data_C7R
#

_chem_comp.id                                   C7R
_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 1)"
_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                    C7R
_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       5JLW
_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
C7R  P       P1   P  0  1  N  N  N   2.932  15.221  -11.136   3.886  -0.560  -0.297  P       C7R   1  
C7R  "C5'"   C1   C  0  1  N  N  N   4.889  15.371  -12.775   1.760   0.916   0.366  "C5'"   C7R   2  
C7R  "O5'"   O1   O  0  1  N  N  N   3.719  14.720  -12.428   2.536   0.250  -0.632  "O5'"   C7R   3  
C7R  "C4'"   C2   C  0  1  N  N  R   5.363  14.960  -14.131   0.549   1.583  -0.290  "C4'"   C7R   4  
C7R  "O4'"   O2   O  0  1  N  N  N   6.448  15.839  -14.503  -0.380   0.588  -0.772  "O4'"   C7R   5  
C7R  "C3'"   C3   C  0  1  N  N  S   5.914  13.538  -14.193  -0.273   2.374   0.759  "C3'"   C7R   6  
C7R  "O3'"   O3   O  0  1  N  N  N   5.661  12.913  -15.460   0.243   3.696   0.920  "O3'"   C7R   7  
C7R  "C2'"   C4   C  0  1  N  N  N   7.398  13.728  -13.923  -1.680   2.404   0.112  "C2'"   C7R   8  
C7R  "C1'"   C5   C  0  1  N  N  R   7.683  15.162  -14.395  -1.659   1.232  -0.894  "C1'"   C7R   9  
C7R  N1      N1   N  0  1  N  N  N   8.590  15.938  -13.480  -2.728   0.282  -0.577  N1      C7R  10  
C7R  C2      C6   C  0  1  N  N  N   9.562  16.764  -14.039  -2.704  -0.387   0.590  C2      C7R  11  
C7R  O2      O4   O  0  1  N  N  N   9.628  16.871  -15.272  -1.790  -0.195   1.374  O2      C7R  12  
C7R  N3      N2   N  0  1  N  N  N  10.398  17.436  -13.221  -3.664  -1.256   0.904  N3      C7R  13  
C7R  C4      C7   C  0  1  N  N  N  10.300  17.314  -11.908  -4.670  -1.484   0.070  C4      C7R  14  
C7R  N4      N3   N  0  1  N  N  N  11.155  18.016  -11.159  -5.655  -2.384   0.405  N4      C7R  15  
C7R  C5      C8   C  0  1  N  N  N   9.325  16.464  -11.305  -4.724  -0.800  -1.161  C5      C7R  16  
C7R  C6      C9   C  0  1  N  N  N   8.496  15.802  -12.123  -3.744   0.085  -1.464  C6      C7R  17  
C7R  OP1     O5   O  0  1  N  N  N   1.464  15.123  -11.470   4.829   0.327   0.419  OP1     C7R  18  
C7R  SP2     S1   S  0  1  N  N  N   3.785  14.369   -9.603   3.424  -2.231   0.922  SP2     C7R  19  
C7R  OP3     O6   O  0  1  N  Y  N   3.309  16.779  -11.110   4.562  -1.067  -1.668  OP3     C7R  20  
C7R  "H5'2"  H1   H  0  0  N  N  N   5.666  15.128  -12.036   1.420   0.191   1.105  "H5'2"  C7R  21  
C7R  "H5'1"  H2   H  0  0  N  N  N   4.708  16.456  -12.773   2.372   1.675   0.855  "H5'1"  C7R  22  
C7R  "H4'"   H3   H  0  1  N  N  N   4.537  15.055  -14.851   0.866   2.237  -1.102  "H4'"   C7R  23  
C7R  "H3'"   H4   H  0  1  N  N  N   5.472  12.945  -13.379  -0.296   1.847   1.713  "H3'"   C7R  24  
C7R  H1      H5   H  0  1  N  Y  N   6.019  12.033  -15.457  -0.239   4.230   1.566  H1      C7R  25  
C7R  "H2'1"  H6   H  0  0  N  N  N   7.995  13.003  -14.495  -2.450   2.247   0.867  "H2'1"  C7R  26  
C7R  "H2'2"  H7   H  0  0  N  N  N   7.617  13.619  -12.851  -1.841   3.350  -0.406  "H2'2"  C7R  27  
C7R  "H1'"   H8   H  0  1  N  N  N   8.159  15.104  -15.385  -1.787   1.613  -1.907  "H1'"   C7R  28  
C7R  H42     H9   H  0  1  N  N  N  11.835  18.605  -11.596  -5.616  -2.853   1.253  H42     C7R  29  
C7R  H41     H10  H  0  1  N  N  N  11.115  17.952  -10.162  -6.390  -2.549  -0.207  H41     C7R  30  
C7R  H5      H11  H  0  1  N  N  N   9.258  16.359  -10.232  -5.536  -0.974  -1.851  H5      C7R  31  
C7R  H6      H12  H  0  1  N  N  N   7.742  15.151  -11.704  -3.766   0.625  -2.398  H6      C7R  32  
C7R  HSP2    H13  H  0  0  N  N  N   3.084  14.832   -8.611   2.573  -2.938   0.157  HSP2    C7R  33  
C7R  HOP3    H14  H  0  0  N  Y  N   2.537  17.296  -11.308   5.382  -1.564  -1.542  HOP3    C7R  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
C7R  "O3'"  "C3'"   SING  N  N   1  
C7R  O2     C2      DOUB  N  N   2  
C7R  "O4'"  "C1'"   SING  N  N   3  
C7R  "O4'"  "C4'"   SING  N  N   4  
C7R  "C1'"  "C2'"   SING  N  N   5  
C7R  "C1'"  N1      SING  N  N   6  
C7R  "C3'"  "C4'"   SING  N  N   7  
C7R  "C3'"  "C2'"   SING  N  N   8  
C7R  "C4'"  "C5'"   SING  N  N   9  
C7R  C2     N1      SING  N  N  10  
C7R  C2     N3      SING  N  N  11  
C7R  N1     C6      SING  N  N  12  
C7R  N3     C4      DOUB  N  N  13  
C7R  "C5'"  "O5'"   SING  N  N  14  
C7R  "O5'"  P       SING  N  N  15  
C7R  C6     C5      DOUB  N  N  16  
C7R  C4     C5      SING  N  N  17  
C7R  C4     N4      SING  N  N  18  
C7R  OP1    P       DOUB  N  N  19  
C7R  P      SP2     SING  N  N  20  
C7R  P      OP3     SING  N  N  21  
C7R  "C5'"  "H5'2"  SING  N  N  22  
C7R  "C5'"  "H5'1"  SING  N  N  23  
C7R  "C4'"  "H4'"   SING  N  N  24  
C7R  "C3'"  "H3'"   SING  N  N  25  
C7R  "O3'"  H1      SING  N  N  26  
C7R  "C2'"  "H2'1"  SING  N  N  27  
C7R  "C2'"  "H2'2"  SING  N  N  28  
C7R  "C1'"  "H1'"   SING  N  N  29  
C7R  N4     H42     SING  N  N  30  
C7R  N4     H41     SING  N  N  31  
C7R  C5     H5      SING  N  N  32  
C7R  C6     H6      SING  N  N  33  
C7R  SP2    HSP2    SING  N  N  34  
C7R  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
C7R  SMILES            ACDLabs               12.01  "P(S)(O)(OCC1OC(CC1O)N2C=CC(=NC2=O)N)=O"  
C7R  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"  
C7R  InChIKey          InChI                 1.03   FHBXKBNKQMSUIJ-SHYZEUOFSA-N  
C7R  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"  
C7R  SMILES            CACTVS                3.385  "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(S)=O)O2"  
C7R  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"  
C7R  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
C7R  "SYSTEMATIC NAME"  ACDLabs               12.01  "2'-deoxy-5'-O-thiophosphonocytidine"  
C7R  "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
C7R  "Create component"  2016-04-28  RCSB  
C7R  "Initial release"   2016-06-22  RCSB  
C7R  "Modify synonyms"   2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     C7R
_pdbx_chem_comp_synonyms.name        "2'-deoxy-5'-O-thiophosphonocytidine (thiophospho connection isoform 1)"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
