data_OIQ # _chem_comp.id OIQ _chem_comp.name ;[(1R,3R,4R,7S)-5-[(E)-N,N'-dimethylcarbamimidoyl]-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-7-oxidanyl-2-oxa-5-azabicyclo[2.2.1]heptan-1-yl]methyl dihydrogen phosphate ; _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C14 H22 N5 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-02-02 _chem_comp.pdbx_modified_date 2023-08-04 _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 419.327 _chem_comp.one_letter_code ? _chem_comp.three_letter_code OIQ _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 8I50 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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 OIQ N1 N1 N 0 1 N N N 14.592 7.696 25.819 -2.307 0.718 0.447 N1 OIQ 1 OIQ C4 C1 C 0 1 N N N 12.755 7.226 27.830 -4.395 2.426 0.118 C4 OIQ 2 OIQ C5 C2 C 0 1 N N N 14.111 6.649 27.912 -3.073 2.861 -0.142 C5 OIQ 3 OIQ C6 C3 C 0 1 N N N 14.970 6.924 26.862 -2.051 1.995 0.027 C6 OIQ 4 OIQ C2 C4 C 0 1 N N N 13.299 8.228 25.766 -3.568 0.317 0.691 C2 OIQ 5 OIQ CD C5 C 0 1 N N N 17.119 10.435 22.733 -0.362 -3.553 0.006 CD OIQ 6 OIQ "C1'" C6 C 0 1 N N R 15.502 7.943 24.685 -1.199 -0.224 0.625 "C1'" OIQ 7 OIQ "C2'" C7 C 0 1 N N R 16.272 9.253 24.762 -1.087 -1.167 -0.613 "C2'" OIQ 8 OIQ "C3'" C8 C 0 1 N N S 17.347 8.857 25.716 -0.172 -0.269 -1.523 "C3'" OIQ 9 OIQ "C4'" C9 C 0 1 N N R 17.744 7.659 24.868 0.891 -0.030 -0.392 "C4'" OIQ 10 OIQ "C5'" C10 C 0 1 N N N 18.812 6.777 25.483 2.113 0.808 -0.773 "C5'" OIQ 11 OIQ C5M C11 C 0 1 N N N 14.535 5.800 29.083 -2.810 4.271 -0.603 C5M OIQ 12 OIQ "C6'" C12 C 0 1 N N N 18.028 8.243 23.497 1.172 -1.509 0.020 "C6'" OIQ 13 OIQ "C7'" C13 C 0 1 N N N 18.457 11.924 21.340 -1.825 -5.453 -0.024 "C7'" OIQ 14 OIQ "C8'" C14 C 0 1 N N N 14.694 10.638 22.234 1.954 -3.834 0.786 "C8'" OIQ 15 OIQ "N2'" N2 N 0 1 N N N 17.108 9.373 23.551 -0.114 -2.213 -0.177 "N2'" OIQ 16 OIQ N3 N3 N 0 1 N N N 12.437 7.961 26.757 -4.606 1.159 0.530 N3 OIQ 17 OIQ "N3'" N4 N 0 1 N N N 18.224 10.801 22.234 -1.522 -4.051 -0.319 "N3'" OIQ 18 OIQ "N4'" N5 N 0 1 N N N 16.034 11.155 22.447 0.613 -4.367 0.531 "N4'" OIQ 19 OIQ O2 O1 O 0 1 N N N 12.972 8.950 24.796 -3.774 -0.822 1.063 O2 OIQ 20 OIQ "O3'" O2 O 0 1 N N N 18.340 9.877 25.779 0.366 -0.988 -2.635 "O3'" OIQ 21 OIQ O4 O3 O 0 1 N N N 11.909 7.017 28.732 -5.332 3.189 -0.028 O4 OIQ 22 OIQ "O4'" O4 O 0 1 N N N 16.517 6.949 24.732 0.054 0.485 0.681 "O4'" OIQ 23 OIQ "O5'" O5 O 0 1 N N N 18.338 6.515 26.797 3.032 0.834 0.320 "O5'" OIQ 24 OIQ OP1 O6 O 0 1 N N N 20.672 6.121 27.754 4.187 3.042 -0.084 OP1 OIQ 25 OIQ OP2 O7 O 0 1 N N N 18.611 5.978 29.243 5.146 1.549 1.711 OP2 OIQ 26 OIQ P P1 P 0 1 N N N 19.222 5.752 27.888 4.433 1.626 0.269 P OIQ 27 OIQ OP3 O8 O 0 1 N Y N 19.059 4.204 27.509 5.389 0.955 -0.839 OP3 OIQ 28 OIQ H1 H1 H 0 1 N N N 15.968 6.511 26.877 -1.036 2.309 -0.166 H1 OIQ 29 OIQ H2 H2 H 0 1 N N N 14.948 7.896 23.736 -1.343 -0.809 1.533 H2 OIQ 30 OIQ H3 H3 H 0 1 N N N 15.679 10.138 25.038 -2.024 -1.513 -1.049 H3 OIQ 31 OIQ H4 H4 H 0 1 N N N 16.953 8.559 26.699 -0.668 0.651 -1.832 H4 OIQ 32 OIQ H5 H5 H 0 1 N N N 18.920 5.842 24.914 2.598 0.368 -1.645 H5 OIQ 33 OIQ H6 H6 H 0 1 N N N 19.779 7.301 25.515 1.798 1.824 -1.008 H6 OIQ 34 OIQ H7 H7 H 0 1 N N N 13.701 5.713 29.794 -3.754 4.811 -0.680 H7 OIQ 35 OIQ H8 H8 H 0 1 N N N 14.819 4.799 28.726 -2.162 4.773 0.115 H8 OIQ 36 OIQ H9 H9 H 0 1 N N N 15.395 6.269 29.583 -2.323 4.250 -1.579 H9 OIQ 37 OIQ H10 H10 H 0 1 N N N 17.777 7.542 22.687 1.942 -1.940 -0.620 H10 OIQ 38 OIQ H11 H11 H 0 1 N N N 19.075 8.565 23.392 1.476 -1.559 1.066 H11 OIQ 39 OIQ H12 H12 H 0 1 N N N 19.526 11.975 21.086 -1.060 -6.091 -0.466 H12 OIQ 40 OIQ H13 H13 H 0 1 N N N 17.868 11.789 20.421 -1.843 -5.602 1.056 H13 OIQ 41 OIQ H14 H14 H 0 1 N N N 18.153 12.857 21.837 -2.798 -5.710 -0.442 H14 OIQ 42 OIQ H15 H15 H 0 1 N N N 14.009 11.471 22.016 1.895 -3.050 1.541 H15 OIQ 43 OIQ H16 H16 H 0 1 N N N 14.702 9.938 21.385 2.602 -4.635 1.143 H16 OIQ 44 OIQ H17 H17 H 0 1 N N N 14.356 10.113 23.139 2.362 -3.420 -0.136 H17 OIQ 45 OIQ H18 H18 H 0 1 N N N 11.510 8.329 26.692 -5.508 0.854 0.710 H18 OIQ 46 OIQ H19 H19 H 0 1 N N N 16.154 12.145 22.372 0.414 -5.295 0.732 H19 OIQ 47 OIQ H20 H20 H 0 1 N Y N 19.022 9.619 26.388 -0.304 -1.338 -3.239 H20 OIQ 48 OIQ H21 H21 H 0 1 N N N 19.266 6.335 29.831 5.997 2.006 1.754 H21 OIQ 49 OIQ H22 H22 H 0 1 N N N 19.907 3.843 27.280 5.593 0.025 -0.671 H22 OIQ 50 # 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 OIQ "C7'" "N3'" SING N N 1 OIQ "N3'" CD DOUB N N 2 OIQ "C8'" "N4'" SING N N 3 OIQ "N4'" CD SING N N 4 OIQ CD "N2'" SING N N 5 OIQ "C6'" "N2'" SING N N 6 OIQ "C6'" "C4'" SING N N 7 OIQ "N2'" "C2'" SING N N 8 OIQ "C1'" "O4'" SING N N 9 OIQ "C1'" "C2'" SING N N 10 OIQ "C1'" N1 SING N N 11 OIQ "O4'" "C4'" SING N N 12 OIQ "C2'" "C3'" SING N N 13 OIQ O2 C2 DOUB N N 14 OIQ "C4'" "C5'" SING N N 15 OIQ "C4'" "C3'" SING N N 16 OIQ "C5'" "O5'" SING N N 17 OIQ "C3'" "O3'" SING N N 18 OIQ C2 N1 SING N N 19 OIQ C2 N3 SING N N 20 OIQ N1 C6 SING N N 21 OIQ N3 C4 SING N N 22 OIQ "O5'" P SING N N 23 OIQ C6 C5 DOUB N N 24 OIQ OP1 P DOUB N N 25 OIQ C4 C5 SING N N 26 OIQ C4 O4 DOUB N N 27 OIQ P OP2 SING N N 28 OIQ C5 C5M SING N N 29 OIQ P OP3 SING N N 30 OIQ C6 H1 SING N N 31 OIQ "C1'" H2 SING N N 32 OIQ "C2'" H3 SING N N 33 OIQ "C3'" H4 SING N N 34 OIQ "C5'" H5 SING N N 35 OIQ "C5'" H6 SING N N 36 OIQ C5M H7 SING N N 37 OIQ C5M H8 SING N N 38 OIQ C5M H9 SING N N 39 OIQ "C6'" H10 SING N N 40 OIQ "C6'" H11 SING N N 41 OIQ "C7'" H12 SING N N 42 OIQ "C7'" H13 SING N N 43 OIQ "C7'" H14 SING N N 44 OIQ "C8'" H15 SING N N 45 OIQ "C8'" H16 SING N N 46 OIQ "C8'" H17 SING N N 47 OIQ N3 H18 SING N N 48 OIQ "N4'" H19 SING N N 49 OIQ "O3'" H20 SING N N 50 OIQ OP2 H21 SING N N 51 OIQ OP3 H22 SING N N 52 # 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 OIQ InChI InChI 1.06 "InChI=1S/C14H22N5O8P/c1-7-4-18(13(22)17-10(7)21)11-8-9(20)14(27-11,6-26-28(23,24)25)5-19(8)12(15-2)16-3/h4,8-9,11,20H,5-6H2,1-3H3,(H,15,16)(H,17,21,22)(H2,23,24,25)/t8-,9+,11-,14-/m1/s1" OIQ InChIKey InChI 1.06 UBEWFRLVLLXNDH-SZRLZVLASA-N OIQ SMILES_CANONICAL CACTVS 3.385 "CNC(=NC)N1C[C@]2(CO[P](O)(O)=O)O[C@H]([C@H]1[C@@H]2O)N3C=C(C)C(=O)NC3=O" OIQ SMILES CACTVS 3.385 "CNC(=NC)N1C[C]2(CO[P](O)(O)=O)O[CH]([CH]1[CH]2O)N3C=C(C)C(=O)NC3=O" OIQ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2[C@H]3[C@@H]([C@@](O2)(CN3/C(=N/C)/NC)COP(=O)(O)O)O" OIQ SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2C3C(C(O2)(CN3C(=NC)NC)COP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id OIQ _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier ;[(1~{R},3~{R},4~{R},7~{S})-5-[(~{E})-~{N},~{N}'-dimethylcarbamimidoyl]-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-7-oxidanyl-2-oxa-5-azabicyclo[2.2.1]heptan-1-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 OIQ "Create component" 2023-02-02 PDBJ OIQ "Initial release" 2023-08-09 RCSB #