data_CVC # _chem_comp.id CVC _chem_comp.name "[(1~{R},5~{R},6~{R},8~{R})-6-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,3-bis(oxidanyl)-2,4,7-trioxa-3$l^{4}-vanadabicyclo[3.3.0]octan-8-yl]methyl dihydrogen phosphate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H14 N3 O10 P V" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-10-19 _chem_comp.pdbx_modified_date 2016-02-19 _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 406.137 _chem_comp.one_letter_code ? _chem_comp.three_letter_code CVC _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 5EAO _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 CVC O01 O1 O 0 1 N N N 102.534 17.930 -0.600 0.957 -1.847 -1.501 O01 CVC 1 CVC C02 C1 C 0 1 N N N 99.683 15.907 -1.503 3.333 -3.846 -0.080 C02 CVC 2 CVC P P1 P 0 1 N N N 103.022 11.245 0.676 -4.780 -0.622 0.039 P CVC 3 CVC "C5'" C2 C 0 1 N N N 104.835 12.741 1.811 -2.323 0.353 -0.349 "C5'" CVC 4 CVC "O5'" O2 O 0 1 N N N 104.190 12.307 0.642 -3.273 -0.294 0.500 "O5'" CVC 5 CVC "C4'" C3 C 0 1 N N R 104.803 14.238 1.869 -0.997 0.511 0.398 "C4'" CVC 6 CVC "O4'" O3 O 0 1 N N N 104.192 14.747 0.646 -0.366 -0.775 0.583 "O4'" CVC 7 CVC "C3'" C4 C 0 1 N N R 103.971 14.783 3.034 0.009 1.320 -0.455 "C3'" CVC 8 CVC "O3'" O4 O 0 1 N N N 104.688 15.824 3.679 -0.104 2.715 -0.090 "O3'" CVC 9 CVC "C2'" C5 C 0 1 N N R 102.709 15.308 2.342 1.360 0.655 -0.180 "C2'" CVC 10 CVC "O2'" O5 O 0 1 N N N 101.966 16.341 2.980 2.377 1.494 0.414 "O2'" CVC 11 CVC "C1'" C6 C 0 1 N N R 103.250 15.729 0.981 1.031 -0.486 0.810 "C1'" CVC 12 CVC C01 C7 C 0 1 N N N 100.050 14.578 -0.678 3.472 -3.225 1.178 C01 CVC 13 CVC N01 N1 N 0 1 N N N 100.484 16.982 -1.474 2.474 -3.354 -0.963 N01 CVC 14 CVC O1V O6 O 0 1 N N N 104.222 18.445 3.116 2.067 4.442 1.241 O1V CVC 15 CVC N02 N2 N 0 1 N N N 98.404 15.877 -2.335 4.089 -4.952 -0.393 N02 CVC 16 CVC O02 O7 O 0 1 N N N 101.836 11.756 1.464 -4.752 -1.696 -1.161 O02 CVC 17 CVC O2V O8 O 0 1 N N N 103.147 17.393 5.518 2.313 3.723 -1.706 O2V CVC 18 CVC N9 N3 N 0 1 N N N 102.137 15.748 0.047 1.850 -1.666 0.520 N9 CVC 19 CVC OP1 O9 O 0 1 N N N 103.615 9.965 1.225 -5.602 -1.230 1.283 OP1 CVC 20 CVC OP2 O10 O 0 1 N N N 102.587 11.233 -0.768 -5.436 0.620 -0.426 OP2 CVC 21 CVC V V1 V 0 1 N N N 103.477 17.264 3.937 1.711 3.184 -0.053 V CVC 22 CVC C4 C8 C 0 1 N N N 101.765 16.971 -0.661 1.741 -2.280 -0.673 C4 CVC 23 CVC C8 C9 C 0 1 N N N 101.208 14.579 0.067 2.720 -2.135 1.458 C8 CVC 24 CVC H1 H1 H 0 1 N N N 104.319 12.328 2.690 -2.166 -0.249 -1.244 H1 CVC 25 CVC H2 H2 H 0 1 N N N 105.879 12.396 1.804 -2.699 1.336 -0.633 H2 CVC 26 CVC H3 H3 H 0 1 N N N 105.831 14.619 1.958 -1.158 0.999 1.359 H3 CVC 27 CVC H4 H4 H 0 1 N N N 103.713 13.971 3.729 -0.234 1.199 -1.511 H4 CVC 28 CVC H5 H5 H 0 1 N N N 102.044 14.447 2.179 1.743 0.216 -1.102 H5 CVC 29 CVC H6 H6 H 0 1 N N N 103.713 16.724 1.056 1.189 -0.156 1.836 H6 CVC 30 CVC H7 H7 H 0 1 N N N 99.408 13.710 -0.707 4.167 -3.614 1.908 H7 CVC 31 CVC H8 H8 H 0 1 N N N 104.915 18.815 3.651 2.996 4.706 1.288 H8 CVC 32 CVC H9 H9 H 0 1 N N N 98.143 16.674 -2.879 3.994 -5.374 -1.261 H9 CVC 33 CVC H10 H10 H 0 1 N N N 97.827 15.060 -2.336 4.717 -5.309 0.254 H10 CVC 34 CVC H11 H11 H 0 1 N N N 101.118 11.942 0.871 -4.335 -2.536 -0.927 H11 CVC 35 CVC H12 H12 H 0 1 N N N 103.867 17.830 5.958 3.247 3.973 -1.723 H12 CVC 36 CVC H13 H13 H 0 1 N N N 103.628 9.304 0.543 -6.520 -1.452 1.077 H13 CVC 37 CVC H14 H14 H 0 1 N N N 101.448 13.720 0.676 2.809 -1.641 2.415 H14 CVC 38 # 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 CVC N02 C02 SING N N 1 CVC C02 N01 DOUB N N 2 CVC C02 C01 SING N N 3 CVC N01 C4 SING N N 4 CVC OP2 P DOUB N N 5 CVC C01 C8 DOUB N N 6 CVC C4 O01 DOUB N N 7 CVC C4 N9 SING N N 8 CVC N9 C8 SING N N 9 CVC N9 "C1'" SING N N 10 CVC "O5'" P SING N N 11 CVC "O5'" "C5'" SING N N 12 CVC "O4'" "C1'" SING N N 13 CVC "O4'" "C4'" SING N N 14 CVC P OP1 SING N N 15 CVC P O02 SING N N 16 CVC "C1'" "C2'" SING N N 17 CVC "C5'" "C4'" SING N N 18 CVC "C4'" "C3'" SING N N 19 CVC "C2'" "O2'" SING N N 20 CVC "C2'" "C3'" SING N N 21 CVC "O2'" V SING N N 22 CVC "C3'" "O3'" SING N N 23 CVC O1V V SING N N 24 CVC "O3'" V SING N N 25 CVC V O2V SING N N 26 CVC "C5'" H1 SING N N 27 CVC "C5'" H2 SING N N 28 CVC "C4'" H3 SING N N 29 CVC "C3'" H4 SING N N 30 CVC "C2'" H5 SING N N 31 CVC "C1'" H6 SING N N 32 CVC C01 H7 SING N N 33 CVC O1V H8 SING N N 34 CVC N02 H9 SING N N 35 CVC N02 H10 SING N N 36 CVC O02 H11 SING N N 37 CVC O2V H12 SING N N 38 CVC OP1 H13 SING N N 39 CVC C8 H14 SING N N 40 # 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 CVC InChI InChI 1.03 "InChI=1S/C9H12N3O8P.2H2O.V/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18;;;/h1-2,4,6-8H,3H2,(H2,10,11,15)(H2,16,17,18);2*1H2;/q-2;;;+4/p-2/t4-,6-,7-,8-;;;/m1.../s1" CVC InChIKey InChI 1.03 RQEDDOKDPWKVRD-LLWADOMFSA-L CVC SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@H]3O[V](O)(O)O[C@@H]23" CVC SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH]3O[V](O)(O)O[CH]23" CVC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "C1=CN(C(=O)N=C1N)[C@H]2[C@H]3[C@@H]([C@H](O2)COP(=O)(O)O)O[V](O3)(O)O" CVC SMILES "OpenEye OEToolkits" 2.0.4 "C1=CN(C(=O)N=C1N)C2C3C(C(O2)COP(=O)(O)O)O[V](O3)(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 CVC "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "[(1~{R},5~{R},6~{R},8~{R})-6-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,3-bis(oxidanyl)-2,4,7-trioxa-3$l^{4}-vanadabicyclo[3.3.0]octan-8-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 CVC "Create component" 2015-10-19 RCSB CVC "Create component" 2015-11-16 RCSB CVC "Initial release" 2016-02-24 RCSB #