data_XCI # _chem_comp.id XCI _chem_comp.name "[(2~{S},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methylselanylphosphonous acid" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H15 N2 O6 P Se" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-07-05 _chem_comp.pdbx_modified_date 2019-11-01 _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 369.170 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XCI _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 6S7D _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 XCI SE1 SE1 SE 0 0 N N N 21.354 -14.005 10.530 2.745 -0.412 -0.711 SE1 XCI 1 XCI "C1'" C1 C 0 1 N N R 20.738 -12.692 14.489 -1.695 1.035 -0.869 "C1'" XCI 2 XCI C2 C2 C 0 1 N N N 21.484 -10.455 14.968 -2.818 -0.147 0.934 C2 XCI 3 XCI "C2'" C3 C 0 1 N N N 19.216 -12.644 14.347 -1.633 2.398 -0.154 "C2'" XCI 4 XCI "C3'" C4 C 0 1 N N S 19.002 -13.330 13.007 -0.224 2.426 0.488 "C3'" XCI 5 XCI C4 C5 C 0 1 N N N 23.145 -9.328 13.566 -4.880 -1.208 0.652 C4 XCI 6 XCI "C4'" C6 C 0 1 N N S 20.058 -14.417 13.106 0.538 1.372 -0.355 "C4'" XCI 7 XCI C5 C7 C 0 1 N N N 23.102 -10.443 12.660 -4.898 -0.789 -0.700 C5 XCI 8 XCI "C5'" C8 C 0 1 N N N 20.445 -15.142 11.840 1.713 0.795 0.437 "C5'" XCI 9 XCI C6 C9 C 0 1 N N N 22.337 -11.487 12.990 -3.862 -0.068 -1.178 C6 XCI 10 XCI C7 C10 C 0 1 N N N 23.997 -10.430 11.463 -6.055 -1.150 -1.596 C7 XCI 11 XCI N1 N1 N 0 1 N N N 21.530 -11.511 14.104 -2.819 0.251 -0.351 N1 XCI 12 XCI N3 N2 N 0 1 N N N 22.267 -9.396 14.619 -3.835 -0.873 1.435 N3 XCI 13 XCI O2 O1 O 0 1 N N N 20.779 -10.441 15.946 -1.882 0.147 1.652 O2 XCI 14 XCI "O3'" O2 O 0 1 N N N 17.714 -13.912 12.768 0.373 3.717 0.351 "O3'" XCI 15 XCI O4 O3 O 0 1 N N N 23.750 -8.297 13.361 -5.802 -1.863 1.105 O4 XCI 16 XCI "O4'" O4 O 0 1 N N N 21.183 -13.784 13.727 -0.457 0.355 -0.601 "O4'" XCI 17 XCI OP1 O5 O 0 1 N N N 23.675 -15.038 8.712 5.239 -2.081 -0.201 OP1 XCI 18 XCI OP2 O6 O 0 1 N N N 22.192 -16.765 9.671 5.319 0.217 0.787 OP2 XCI 19 XCI P P1 P 0 1 N N N 22.906 -15.533 9.796 4.373 -1.085 0.721 P XCI 20 XCI "H1'" H1 H 0 1 N N N 20.951 -12.900 15.548 -1.811 1.184 -1.942 "H1'" XCI 21 XCI "H2''" H2 H 0 0 N N N 18.849 -11.607 14.328 -1.741 3.211 -0.872 "H2''" XCI 22 XCI "H2'" H3 H 0 1 N N N 18.721 -13.194 15.161 -2.405 2.463 0.613 "H2'" XCI 23 XCI "H3'" H4 H 0 1 N N N 19.268 -12.636 12.196 -0.268 2.128 1.536 "H3'" XCI 24 XCI "H4'" H5 H 0 1 N N N 19.670 -15.175 13.803 0.882 1.806 -1.293 "H4'" XCI 25 XCI "H5'" H6 H 0 1 N N N 19.532 -15.544 11.377 1.335 0.243 1.298 "H5'" XCI 26 XCI "H5''" H7 H 0 0 N N N 21.117 -15.971 12.106 2.354 1.607 0.780 "H5''" XCI 27 XCI H6 H8 H 0 1 N N N 22.353 -12.357 12.350 -3.858 0.261 -2.207 H6 XCI 28 XCI H72 H9 H 0 1 N N N 24.520 -9.464 11.406 -5.854 -2.105 -2.082 H72 XCI 29 XCI H73 H10 H 0 1 N N N 24.734 -11.242 11.548 -6.964 -1.230 -1.001 H73 XCI 30 XCI H71 H11 H 0 1 N N N 23.395 -10.575 10.554 -6.183 -0.377 -2.353 H71 XCI 31 XCI H3 H12 H 0 1 N N N 22.194 -8.580 15.192 -3.816 -1.156 2.362 H3 XCI 32 XCI H1 H13 H 0 1 N N N 17.061 -13.224 12.708 -0.068 4.410 0.860 H1 XCI 33 XCI H2 H14 H 0 1 N N N 24.081 -14.216 8.961 5.997 -2.476 0.251 H2 XCI 34 XCI H4 H15 H 0 1 N N N 21.733 -16.949 10.482 4.954 0.942 1.312 H4 XCI 35 # # 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 XCI OP1 P SING N N 1 XCI OP2 P SING N N 2 XCI P SE1 SING N N 3 XCI SE1 "C5'" SING N N 4 XCI C7 C5 SING N N 5 XCI "C5'" "C4'" SING N N 6 XCI C5 C6 DOUB N N 7 XCI C5 C4 SING N N 8 XCI "O3'" "C3'" SING N N 9 XCI C6 N1 SING N N 10 XCI "C3'" "C4'" SING N N 11 XCI "C3'" "C2'" SING N N 12 XCI "C4'" "O4'" SING N N 13 XCI O4 C4 DOUB N N 14 XCI C4 N3 SING N N 15 XCI "O4'" "C1'" SING N N 16 XCI N1 "C1'" SING N N 17 XCI N1 C2 SING N N 18 XCI "C2'" "C1'" SING N N 19 XCI N3 C2 SING N N 20 XCI C2 O2 DOUB N N 21 XCI "C1'" "H1'" SING N N 22 XCI "C2'" "H2''" SING N N 23 XCI "C2'" "H2'" SING N N 24 XCI "C3'" "H3'" SING N N 25 XCI "C4'" "H4'" SING N N 26 XCI "C5'" "H5'" SING N N 27 XCI "C5'" "H5''" SING N N 28 XCI C6 H6 SING N N 29 XCI C7 H72 SING N N 30 XCI C7 H73 SING N N 31 XCI C7 H71 SING N N 32 XCI N3 H3 SING N N 33 XCI "O3'" H1 SING N N 34 XCI OP1 H2 SING N N 35 XCI OP2 H4 SING N N 36 # # 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 XCI InChI InChI 1.03 "InChI=1S/C10H15N2O6PSe/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(18-8)4-20-19(16)17/h3,6-8,13,16-17H,2,4H2,1H3,(H,11,14,15)/t6-,7+,8+/m0/s1" XCI InChIKey InChI 1.03 HCHHJSSYSFJUHX-XLPZGREQSA-N XCI SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](C[Se]P(O)O)O2)C(=O)NC1=O" XCI SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](C[Se]P(O)O)O2)C(=O)NC1=O" XCI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)C[Se]P(O)O)O" XCI SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)C[Se]P(O)O)O" # _pdbx_chem_comp_identifier.comp_id XCI _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~{S},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methylselanylphosphonous acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site XCI "Create component" 2019-07-05 EBI XCI "Initial release" 2019-11-06 RCSB ##