data_N7X
#

_chem_comp.id                                   N7X
_chem_comp.name                                 "5'-O-[(R)-hydroxy(sulfanylidene)-lambda~5~-phosphanyl]-2'-O-(2-methoxyethyl)-5-methylcytidine"
_chem_comp.type                                 "RNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C13 H22 N3 O8 P S"
_chem_comp.mon_nstd_parent_comp_id              C
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-02-11
_chem_comp.pdbx_modified_date                   2021-02-05
_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                       411.368
_chem_comp.one_letter_code                      C
_chem_comp.three_letter_code                    N7X
_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       6VRD
_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
N7X  C       C1   C  0  1  N  N  N   8.557  42.695  20.925  -2.778  -2.710  -1.043  C      N7X   1  
N7X  C1      C2   C  0  1  N  N  N   8.082  44.129  21.033  -3.727  -3.733  -0.415  C1     N7X   2  
N7X  "C1'"   C3   C  0  1  N  N  R   8.203  39.793  21.661  -0.904   0.033   0.553  "C1'"  N7X   3  
N7X  C12     C4   C  0  1  N  N  N   6.313  45.183  22.370  -5.632  -3.924   1.027  C12    N7X   4  
N7X  C2      C5   C  0  1  N  N  N  10.533  39.137  21.365  -1.542   1.856  -0.927  C2     N7X   5  
N7X  "C2'"   C6   C  0  1  N  N  R   7.804  40.509  20.239  -1.104  -1.084  -0.496  "C2'"  N7X   6  
N7X  "C3'"   C7   C  0  1  N  N  R   6.827  39.794  19.826   0.303  -1.699  -0.662  "C3'"  N7X   7  
N7X  C4      C8   C  0  1  N  N  N  11.195  36.917  21.271  -3.237   3.345  -0.431  C4     N7X   8  
N7X  "C4'"   C9   C  0  1  N  N  R   5.972  39.569  21.126   1.187  -0.882   0.306  "C4'"  N7X   9  
N7X  C5      C10  C  0  1  N  N  N   9.863  36.522  21.405  -3.466   2.674   0.788  C5     N7X  10  
N7X  "C5'"   C11  C  0  1  N  N  N   5.089  38.470  21.014   2.573  -0.655  -0.301  "C5'"  N7X  11  
N7X  C6      C12  C  0  1  N  N  N   8.866  37.474  21.514  -2.703   1.600   1.099  C6     N7X  12  
N7X  C7      C13  C  0  1  N  N  N   9.479  35.021  21.432  -4.543   3.147   1.731  C7     N7X  13  
N7X  N1      N1   N  0  1  N  N  N   9.237  38.786  21.507  -1.736   1.195   0.228  N1     N7X  14  
N7X  N3      N2   N  0  1  N  N  N  11.499  38.204  21.254  -2.284   2.914  -1.247  N3     N7X  15  
N7X  N4      N3   N  0  1  N  N  N  12.280  35.983  21.153  -3.997   4.439  -0.772  N4     N7X  16  
N7X  O12     O1   O  0  1  N  N  N   7.345  44.170  22.310  -4.693  -3.055   0.391  O12    N7X  17  
N7X  O2      O2   O  0  1  N  N  N  10.825  40.317  21.318  -0.668   1.482  -1.692  O2     N7X  18  
N7X  "O2'"   O3   O  0  1  N  N  N   7.406  41.880  20.632  -2.026  -2.064  -0.014  "O2'"  N7X  19  
N7X  "O3'"   O4   O  0  1  N  N  N   5.988  40.431  18.785   0.294  -3.078  -0.287  "O3'"  N7X  20  
N7X  "O4'"   O5   O  0  1  N  N  N   7.092  39.260  22.106   0.496   0.377   0.463  "O4'"  N7X  21  
N7X  "O5'"   O6   O  0  1  N  N  N   5.884  37.300  20.878   3.410  -0.000   0.654  "O5'"  N7X  22  
N7X  OP2     O7   O  0  1  N  N  N   6.214  34.728  20.372   5.688   0.745   1.737  OP2    N7X  23  
N7X  P       P1   P  0  1  N  N  N   5.212  35.776  20.946   4.942   0.394   0.354  P      N7X  24  
N7X  S       S1   S  0  1  N  N  N   3.291  35.930  20.154   5.802  -1.038  -0.470  S      N7X  25  
N7X  H1      H1   H  0  1  N  N  N   9.011  42.377  21.875  -2.098  -3.217  -1.727  H1     N7X  26  
N7X  H2      H2   H  0  1  N  N  N   9.297  42.604  20.117  -3.357  -1.966  -1.591  H2     N7X  27  
N7X  H3      H3   H  0  1  N  N  N   8.936  44.822  21.053  -4.236  -4.287  -1.203  H3     N7X  28  
N7X  H4      H4   H  0  1  N  N  N   7.421  44.385  20.192  -3.156  -4.424   0.205  H4     N7X  29  
N7X  H5      H5   H  0  1  N  N  N   8.565  40.587  22.330  -1.141  -0.336   1.550  H5     N7X  30  
N7X  H6      H6   H  0  1  N  N  N   5.817  45.144  23.351  -5.101  -4.620   1.677  H6     N7X  31  
N7X  H7      H7   H  0  1  N  N  N   6.765  46.176  22.227  -6.330  -3.334   1.619  H7     N7X  32  
N7X  H8      H8   H  0  1  N  N  N   5.573  45.000  21.577  -6.181  -4.483   0.269  H8     N7X  33  
N7X  H9      H9   H  0  1  N  N  N   8.684  40.520  19.579  -1.453  -0.664  -1.439  H9     N7X  34  
N7X  H10     H10  H  0  1  N  N  N   7.158  38.809  19.466   0.652  -1.584  -1.688  H10    N7X  35  
N7X  H11     H11  H  0  1  N  N  N   5.454  40.499  21.404   1.271  -1.391   1.266  H11    N7X  36  
N7X  H12     H12  H  0  1  N  N  N   4.446  38.593  20.130   3.013  -1.616  -0.571  H12    N7X  37  
N7X  H13     H13  H  0  1  N  N  N   4.463  38.397  21.916   2.483  -0.034  -1.192  H13    N7X  38  
N7X  H14     H14  H  0  1  N  N  N   7.828  37.188  21.602  -2.859   1.069   2.027  H14    N7X  39  
N7X  H15     H15  H  0  1  N  N  N   8.389  34.923  21.544  -5.041   4.018   1.306  H15    N7X  40  
N7X  H16     H16  H  0  1  N  N  N   9.796  34.545  20.492  -5.270   2.349   1.880  H16    N7X  41  
N7X  H17     H17  H  0  1  N  N  N   9.980  34.530  22.279  -4.096   3.415   2.688  H17    N7X  42  
N7X  H18     H18  H  0  1  N  N  N  13.219  36.316  21.063  -4.694   4.752  -0.173  H18    N7X  43  
N7X  H19     H19  H  0  1  N  N  N  12.097  35.000  21.161  -3.837   4.899  -1.611  H19    N7X  44  
N7X  "HO3'"  H20  H  0  0  N  Y  N   5.289  39.838  18.534   1.153  -3.515  -0.372  H20    N7X  45  
N7X  HOP2    H21  H  0  0  N  N  N   7.038  34.788  20.840   6.616   0.992   1.631  H21    N7X  46  
N7X  OP3     OP3  O  0  1  N  Y  N       ?       ?       ?   4.984   1.677  -0.619  OP3    N7X  47  
N7X  HOP3    H22  H  0  0  N  Y  N       ?       ?       ?   4.554   2.462  -0.254  H22    N7X  48  
#   #
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
N7X  "O3'"  "C3'"   SING  N  N   1  
N7X  "C3'"  "C2'"   SING  N  N   2  
N7X  "C3'"  "C4'"   SING  N  N   3  
N7X  S      P       DOUB  N  N   4  
N7X  "C2'"  "O2'"   SING  N  N   5  
N7X  "C2'"  "C1'"   SING  N  N   6  
N7X  OP2    P       SING  N  N   7  
N7X  "O2'"  C       SING  N  N   8  
N7X  "O5'"  P       SING  N  N   9  
N7X  "O5'"  "C5'"   SING  N  N  10  
N7X  C      C1      SING  N  N  11  
N7X  "C5'"  "C4'"   SING  N  N  12  
N7X  C1     O12     SING  N  N  13  
N7X  "C4'"  "O4'"   SING  N  N  14  
N7X  N4     C4      SING  N  N  15  
N7X  N3     C4      DOUB  N  N  16  
N7X  N3     C2      SING  N  N  17  
N7X  C4     C5      SING  N  N  18  
N7X  O2     C2      DOUB  N  N  19  
N7X  C2     N1      SING  N  N  20  
N7X  C5     C7      SING  N  N  21  
N7X  C5     C6      DOUB  N  N  22  
N7X  N1     C6      SING  N  N  23  
N7X  N1     "C1'"   SING  N  N  24  
N7X  "C1'"  "O4'"   SING  N  N  25  
N7X  O12    C12     SING  N  N  26  
N7X  C      H1      SING  N  N  27  
N7X  C      H2      SING  N  N  28  
N7X  C1     H3      SING  N  N  29  
N7X  C1     H4      SING  N  N  30  
N7X  "C1'"  H5      SING  N  N  31  
N7X  C12    H6      SING  N  N  32  
N7X  C12    H7      SING  N  N  33  
N7X  C12    H8      SING  N  N  34  
N7X  "C2'"  H9      SING  N  N  35  
N7X  "C3'"  H10     SING  N  N  36  
N7X  "C4'"  H11     SING  N  N  37  
N7X  "C5'"  H12     SING  N  N  38  
N7X  "C5'"  H13     SING  N  N  39  
N7X  C6     H14     SING  N  N  40  
N7X  C7     H15     SING  N  N  41  
N7X  C7     H16     SING  N  N  42  
N7X  C7     H17     SING  N  N  43  
N7X  N4     H18     SING  N  N  44  
N7X  N4     H19     SING  N  N  45  
N7X  "O3'"  "HO3'"  SING  N  N  46  
N7X  OP2    HOP2    SING  N  N  47  
N7X  P      OP3     SING  N  N  48  
N7X  OP3    HOP3    SING  N  N  49  
#   #
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
N7X  SMILES            ACDLabs               12.01  "C(COC)OC1C(OC(C1O)COP(O)(O)=S)N2C(N=C(C(C)=C2)N)=O"  
N7X  InChI             InChI                 1.03   "InChI=1S/C13H22N3O8PS/c1-7-5-16(13(18)15-11(7)14)12-10(22-4-3-21-2)9(17)8(24-12)6-23-25(19,20)26/h5,8-10,12,17H,3-4,6H2,1-2H3,(H2,14,15,18)(H2,19,20,26)/t8-,9-,10-,12-/m1/s1"  
N7X  InChIKey          InChI                 1.03   UINDLFLAAYRFRN-DNRKLUKYSA-N  
N7X  SMILES_CANONICAL  CACTVS                3.385  "COCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=S)O[C@H]1N2C=C(C)C(=NC2=O)N"  
N7X  SMILES            CACTVS                3.385  "COCCO[CH]1[CH](O)[CH](CO[P](O)(O)=S)O[CH]1N2C=C(C)C(=NC2=O)N"  
N7X  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CC1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=S)(O)O)O)OCCOC"  
N7X  SMILES            "OpenEye OEToolkits"  2.0.7  "CC1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=S)(O)O)O)OCCOC"  
#   #
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
N7X  "SYSTEMATIC NAME"  ACDLabs               12.01  "2'-O-(2-methoxyethyl)-5-methyl-5'-O-thiophosphonocytidine"  
N7X  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "4-azanyl-1-[(2~{R},3~{R},4~{R},5~{R})-5-[bis(oxidanyl)phosphinothioyloxymethyl]-3-(2-methoxyethoxy)-4-oxidanyl-oxolan-2-yl]-5-methyl-pyrimidin-2-one"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
N7X  "Create component"  2020-02-11  RCSB  
N7X  "Initial release"   2021-02-10  RCSB  
##
