data_GMS # _chem_comp.id GMS _chem_comp.name "2'-DEOXYGUANOSINE-5'-MONOSELENOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H14 N5 O6 P Se" _chem_comp.mon_nstd_parent_comp_id DG _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2002-11-18 _chem_comp.pdbx_modified_date 2012-01-05 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 410.182 _chem_comp.one_letter_code G _chem_comp.three_letter_code GMS _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1VRO _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal GMS P P P 0 1 N N R 2.383 9.457 37.225 3.960 -1.107 -0.153 P GMS 1 GMS OP1 O1P O 0 1 N N N 1.424 8.908 38.227 3.951 -1.760 1.176 OP1 GMS 2 GMS SE SE SE 0 0 N N N 4.406 8.874 37.554 5.690 0.357 -0.265 SE GMS 3 GMS "O5'" "O5'" O 0 1 N N N 1.828 8.959 35.812 2.573 -0.319 -0.372 "O5'" GMS 4 GMS N9 N9 N 0 1 Y N N -0.838 11.147 32.374 -2.660 -0.206 0.165 N9 GMS 5 GMS C4 C4 C 0 1 Y N N -0.105 12.281 32.525 -3.984 -0.037 -0.135 C4 GMS 6 GMS N3 N3 N 0 1 N N N 1.235 12.392 32.577 -4.691 0.935 -0.724 N3 GMS 7 GMS C2 C2 C 0 1 N N N 1.640 13.615 32.730 -5.990 0.827 -0.886 C2 GMS 8 GMS N2 N2 N 0 1 N N N 2.924 13.886 32.805 -6.673 1.850 -1.496 N2 GMS 9 GMS N1 N1 N 0 1 N N N 0.773 14.693 32.805 -6.680 -0.271 -0.468 N1 GMS 10 GMS C6 C6 C 0 1 N N N -0.601 14.614 32.750 -6.034 -1.293 0.136 C6 GMS 11 GMS O6 O6 O 0 1 N N N -1.298 15.646 32.839 -6.642 -2.280 0.514 O6 GMS 12 GMS C5 C5 C 0 1 Y N N -1.042 13.275 32.599 -4.635 -1.190 0.317 C5 GMS 13 GMS N7 N7 N 0 1 Y N N -2.344 12.783 32.497 -3.692 -1.996 0.863 N7 GMS 14 GMS C8 C8 C 0 1 Y N N -2.143 11.520 32.372 -2.529 -1.419 0.776 C8 GMS 15 GMS "C2'" "C2'" C 0 1 N N N 0.712 9.504 31.273 -1.475 1.796 1.003 "C2'" GMS 16 GMS "C5'" "C5'" C 0 1 N N N 2.417 9.373 34.549 1.982 0.509 0.631 "C5'" GMS 17 GMS "C4'" "C4'" C 0 1 N N R 1.511 8.887 33.413 0.678 1.105 0.097 "C4'" GMS 18 GMS "O4'" "O4'" O 0 1 N N N 0.236 9.453 33.570 -0.303 0.065 -0.111 "O4'" GMS 19 GMS "C1'" "C1'" C 0 1 N N R -0.362 9.783 32.251 -1.579 0.741 -0.121 "C1'" GMS 20 GMS "C3'" "C3'" C 0 1 N N S 1.986 9.315 32.071 0.043 2.041 1.149 "C3'" GMS 21 GMS "O3'" "O3'" O 0 1 N N N 2.856 8.306 31.483 0.360 3.405 0.863 "O3'" GMS 22 GMS OP2 O2P O 0 1 N N N ? ? ? 4.128 -2.226 -1.298 OP2 GMS 23 GMS HS HS H 0 1 N N N 5.108 8.737 36.236 5.514 0.915 -1.711 HS GMS 24 GMS H21 H21 H 0 1 N N N 3.084 14.866 32.922 -6.196 2.638 -1.800 H21 GMS 25 GMS H22 H22 H 0 1 N N N 3.649 13.199 32.752 -7.632 1.785 -1.623 H22 GMS 26 GMS H1 H1 H 0 1 N N N 1.177 15.602 32.907 -7.639 -0.319 -0.603 H1 GMS 27 GMS H8 H8 H 0 1 N N N -2.951 10.810 32.273 -1.600 -1.838 1.132 H8 GMS 28 GMS "H2'" "H2'1" H 0 1 N N N 0.481 8.595 30.698 -1.984 2.715 0.712 "H2'" GMS 29 GMS "H2''" "H2'2" H 0 0 N N N 0.815 10.329 30.553 -1.891 1.406 1.932 "H2''" GMS 30 GMS "H5'" "H5'1" H 0 1 N N N 2.501 10.469 34.517 1.771 -0.089 1.518 "H5'" GMS 31 GMS "H5''" "H5'2" H 0 0 N N N 3.423 8.942 34.441 2.669 1.314 0.890 "H5''" GMS 32 GMS "H4'" "H4'" H 0 1 N N N 1.508 7.788 33.467 0.861 1.645 -0.832 "H4'" GMS 33 GMS "H1'" "H1'" H 0 1 N N N -1.234 9.205 31.911 -1.745 1.226 -1.083 "H1'" GMS 34 GMS "H3'" "H3'" H 0 1 N N N 2.590 10.234 32.101 0.378 1.772 2.151 "H3'" GMS 35 GMS "HO3'" H3T H 0 0 N Y N 3.045 8.537 30.581 -0.062 4.040 1.457 "HO3'" GMS 36 GMS HOP2 HOP2 H 0 0 N N N 0.610 0.349 -0.638 4.943 -2.742 -1.228 HOP2 GMS 37 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal GMS P OP1 DOUB N N 1 GMS P SE SING N N 2 GMS P "O5'" SING N N 3 GMS P OP2 SING N N 4 GMS SE HS SING N N 5 GMS "O5'" "C5'" SING N N 6 GMS N9 C4 SING Y N 7 GMS N9 C8 SING Y N 8 GMS N9 "C1'" SING N N 9 GMS C4 N3 SING N N 10 GMS C4 C5 DOUB Y N 11 GMS N3 C2 DOUB N N 12 GMS C2 N2 SING N N 13 GMS C2 N1 SING N N 14 GMS N2 H21 SING N N 15 GMS N2 H22 SING N N 16 GMS N1 C6 SING N N 17 GMS N1 H1 SING N N 18 GMS C6 O6 DOUB N N 19 GMS C6 C5 SING N N 20 GMS C5 N7 SING Y N 21 GMS N7 C8 DOUB Y N 22 GMS C8 H8 SING N N 23 GMS "C2'" "C1'" SING N N 24 GMS "C2'" "C3'" SING N N 25 GMS "C2'" "H2'" SING N N 26 GMS "C2'" "H2''" SING N N 27 GMS "C5'" "C4'" SING N N 28 GMS "C5'" "H5'" SING N N 29 GMS "C5'" "H5''" SING N N 30 GMS "C4'" "O4'" SING N N 31 GMS "C4'" "C3'" SING N N 32 GMS "C4'" "H4'" SING N N 33 GMS "O4'" "C1'" SING N N 34 GMS "C1'" "H1'" SING N N 35 GMS "C3'" "O3'" SING N N 36 GMS "C3'" "H3'" SING N N 37 GMS "O3'" "HO3'" SING N N 38 GMS OP2 HOP2 SING N N 39 # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor GMS SMILES ACDLabs 10.04 "O=P(O)([SeH])OCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O" GMS InChI InChI 1.03 "InChI=1S/C10H14N5O6PSe/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(21-6)2-20-22(18,19)23/h3-6,16H,1-2H2,(H2,18,19,23)(H3,11,13,14,17)/t4-,5+,6+/m0/s1" GMS InChIKey InChI 1.03 MMKHSOCVUGNOOR-KVQBGUIXSA-N GMS SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)([SeH])=O)O3" GMS SMILES CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)([SeH])=O)O3" GMS SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 "c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)[SeH])O)N=C(NC2=O)N" GMS SMILES "OpenEye OEToolkits" 1.7.5 "c1nc2c(n1C3CC(C(O3)COP(=O)(O)[SeH])O)N=C(NC2=O)N" # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier GMS "SYSTEMATIC NAME" ACDLabs 10.04 "2'-deoxy-5'-O-selenophosphonoguanosine" GMS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methoxy-selanyl-phosphinic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site GMS "Create component" 2002-11-18 RCSB GMS "Modify descriptor" 2011-06-04 RCSB GMS "Modify descriptor" 2012-01-05 RCSB GMS "Modify coordinates" 2012-01-05 RCSB #