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 
# 
