data_GDO # _chem_comp.id GDO _chem_comp.name ;3'-deoxy-guanosine 5'-monophosphate ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H14 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id G _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-04-11 _chem_comp.pdbx_modified_date 2012-04-13 _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 347.221 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GDO _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4E78 _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 GDO C4 C4 C 0 1 Y N N 41.126 -46.619 10.317 2.815 -0.107 0.132 C4 GDO 1 GDO C5 C5 C 0 1 Y N N 41.747 -45.841 11.272 3.343 -1.304 -0.363 C5 GDO 2 GDO C6 C6 C 0 1 N N N 40.982 -45.370 12.375 4.729 -1.546 -0.213 C6 GDO 3 GDO N1 N1 N 0 1 N N N 39.659 -45.799 12.301 5.481 -0.607 0.403 N1 GDO 4 GDO C8 C8 C 0 1 Y N N 43.252 -46.306 9.840 1.216 -1.322 -0.778 C8 GDO 5 GDO N2 N2 N 0 1 N N N 37.837 -46.893 11.404 5.696 1.475 1.487 N2 GDO 6 GDO O6 O6 O 0 1 N N N 41.351 -44.670 13.327 5.232 -2.576 -0.629 O6 GDO 7 GDO N3 N3 N 0 1 N N N 39.838 -47.024 10.265 3.622 0.776 0.732 N3 GDO 8 GDO P P P 0 1 N N N 46.954 -46.186 7.394 -5.135 -0.660 0.338 P GDO 9 GDO OP1 OP1 O 0 1 N N N 47.655 -45.691 6.180 -5.024 -1.752 -0.655 OP1 GDO 10 GDO OP2 OP2 O 0 1 N N N 46.903 -45.318 8.594 -5.529 -1.278 1.772 OP2 GDO 11 GDO "O5'" "O5'" O 0 1 N N N 45.412 -46.392 7.033 -3.724 0.106 0.452 "O5'" GDO 12 GDO "C5'" "C5'" C 0 1 N N N 44.941 -47.492 6.222 -3.052 0.673 -0.674 "C5'" GDO 13 GDO "C4'" "C4'" C 0 1 N N S 43.452 -47.693 6.407 -1.745 1.322 -0.215 "C4'" GDO 14 GDO "O4'" "O4'" O 0 1 N N N 43.178 -48.182 7.748 -0.821 0.322 0.263 "O4'" GDO 15 GDO "C3'" "C3'" C 0 1 N N N 42.591 -46.448 6.283 -1.000 1.958 -1.417 "C3'" GDO 16 GDO "C2'" "C2'" C 0 1 N N R 41.335 -46.851 7.047 0.467 1.963 -0.923 "C2'" GDO 17 GDO "O2'" "O2'" O 0 1 N N N 40.399 -47.577 6.277 0.812 3.245 -0.395 "O2'" GDO 18 GDO "C1'" "C1'" C 0 1 N N R 41.918 -47.700 8.180 0.495 0.896 0.189 "C1'" GDO 19 GDO N9 N9 N 0 1 Y N N 42.104 -46.924 9.401 1.474 -0.142 -0.141 N9 GDO 20 GDO N7 N7 N 0 1 Y N N 43.086 -45.651 10.957 2.318 -2.001 -0.911 N7 GDO 21 GDO C2 C2 C 0 1 N N N 39.138 -46.582 11.298 4.908 0.540 0.865 C2 GDO 22 GDO OP3 O1 O 0 1 N Y N 47.605 -47.632 7.754 -6.273 0.378 -0.130 O1 GDO 23 GDO H1 H1 H 0 1 N N N 39.040 -45.516 13.034 6.433 -0.751 0.518 H1 GDO 24 GDO H2 H2 H 0 1 N N N 44.194 -46.357 9.314 0.244 -1.640 -1.125 H2 GDO 25 GDO H3 H3 H 0 1 N N N 37.399 -47.457 10.704 5.302 2.296 1.821 H3 GDO 26 GDO H4 H4 H 0 1 N N N 37.305 -46.561 12.183 6.647 1.315 1.593 H4 GDO 27 GDO H5 H5 H 0 1 N N N 47.357 -44.503 8.415 -6.370 -1.755 1.777 H5 GDO 28 GDO H6 H6 H 0 1 N N N 45.469 -48.411 6.518 -2.833 -0.112 -1.399 H6 GDO 29 GDO H7 H7 H 0 1 N N N 45.147 -47.275 5.164 -3.690 1.426 -1.137 H7 GDO 30 GDO H8 H8 H 0 1 N N N 43.104 -48.433 5.671 -1.938 2.067 0.557 H8 GDO 31 GDO H9 H9 H 0 1 N N N 43.078 -45.578 6.747 -1.107 1.343 -2.310 H9 GDO 32 GDO H10 H10 H 0 1 N N N 42.363 -46.223 5.231 -1.352 2.973 -1.600 H10 GDO 33 GDO H11 H11 H 0 1 N N N 40.870 -45.951 7.476 1.143 1.688 -1.732 H11 GDO 34 GDO H12 H12 H 0 1 N N N 39.646 -47.793 6.814 0.755 3.964 -1.039 H12 GDO 35 GDO H13 H13 H 0 1 N N N 41.236 -48.541 8.377 0.751 1.360 1.141 H13 GDO 36 GDO H14 H14 H 0 1 N N N 48.281 -47.842 7.120 -6.400 1.121 0.475 H14 GDO 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 GDO OP1 P DOUB N N 1 GDO "C5'" "C4'" SING N N 2 GDO "C5'" "O5'" SING N N 3 GDO "O2'" "C2'" SING N N 4 GDO "C3'" "C4'" SING N N 5 GDO "C3'" "C2'" SING N N 6 GDO "C4'" "O4'" SING N N 7 GDO "O5'" P SING N N 8 GDO "C2'" "C1'" SING N N 9 GDO P OP2 SING N N 10 GDO "O4'" "C1'" SING N N 11 GDO "C1'" N9 SING N N 12 GDO N9 C8 SING Y N 13 GDO N9 C4 SING Y N 14 GDO C8 N7 DOUB Y N 15 GDO N3 C4 SING N N 16 GDO N3 C2 DOUB N N 17 GDO C4 C5 DOUB Y N 18 GDO N7 C5 SING Y N 19 GDO C5 C6 SING N N 20 GDO C2 N2 SING N N 21 GDO C2 N1 SING N N 22 GDO N1 C6 SING N N 23 GDO C6 O6 DOUB N N 24 GDO P OP3 SING N N 25 GDO N1 H1 SING N N 26 GDO C8 H2 SING N N 27 GDO N2 H3 SING N N 28 GDO N2 H4 SING N N 29 GDO OP2 H5 SING N N 30 GDO "C5'" H6 SING N N 31 GDO "C5'" H7 SING N N 32 GDO "C4'" H8 SING N N 33 GDO "C3'" H9 SING N N 34 GDO "C3'" H10 SING N N 35 GDO "C2'" H11 SING N N 36 GDO "O2'" H12 SING N N 37 GDO "C1'" H13 SING N N 38 GDO OP3 H14 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 GDO SMILES ACDLabs 12.01 "O=P(O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3" GDO InChI InChI 1.03 "InChI=1S/C10H14N5O7P/c11-10-13-7-6(8(17)14-10)12-3-15(7)9-5(16)1-4(22-9)2-21-23(18,19)20/h3-5,9,16H,1-2H2,(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,9+/m0/s1" GDO InChIKey InChI 1.03 FDFODSATEZEUMJ-OBXARNEKSA-N GDO SMILES_CANONICAL CACTVS 3.370 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(O)=O)C[C@H]3O" GDO SMILES CACTVS 3.370 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(O)=O)C[CH]3O" GDO SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1nc2c(n1[C@H]3[C@@H](C[C@H](O3)COP(=O)(O)O)O)N=C(NC2=O)N" GDO SMILES "OpenEye OEToolkits" 1.7.6 "c1nc2c(n1C3C(CC(O3)COP(=O)(O)O)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 GDO "SYSTEMATIC NAME" ACDLabs 12.01 ;3'-deoxy-5'-guanylic acid ; GDO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2S,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site GDO "Create component" 2012-04-11 RCSB #