data_VSN # _chem_comp.id VSN _chem_comp.name "5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]guanosine" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N5 O10 P2 S" _chem_comp.mon_nstd_parent_comp_id G _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-09-16 _chem_comp.pdbx_modified_date 2023-11-17 _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 459.266 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VSN _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 8SQJ _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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 VSN "C3'" C1 C 0 1 N N S N N N 142.735 138.488 140.688 -1.013 -2.787 -0.486 "C3'" VSN 1 VSN "C4'" C2 C 0 1 N N R N N N 143.924 139.080 139.897 -0.095 -1.737 0.170 "C4'" VSN 2 VSN "C5'" C3 C 0 1 N N N N N N 145.064 138.347 140.117 1.159 -1.537 -0.682 "C5'" VSN 3 VSN "C1'" C4 C 0 1 N N R N N N 142.335 138.435 138.327 -2.241 -0.864 0.288 "C1'" VSN 4 VSN "C2'" C5 C 0 1 N N R N N N 142.119 137.700 139.812 -2.347 -2.036 -0.720 "C2'" VSN 5 VSN C8 C6 C 0 1 Y N N N N N 143.239 136.715 136.798 -2.678 1.302 -0.934 C8 VSN 6 VSN C5 C7 C 0 1 Y N N N N N 141.442 136.076 135.807 -4.755 1.668 -0.436 C5 VSN 7 VSN C4 C8 C 0 1 Y N N N N N 141.119 137.054 136.706 -4.385 0.470 0.185 C4 VSN 8 VSN C2 C9 C 0 1 N N N N N N 138.880 136.893 136.101 -6.507 0.250 1.073 C2 VSN 9 VSN C6 C10 C 0 1 N N N N N N 140.388 135.510 135.037 -6.079 2.138 -0.268 C6 VSN 10 VSN N9 N1 N 0 1 Y N N N N N 142.250 137.426 137.302 -3.072 0.264 -0.139 N9 VSN 11 VSN N7 N2 N 0 1 Y N N N N N 142.763 135.890 135.887 -3.670 2.126 -1.107 N7 VSN 12 VSN N3 N3 N 0 1 N N N N N N 139.832 137.451 136.844 -5.281 -0.199 0.921 N3 VSN 13 VSN N2 N4 N 0 1 N N N N N N 137.502 137.348 136.274 -7.390 -0.470 1.837 N2 VSN 14 VSN N1 N5 N 0 1 N N N N N N 139.146 135.940 135.213 -6.927 1.408 0.491 N1 VSN 15 VSN "O3'" O1 O 0 1 N N N N N N 141.819 139.572 141.130 -1.211 -3.897 0.392 "O3'" VSN 16 VSN "O5'" O2 O 0 1 N N N N N N 145.952 138.571 139.023 2.056 -0.651 -0.009 "O5'" VSN 17 VSN OP2 O3 O 0 1 N N N N N N 148.557 138.676 138.805 3.251 0.642 -1.962 OP2 VSN 18 VSN OP3 O4 O 0 1 N N N N N N 147.551 136.921 140.453 4.275 0.678 0.459 OP3 VSN 19 VSN O3B O5 O 0 1 N N N N N N 146.896 134.809 142.017 6.227 2.021 -0.682 O3B VSN 20 VSN O2B O6 O 0 1 N N N N N N 146.955 134.519 139.334 5.964 2.051 1.934 O2B VSN 21 VSN OP1 O7 O 0 1 N N N N N N 147.362 136.702 137.859 4.272 -1.426 -0.936 OP1 VSN 22 VSN "O4'" O8 O 0 1 N N N N N N 143.512 138.970 138.344 -0.837 -0.508 0.245 "O4'" VSN 23 VSN "O2'" O9 O 0 1 N N N N N N 140.735 137.619 140.120 -3.464 -2.872 -0.414 "O2'" VSN 24 VSN O6 O10 O 0 1 N N N N N N 140.619 134.639 134.220 -6.446 3.174 -0.795 O6 VSN 25 VSN P P1 P 0 1 N N N N N N 147.393 137.707 139.004 3.481 -0.216 -0.619 P VSN 26 VSN PB P2 P 0 1 N N N N N N 147.664 135.266 140.634 5.807 1.153 0.607 PB VSN 27 VSN S1B S1 S 0 1 N N N N N N 149.507 134.757 140.734 6.911 -0.343 0.735 S1B VSN 28 VSN "H3'" H1 H 0 1 N N N N N N 143.116 137.936 141.559 -0.592 -3.122 -1.434 "H3'" VSN 29 VSN "H4'" H2 H 0 1 N N N N N N 144.052 140.141 140.158 0.185 -2.065 1.171 "H4'" VSN 30 VSN "H5'" H3 H 0 1 N N N N N N 144.813 137.278 140.181 1.648 -2.498 -0.840 "H5'" VSN 31 VSN "H5''" H4 H 0 0 N N N N N N 145.539 138.669 141.055 0.880 -1.109 -1.645 "H5''" VSN 32 VSN "H1'" H5 H 0 1 N N N N N N 141.531 139.175 138.204 -2.523 -1.193 1.288 "H1'" VSN 33 VSN "H2'" H6 H 0 1 N N N N N N 142.570 136.698 139.758 -2.409 -1.665 -1.743 "H2'" VSN 34 VSN H8 H7 H 0 1 N N N N N N 144.277 136.796 137.086 -1.690 1.423 -1.352 H8 VSN 35 VSN H22 H8 H 0 1 N N N N N N 137.292 138.064 136.940 -7.106 -1.298 2.257 H22 VSN 36 VSN H21 H9 H 0 1 N N N N N N 136.769 136.943 135.727 -8.298 -0.152 1.958 H21 VSN 37 VSN HOP3 H10 H 0 0 N N N N N N 138.403 135.544 134.673 -7.840 1.710 0.620 HOP3 VSN 38 VSN "HO3'" H11 H 0 0 N N N N N N 142.266 140.130 141.755 -1.804 -4.575 0.040 "HO3'" VSN 39 VSN HOP2 H12 H 0 0 N N N N N N 149.023 138.453 138.008 2.738 1.451 -1.829 HOP2 VSN 40 VSN HOB3 H13 H 0 0 N N N N N N 147.515 134.381 142.597 5.693 2.817 -0.811 HOB3 VSN 41 VSN HOB2 H14 H 0 0 N N N N N N 146.956 135.109 138.590 6.863 2.372 2.087 HOB2 VSN 42 VSN "HO2'" H15 H 0 0 N N N N N N 140.622 137.200 140.965 -3.573 -3.620 -1.017 "HO2'" VSN 43 # 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 VSN O6 C6 DOUB N N 1 VSN C6 N1 SING N N 2 VSN C6 C5 SING N N 3 VSN N1 C2 SING N N 4 VSN C5 N7 SING Y N 5 VSN C5 C4 DOUB Y N 6 VSN N7 C8 DOUB Y N 7 VSN C2 N2 SING N N 8 VSN C2 N3 DOUB N N 9 VSN C4 N3 SING N N 10 VSN C4 N9 SING Y N 11 VSN C8 N9 SING Y N 12 VSN N9 "C1'" SING N N 13 VSN OP1 P DOUB N N 14 VSN "C1'" "O4'" SING N N 15 VSN "C1'" "C2'" SING N N 16 VSN "O4'" "C4'" SING N N 17 VSN OP2 P SING N N 18 VSN P "O5'" SING N N 19 VSN P OP3 SING N N 20 VSN "O5'" "C5'" SING N N 21 VSN O2B PB SING N N 22 VSN "C2'" "O2'" SING N N 23 VSN "C2'" "C3'" SING N N 24 VSN "C4'" "C5'" SING N N 25 VSN "C4'" "C3'" SING N N 26 VSN OP3 PB SING N N 27 VSN PB S1B DOUB N N 28 VSN PB O3B SING N N 29 VSN "C3'" "O3'" SING N N 30 VSN "C3'" "H3'" SING N N 31 VSN "C4'" "H4'" SING N N 32 VSN "C5'" "H5'" SING N N 33 VSN "C5'" "H5''" SING N N 34 VSN "C1'" "H1'" SING N N 35 VSN "C2'" "H2'" SING N N 36 VSN C8 H8 SING N N 37 VSN N2 H22 SING N N 38 VSN N2 H21 SING N N 39 VSN N1 HOP3 SING N N 40 VSN "O3'" "HO3'" SING N N 41 VSN OP2 HOP2 SING N N 42 VSN O3B HOB3 SING N N 43 VSN O2B HOB2 SING N N 44 VSN "O2'" "HO2'" SING N N 45 # 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 VSN SMILES ACDLabs 12.01 "OP(O)(=S)OP(=O)(O)OCC1OC(n2cnc3c2N=C(N)NC3=O)C(O)C1O" VSN InChI InChI 1.06 "InChI=1S/C10H15N5O10P2S/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(24-9)1-23-26(19,20)25-27(21,22)28/h2-3,5-6,9,16-17H,1H2,(H,19,20)(H2,21,22,28)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1" VSN InChIKey InChI 1.06 QJXJXBXFIOTYHB-UUOKFMHZSA-N VSN SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O" VSN SMILES CACTVS 3.385 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O" VSN SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=S)(O)O)O)O)N=C(NC2=O)N" VSN SMILES "OpenEye OEToolkits" 2.0.7 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=S)(O)O)O)O)N=C(NC2=O)N" # 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 VSN "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]guanosine" VSN "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl bis(oxidanyl)phosphinothioyl hydrogen 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 VSN "Create component" 2023-09-16 RCSB VSN "Initial release" 2023-11-22 RCSB #