data_TC # _chem_comp.id TC _chem_comp.name "4-azanyl-1-[(2~{R},3~{R},4~{S})-3-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-oxolan-2-yl]pyrimidin-2-one" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C8 H11 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id C _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-10-23 _chem_comp.pdbx_modified_date 2019-05-30 _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 292.163 _chem_comp.one_letter_code ? _chem_comp.three_letter_code TC _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 6MU5 _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 TC "C1'" C1 C 0 1 N N R -36.757 -19.496 18.406 0.929 -1.702 -0.236 "C1'" TC 1 TC C2 C2 C 0 1 N N N -34.843 -20.556 19.430 1.735 0.590 -0.370 C2 TC 2 TC "C2'" C3 C 0 1 N N R -38.049 -18.846 18.713 -0.194 -1.424 0.781 "C2'" TC 3 TC "C3'" C4 C 0 1 N N S -37.854 -17.455 18.568 -1.457 -1.226 -0.093 "C3'" TC 4 TC C4 C5 C 0 1 N N N -34.269 -20.217 21.772 3.903 1.194 0.154 C4 TC 5 TC "C4'" C6 C 0 1 N N N -36.511 -17.215 17.945 -1.052 -1.932 -1.412 "C4'" TC 6 TC C5 C7 C 0 1 N N N -35.411 -19.361 21.907 4.203 -0.152 0.452 C5 TC 7 TC C6 C8 C 0 1 N N N -36.233 -19.132 20.798 3.231 -1.085 0.322 C6 TC 8 TC N1 N1 N 0 1 N N N -35.959 -19.729 19.551 1.990 -0.702 -0.092 N1 TC 9 TC N3 N2 N 0 1 N N N -33.997 -20.793 20.567 2.681 1.519 -0.247 N3 TC 10 TC N4 N3 N 0 1 N N N -33.407 -20.468 22.912 4.872 2.162 0.277 N4 TC 11 TC O1P O1 O 0 1 N N N -39.044 -15.445 21.518 -4.170 0.506 -0.772 O1P TC 12 TC O2 O2 O 0 1 N N N -34.557 -21.155 18.200 0.620 0.914 -0.744 O2 TC 13 TC "O2'" O3 O 0 1 N N N -38.862 -19.151 17.899 -0.360 -2.538 1.660 "O2'" TC 14 TC O2P O4 O 0 1 N N N -39.228 -14.905 19.222 -3.414 0.471 1.523 O2P TC 15 TC "O3'" O5 O 0 1 N N N -37.917 -16.941 19.897 -1.711 0.162 -0.315 "O3'" TC 16 TC "O4'" O6 O 0 1 N N N -35.950 -18.554 17.507 0.350 -1.614 -1.548 "O4'" TC 17 TC P P1 P 0 1 N N N -38.297 -15.437 20.241 -3.073 0.888 0.145 P TC 18 TC H1 H1 H 0 1 N N N -36.937 -20.436 17.865 1.337 -2.700 -0.075 H1 TC 19 TC H2 H2 H 0 1 N N N -38.337 -19.083 19.748 0.021 -0.519 1.350 H2 TC 20 TC H3 H3 H 0 1 N N N -38.640 -17.010 17.940 -2.322 -1.711 0.359 H3 TC 21 TC H4 H4 H 0 1 N N N -35.837 -16.750 18.679 -1.195 -3.010 -1.330 H4 TC 22 TC H5 H5 H 0 1 N N N -36.617 -16.552 17.074 -1.622 -1.534 -2.251 H5 TC 23 TC H6 H6 H 0 1 N N N -35.635 -18.897 22.856 5.193 -0.433 0.779 H6 TC 24 TC H7 H7 H 0 1 N N N -37.093 -18.486 20.899 3.436 -2.122 0.545 H7 TC 25 TC H8 H8 H 0 1 N N N -32.611 -21.065 22.815 5.764 1.921 0.570 H8 TC 26 TC H9 H9 H 0 1 N N N -33.609 -20.044 23.795 4.662 3.087 0.071 H9 TC 27 TC H11 H11 H 0 1 N N N -39.689 -18.730 18.103 -1.055 -2.417 2.321 H11 TC 28 TC O3P O3P O 0 1 N Y N -36.874 -14.707 20.361 -2.870 2.485 0.102 O3P TC 29 TC H10 H10 H 0 1 N N N -36.750 -14.397 21.251 -3.652 2.988 0.367 H10 TC 30 # # 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 TC "O4'" "C4'" SING N N 1 TC "O4'" "C1'" SING N N 2 TC "O2'" "C2'" SING N N 3 TC "C4'" "C3'" SING N N 4 TC O2 C2 DOUB N N 5 TC "C1'" "C2'" SING N N 6 TC "C1'" N1 SING N N 7 TC "C3'" "C2'" SING N N 8 TC "C3'" "O3'" SING N N 9 TC O2P P DOUB N N 10 TC C2 N1 SING N N 11 TC C2 N3 SING N N 12 TC N1 C6 SING N N 13 TC "O3'" P SING N N 14 TC P O1P DOUB N N 15 TC N3 C4 DOUB N N 16 TC C6 C5 DOUB N N 17 TC C4 C5 SING N N 18 TC C4 N4 SING N N 19 TC "C1'" H1 SING N N 20 TC "C2'" H2 SING N N 21 TC "C3'" H3 SING N N 22 TC "C4'" H4 SING N N 23 TC "C4'" H5 SING N N 24 TC C5 H6 SING N N 25 TC C6 H7 SING N N 26 TC N4 H8 SING N N 27 TC N4 H9 SING N N 28 TC "O2'" H11 SING N N 29 TC P O3P SING N N 30 TC O3P H10 SING N N 31 # # 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 TC InChI InChI 1.03 "InChI=1S/C8H11N3O7P/c9-5-1-2-11(8(13)10-5)7-6(12)4(3-17-7)18-19(14,15)16/h1-2,4,6-7,12H,3H2,(H2,9,10,13)(H,14,15,16)/t4-,6+,7+/m0/s1" TC InChIKey InChI 1.03 QZXAIPJUSZWLSS-UBKIQSJTSA-N TC SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@@H]2OC[C@H](O[P](O)(=O)=O)[C@H]2O" TC SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2OC[CH](O[P](O)(=O)=O)[CH]2O" TC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1[C@@H]([C@H]([C@@H](O1)N2C=CC(=NC2=O)N)O)OP(=O)(=O)O" TC SMILES "OpenEye OEToolkits" 2.0.6 "C1C(C(C(O1)N2C=CC(=NC2=O)N)O)OP(=O)(=O)O" # _pdbx_chem_comp_identifier.comp_id TC _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _pdbx_chem_comp_identifier.identifier "4-azanyl-1-[(2~{R},3~{R},4~{S})-3-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-oxolan-2-yl]pyrimidin-2-one" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site TC "Create component" 2018-10-23 RCSB TC "Initial release" 2019-06-05 RCSB ##