data_XEC # _chem_comp.id XEC _chem_comp.name "1-(2-O-methyl-5-O-phosphono-beta-L-ribofuranosyl)pyrimidine-2,4(1H,3H)-dione" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-11-14 _chem_comp.pdbx_modified_date 2023-04-07 _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 338.208 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XEC _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 8F27 _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 XEC N1 N1 N 0 1 N N N 21.099 1.358 -7.711 2.199 -0.552 -0.338 N1 XEC 1 XEC C2 C1 C 0 1 N N N 21.514 2.259 -6.796 3.501 -0.215 -0.374 C2 XEC 2 XEC N3 N2 N 0 1 N N N 22.372 1.905 -5.809 4.457 -1.115 -0.076 N3 XEC 3 XEC C4 C2 C 0 1 N N N 22.887 0.634 -5.689 4.121 -2.375 0.265 C4 XEC 4 XEC C5 C3 C 0 1 N N N 22.492 -0.323 -6.670 2.755 -2.743 0.307 C5 XEC 5 XEC C6 C4 C 0 1 N N N 21.614 0.040 -7.668 1.817 -1.821 0.004 C6 XEC 6 XEC O2 O1 O 0 1 N N N 21.095 3.407 -6.840 3.819 0.917 -0.681 O2 XEC 7 XEC O4 O2 O 0 1 N N N 23.704 0.384 -4.791 4.985 -3.190 0.535 O4 XEC 8 XEC "C1'" C5 C 0 1 N N S 20.154 1.812 -8.801 1.181 0.450 -0.662 "C1'" XEC 9 XEC "C2'" C6 C 0 1 N N S 18.739 1.857 -8.361 1.278 1.648 0.308 "C2'" XEC 10 XEC "O2'" O3 O 0 1 N N N 17.883 2.698 -9.188 2.009 2.720 -0.291 "O2'" XEC 11 XEC CM2 C7 C 0 1 N N N 18.007 4.133 -8.943 2.721 3.532 0.645 CM2 XEC 12 XEC "C3'" C8 C 0 1 N N S 18.400 0.392 -8.602 -0.192 2.058 0.546 "C3'" XEC 13 XEC "C4'" C9 C 0 1 N N S 18.919 0.261 -10.013 -1.004 1.060 -0.308 "C4'" XEC 14 XEC "O3'" O4 O 0 1 N N N 17.001 0.233 -8.585 -0.417 3.397 0.100 "O3'" XEC 15 XEC "O4'" O5 O 0 1 N N N 20.253 0.855 -9.881 -0.141 -0.090 -0.451 "O4'" XEC 16 XEC "C5'" C10 C 0 1 N N N 19.032 -1.156 -10.542 -2.297 0.670 0.411 "C5'" XEC 17 XEC "O5'" O6 O 0 1 N N N 19.888 -1.834 -9.641 -3.052 -0.219 -0.413 "O5'" XEC 18 XEC P P1 P 0 1 N N N 20.423 -3.335 -10.019 -4.473 -0.833 0.030 P XEC 19 XEC OP1 O7 O 0 1 N N N 21.015 -3.915 -8.799 -4.330 -1.517 1.334 OP1 XEC 20 XEC OP2 O8 O 0 1 N N N 19.354 -4.065 -10.732 -5.552 0.355 0.162 OP2 XEC 21 XEC H1 H1 H 0 1 N N N 22.643 2.596 -5.139 5.391 -0.855 -0.107 H1 XEC 22 XEC H2 H2 H 0 1 N N N 22.880 -1.330 -6.631 2.467 -3.748 0.578 H2 XEC 23 XEC H3 H3 H 0 1 N N N 21.319 -0.680 -8.417 0.769 -2.083 0.031 H3 XEC 24 XEC H4 H4 H 0 1 N N N 20.461 2.808 -9.152 1.295 0.786 -1.693 H4 XEC 25 XEC H5 H5 H 0 1 N N N 18.656 2.110 -7.294 1.746 1.344 1.245 H5 XEC 26 XEC H6 H6 H 0 1 N N N 17.326 4.680 -9.611 3.250 4.323 0.111 H6 XEC 27 XEC H7 H7 H 0 1 N N N 17.747 4.350 -7.897 2.017 3.977 1.349 H7 XEC 28 XEC H8 H8 H 0 1 N N N 19.042 4.450 -9.136 3.439 2.918 1.188 H8 XEC 29 XEC H9 H9 H 0 1 N N N 18.930 -0.272 -7.903 -0.450 1.960 1.601 H9 XEC 30 XEC H10 H10 H 0 1 N N N 18.299 0.862 -10.694 -1.227 1.490 -1.285 H10 XEC 31 XEC H11 H11 H 0 1 N N N 16.683 0.317 -7.694 -1.325 3.707 0.226 H11 XEC 32 XEC H12 H12 H 0 1 N N N 18.043 -1.636 -10.566 -2.054 0.176 1.352 H12 XEC 33 XEC H13 H13 H 0 1 N N N 19.464 -1.154 -11.554 -2.884 1.566 0.613 H13 XEC 34 XEC H15 H15 H 0 1 N N N 19.169 -4.879 -10.279 -5.697 0.848 -0.657 H15 XEC 35 XEC OP3 O9 O 0 1 N Y N 21.624 -3.046 -11.097 -4.970 -1.889 -1.079 OP3 XEC 36 XEC H14 H14 H 0 1 N Y N 22.457 -3.309 -10.722 -5.823 -2.299 -0.877 H14 XEC 37 # 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 XEC OP2 P SING N N 1 XEC "C5'" "C4'" SING N N 2 XEC "C5'" "O5'" SING N N 3 XEC P "O5'" SING N N 4 XEC P OP1 DOUB N N 5 XEC "C4'" "O4'" SING N N 6 XEC "C4'" "C3'" SING N N 7 XEC "O4'" "C1'" SING N N 8 XEC "O2'" CM2 SING N N 9 XEC "O2'" "C2'" SING N N 10 XEC "C1'" "C2'" SING N N 11 XEC "C1'" N1 SING N N 12 XEC "C3'" "O3'" SING N N 13 XEC "C3'" "C2'" SING N N 14 XEC N1 C6 SING N N 15 XEC N1 C2 SING N N 16 XEC C6 C5 DOUB N N 17 XEC O2 C2 DOUB N N 18 XEC C2 N3 SING N N 19 XEC C5 C4 SING N N 20 XEC N3 C4 SING N N 21 XEC C4 O4 DOUB N N 22 XEC N3 H1 SING N N 23 XEC C5 H2 SING N N 24 XEC C6 H3 SING N N 25 XEC "C1'" H4 SING N N 26 XEC "C2'" H5 SING N N 27 XEC CM2 H6 SING N N 28 XEC CM2 H7 SING N N 29 XEC CM2 H8 SING N N 30 XEC "C3'" H9 SING N N 31 XEC "C4'" H10 SING N N 32 XEC "O3'" H11 SING N N 33 XEC "C5'" H12 SING N N 34 XEC "C5'" H13 SING N N 35 XEC OP2 H15 SING N N 36 XEC P OP3 SING N N 37 XEC OP3 H14 SING N N 38 # 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 XEC SMILES ACDLabs 12.01 "O=P(O)(O)OCC1OC(N2C=CC(=O)NC2=O)C(OC)C1O" XEC InChI InChI 1.06 "InChI=1S/C10H15N2O9P/c1-19-8-7(14)5(4-20-22(16,17)18)21-9(8)12-3-2-6(13)11-10(12)15/h2-3,5,7-9,14H,4H2,1H3,(H,11,13,15)(H2,16,17,18)/t5-,7-,8-,9-/m0/s1" XEC InChIKey InChI 1.06 FHMMECZNEPGJSJ-ZITKLIBNSA-N XEC SMILES_CANONICAL CACTVS 3.385 "CO[C@H]1[C@@H](O)[C@H](CO[P](O)(O)=O)O[C@@H]1N2C=CC(=O)NC2=O" XEC SMILES CACTVS 3.385 "CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)NC2=O" XEC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CO[C@H]1[C@H]([C@@H](O[C@@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O" XEC SMILES "OpenEye OEToolkits" 2.0.7 "COC1C(C(OC1N2C=CC(=O)NC2=O)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 XEC "SYSTEMATIC NAME" ACDLabs 12.01 "1-(2-O-methyl-5-O-phosphono-beta-L-ribofuranosyl)pyrimidine-2,4(1H,3H)-dione" XEC "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{S},3~{S},4~{S},5~{S})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-methoxy-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 XEC "Create component" 2022-11-14 RCSB XEC "Initial release" 2023-04-12 RCSB #