC ANGLE HAA CAA CAC ANGLE HAB CAA HAC ANGLE HAB CAA CAC ANGLE HAC CAA CAC ANGLE CAA CAC OAD ANGLE CAA CAC CAB ANGLE OAD CAC CAB ANGLE CAC CAB HAE ANGLE CAC CAB HAF ANGLE CAC CAB HAD ANGLE HAE CAB HAF ANGLE HAE CAB HAD ANGLE HAF CAB HAD IMPROPER CAA HAA HAC HAB IMPROPER CAC CAA OAD CAB IMPROPER CAB CAC HAE HAF DIHEDRAL HAA CAA CAC CAB DIHEDRAL HAD CAB CAC CAA END set echo=true end -------------------------------------------------------------------------------- The CIF topology (general) # # # WARNING: REFMAC5 uses columns 77-78 of PDB ATOM records to # establish equivalence between model and topology. If # you use O or other programmes that produce defective # PDB files you must restore these columns, otherwise # REFMAC5 will not recognise this 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. # # global_ _lib_name prodrg_lib _lib_version 100323 _lib_update ? # # --------------- # data_comp_list # loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level UNK UNK 'UNK ' non-polymer 10 4 . # # --------------- # data_comp_UNK # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge UNK CAA C CH3 0.084 UNK HAA H HCH3 0.004 UNK HAB H HCH3 0.004 UNK HAC H HCH3 0.004 UNK CAC C C 0.224 UNK OAD O O -0.416 UNK CAB C CH3 0.084 UNK HAE H HCH3 0.004 UNK HAF H HCH3 0.004 UNK HAD H HCH3 0.004 loop_ _chem_comp_tree.comp_id _chem_comp_tree.atom_id _chem_comp_tree.atom_back _chem_comp_tree.atom_forward _chem_comp_tree.connect_type UNK CAA n/a CAC START UNK HAA CAA . . UNK HAB CAA . . UNK HAC CAA . . UNK CAC CAA CAB . UNK OAD CAC . . UNK CAB CAC HAD . UNK HAE CAB . . UNK HAF CAB . . UNK HAD CAB . END loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd UNK CAA HAA single 1.090 0.029 UNK CAA HAB single 1.090 0.029 UNK CAA HAC single 1.090 0.029 UNK CAC CAA single 1.530 0.025 UNK CAC OAD double 1.230 0.017 UNK CAC CAB single 1.530 0.025 UNK CAB HAE single 1.090 0.029 UNK CAB HAF single 1.090 0.029 UNK CAB HAD single 1.090 0.029 loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd UNK HAA CAA HAB 109.500 3.333 UNK HAA CAA HAC 109.500 3.333 UNK HAA CAA CAC 109.500 3.333 UNK HAB CAA HAC 109.500 3.333 UNK HAB CAA CAC 109.500 3.333 UNK HAC CAA CAC 109.500 3.333 UNK CAA CAC OAD 121.000 2.494 UNK CAA CAC CAB 115.000 2.505 UNK OAD CAC CAB 121.000 2.494 UNK CAC CAB HAE 109.500 3.333 UNK CAC CAB HAF 109.500 3.333 UNK CAC CAB HAD 109.500 3.333 UNK HAE CAB HAF 109.500 3.333 UNK HAE CAB HAD 109.500 3.333 UNK HAF CAB HAD 109.500 3.333 loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period UNK var_001 HAA CAA CAC CAB 30.000 16.736 6 UNK var_002 HAD CAB CAC CAA 30.000 16.736 6 loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign UNK chir_001 CAA HAA HAC HAB positiv UNK chir_002 CAB CAC HAE HAF positiv loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd UNK plan-01 CAA 0.030 UNK plan-01 CAC 0.030 UNK plan-01 OAD 0.030 UNK plan-01 CAB 0.030 # # --------------- # -------------------------------------------------------------------------------- The CIF topology (PHENIX) # # # WARNING: REFMAC5 uses columns 77-78 of PDB ATOM records to # establish equivalence between model and topology. If # you use O or other programmes that produce defective # PDB files you must restore these columns, otherwise # REFMAC5 will not recognise this 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. # # global_ _lib_name prodrg_lib _lib_version 100323 _lib_update ? # # --------------- # data_comp_list # loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level UNK UNK 'UNK ' non-polymer 10 4 . # # --------------- # data_comp_UNK # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge UNK CAA C CH3 0.084 UNK HAA H HCH3 0.004 UNK HAB H HCH3 0.004 UNK HAC H HCH3 0.004 UNK CAC C C 0.224 UNK OAD O O -0.416 UNK CAB C CH3 0.084 UNK HAE H HCH3 0.004 UNK HAF H HCH3 0.004 UNK HAD H HCH3 0.004 loop_ _chem_comp_tree.comp_id _chem_comp_tree.atom_id _chem_comp_tree.atom_back _chem_comp_tree.atom_forward _chem_comp_tree.connect_type UNK CAA n/a CAC START UNK HAA CAA . . UNK HAB CAA . . UNK HAC CAA . . UNK CAC CAA CAB . UNK OAD CAC . . UNK CAB CAC HAD . UNK HAE CAB . . UNK HAF CAB . . UNK HAD CAB . END loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd UNK CAA HAA single 1.090 0.029 UNK CAA HAB single 1.090 0.029 UNK CAA HAC single 1.090 0.029 UNK CAC CAA single 1.530 0.025 UNK CAC OAD double 1.230 0.017 UNK CAC CAB single 1.530 0.025 UNK CAB HAE single 1.090 0.029 UNK CAB HAF single 1.090 0.029 UNK CAB HAD single 1.090 0.029 loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd UNK HAA CAA HAB 109.500 3.333 UNK HAA CAA HAC 109.500 3.333 UNK HAA CAA CAC 109.500 3.333 UNK HAB CAA HAC 109.500 3.333 UNK HAB CAA CAC 109.500 3.333 UNK HAC CAA CAC 109.500 3.333 UNK CAA CAC OAD 121.000 2.494 UNK CAA CAC CAB 115.000 2.505 UNK OAD CAC CAB 121.000 2.494 UNK CAC CAB HAE 109.500 3.333 UNK CAC CAB HAF 109.500 3.333 UNK CAC CAB HAD 109.500 3.333 UNK HAE CAB HAF 109.500 3.333 UNK HAE CAB HAD 109.500 3.333 UNK HAF CAB HAD 109.500 3.333 loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period UNK var_001 HAA CAA CAC CAB 30.000 30.000 6 UNK var_002 HAA CAA CAC OAD 30.000 30.000 6 UNK var_003 HAB CAA CAC OAD 30.000 30.000 6 UNK var_004 HAB CAA CAC CAB 30.000 30.000 6 UNK var_005 HAC CAA CAC OAD 30.000 30.000 6 UNK var_006 HAC CAA CAC CAB 30.000 30.000 6 UNK var_007 HAD CAB CAC CAA 30.000 30.000 6 UNK var_008 HAE CAB CAC CAA 30.000 30.000 6 UNK var_009 HAE CAB CAC OAD 30.000 30.000 6 UNK var_010 HAF CAB CAC CAA 30.000 30.000 6 UNK var_011 HAF CAB CAC OAD 30.000 30.000 6 UNK var_012 HAD CAB CAC OAD 30.000 30.000 6 loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign UNK chir_001 CAA HAA HAC HAB positiv UNK chir_002 CAB CAC HAE HAF positiv loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd UNK plan-01 CAA 0.030 UNK plan-01 CAC 0.030 UNK plan-01 OAD 0.030 UNK plan-01 CAB 0.030 # # --------------- # -------------------------------------------------------------------------------- The SHELX topology REM REM REM This file was generated by PRODRG version AA100323.0717 REM PRODRG written/copyrighted by Daan van Aalten REM and Alexander Schuettelkopf REM REM Questions/comments to dava@davapc1.bioch.dundee.ac.uk REM REM When using this software in a publication, cite: REM A. W. Schuettelkopf and D. M. F. van Aalten (2004). REM PRODRG - a tool for high-throughput crystallography REM of protein-ligand complexes. REM Acta Crystallogr. D60, 1355--1363. REM REM DFIX_UNK 1.090 CAA HAA DFIX_UNK 1.090 CAA HAB DFIX_UNK 1.090 CAA HAC DFIX_UNK 1.530 CAC CAA DFIX_UNK 1.230 CAC OAD DFIX_UNK 1.530 CAC CAB DFIX_UNK 1.090 CAB HAE DFIX_UNK 1.090 CAB HAF DFIX_UNK 1.090 CAB HAD DANG_UNK 1.780 HAA HAB DANG_UNK 1.780 HAA HAC DANG_UNK 2.155 HAA CAC DANG_UNK 1.780 HAB HAC DANG_UNK 2.155 HAB CAC DANG_UNK 2.155 HAC CAC DANG_UNK 2.407 CAA OAD DANG_UNK 2.581 CAA CAB DANG_UNK 2.407 OAD CAB DANG_UNK 2.155 CAC HAE DANG_UNK 2.155 CAC HAF DANG_UNK 2.155 CAC HAD DANG_UNK 1.780 HAE HAF DANG_UNK 1.780 HAE HAD DANG_UNK 1.780 HAF HAD FLAT_UNK CAC CAA OAD CAB -------------------------------------------------------------------------------- The O torsion database (pre-9.x) ! ! ! 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. ! ! ! To use this file add the data _after_ the line starting with ! '.torsion_information' to your current .torsion_information datablock ! (e.g. in torsions.o) and update the datablock header. ! ! .torsion_information t 1 72 residue UNK -------------------------------------------------------------------------------- The O refi dictionary (pre-9.x) ! ! ! 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. ! ! ! To use this file add the data _after_ the line starting with ! '.bonds_angles' to your current .bonds_angles datablock ! (e.g. in stereo_chem.odb) and update the datablock header. ! ! .bonds_angles t 8 72 residue UNK bond_distance CAC CAA 1.530 0.019 bond_distance CAC OAD 1.230 0.012 bond_distance CAC CAB 1.530 0.019 bond_angle CAA CAC OAD 121.000 1.663 bond_angle CAA CAC CAB 115.000 1.670 bond_angle OAD CAC CAB 121.000 1.663 torsion_fixed CAC CAA OAD CAB 0.000 1.100 -------------------------------------------------------------------------------- The O dictionary (9.x) ! ! ! 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. ! ! ! To use this file add the data _after_ the line starting with ! '.bonds_angles' to your current .bonds_angles datablock ! (e.g. in stereo_chem.odb) and update the datablock header. ! ! .bonds_angles t 15 72 residue UNK centre CAA atom CAA CAC OAD CAB fragment_all CAA CAC OAD CAB fragment_mc CAA CAC OAD CAB main-chain CAA CAC OAD CAB connect_all CAA CAC OAD connect_all CAC CAB bond_distance CAC CAA 1.530 0.019 bond_distance CAC OAD 1.230 0.012 bond_distance CAC CAB 1.530 0.019 bond_angle CAA CAC OAD 121.000 1.663 bond_angle CAA CAC CAB 115.000 1.670 bond_angle OAD CAC CAB 121.000 1.663 torsion_fixed CAC CAA OAD CAB 0.000 1.100 -------------------------------------------------------------------------------- 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 UNK 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 UNK CAA 1 0.096 15.0350 2 C 1 UNK CAC 1 0.224 12.0110 3 O 1 UNK OAD 1 -0.416 15.9994 4 CH3 1 UNK CAB 1 0.096 15.0350 [ bonds ] ; ai aj fu c0, c1, ... 2 1 2 0.153 7150000.0 0.153 7150000.0 ; CAC CAA 2 3 2 0.123 16600000.0 0.123 16600000.0 ; CAC OAD 2 4 2 0.153 7150000.0 0.153 7150000.0 ; CAC CAB [ pairs ] ; ai aj fu c0, c1, ... [ angles ] ; ai aj ak fu c0, c1, ... 1 2 3 2 121.0 685.0 121.0 685.0 ; CAA CAC OAD 1 2 4 2 115.0 610.0 115.0 610.0 ; CAA CAC CAB 3 2 4 2 121.0 685.0 121.0 685.0 ; OAD CAC CAB [ dihedrals ] ; ai aj ak al fu c0, c1, m, ... 2 1 3 4 2 0.0 167.4 0.0 167.4 ; imp CAC CAA OAD CAB -------------------------------------------------------------------------------- The WHAT IF topology * UNK 1 # AT BND CHI TRS CRD #BL HGR HAT ANG 1-3 PAR PC HANG TYP 4 3 0 0 1 3 0 4 3 1 1 1 3 6 #===== Atom names CAA CAC OAD CAB #===== Bonds 2 1 2 3 2 4 #===== Rotatable bonds #===== Torsion angles #===== Coordinates, hydrogen bonding and planarity 44.88095 44.33442 46.12780 F 45.40095 44.60442 44.70779 F 46.19094 43.84442 44.14780 T- 44.89095 45.88442 44.03780 F #===== Standard bond lengths 1.530 0.020 1.230 0.020 1.530 0.020 #===== Standard bond angles 1 2 3 121.0 2.0 1 2 4 115.0 2.0 3 2 4 121.0 2.0 #===== 1--3 connections 3 3 4 1 3 1 4 3 1 3 #===== Charges 0.096 0.224 -0.416 0.096 *END -------------------------------------------------------------------------------- The SYBYL2 topology (all hydrogens) # # # 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. # # @<TRIPOS>MOLECULE UNK 10 9 1 SMALL USER_CHARGES PRODRG MOLECULE @<TRIPOS>ATOM 1 CAA -3.050 2.220 1.930 C.3 1 UNK 0.084 2 HAA -2.759 3.041 2.585 H 1 UNK 0.004 3 HAB -2.623 1.289 2.303 H 1 UNK 0.004 4 HAC -4.133 2.152 1.828 H 1 UNK 0.004 5 CAC -2.530 2.490 0.510 C.2 1 UNK 0.224 6 OAD -1.740 1.730 -0.050 O.2 1 UNK -0.416 7 CAB -3.040 3.770 -0.160 C.3 1 UNK 0.084 8 HAE -3.725 4.285 0.513 H 1 UNK 0.004 9 HAF -3.562 3.514 -1.082 H 1 UNK 0.004 10 HAD -2.148 4.364 -0.356 H 1 UNK 0.004 @<TRIPOS>BOND 1 1 2 1 2 1 3 1 3 1 4 1 4 5 1 1 5 5 6 2 6 5 7 1 7 7 8 1 8 7 9 1 9 7 10 1 @<TRIPOS>SUBSTRUCTURE 1 UNK 1 -------------------------------------------------------------------------------- The SYBYL2 topology (polar hydrogens) # # # 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. # # @<TRIPOS>MOLECULE UNK 4 3 1 SMALL USER_CHARGES PRODRG MOLECULE @<TRIPOS>ATOM 1 CAA -3.050 2.220 1.930 C.3 1 UNK 0.084 2 CAC -2.530 2.490 0.510 C.2 1 UNK 0.224 3 OAD -1.740 1.730 -0.050 O.2 1 UNK -0.416 4 CAB -3.040 3.770 -0.160 C.3 1 UNK 0.084 @<TRIPOS>BOND 1 2 1 1 2 2 3 2 3 2 4 1 @<TRIPOS>SUBSTRUCTURE 1 UNK 1 -------------------------------------------------------------------------------- The AUTODOCK 2.4 PDBQ 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 REMARK 0 active torsions: REMARK ------- TDOF 0 ROOT ATOM 1 CAA UNK 1 -3.050 2.220 1.930 1.00 20.00 0.096 C ATOM 2 CAC UNK 1 -2.530 2.490 0.510 1.00 20.00 0.224 C ATOM 3 OAD UNK 1 -1.740 1.730 -0.050 1.00 20.00 -0.416 O ATOM 4 CAB UNK 1 -3.040 3.770 -0.160 1.00 20.00 0.096 C ENDROOT TORSDOF 0 (for dpf3gen and similarly broken stuff) END -------------------------------------------------------------------------------- The AUTODOCK 3.0 PDBQ 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 REMARK 0 active torsions: REMARK ------- TDOF 0 ROOT ATOM 1 CAA UNK 1 -3.050 2.220 1.930 1.00 20.00 0.096 C ATOM 2 CAC UNK 1 -2.530 2.490 0.510 1.00 20.00 0.224 C ATOM 3 OAD UNK 1 -1.740 1.730 -0.050 1.00 20.00 -0.416 O ATOM 4 CAB UNK 1 -3.040 3.770 -0.160 1.00 20.00 0.096 C ENDROOT TORSDOF 0 (for dpf3gen and similarly broken stuff) END -------------------------------------------------------------------------------- The HEX topology UNK CAA 1.40 0.096 b -1 -1 -1 UNK CAC 1.40 0.224 b -1 -1 -1 UNK OAD 1.60 -0.416 b -1 -1 -1 UNK CAB 1.40 0.096 b -1 -1 -1 -------------------------------------------------------------------------------- Copyright © 2010-2014 GlycoBioChem Ltd. |
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