data_XY7 # _chem_comp.id XY7 _chem_comp.name "1-[2-deoxy-5-O-(dihydroxyphosphanyl)-2-fluoro-beta-L-ribofuranosyl]pyrimidine-2,4(1H,3H)-dione" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H12 F N2 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-01-19 _chem_comp.pdbx_modified_date 2021-08-27 _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 310.173 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XY7 _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 7KW4 _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 XY7 C4 C1 C 0 1 N N N -19.769 7.333 11.815 4.242 -1.705 0.189 C4 XY7 1 XY7 N3 N1 N 0 1 N N N -20.048 8.141 12.903 2.969 -2.143 0.120 N3 XY7 2 XY7 C2 C2 C 0 1 N N N -19.119 8.446 13.876 1.968 -1.280 -0.137 C2 XY7 3 XY7 N1 N2 N 0 1 N N N -17.860 7.925 13.760 2.215 0.028 -0.329 N1 XY7 4 XY7 C6 C3 C 0 1 N N N -17.541 7.084 12.671 3.493 0.513 -0.267 C6 XY7 5 XY7 C5 C4 C 0 1 N N N -18.467 6.795 11.706 4.516 -0.330 -0.011 C5 XY7 6 XY7 O4 O1 O 0 1 N N N -20.657 7.104 11.018 5.148 -2.484 0.426 O4 XY7 7 XY7 O2 O2 O 0 1 N N N -19.374 9.219 14.785 0.825 -1.690 -0.197 O2 XY7 8 XY7 "C1'" C5 C 0 1 N N S -16.905 8.212 14.837 1.105 0.943 -0.606 "C1'" XY7 9 XY7 "O4'" O3 O 0 1 N N N -15.832 7.240 14.772 -0.157 0.244 -0.545 "O4'" XY7 10 XY7 "C2'" C6 C 0 1 N N S -16.286 9.555 14.701 0.985 2.012 0.510 "C2'" XY7 11 XY7 "F2'" F1 F 0 1 N N N -15.898 9.993 15.916 1.822 3.102 0.249 "F2'" XY7 12 XY7 "C3'" C7 C 0 1 N N S -15.084 9.237 13.793 -0.504 2.421 0.409 "C3'" XY7 13 XY7 "O3'" O4 O 0 1 N N N -14.095 10.266 13.787 -0.643 3.619 -0.358 "O3'" XY7 14 XY7 "C4'" C8 C 0 1 N N S -14.596 7.959 14.500 -1.174 1.234 -0.317 "C4'" XY7 15 XY7 "C5'" C9 C 0 1 N N N -13.665 7.084 13.639 -2.284 0.648 0.559 "C5'" XY7 16 XY7 "O5'" O5 O 0 1 N N N -14.251 6.908 12.354 -2.974 -0.372 -0.166 "O5'" XY7 17 XY7 P P1 P 0 1 N N N -13.492 6.096 11.234 -4.206 -1.205 0.451 P XY7 18 XY7 OP1 O6 O 0 1 N N N -14.274 6.324 10.002 -5.468 -0.299 0.029 OP1 XY7 19 XY7 OP2 O7 O 0 1 N N N -12.067 6.438 11.259 -4.322 -2.440 -0.575 OP2 XY7 20 XY7 H1 H1 H 0 1 N N N -20.968 8.523 12.988 2.773 -3.083 0.255 H1 XY7 21 XY7 H2 H2 H 0 1 N N N -16.550 6.662 12.599 3.682 1.565 -0.422 H2 XY7 22 XY7 H3 H3 H 0 1 N N N -18.206 6.163 10.870 5.530 0.039 0.041 H3 XY7 23 XY7 H4 H4 H 0 1 N N N -17.414 8.142 15.810 1.234 1.417 -1.579 H4 XY7 24 XY7 H5 H5 H 0 1 N N N -16.969 10.250 14.191 1.205 1.580 1.487 H5 XY7 25 XY7 H6 H6 H 0 1 N N N -15.430 8.998 12.777 -0.933 2.552 1.403 H6 XY7 26 XY7 H7 H7 H 0 1 N N N -14.438 11.033 13.343 -0.240 4.397 0.051 H7 XY7 27 XY7 H8 H8 H 0 1 N N N -14.087 8.228 15.437 -1.588 1.567 -1.269 H8 XY7 28 XY7 H9 H9 H 0 1 N N N -13.531 6.104 14.120 -1.847 0.221 1.461 H9 XY7 29 XY7 H10 H10 H 0 1 N N N -12.688 7.578 13.534 -2.985 1.437 0.833 H10 XY7 30 XY7 H11 H11 H 0 1 N N N -15.174 6.054 10.143 -5.564 0.509 0.551 H11 XY7 31 XY7 H12 H12 H 0 1 N N N -11.707 6.235 12.114 -5.028 -3.065 -0.360 H12 XY7 32 # # 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 XY7 OP1 P SING N N 1 XY7 O4 C4 DOUB N N 2 XY7 P OP2 SING N N 3 XY7 P "O5'" SING N N 4 XY7 C5 C4 SING N N 5 XY7 C5 C6 DOUB N N 6 XY7 C4 N3 SING N N 7 XY7 "O5'" "C5'" SING N N 8 XY7 C6 N1 SING N N 9 XY7 N3 C2 SING N N 10 XY7 "C5'" "C4'" SING N N 11 XY7 N1 C2 SING N N 12 XY7 N1 "C1'" SING N N 13 XY7 "O3'" "C3'" SING N N 14 XY7 "C3'" "C4'" SING N N 15 XY7 "C3'" "C2'" SING N N 16 XY7 C2 O2 DOUB N N 17 XY7 "C4'" "O4'" SING N N 18 XY7 "C2'" "C1'" SING N N 19 XY7 "C2'" "F2'" SING N N 20 XY7 "O4'" "C1'" SING N N 21 XY7 N3 H1 SING N N 22 XY7 C6 H2 SING N N 23 XY7 C5 H3 SING N N 24 XY7 "C1'" H4 SING N N 25 XY7 "C2'" H5 SING N N 26 XY7 "C3'" H6 SING N N 27 XY7 "O3'" H7 SING N N 28 XY7 "C4'" H8 SING N N 29 XY7 "C5'" H9 SING N N 30 XY7 "C5'" H10 SING N N 31 XY7 OP1 H11 SING N N 32 XY7 OP2 H12 SING N N 33 # # 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 XY7 SMILES ACDLabs 12.01 "C2(NC(=O)N(C1OC(C(C1F)O)COP(O)O)C=C2)=O" XY7 InChI InChI 1.03 "InChI=1S/C9H12FN2O7P/c10-6-7(14)4(3-18-20(16)17)19-8(6)12-2-1-5(13)11-9(12)15/h1-2,4,6-8,14,16-17H,3H2,(H,11,13,15)/t4-,6-,7-,8-/m0/s1" XY7 InChIKey InChI 1.03 SAPVPALVILMUHE-PSQAKQOGSA-N XY7 SMILES_CANONICAL CACTVS 3.385 "O[C@@H]1[C@H](F)[C@H](O[C@H]1COP(O)O)N2C=CC(=O)NC2=O" XY7 SMILES CACTVS 3.385 "O[CH]1[CH](F)[CH](O[CH]1COP(O)O)N2C=CC(=O)NC2=O" XY7 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)O)F" XY7 SMILES "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(O)O)O)F" # # 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 XY7 "SYSTEMATIC NAME" ACDLabs 12.01 "1-[2-deoxy-5-O-(dihydroxyphosphanyl)-2-fluoro-beta-L-ribofuranosyl]pyrimidine-2,4(1H,3H)-dione" XY7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{S},3~{S},4~{S},5~{S})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site XY7 "Create component" 2021-01-19 RCSB XY7 "Initial release" 2021-09-01 RCSB ##