data_UOA # _chem_comp.id UOA _chem_comp.name "[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3-hydroxy-2,4-dimethoxytetrahydrofuran-2-yl]methyl dihydrogen phosphate (non-preferred name)" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H17 N2 O10 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-04-06 _chem_comp.pdbx_modified_date 2018-09-27 _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 368.234 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UOA _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 6CY2 _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 UOA "C''" C1 C 0 1 N N N 9.088 -7.603 -10.607 3.555 -2.356 1.239 "C''" UOA 1 UOA "C1'" C2 C 0 1 N N R 11.967 -7.467 -10.278 1.333 -0.821 -0.544 "C1'" UOA 2 UOA C2 C3 C 0 1 N N N 12.159 -5.174 -9.625 2.234 1.172 0.517 C2 UOA 3 UOA "C2'" C4 C 0 1 N N R 11.178 -7.594 -11.517 1.310 -1.667 0.755 "C2'" UOA 4 UOA "C3'" C5 C 0 1 N N S 12.169 -8.277 -12.430 -0.126 -2.244 0.741 "C3'" UOA 5 UOA C4 C6 C 0 1 N N N 14.209 -3.939 -9.692 4.178 2.228 -0.233 C4 UOA 6 UOA "C4'" C7 C 0 1 N N R 12.820 -9.271 -11.518 -0.906 -1.293 -0.189 "C4'" UOA 7 UOA C5 C8 C 0 1 N N N 14.880 -5.044 -10.219 4.302 1.253 -1.251 C5 UOA 8 UOA "C5'" C9 C 0 1 N N N 14.042 -9.941 -12.029 -2.085 -0.678 0.567 "C5'" UOA 9 UOA C6 C10 C 0 1 N N N 14.152 -6.210 -10.436 3.371 0.279 -1.345 C6 UOA 10 UOA CMC C11 C 0 1 N N N 12.149 -11.161 -10.063 -2.047 -1.194 -2.294 CMC UOA 11 UOA N1 N1 N 0 1 N N N 12.778 -6.245 -10.127 2.337 0.242 -0.449 N1 UOA 12 UOA N3 N2 N 0 1 N N N 12.865 -4.017 -9.404 3.142 2.159 0.627 N3 UOA 13 UOA O2 O1 O 0 1 N N N 10.959 -5.196 -9.354 1.305 1.122 1.300 O2 UOA 14 UOA "O2'" O2 O 0 1 N N N 10.020 -8.447 -11.241 2.281 -2.714 0.698 "O2'" UOA 15 UOA "O3'" O3 O 0 1 N N N 11.469 -8.917 -13.480 -0.127 -3.572 0.213 "O3'" UOA 16 UOA O4 O4 O 0 1 N N N 14.772 -2.871 -9.450 5.001 3.121 -0.134 O4 UOA 17 UOA "O4'" O5 O 0 1 N N N 12.971 -8.567 -10.276 0.004 -0.261 -0.604 "O4'" UOA 18 UOA "O5'" O6 O 0 1 N N N 14.999 -8.789 -12.141 -2.719 0.303 -0.256 "O5'" UOA 19 UOA OP1 O7 O 0 1 N N N 16.940 -10.040 -13.189 -4.526 2.062 -0.999 OP1 UOA 20 UOA OP2 O8 O 0 1 N N N 17.177 -7.641 -12.321 -5.075 0.228 0.646 OP2 UOA 21 UOA P P1 P 0 1 N N N 16.582 -8.998 -12.206 -4.000 1.153 0.221 P UOA 22 UOA OCM O9 O 0 1 N N N 11.856 -10.407 -11.352 -1.381 -2.011 -1.329 OCM UOA 23 UOA "H''" H1 H 0 1 N N N 8.180 -8.175 -10.365 4.235 -3.204 1.159 "H''" UOA 24 UOA H5X H2 H 0 1 N N N 9.527 -7.202 -9.681 3.961 -1.511 0.683 H5X UOA 25 UOA H5W H3 H 0 1 N N N 8.829 -6.772 -11.280 3.440 -2.080 2.287 H5W UOA 26 UOA "H1'" H4 H 0 1 N N N 11.304 -7.578 -9.407 1.524 -1.452 -1.412 "H1'" UOA 27 UOA "H2'" H5 H 0 1 N N N 10.880 -6.612 -11.914 1.469 -1.039 1.631 "H2'" UOA 28 UOA "H3'" H6 H 0 1 N N N 12.907 -7.554 -12.808 -0.552 -2.231 1.744 "H3'" UOA 29 UOA H5 H7 H 0 1 N N N 15.934 -4.995 -10.452 5.126 1.291 -1.949 H5 UOA 30 UOA H5S H8 H 0 1 N N N 13.862 -10.409 -13.008 -2.803 -1.460 0.819 H5S UOA 31 UOA "H5'" H9 H 0 1 N N N 14.409 -10.699 -11.322 -1.725 -0.207 1.482 "H5'" UOA 32 UOA H6 H10 H 0 1 N N N 14.639 -7.085 -10.840 3.449 -0.474 -2.115 H6 UOA 33 UOA HMC H11 H 0 1 N N N 11.436 -11.991 -9.953 -2.264 -1.785 -3.184 HMC UOA 34 UOA H5U H12 H 0 1 N N N 13.173 -11.560 -10.097 -2.980 -0.820 -1.871 H5U UOA 35 UOA H5V H13 H 0 1 N N N 12.050 -10.477 -9.207 -1.407 -0.354 -2.563 H5V UOA 36 UOA H3 H14 H 0 1 N N N 12.395 -3.218 -9.028 3.050 2.824 1.327 H3 UOA 37 UOA H1 H15 H 0 1 N N N 11.068 -8.262 -14.039 0.350 -4.212 0.758 H1 UOA 38 UOA H2 H16 H 0 1 N N N 17.554 -9.683 -13.820 -5.298 2.603 -0.782 H2 UOA 39 UOA OP3 OP3 O 0 1 N Y N 16.944 -9.639 -10.778 -3.587 2.099 1.457 OP3 UOA 40 UOA HOP3 HOP3 H 0 0 N Y N 17.471 -9.025 -10.279 -2.886 2.731 1.250 HOP3 UOA 41 # 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 UOA "O3'" "C3'" SING N N 1 UOA OP1 P SING N N 2 UOA "C3'" "C4'" SING N N 3 UOA "C3'" "C2'" SING N N 4 UOA OP2 P DOUB N N 5 UOA P "O5'" SING N N 6 UOA "O5'" "C5'" SING N N 7 UOA "C5'" "C4'" SING N N 8 UOA "C4'" OCM SING N N 9 UOA "C4'" "O4'" SING N N 10 UOA "C2'" "O2'" SING N N 11 UOA "C2'" "C1'" SING N N 12 UOA OCM CMC SING N N 13 UOA "O2'" "C''" SING N N 14 UOA C6 C5 DOUB N N 15 UOA C6 N1 SING N N 16 UOA "C1'" "O4'" SING N N 17 UOA "C1'" N1 SING N N 18 UOA C5 C4 SING N N 19 UOA N1 C2 SING N N 20 UOA C4 O4 DOUB N N 21 UOA C4 N3 SING N N 22 UOA C2 N3 SING N N 23 UOA C2 O2 DOUB N N 24 UOA "C''" "H''" SING N N 25 UOA "C''" H5X SING N N 26 UOA "C''" H5W SING N N 27 UOA "C1'" "H1'" SING N N 28 UOA "C2'" "H2'" SING N N 29 UOA "C3'" "H3'" SING N N 30 UOA C5 H5 SING N N 31 UOA "C5'" H5S SING N N 32 UOA "C5'" "H5'" SING N N 33 UOA C6 H6 SING N N 34 UOA CMC HMC SING N N 35 UOA CMC H5U SING N N 36 UOA CMC H5V SING N N 37 UOA N3 H3 SING N N 38 UOA "O3'" H1 SING N N 39 UOA OP1 H2 SING N N 40 UOA P OP3 SING N N 41 UOA OP3 HOP3 SING N N 42 # 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 UOA SMILES ACDLabs 12.01 "COC1C(OC(C1O)(OC)COP(O)(=O)O)N2C(NC(=O)C=C2)=O" UOA InChI InChI 1.03 "InChI=1S/C11H17N2O10P/c1-20-7-8(15)11(21-2,5-22-24(17,18)19)23-9(7)13-4-3-6(14)12-10(13)16/h3-4,7-9,15H,5H2,1-2H3,(H,12,14,16)(H2,17,18,19)/t7-,8+,9-,11-/m1/s1" UOA InChIKey InChI 1.03 PQPFDVLUCHRYPP-PKIKSRDPSA-N UOA SMILES_CANONICAL CACTVS 3.385 "CO[C@@H]1[C@H](O)[C@](CO[P](O)(O)=O)(OC)O[C@H]1N2C=CC(=O)NC2=O" UOA SMILES CACTVS 3.385 "CO[CH]1[CH](O)[C](CO[P](O)(O)=O)(OC)O[CH]1N2C=CC(=O)NC2=O" UOA SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CO[C@@H]1[C@@H]([C@](O[C@H]1N2C=CC(=O)NC2=O)(COP(=O)(O)O)OC)O" UOA SMILES "OpenEye OEToolkits" 2.0.6 "COC1C(C(OC1N2C=CC(=O)NC2=O)(COP(=O)(O)O)OC)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 UOA "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3-hydroxy-2,4-dimethoxytetrahydrofuran-2-yl]methyl dihydrogen phosphate (non-preferred name)" UOA "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-2,4-dimethoxy-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 UOA "Create component" 2018-04-06 RCSB UOA "Initial release" 2018-08-29 RCSB UOA "Modify atom id" 2018-09-27 RCSB #