data_OKQ
#

_chem_comp.id                                   OKQ
_chem_comp.name                                 "2'-O-methylcytidine-5'-phosphorothioate"
_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C10 H16 N3 O7 P S"
_chem_comp.mon_nstd_parent_comp_id              DC
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-03-19
_chem_comp.pdbx_modified_date                   2020-04-24
_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                       353.289
_chem_comp.one_letter_code                      C
_chem_comp.three_letter_code                    OKQ
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  Y
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       6YCS
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBE
#   #
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
OKQ  C2      C1   C  0  1  N  N  N   8.316  -34.825  34.780  -2.235  -1.139   0.447  C2      OKQ   1  
OKQ  C4      C2   C  0  1  N  N  N   9.454  -36.701  34.090  -4.139  -2.341  -0.071  C4      OKQ   2  
OKQ  C5      C3   C  0  1  N  N  N  10.143  -35.948  33.168  -4.407  -1.454  -1.134  C5      OKQ   3  
OKQ  C6      C4   C  0  1  N  N  N   9.881  -34.601  33.087  -3.549  -0.433  -1.368  C6      OKQ   4  
OKQ  O2      O1   O  0  1  N  N  N   7.515  -34.312  35.483  -1.253  -0.989   1.154  O2      OKQ   5  
OKQ  "C1'"   C5   C  0  1  N  N  R   8.655  -32.648  33.852  -1.532   0.830  -0.798  "C1'"   OKQ   6  
OKQ  "C2'"   C6   C  0  1  N  N  R   9.869  -31.725  33.787  -1.508   1.789   0.419  "C2'"   OKQ   7  
OKQ  "C3'"   C7   C  0  1  N  N  R   9.243  -30.489  33.166  -0.113   2.447   0.286  "C3'"   OKQ   8  
OKQ  "C4'"   C8   C  0  1  N  N  R   8.317  -31.105  32.122   0.685   1.465  -0.592  "C4'"   OKQ   9  
OKQ  "C5'"   C9   C  0  1  N  N  N   8.937  -31.330  30.762   1.932   0.988   0.155  "C5'"   OKQ  10  
OKQ  CM2     C10  C  0  1  N  N  N  11.596  -30.722  35.037  -3.042   3.221   1.579  CM2     OKQ  11  
OKQ  N1      N1   N  0  1  N  N  N   8.976  -34.082  33.897  -2.461  -0.278  -0.563  N1      OKQ  12  
OKQ  N3      N2   N  0  1  N  N  N   8.560  -36.129  34.874  -3.063  -2.155   0.683  N3      OKQ  13  
OKQ  N4      N3   N  0  1  N  N  N   9.713  -38.123  34.202  -4.987  -3.394   0.182  N4      OKQ  14  
OKQ  "O2'"   O2   O  0  1  N  N  N  10.447  -31.517  35.059  -2.546   2.767   0.318  "O2'"   OKQ  15  
OKQ  "O3'"   O3   O  0  1  N  N  N   8.451  -29.837  34.157  -0.220   3.720  -0.355  "O3'"   OKQ  16  
OKQ  "O4'"   O4   O  0  1  N  N  N   7.915  -32.390  32.671  -0.174   0.347  -0.877  "O4'"   OKQ  17  
OKQ  "O5'"   O5   O  0  1  N  N  N   8.246  -32.335  30.020   2.717   0.161  -0.707  "O5'"   OKQ  18  
OKQ  H1      H1   H  0  1  N  N  N  10.876  -36.406  32.520  -5.278  -1.592  -1.757  H1      OKQ  19  
OKQ  H2      H2   H  0  1  N  N  N  10.405  -33.980  32.375  -3.733   0.260  -2.176  H2      OKQ  20  
OKQ  H3      H3   H  0  1  N  N  N   8.059  -32.381  34.737  -1.801   1.369  -1.706  H3      OKQ  21  
OKQ  H4      H4   H  0  1  N  N  N  10.606  -32.148  33.089  -1.590   1.234   1.354  H4      OKQ  22  
OKQ  H5      H5   H  0  1  N  N  N   9.997  -29.833  32.707   0.354   2.553   1.265  H5      OKQ  23  
OKQ  H6      H6   H  0  1  N  N  N   7.434  -30.459  32.008   0.974   1.957  -1.522  H6      OKQ  24  
OKQ  H7      H7   H  0  1  N  N  N   9.983  -31.643  30.896   2.521   1.850   0.467  H7      OKQ  25  
OKQ  H8      H8   H  0  1  N  N  N   8.906  -30.387  30.197   1.632   0.415   1.033  H8      OKQ  26  
OKQ  H9      H9   H  0  1  N  N  N  11.983  -30.608  36.060  -3.825   3.961   1.416  H9      OKQ  27  
OKQ  H10     H10  H  0  1  N  N  N  12.360  -31.200  34.407  -3.449   2.376   2.134  H10     OKQ  28  
OKQ  H11     H11  H  0  1  N  N  N  11.349  -29.732  34.626  -2.229   3.672   2.148  H11     OKQ  29  
OKQ  H12     H12  H  0  1  N  N  N   9.214  -38.671  34.874  -4.800  -4.002   0.914  H12     OKQ  30  
OKQ  H13     H13  H  0  1  N  N  N  10.391  -38.556  33.608  -5.773  -3.527  -0.371  H13     OKQ  31  
OKQ  H14     H14  H  0  1  N  N  N   9.019  -29.450  34.813   0.625   4.177  -0.465  H14     OKQ  32  
OKQ  P1      P1   P  0  1  N  N  N   7.331  -32.051  29.865   4.103  -0.517  -0.248  P1      OKQ  33  
OKQ  O1      O6   O  0  1  N  N  N       ?        ?       ?   5.022   0.530   0.253  O1      OKQ  34  
OKQ  H17     H17  H  0  1  N  N  N       ?        ?       ?   4.951  -2.402   1.572  H17     OKQ  35  
OKQ  S1      S1   S  0  1  N  N  N       ?        ?       ?   3.726  -1.923   1.293  S1      OKQ  36  
OKQ  OP3     O7   O  0  1  N  Y  N       ?        ?       ?   4.776  -1.265  -1.505  OP3     OKQ  37  
OKQ  HOP3    H18  H  0  0  N  Y  N       ?        ?       ?   4.228  -1.965  -1.885  HOP3    OKQ  38  
#   #
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
OKQ  "O5'"   "C5'"  SING  N  N   1  
OKQ  "C5'"   "C4'"  SING  N  N   2  
OKQ  "C4'"   "O4'"  SING  N  N   3  
OKQ  "C4'"   "C3'"  SING  N  N   4  
OKQ  "O4'"   "C1'"  SING  N  N   5  
OKQ  C6      C5     DOUB  N  N   6  
OKQ  C6      N1     SING  N  N   7  
OKQ  "C3'"   "C2'"  SING  N  N   8  
OKQ  "C3'"   "O3'"  SING  N  N   9  
OKQ  C5      C4     SING  N  N  10  
OKQ  "C2'"   "C1'"  SING  N  N  11  
OKQ  "C2'"   "O2'"  SING  N  N  12  
OKQ  "C1'"   N1     SING  N  N  13  
OKQ  N1      C2     SING  N  N  14  
OKQ  C4      N4     SING  N  N  15  
OKQ  C4      N3     DOUB  N  N  16  
OKQ  C2      N3     SING  N  N  17  
OKQ  C2      O2     DOUB  N  N  18  
OKQ  CM2     "O2'"  SING  N  N  19  
OKQ  C5      H1     SING  N  N  20  
OKQ  C6      H2     SING  N  N  21  
OKQ  "C1'"   H3     SING  N  N  22  
OKQ  "C2'"   H4     SING  N  N  23  
OKQ  "C3'"   H5     SING  N  N  24  
OKQ  "C4'"   H6     SING  N  N  25  
OKQ  "C5'"   H7     SING  N  N  26  
OKQ  "C5'"   H8     SING  N  N  27  
OKQ  CM2     H9     SING  N  N  28  
OKQ  CM2     H10    SING  N  N  29  
OKQ  CM2     H11    SING  N  N  30  
OKQ  N4      H12    SING  N  N  31  
OKQ  N4      H13    SING  N  N  32  
OKQ  "O3'"   H14    SING  N  N  33  
OKQ  "O5'"   P1     SING  N  N  34  
OKQ  O1      P1     DOUB  N  N  35  
OKQ  H17     S1     SING  N  N  36  
OKQ  S1      P1     SING  N  N  37  
OKQ  OP3     P1     SING  N  N  38  
OKQ  HOP3    OP3    SING  N  N  39  
#   #
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
OKQ  InChI             InChI                 1.03   "InChI=1S/C10H16N3O7PS/c1-18-8-7(14)5(4-19-21(16,17)22)20-9(8)13-3-2-6(11)12-10(13)15/h2-3,5,7-9,14H,4H2,1H3,(H2,11,12,15)(H2,16,17,22)/t5-,7-,8-,9-/m1/s1"  
OKQ  InChIKey          InChI                 1.03   JKIZWHJBBPPNBB-ZOQUXTDFSA-N  
OKQ  SMILES_CANONICAL  CACTVS                3.385  "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(S)=O)O[C@H]1N2C=CC(=NC2=O)N"  
OKQ  SMILES            CACTVS                3.385  "CO[CH]1[CH](O)[CH](CO[P](O)(S)=O)O[CH]1N2C=CC(=NC2=O)N"  
OKQ  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)S)O"  
OKQ  SMILES            "OpenEye OEToolkits"  2.0.7  "COC1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)S)O"  
#
_pdbx_chem_comp_identifier.comp_id          OKQ
_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~{R},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4-methoxy-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
OKQ  "Create component"  2020-03-19  PDBE  
OKQ  "Initial release"   2020-04-29  RCSB  
##
