data_YQS
# 
_chem_comp.id                                    YQS 
_chem_comp.name                                  "[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H17 N2 O13 P3 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-03-23 
_chem_comp.pdbx_modified_date                    2022-07-01 
_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                        498.234 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YQS 
_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        7M4K 
_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 
YQS "C1'" C1  C 0 1 N N R -15.667 -7.396  18.264 3.983  -0.289 -1.367 "C1'" YQS 1  
YQS C2    C2  C 0 1 N N N -17.162 -9.337  18.511 5.064  0.289  0.732  C2    YQS 2  
YQS "C2'" C3  C 0 1 N N N -14.419 -7.465  19.166 4.503  -1.738 -1.427 "C2'" YQS 3  
YQS "C3'" C4  C 0 1 N N S -13.308 -7.254  18.159 3.353  -2.579 -0.819 "C3'" YQS 4  
YQS C4    C5  C 0 1 N N N -16.842 -11.334 17.205 6.590  2.049  0.919  C4    YQS 5  
YQS "C4'" C6  C 0 1 N N R -13.930 -6.197  17.256 2.136  -1.634 -0.986 "C4'" YQS 6  
YQS C5    C7  C 0 1 N N N -15.731 -10.713 16.551 6.432  2.317  -0.462 C5    YQS 7  
YQS "C5'" C8  C 0 1 N N N -13.265 -6.083  15.884 1.051  -1.966 0.040  "C5'" YQS 8  
YQS C5M   C9  C 0 1 N N N -14.962 -11.470 15.493 7.195  3.443  -1.112 C5M   YQS 9  
YQS C6    C10 C 0 1 N N N -15.375 -9.468  16.905 5.586  1.556  -1.187 C6    YQS 10 
YQS N1    N1  N 0 1 N N N -16.071 -8.771  17.878 4.901  0.538  -0.581 N1    YQS 11 
YQS N3    N2  N 0 1 N N N -17.622 -10.585 18.166 5.897  1.036  1.479  N3    YQS 12 
YQS O1A   O1  O 0 1 N N N -11.462 -6.742  13.542 -1.101 -1.033 2.105  O1A   YQS 13 
YQS O1B   O2  O 0 1 N N N -9.218  -6.271  16.053 -4.755 -0.891 0.967  O1B   YQS 14 
YQS O1G   O3  O 0 1 N N N -8.571  -7.793  13.450 -7.102 0.483  -0.461 O1G   YQS 15 
YQS O2    O4  O 0 1 N N N -17.737 -8.699  19.380 4.446  -0.621 1.250  O2    YQS 16 
YQS O2B   O5  O 0 1 N N N -9.802  -7.938  17.880 -3.856 1.233  1.991  O2B   YQS 17 
YQS O2G   O6  O 0 1 N N N -6.360  -7.953  14.558 -6.558 2.887  0.085  O2G   YQS 18 
YQS "O3'" O7  O 0 1 N N N -12.094 -6.816  18.830 3.163  -3.789 -1.554 "O3'" YQS 19 
YQS O3A   O8  O 0 1 N N N -10.876 -8.298  15.635 -2.479 -0.114 0.201  O3A   YQS 20 
YQS O3B   O9  O 0 1 N N N -8.333  -8.614  15.918 -4.670 1.156  -0.508 O3B   YQS 21 
YQS O3G   O10 O 0 1 N N N -7.662  -10.030 14.018 -6.348 1.957  -2.366 O3G   YQS 22 
YQS O4    O11 O 0 1 N N N -17.197 -12.471 16.946 7.344  2.725  1.595  O4    YQS 23 
YQS "O4'" O12 O 0 1 N N N -15.323 -6.613  17.120 2.691  -0.324 -0.738 "O4'" YQS 24 
YQS "O5'" O13 O 0 1 N N N -13.272 -7.349  15.234 -0.103 -1.161 -0.209 "O5'" YQS 25 
YQS PA    P1  P 0 1 N N S -11.921 -7.829  14.469 -1.441 -1.247 0.681  PA    YQS 26 
YQS PB    P2  P 0 1 N N N -9.552  -7.704  16.376 -3.957 0.319  0.669  PB    YQS 27 
YQS PG    P3  P 0 1 N N N -7.731  -8.578  14.435 -6.189 1.596  -0.805 PG    YQS 28 
YQS S2A   S1  S 0 1 N N N -12.362 -9.407  13.505 -2.325 -3.160 0.446  S2A   YQS 29 
YQS H1    H1  H 0 1 N N N -16.483 -6.916  18.824 3.893  0.114  -2.376 H1    YQS 30 
YQS H2    H2  H 0 1 N N N -14.333 -8.444  19.660 4.688  -2.035 -2.459 H2    YQS 31 
YQS H3    H3  H 0 1 N N N -14.428 -6.670  19.927 5.410  -1.843 -0.832 H3    YQS 32 
YQS H4    H4  H 0 1 N N N -13.132 -8.179  17.590 3.541  -2.791 0.233  H4    YQS 33 
YQS H5    H5  H 0 1 N N N -13.879 -5.220  17.760 1.738  -1.696 -1.999 H5    YQS 34 
YQS H6    H6  H 0 1 N N N -12.226 -5.744  16.010 0.784  -3.020 -0.043 H6    YQS 35 
YQS H7    H7  H 0 1 N N N -13.817 -5.355  15.271 1.426  -1.764 1.043  H7    YQS 36 
YQS H8    H8  H 0 1 N N N -15.412 -12.464 15.352 6.611  4.360  -1.052 H8    YQS 37 
YQS H9    H9  H 0 1 N N N -14.998 -10.914 14.545 8.146  3.582  -0.598 H9    YQS 38 
YQS H10   H10 H 0 1 N N N -13.915 -11.583 15.811 7.381  3.199  -2.158 H10   YQS 39 
YQS H11   H11 H 0 1 N N N -14.530 -9.001  16.422 5.453  1.746  -2.242 H11   YQS 40 
YQS H12   H12 H 0 1 N N N -18.460 -10.960 18.562 5.999  0.846  2.425  H12   YQS 41 
YQS H13   H13 H 0 1 N N N -9.699  -7.119  18.350 -3.345 2.045  1.869  H13   YQS 42 
YQS H14   H14 H 0 1 N N N -6.306  -7.193  13.990 -5.998 3.657  -0.089 H14   YQS 43 
YQS H15   H15 H 0 1 N N N -11.761 -7.520  19.374 3.933  -4.375 -1.555 H15   YQS 44 
YQS H16   H16 H 0 1 N N N -8.162  -10.155 13.220 -7.240 2.232  -2.617 H16   YQS 45 
YQS H17   H17 H 0 1 N N N -12.121 -9.050  12.278 -2.577 -3.216 -0.874 H17   YQS 46 
# 
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 
YQS O1G   PG    DOUB N N 1  
YQS S2A   PA    SING N N 2  
YQS O1A   PA    DOUB N N 3  
YQS O3G   PG    SING N N 4  
YQS PG    O2G   SING N N 5  
YQS PG    O3B   SING N N 6  
YQS PA    "O5'" SING N N 7  
YQS PA    O3A   SING N N 8  
YQS "O5'" "C5'" SING N N 9  
YQS C5M   C5    SING N N 10 
YQS O3A   PB    SING N N 11 
YQS "C5'" "C4'" SING N N 12 
YQS O3B   PB    SING N N 13 
YQS O1B   PB    DOUB N N 14 
YQS PB    O2B   SING N N 15 
YQS C5    C6    DOUB N N 16 
YQS C5    C4    SING N N 17 
YQS C6    N1    SING N N 18 
YQS O4    C4    DOUB N N 19 
YQS "O4'" "C4'" SING N N 20 
YQS "O4'" "C1'" SING N N 21 
YQS C4    N3    SING N N 22 
YQS "C4'" "C3'" SING N N 23 
YQS N1    "C1'" SING N N 24 
YQS N1    C2    SING N N 25 
YQS "C3'" "O3'" SING N N 26 
YQS "C3'" "C2'" SING N N 27 
YQS N3    C2    SING N N 28 
YQS "C1'" "C2'" SING N N 29 
YQS C2    O2    DOUB N N 30 
YQS "C1'" H1    SING N N 31 
YQS "C2'" H2    SING N N 32 
YQS "C2'" H3    SING N N 33 
YQS "C3'" H4    SING N N 34 
YQS "C4'" H5    SING N N 35 
YQS "C5'" H6    SING N N 36 
YQS "C5'" H7    SING N N 37 
YQS C5M   H8    SING N N 38 
YQS C5M   H9    SING N N 39 
YQS C5M   H10   SING N N 40 
YQS C6    H11   SING N N 41 
YQS N3    H12   SING N N 42 
YQS O2B   H13   SING N N 43 
YQS O2G   H14   SING N N 44 
YQS "O3'" H15   SING N N 45 
YQS O3G   H16   SING N N 46 
YQS S2A   H17   SING N N 47 
# 
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 
YQS InChI            InChI                1.03  "InChI=1S/C10H17N2O13P3S/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(23-8)4-22-28(21,29)25-27(19,20)24-26(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,29)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+,28-/m0/s1" 
YQS InChIKey         InChI                1.03  PXHHTOSRELKWOE-ISVKTPMGSA-N                                                                                                                                                                       
YQS SMILES_CANONICAL CACTVS               3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](S)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                                
YQS SMILES           CACTVS               3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](S)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                                      
YQS SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@@](=O)(OP(=O)(O)OP(=O)(O)O)S)O"                                                                                                                    
YQS SMILES           "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(OP(=O)(O)OP(=O)(O)O)S)O"                                                                                                                                     
# 
_pdbx_chem_comp_identifier.comp_id           YQS 
_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~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono 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 
YQS "Create component" 2021-03-23 RCSB 
YQS "Initial release"  2022-07-06 RCSB 
# 
