data_C7S
#

_chem_comp.id                                   C7S
_chem_comp.name                                 "2'-deoxy-5'-O-thiophosphonocytidine"
_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C9 H14 N3 O6 P S"
_chem_comp.mon_nstd_parent_comp_id              DC
_chem_comp.pdbx_synonyms                        "2'-deoxy-5'-O-thiophosphonocytidine (thiophospho connection isoform 2)"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2016-04-28
_chem_comp.pdbx_modified_date                   2021-03-01
_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                       323.263
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    C7S
_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       5JLX
_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
C7S  P       P1   P  0  1  N  N  N   3.050  14.932  -11.305   3.706   1.116   0.093  P       C7S   1  
C7S  "C5'"   C1   C  0  1  N  N  N   3.810  15.138  -13.784   1.761  -0.661  -0.355  "C5'"   C7S   2  
C7S  "O5'"   O1   O  0  1  N  N  N   3.636  14.305  -12.656   2.408   0.265   0.521  "O5'"   C7S   3  
C7S  "C4'"   C2   C  0  1  N  N  R   5.118  14.844  -14.498   0.567  -1.294   0.363  "C4'"   C7S   4  
C7S  "O4'"   O2   O  0  1  N  N  N   6.132  15.765  -14.068  -0.479  -0.317   0.555  "O4'"   C7S   5  
C7S  "C3'"   C3   C  0  1  N  N  S   5.705  13.445  -14.277  -0.072  -2.389  -0.518  "C3'"   C7S   6  
C7S  "O3'"   O3   O  0  1  N  N  N   5.513  12.657  -15.461   0.389  -3.683  -0.123  "O3'"   C7S   7  
C7S  "C2'"   C4   C  0  1  N  N  N   7.203  13.702  -13.992  -1.587  -2.249  -0.251  "C2'"   C7S   8  
C7S  "C1'"   C5   C  0  1  N  N  R   7.376  15.179  -14.336  -1.684  -1.086   0.760  "C1'"   C7S   9  
C7S  N1      N1   N  0  1  N  N  N   8.435  15.894  -13.527  -2.866  -0.266   0.482  N1      C7S  10  
C7S  C2      C6   C  0  1  N  N  N   9.404  16.663  -14.180  -2.978   0.369  -0.699  C2      C7S  11  
C7S  O2      O4   O  0  1  N  N  N   9.384  16.736  -15.413  -2.090   0.255  -1.528  O2      C7S  12  
C7S  N3      N2   N  0  1  N  N  N  10.340  17.307  -13.442  -4.041   1.120  -0.978  N3      C7S  13  
C7S  C4      C7   C  0  1  N  N  N  10.334  17.208  -12.115  -5.021   1.262  -0.095  C4      C7S  14  
C7S  N4      N3   N  0  1  N  N  N  11.280  17.864  -11.434  -6.115   2.040  -0.394  N4      C7S  15  
C7S  C5      C8   C  0  1  N  N  N   9.355  16.434  -11.426  -4.935   0.610   1.153  C5      C7S  16  
C7S  C6      C9   C  0  1  N  N  N   8.431  15.802  -12.164  -3.849  -0.154   1.419  C6      C7S  17  
C7S  SP1     S1   S  0  1  N  N  N   1.101  14.689  -11.338   5.333  -0.200  -0.245  SP1     C7S  18  
C7S  OP2     O5   O  0  1  N  N  N   3.938  14.445  -10.197   3.415   1.870  -1.147  OP2     C7S  19  
C7S  OP3     O6   O  0  1  N  Y  N   3.307  16.504  -11.464   4.084   2.146   1.271  OP3     C7S  20  
C7S  H1      H1   H  0  1  N  N  N   3.810  16.188  -13.456   1.413  -0.138  -1.245  H1      C7S  21  
C7S  H2      H2   H  0  1  N  N  N   2.977  14.972  -14.483   2.466  -1.441  -0.644  H2      C7S  22  
C7S  H3      H3   H  0  1  N  N  N   4.951  14.972  -15.578   0.877  -1.711   1.321  H3      C7S  23  
C7S  H4      H4   H  0  1  N  N  N   5.235  12.974  -13.401   0.148  -2.210  -1.571  H4      C7S  24  
C7S  H5      H5   H  0  1  N  Y  N   5.876  11.789  -15.327   0.019  -4.409  -0.644  H5      C7S  25  
C7S  H6      H6   H  0  1  N  N  N   7.840  13.071  -14.630  -2.116  -2.001  -1.171  H6      C7S  26  
C7S  H7      H7   H  0  1  N  N  N   7.441  13.513  -12.935  -1.986  -3.168   0.180  H7      C7S  27  
C7S  H8      H8   H  0  1  N  N  N   7.622  15.267  -15.404  -1.720  -1.471   1.779  H8      C7S  28  
C7S  H9      H9   H  0  1  N  N  N  11.962  18.407  -11.923  -6.172   2.487  -1.253  H9      C7S  29  
C7S  H10     H10  H  0  1  N  N  N  11.305  17.811  -10.436  -6.830   2.142   0.254  H10     C7S  30  
C7S  H11     H11  H  0  1  N  N  N   9.357  16.359  -10.349  -5.724   0.716   1.882  H11     C7S  31  
C7S  H12     H12  H  0  1  N  N  N   7.672  15.211  -11.673  -3.762  -0.668   2.366  H12     C7S  32  
C7S  HSP1    H13  H  0  0  N  N  N   0.742  15.227  -10.210   5.483  -0.809   0.945  HSP1    C7S  33  
C7S  HOP3    H14  H  0  0  N  Y  N   3.957  16.785  -10.831   4.859   2.693   1.082  HOP3    C7S  34  
#   #
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
C7S  "O3'"  "C3'"   SING  N  N   1  
C7S  O2     C2      DOUB  N  N   2  
C7S  "C4'"  "C3'"   SING  N  N   3  
C7S  "C4'"  "O4'"   SING  N  N   4  
C7S  "C4'"  "C5'"   SING  N  N   5  
C7S  "C1'"  "O4'"   SING  N  N   6  
C7S  "C1'"  "C2'"   SING  N  N   7  
C7S  "C1'"  N1      SING  N  N   8  
C7S  "C3'"  "C2'"   SING  N  N   9  
C7S  C2     N1      SING  N  N  10  
C7S  C2     N3      SING  N  N  11  
C7S  "C5'"  "O5'"   SING  N  N  12  
C7S  N1     C6      SING  N  N  13  
C7S  N3     C4      DOUB  N  N  14  
C7S  "O5'"  P       SING  N  N  15  
C7S  C6     C5      DOUB  N  N  16  
C7S  C4     N4      SING  N  N  17  
C7S  C4     C5      SING  N  N  18  
C7S  SP1    P       SING  N  N  19  
C7S  P      OP2     DOUB  N  N  20  
C7S  P      OP3     SING  N  N  21  
C7S  "C5'"  H1      SING  N  N  22  
C7S  "C5'"  H2      SING  N  N  23  
C7S  "C4'"  H3      SING  N  N  24  
C7S  "C3'"  H4      SING  N  N  25  
C7S  "O3'"  H5      SING  N  N  26  
C7S  "C2'"  H6      SING  N  N  27  
C7S  "C2'"  H7      SING  N  N  28  
C7S  "C1'"  H8      SING  N  N  29  
C7S  N4     H9      SING  N  N  30  
C7S  N4     H10     SING  N  N  31  
C7S  C5     H11     SING  N  N  32  
C7S  C6     H12     SING  N  N  33  
C7S  SP1    HSP1    SING  N  N  34  
C7S  OP3    HOP3    SING  N  N  35  
#   #
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
C7S  SMILES            ACDLabs               12.01  "P(=O)(O)(OCC1C(CC(O1)N2C=CC(=NC2=O)N)O)S"  
C7S  InChI             InChI                 1.03   "InChI=1S/C9H14N3O6PS/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(18-8)4-17-19(15,16)20/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,20)/t5-,6+,8+/m0/s1"  
C7S  InChIKey          InChI                 1.03   FHBXKBNKQMSUIJ-SHYZEUOFSA-N  
C7S  SMILES_CANONICAL  CACTVS                3.385  "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(S)=O)O2"  
C7S  SMILES            CACTVS                3.385  "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(S)=O)O2"  
C7S  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.4  "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)S)O"  
C7S  SMILES            "OpenEye OEToolkits"  2.0.4  "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)S)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
C7S  "SYSTEMATIC NAME"  ACDLabs               12.01  "2'-deoxy-5'-O-thiophosphonocytidine"  
C7S  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.4  "[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-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
C7S  "Create component"  2016-04-28  RCSB  
C7S  "Initial release"   2016-06-22  RCSB  
C7S  "Modify synonyms"   2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     C7S
_pdbx_chem_comp_synonyms.name        "2'-deoxy-5'-O-thiophosphonocytidine (thiophospho connection isoform 2)"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
