data_OWR # _chem_comp.id OWR _chem_comp.name "1-[2-deoxy-5-O-(dihydroxyphosphanyl)-beta-D-erythro-pentofuranosyl]-1H-naphtho[2,3-d]imidazole" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C16 H17 N2 O6 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-05-18 _chem_comp.pdbx_modified_date 2022-08-26 _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 364.290 _chem_comp.one_letter_code ? _chem_comp.three_letter_code OWR _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 8CTZ _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 OWR C1 C1 C 0 1 Y N N 3.367 35.620 14.066 5.211 0.824 0.145 C1 OWR 1 OWR "C1'" C2 C 0 1 N N R 6.084 39.537 15.891 0.141 -0.710 -0.260 "C1'" OWR 2 OWR C10 C3 C 0 1 Y N N 2.777 35.338 16.371 5.590 -1.102 -1.359 C10 OWR 3 OWR C11 C4 C 0 1 Y N N 1.982 34.236 16.048 6.918 -0.806 -1.333 C11 OWR 4 OWR C12 C5 C 0 1 Y N N 1.880 33.819 14.726 7.414 0.269 -0.598 C12 OWR 5 OWR C13 C6 C 0 1 Y N N 2.572 34.516 13.734 6.596 1.075 0.129 C13 OWR 6 OWR C2 C7 C 0 1 Y N N 3.469 36.032 15.382 4.690 -0.306 -0.628 C2 OWR 7 OWR "C2'" C8 C 0 1 N N N 7.538 39.276 16.284 0.062 -1.972 0.622 "C2'" OWR 8 OWR C3 C9 C 0 1 Y N N 4.265 37.138 15.680 3.314 -0.568 -0.621 C3 OWR 9 OWR "C3'" C10 C 0 1 N N S 8.013 40.647 16.771 -1.429 -2.053 1.033 "C3'" OWR 10 OWR C4 C11 C 0 1 Y N N 4.912 37.776 14.693 2.472 0.240 0.111 C4 OWR 11 OWR "C4'" C12 C 0 1 N N R 6.840 41.601 16.572 -2.115 -1.193 -0.058 "C4'" OWR 12 OWR C5 C13 C 0 1 Y N N 4.811 37.373 13.419 2.969 1.332 0.859 C5 OWR 13 OWR "C5'" C14 C 0 1 N N N 7.319 42.932 15.998 -3.448 -0.640 0.450 "C5'" OWR 14 OWR C6 C15 C 0 1 Y N N 4.062 36.316 13.089 4.326 1.619 0.880 C6 OWR 15 OWR C8 C16 C 0 1 Y N N 6.120 39.108 13.466 0.811 1.279 1.138 C8 OWR 16 OWR N7 N1 N 0 1 Y N N 5.550 38.209 12.669 1.896 1.918 1.458 N7 OWR 17 OWR N9 N2 N 0 1 Y N N 5.724 38.831 14.701 1.101 0.238 0.312 N9 OWR 18 OWR "O3'" O1 O 0 1 N N N 8.384 40.615 18.158 -1.897 -3.403 0.988 "O3'" OWR 19 OWR "O4'" O2 O 0 1 N N N 5.978 40.944 15.638 -1.171 -0.125 -0.287 "O4'" OWR 20 OWR "O5'" O3 O 0 1 N N N 8.171 42.667 14.877 -4.112 0.049 -0.611 "O5'" OWR 21 OWR OP3 O4 O 0 1 N Y N 9.203 45.021 14.785 -5.928 1.546 -1.784 OP3 OWR 22 OWR OP2 O5 O 0 1 N N N 9.472 43.468 12.797 -6.664 -0.357 -0.126 OP2 OWR 23 OWR P P1 P 0 1 N N N 8.591 43.922 13.945 -5.546 0.760 -0.431 P OWR 24 OWR H1 H1 H 0 1 N N N 5.428 39.246 16.725 0.447 -0.983 -1.270 H1 OWR 25 OWR H2 H2 H 0 1 N N N 2.856 35.656 17.400 5.231 -1.940 -1.937 H2 OWR 26 OWR H3 H3 H 0 1 N N N 1.447 33.709 16.824 7.605 -1.420 -1.896 H3 OWR 27 OWR H4 H4 H 0 1 N N N 1.272 32.965 14.469 8.476 0.466 -0.607 H4 OWR 28 OWR H5 H5 H 0 1 N N N 2.494 34.202 12.704 7.005 1.903 0.690 H5 OWR 29 OWR H6 H6 H 0 1 N N N 7.602 38.527 17.087 0.349 -2.855 0.052 H6 OWR 30 OWR H7 H7 H 0 1 N N N 8.127 38.938 15.419 0.695 -1.862 1.503 H7 OWR 31 OWR H8 H8 H 0 1 N N N 4.360 37.479 16.700 2.915 -1.397 -1.186 H8 OWR 32 OWR H9 H9 H 0 1 N N N 8.860 40.978 16.152 -1.584 -1.623 2.023 H9 OWR 33 OWR H10 H10 H 0 1 N N N 6.330 41.771 17.532 -2.264 -1.775 -0.968 H10 OWR 34 OWR H11 H11 H 0 1 N N N 7.879 43.487 16.766 -4.074 -1.462 0.797 H11 OWR 35 OWR H12 H12 H 0 1 N N N 6.454 43.528 15.673 -3.264 0.050 1.273 H12 OWR 36 OWR H13 H13 H 0 1 N N N 3.998 36.003 12.057 4.696 2.455 1.454 H13 OWR 37 OWR H14 H14 H 0 1 N N N 6.779 39.909 13.165 -0.181 1.538 1.480 H14 OWR 38 OWR H15 H15 H 0 1 N N N 8.673 41.478 18.429 -1.434 -4.000 1.592 H15 OWR 39 OWR H16 H16 H 0 1 N Y N 8.631 45.779 14.781 -6.781 1.999 -1.747 H16 OWR 40 OWR H17 H17 H 0 1 N N N 9.013 43.595 11.975 -6.759 -1.020 -0.824 H17 OWR 41 OWR OP1 O6 O 0 1 N N N 7.202 44.453 13.363 -5.484 1.717 0.695 OP1 OWR 42 # 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 OWR N7 C5 SING Y N 1 OWR N7 C8 DOUB Y N 2 OWR OP2 P SING N N 3 OWR C6 C5 DOUB Y N 4 OWR C6 C1 SING Y N 5 OWR C5 C4 SING Y N 6 OWR C8 N9 SING Y N 7 OWR C13 C1 DOUB Y N 8 OWR C13 C12 SING Y N 9 OWR P OP3 SING N N 10 OWR P "O5'" SING N N 11 OWR C1 C2 SING Y N 12 OWR C4 N9 SING Y N 13 OWR C4 C3 DOUB Y N 14 OWR N9 "C1'" SING N N 15 OWR C12 C11 DOUB Y N 16 OWR "O5'" "C5'" SING N N 17 OWR C2 C3 SING Y N 18 OWR C2 C10 DOUB Y N 19 OWR "O4'" "C1'" SING N N 20 OWR "O4'" "C4'" SING N N 21 OWR "C1'" "C2'" SING N N 22 OWR "C5'" "C4'" SING N N 23 OWR C11 C10 SING Y N 24 OWR "C2'" "C3'" SING N N 25 OWR "C4'" "C3'" SING N N 26 OWR "C3'" "O3'" SING N N 27 OWR "C1'" H1 SING N N 28 OWR C10 H2 SING N N 29 OWR C11 H3 SING N N 30 OWR C12 H4 SING N N 31 OWR C13 H5 SING N N 32 OWR "C2'" H6 SING N N 33 OWR "C2'" H7 SING N N 34 OWR C3 H8 SING N N 35 OWR "C3'" H9 SING N N 36 OWR "C4'" H10 SING N N 37 OWR "C5'" H11 SING N N 38 OWR "C5'" H12 SING N N 39 OWR C6 H13 SING N N 40 OWR C8 H14 SING N N 41 OWR "O3'" H15 SING N N 42 OWR OP3 H16 SING N N 43 OWR OP2 H17 SING N N 44 OWR P OP1 DOUB N N 45 # 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 OWR SMILES ACDLabs 12.01 "O=P(O)(O)OCC1OC(CC1O)n1cnc2cc3ccccc3cc21" OWR InChI InChI 1.03 "InChI=1S/C16H17N2O6P/c19-14-7-16(24-15(14)8-23-25(20,21)22)18-9-17-12-5-10-3-1-2-4-11(10)6-13(12)18/h1-6,9,14-16,19H,7-8H2,(H2,20,21,22)/t14-,15+,16+/m0/s1" OWR InChIKey InChI 1.03 HNXFPKXDQSBACZ-ARFHVFGLSA-N OWR SMILES_CANONICAL CACTVS 3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3cc4ccccc4cc23" OWR SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2cnc3cc4ccccc4cc23" OWR SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc2cc3c(cc2c1)ncn3[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)O" OWR SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc2cc3c(cc2c1)ncn3C4CC(C(O4)COP(=O)(O)O)O" # 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 OWR "SYSTEMATIC NAME" ACDLabs 12.01 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-naphtho[2,3-d]imidazole" OWR "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},5~{R})-5-benzo[f]benzimidazol-3-yl-3-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 OWR "Create component" 2022-05-18 RCSB OWR "Initial release" 2022-08-31 RCSB #