data_NE0 # _chem_comp.id NE0 _chem_comp.name "[[(2R,3R,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H16 N2 O18 P4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-01-12 _chem_comp.pdbx_modified_date 2023-06-30 _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 564.121 _chem_comp.one_letter_code ? _chem_comp.three_letter_code NE0 _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 8HYK _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 NE0 O01 O1 O 0 1 N N N 4.698 1.406 17.336 -4.259 -5.170 1.114 O01 NE0 1 NE0 C02 C1 C 0 1 N N N 4.797 0.222 17.468 -3.941 -4.073 0.692 C02 NE0 2 NE0 C03 C2 C 0 1 N N N 3.814 -0.475 18.195 -4.056 -3.777 -0.688 C03 NE0 3 NE0 C04 C3 C 0 1 N N N 3.938 -1.859 18.362 -3.697 -2.553 -1.130 C04 NE0 4 NE0 N05 N1 N 0 1 N N N 5.012 -2.499 17.800 -3.231 -1.622 -0.242 N05 NE0 5 NE0 C06 C4 C 0 1 N N R 5.172 -3.864 17.873 -2.841 -0.294 -0.722 C06 NE0 6 NE0 O07 O2 O 0 1 N N N 3.832 -4.673 18.119 -1.497 0.021 -0.296 O07 NE0 7 NE0 C08 C5 C 0 1 N N R 3.943 -5.319 19.250 -1.402 1.460 -0.369 C08 NE0 8 NE0 C09 C6 C 0 1 N N N 2.703 -5.163 20.107 -0.256 1.963 0.512 C09 NE0 9 NE0 O10 O3 O 0 1 N N N 2.608 -3.803 20.560 0.990 1.513 -0.024 O10 NE0 10 NE0 P11 P1 P 0 1 N N N 1.136 -3.210 21.067 2.410 1.858 0.651 P11 NE0 11 NE0 O12 O4 O 0 1 N N N 1.240 -1.727 21.379 2.401 1.427 2.067 O12 NE0 12 NE0 O13 O5 O 0 1 N N N 0.606 -3.931 22.306 2.669 3.445 0.574 O13 NE0 13 NE0 O14 O6 O 0 1 N N N 0.183 -3.458 19.764 3.581 1.085 -0.138 O14 NE0 14 NE0 P15 P2 P 0 1 N N N -1.381 -3.809 19.830 5.093 0.670 0.229 P15 NE0 15 NE0 O16 O7 O 0 1 N N N -1.979 -3.496 21.213 6.036 1.973 0.169 O16 NE0 16 NE0 O17 O8 O 0 1 N N N -2.124 -3.108 18.706 5.129 0.097 1.594 O17 NE0 17 NE0 O18 O9 O 0 1 N N N -1.446 -5.383 19.529 5.621 -0.424 -0.826 O18 NE0 18 NE0 P19 P3 P 0 1 N N N -1.798 -6.621 20.607 6.809 -1.511 -0.811 P19 NE0 19 NE0 O20 O10 O 0 1 N N N -3.275 -6.805 20.363 6.340 -2.808 0.020 O20 NE0 20 NE0 O21 O11 O 0 1 N N N -1.503 -6.142 22.088 7.163 -1.940 -2.322 O21 NE0 21 NE0 O22 O12 O 0 1 N N N -0.879 -7.690 20.039 8.007 -0.922 -0.172 O22 NE0 22 NE0 C23 C7 C 0 1 N N R 5.262 -4.575 19.961 -2.757 1.973 0.166 C23 NE0 23 NE0 O24 O13 O 0 1 N N N 5.730 -5.376 21.109 -3.181 3.124 -0.567 O24 NE0 24 NE0 C25 C8 C 0 1 N N R 6.114 -4.425 18.959 -3.726 0.793 -0.072 C25 NE0 25 NE0 O26 O14 O 0 1 N N N 6.537 -5.735 18.402 -4.778 1.179 -0.959 O26 NE0 26 NE0 P27 P4 P 0 1 N N N 7.960 -6.328 18.965 -6.337 1.025 -0.590 P27 NE0 27 NE0 O28 O15 O 0 1 N N N 8.952 -5.275 18.441 -6.619 -0.380 -0.218 O28 NE0 28 NE0 O29 O16 O 0 1 N N N 7.821 -6.327 20.487 -6.693 1.990 0.649 O29 NE0 29 NE0 O30 O17 O 0 1 N N N 8.229 -7.757 18.532 -7.233 1.434 -1.863 O30 NE0 30 NE0 C31 C9 C 0 1 N N N 5.915 -1.803 17.080 -3.127 -1.915 1.067 C31 NE0 31 NE0 O32 O18 O 0 1 N N N 6.835 -2.403 16.610 -2.711 -1.072 1.838 O32 NE0 32 NE0 N33 N2 N 0 1 N N N 5.856 -0.463 16.948 -3.483 -3.126 1.535 N33 NE0 33 NE0 H1 H1 H 0 1 N N N 2.973 0.053 18.620 -4.425 -4.522 -1.378 H1 NE0 34 NE0 H2 H2 H 0 1 N N N 3.200 -2.413 18.924 -3.777 -2.310 -2.180 H2 NE0 35 NE0 H3 H3 H 0 1 N N N 5.565 -4.219 16.909 -2.916 -0.246 -1.808 H3 NE0 36 NE0 H4 H4 H 0 1 N N N 4.181 -6.385 19.122 -1.256 1.778 -1.401 H4 NE0 37 NE0 H5 H5 H 0 1 N N N 1.812 -5.416 19.514 -0.269 3.053 0.536 H5 NE0 38 NE0 H6 H6 H 0 1 N N N 2.769 -5.836 20.975 -0.378 1.575 1.523 H6 NE0 39 NE0 H7 H7 H 0 1 N N N 0.457 -3.300 23.000 2.687 3.798 -0.326 H7 NE0 40 NE0 H8 H8 H 0 1 N N N -2.720 -2.909 21.113 6.061 2.401 -0.698 H8 NE0 41 NE0 H9 H9 H 0 1 N N N -3.417 -7.602 19.866 5.558 -3.246 -0.343 H9 NE0 42 NE0 H10 H10 H 0 1 N N N -0.754 -6.615 22.431 7.873 -2.594 -2.389 H10 NE0 43 NE0 H11 H11 H 0 1 N N N 4.910 -3.600 20.329 -2.686 2.204 1.229 H11 NE0 44 NE0 H12 H12 H 0 1 N N N 5.045 -5.419 21.766 -2.577 3.876 -0.503 H12 NE0 45 NE0 H13 H13 H 0 1 N N N 6.962 -3.752 19.152 -4.134 0.438 0.875 H13 NE0 46 NE0 H14 H14 H 0 1 N N N 8.386 -5.659 20.857 -6.533 2.928 0.476 H14 NE0 47 NE0 H15 H15 H 0 1 N N N 9.002 -7.781 17.980 -8.186 1.364 -1.712 H15 NE0 48 NE0 H16 H16 H 0 1 N N N 6.585 0.027 16.471 -3.402 -3.320 2.482 H16 NE0 49 # 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 NE0 O32 C31 DOUB N N 1 NE0 N33 C31 SING N N 2 NE0 N33 C02 SING N N 3 NE0 C31 N05 SING N N 4 NE0 O01 C02 DOUB N N 5 NE0 C02 C03 SING N N 6 NE0 N05 C06 SING N N 7 NE0 N05 C04 SING N N 8 NE0 C06 O07 SING N N 9 NE0 C06 C25 SING N N 10 NE0 O07 C08 SING N N 11 NE0 C03 C04 DOUB N N 12 NE0 O26 C25 SING N N 13 NE0 O26 P27 SING N N 14 NE0 O28 P27 DOUB N N 15 NE0 O30 P27 SING N N 16 NE0 O17 P15 DOUB N N 17 NE0 C25 C23 SING N N 18 NE0 P27 O29 SING N N 19 NE0 C08 C23 SING N N 20 NE0 C08 C09 SING N N 21 NE0 O18 P15 SING N N 22 NE0 O18 P19 SING N N 23 NE0 O14 P15 SING N N 24 NE0 O14 P11 SING N N 25 NE0 P15 O16 SING N N 26 NE0 C23 O24 SING N N 27 NE0 O22 P19 DOUB N N 28 NE0 C09 O10 SING N N 29 NE0 O20 P19 SING N N 30 NE0 O10 P11 SING N N 31 NE0 P19 O21 SING N N 32 NE0 P11 O12 DOUB N N 33 NE0 P11 O13 SING N N 34 NE0 C03 H1 SING N N 35 NE0 C04 H2 SING N N 36 NE0 C06 H3 SING N N 37 NE0 C08 H4 SING N N 38 NE0 C09 H5 SING N N 39 NE0 C09 H6 SING N N 40 NE0 O13 H7 SING N N 41 NE0 O16 H8 SING N N 42 NE0 O20 H9 SING N N 43 NE0 O21 H10 SING N N 44 NE0 C23 H11 SING N N 45 NE0 O24 H12 SING N N 46 NE0 C25 H13 SING N N 47 NE0 O29 H14 SING N N 48 NE0 O30 H15 SING N N 49 NE0 N33 H16 SING N N 50 # 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 NE0 InChI InChI 1.06 "InChI=1S/C9H16N2O18P4/c12-5-1-2-11(9(14)10-5)8-7(27-30(15,16)17)6(13)4(26-8)3-25-32(21,22)29-33(23,24)28-31(18,19)20/h1-2,4,6-8,13H,3H2,(H,21,22)(H,23,24)(H,10,12,14)(H2,15,16,17)(H2,18,19,20)/t4-,6-,7-,8-/m1/s1" NE0 InChIKey InChI 1.06 OATQDFNIQGUFQP-XVFCMESISA-N NE0 SMILES_CANONICAL CACTVS 3.385 "O[C@@H]1[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O[C@H]([C@@H]1O[P](O)(O)=O)N2C=CC(=O)NC2=O" NE0 SMILES CACTVS 3.385 "O[CH]1[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O[CH]([CH]1O[P](O)(O)=O)N2C=CC(=O)NC2=O" NE0 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)OP(=O)(O)O" NE0 SMILES "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)OP(=O)(O)O" # _pdbx_chem_comp_identifier.comp_id NE0 _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 "[[(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen 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 NE0 "Create component" 2023-01-12 PDBJ NE0 "Initial release" 2023-07-05 RCSB #