data_YA4
#

_chem_comp.id                                   YA4
_chem_comp.name                                 "[(2~{R},3~{S},4~{S})-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphinic acid"
_chem_comp.type                                 "RNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C5 H11 O6 P S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-02-12
_chem_comp.pdbx_modified_date                   2021-07-30
_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                       230.176
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    YA4
_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       7LPJ
_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
YA4  "C1'"   C1   C  0  1  N  N  N  -149.244  -52.772  -68.581   3.204   1.489  -0.247  "C1'"   YA4   1  
YA4  "C2'"   C2   C  0  1  N  N  S  -149.870  -54.239  -68.635   3.719   0.218   0.465  "C2'"   YA4   2  
YA4  "C3'"   C3   C  0  1  N  N  S  -149.796  -54.681  -67.469   2.501  -0.734   0.462  "C3'"   YA4   3  
YA4  "C4'"   C4   C  0  1  N  N  R  -149.814  -53.348  -66.463   1.395   0.075  -0.252  "C4'"   YA4   4  
YA4  "C5'"   C5   C  0  1  N  N  N  -148.736  -53.596  -65.491   0.035  -0.198   0.395  "C5'"   YA4   5  
YA4  "O2'"   O1   O  0  1  N  N  N  -151.307  -54.177  -68.963   4.806  -0.357  -0.262  "O2'"   YA4   6  
YA4  "O3'"   O2   O  0  1  N  N  N  -150.995  -55.476  -67.231   2.800  -1.926  -0.267  "O3'"   YA4   7  
YA4  "O4'"   O3   O  0  1  N  N  N  -149.574  -52.287  -67.156   1.771   1.457  -0.068  "O4'"   YA4   8  
YA4  "O5'"   O4   O  0  1  N  N  N  -148.447  -52.418  -64.828  -0.988   0.465  -0.350  "O5'"   YA4   9  
YA4  OP1     O5   O  0  1  N  N  N  -147.902  -50.923  -62.634  -2.719   0.836   1.449  OP1     YA4  10  
YA4  P       P1   P  0  1  N  N  N  -147.850  -52.411  -63.410  -2.547   0.395   0.047  P       YA4  11  
YA4  SP3     S1   S  0  1  N  N  N  -145.888  -53.215  -63.680  -3.239  -1.598  -0.157  SP3     YA4  12  
YA4  "H1'"   H1   H  0  1  N  N  N  -148.156  -52.803  -68.743   3.624   2.381   0.217  H1      YA4  13  
YA4  "H1''"  H2   H  0  0  N  N  N  -149.708  -52.119  -69.335   3.454   1.459  -1.307  H2      YA4  14  
YA4  "H2'"   H3   H  0  1  N  N  N  -149.327  -54.833  -69.385   4.021   0.449   1.487  H3      YA4  15  
YA4  "H3'"   H4   H  0  1  N  N  N  -148.888  -55.263  -67.254   2.203  -0.976   1.482  H4      YA4  16  
YA4  "H4'"   H5   H  0  1  N  N  N  -150.789  -53.324  -65.954   1.367  -0.175  -1.312  H5      YA4  17  
YA4  "H5'"   H6   H  0  1  N  N  N  -149.061  -54.357  -64.766  -0.156  -1.271   0.399  H6      YA4  18  
YA4  "H5''"  H7   H  0  0  N  N  N  -147.839  -53.952  -66.018   0.039   0.174   1.419  H7      YA4  19  
YA4  "HO2'"  H8   H  0  0  N  N  N  -151.664  -55.057  -68.991   5.576   0.223  -0.343  H8      YA4  20  
YA4  "HO3'"  H9   H  0  0  N  Y  N  -150.972  -55.829  -66.349   3.529  -2.441   0.104  H9      YA4  21  
YA4  HSP3    H11  H  0  0  N  N  N  -145.418  -53.193  -62.468  -4.532  -1.507   0.201  H11     YA4  22  
YA4  OP3     OP3  O  0  1  N  Y  N  -148.847  -53.399  -62.731  -3.392   1.359  -0.927  OP3     YA4  23  
YA4  HOP3    H10  H  0  0  N  Y  N  -149.287  -52.961  -62.011  -3.326   1.128  -1.863  "HO3'"  YA4  24  
#   #
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
YA4  "O2'"  "C2'"   SING  N  N   1  
YA4  "C2'"  "C1'"   SING  N  N   2  
YA4  "C2'"  "C3'"   SING  N  N   3  
YA4  "C1'"  "O4'"   SING  N  N   4  
YA4  "C3'"  "O3'"   SING  N  N   5  
YA4  "C3'"  "C4'"   SING  N  N   6  
YA4  "O4'"  "C4'"   SING  N  N   7  
YA4  "C4'"  "C5'"   SING  N  N   8  
YA4  "C5'"  "O5'"   SING  N  N   9  
YA4  "O5'"  P       SING  N  N  10  
YA4  SP3    P       SING  N  N  11  
YA4  P      OP1     DOUB  N  N  12  
YA4  "C1'"  "H1'"   SING  N  N  13  
YA4  "C1'"  "H1''"  SING  N  N  14  
YA4  "C2'"  "H2'"   SING  N  N  15  
YA4  "C3'"  "H3'"   SING  N  N  16  
YA4  "C4'"  "H4'"   SING  N  N  17  
YA4  "C5'"  "H5'"   SING  N  N  18  
YA4  "C5'"  "H5''"  SING  N  N  19  
YA4  "O2'"  "HO2'"  SING  N  N  20  
YA4  "O3'"  "HO3'"  SING  N  N  21  
YA4  SP3    HSP3    SING  N  N  22  
YA4  P      OP3     SING  N  N  23  
YA4  OP3    HOP3    SING  N  N  24  
#   #
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
YA4  InChI             InChI                 1.03   "InChI=1S/C5H11O6PS/c6-3-1-10-4(5(3)7)2-11-12(8,9)13/h3-7H,1-2H2,(H2,8,9,13)/t3-,4+,5-/m0/s1"  
YA4  InChIKey          InChI                 1.03   HBCHIJUQXWEATM-LMVFSUKVSA-N  
YA4  SMILES_CANONICAL  CACTVS                3.385  "O[C@H]1CO[C@H](CO[P](O)(S)=O)[C@H]1O"  
YA4  SMILES            CACTVS                3.385  "O[CH]1CO[CH](CO[P](O)(S)=O)[CH]1O"  
YA4  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C1[C@@H]([C@@H]([C@H](O1)COP(=O)(O)S)O)O"  
YA4  SMILES            "OpenEye OEToolkits"  2.0.7  "C1C(C(C(O1)COP(=O)(O)S)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          YA4
_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},4~{S})-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphinic acid"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
YA4  "Create component"  2021-02-12  RCSB  
YA4  "Initial release"   2021-08-04  RCSB  
##
