data_JMC
#

_chem_comp.id                                   JMC
_chem_comp.name                                 "[(2~{R},3~{R},4~{R},5~{R})-5-(4-azanyl-3-methyl-2-oxidanylidene-4~{H}-pyrimidin-1-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C11 H20 N3 O8 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-06-29
_chem_comp.pdbx_modified_date                   2020-10-02
_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                       353.266
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    JMC
_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       6ZJ3
_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
JMC  C1     C1   C  0  1  N  N  N  272.522  209.037  213.945   5.371   1.277  -1.157  C1     JMC   1  
JMC  "C1'"  C2   C  0  1  N  N  R  275.946  207.626  210.549   1.010  -0.747  -0.503  "C1'"  JMC   2  
JMC  C2     C3   C  0  1  N  N  N  274.184  208.319  212.271   3.158   0.318  -0.740  C2     JMC   3  
JMC  "C2'"  C4   C  0  1  N  N  R  277.221  206.903  210.965   0.817  -1.883   0.533  "C2'"  JMC   4  
JMC  C3     C5   C  0  1  N  N  N  278.578  208.118  209.504   2.131  -3.635   1.509  C3     JMC   5  
JMC  "C3'"  C6   C  0  1  N  N  R  276.695  205.525  211.337  -0.622  -2.364   0.223  "C3'"  JMC   6  
JMC  C4     C7   C  0  1  N  N  R  274.599  210.334  213.537   3.929   2.000   0.825  C4     JMC   7  
JMC  "C4'"  C8   C  0  1  N  N  R  275.536  205.332  210.376  -1.266  -1.175  -0.517  "C4'"  JMC   8  
JMC  C5     C9   C  0  1  N  N  N  275.798  210.503  212.874   2.622   1.825   1.569  C5     JMC   9  
JMC  "C5'"  C10  C  0  1  N  N  N  274.449  204.398  210.839  -2.508  -0.702   0.242  "C5'"  JMC  10  
JMC  C6     C11  C  0  1  N  N  N  276.173  209.577  211.912   1.752   0.948   1.100  C6     JMC  11  
JMC  N1     N1   N  0  1  N  N  N  275.417  208.515  211.608   2.021   0.207  -0.040  N1     JMC  12  
JMC  N3     N2   N  0  1  N  N  N  273.784  209.237  213.242   4.135   1.173  -0.376  N3     JMC  13  
JMC  N4     N3   N  0  1  N  N  N  274.213  211.213  214.474   4.037   3.410   0.426  N4     JMC  14  
JMC  O2     O1   O  0  1  N  N  N  273.414  207.368  212.046   3.315  -0.375  -1.727  O2     JMC  15  
JMC  "O2'"  O2   O  0  1  N  N  N  278.073  206.830  209.837   1.763  -2.933   0.319  "O2'"  JMC  16  
JMC  "O3'"  O3   O  0  1  N  N  N  277.670  204.506  211.218  -0.592  -3.521  -0.615  "O3'"  JMC  17  
JMC  "O4'"  O4   O  0  1  N  N  N  274.987  206.658  210.205  -0.290  -0.121  -0.562  "O4'"  JMC  18  
JMC  "O5'"  O5   O  0  1  N  N  N  274.976  203.151  211.250  -3.163   0.321  -0.510  "O5'"  JMC  19  
JMC  OP1    O6   O  0  1  N  N  N  275.059  202.781  213.738  -5.710  -0.021   0.047  OP1    JMC  20  
JMC  OP2    O7   O  0  1  N  N  N  274.274  200.916  212.101  -4.291   1.618   1.339  OP2    JMC  21  
JMC  P      P1   P  0  1  N  N  N  274.348  202.368  212.480  -4.509   1.050  -0.010  P      JMC  22  
JMC  O1     O8   O  0  1  N  Y  N  272.849  202.919  212.558  -4.891   2.232  -1.034  O1     JMC  23  
JMC  H1     H1   H  0  1  N  N  N  272.371  209.852  214.668   5.327   0.587  -2.000  H1     JMC  24  
JMC  H2     H2   H  0  1  N  N  N  271.695  209.033  213.220   5.482   2.296  -1.527  H2     JMC  25  
JMC  H3     H3   H  0  1  N  N  N  272.547  208.075  214.477   6.222   1.025  -0.525  H3     JMC  26  
JMC  H4     H4   H  0  1  N  N  N  276.179  208.239  209.666   1.286  -1.155  -1.475  H4     JMC  27  
JMC  H5     H5   H  0  1  N  N  N  277.694  207.395  211.828   0.888  -1.499   1.550  H5     JMC  28  
JMC  H6     H6   H  0  1  N  N  N  279.236  208.039  208.626   2.578  -2.938   2.218  H6     JMC  29  
JMC  H7     H7   H  0  1  N  N  N  277.740  208.792  209.274   1.243  -4.086   1.953  H7     JMC  30  
JMC  H8     H8   H  0  1  N  N  N  279.148  208.519  210.355   2.851  -4.415   1.262  H8     JMC  31  
JMC  H9     H9   H  0  1  N  N  N  276.303  205.560  212.364  -1.160  -2.576   1.146  H9     JMC  32  
JMC  H10    H10  H  0  1  N  N  N  274.086  210.927  212.765   4.741   1.788   1.520  H10    JMC  33  
JMC  H11    H11  H  0  1  N  N  N  275.931  204.969  209.416  -1.541  -1.473  -1.529  H11    JMC  34  
JMC  H12    H12  H  0  1  N  N  N  276.435  211.345  213.101   2.407   2.400   2.457  H12    JMC  35  
JMC  H13    H13  H  0  1  N  N  N  273.919  204.858  211.686  -3.188  -1.542   0.383  H13    JMC  36  
JMC  H14    H14  H  0  1  N  N  N  273.744  204.232  210.011  -2.211  -0.307   1.213  H14    JMC  37  
JMC  H15    H15  H  0  1  N  N  N  277.108  209.718  211.390   0.813   0.807   1.614  H15    JMC  38  
JMC  H16    H16  H  0  1  N  N  N  273.327  210.936  214.846   3.964   4.018   1.228  H16    JMC  39  
JMC  H17    H17  H  0  1  N  N  N  274.891  211.236  215.209   4.895   3.578  -0.078  H17    JMC  40  
JMC  H19    H19  H  0  1  N  N  N  278.374  204.667  211.836  -1.468  -3.865  -0.841  H19    JMC  41  
JMC  H20    H20  H  0  1  N  N  N  275.403  202.011  214.175  -5.909  -0.434  -0.805  H20    JMC  42  
JMC  H21    H21  H  0  1  N  N  N  272.242  202.218  212.350  -5.694   2.716  -0.795  H21    JMC  43  
#   #
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
JMC  C3     "O2'"  SING  N  N   1  
JMC  "O2'"  "C2'"  SING  N  N   2  
JMC  "O4'"  "C4'"  SING  N  N   3  
JMC  "O4'"  "C1'"  SING  N  N   4  
JMC  "C4'"  "C5'"  SING  N  N   5  
JMC  "C4'"  "C3'"  SING  N  N   6  
JMC  "C1'"  "C2'"  SING  N  N   7  
JMC  "C1'"  N1     SING  N  N   8  
JMC  "C5'"  "O5'"  SING  N  N   9  
JMC  "C2'"  "C3'"  SING  N  N  10  
JMC  "O3'"  "C3'"  SING  N  N  11  
JMC  "O5'"  P      SING  N  N  12  
JMC  N1     C6     SING  N  N  13  
JMC  N1     C2     SING  N  N  14  
JMC  C6     C5     DOUB  N  N  15  
JMC  O2     C2     DOUB  N  N  16  
JMC  OP2    P      DOUB  N  N  17  
JMC  C2     N3     SING  N  N  18  
JMC  P      OP1    SING  N  N  19  
JMC  C5     C4     SING  N  N  20  
JMC  N3     C4     SING  N  N  21  
JMC  N3     C1     SING  N  N  22  
JMC  C4     N4     SING  N  N  23  
JMC  P      O1     SING  N  N  24  
JMC  C1     H1     SING  N  N  25  
JMC  C1     H2     SING  N  N  26  
JMC  C1     H3     SING  N  N  27  
JMC  "C1'"  H4     SING  N  N  28  
JMC  "C2'"  H5     SING  N  N  29  
JMC  C3     H6     SING  N  N  30  
JMC  C3     H7     SING  N  N  31  
JMC  C3     H8     SING  N  N  32  
JMC  "C3'"  H9     SING  N  N  33  
JMC  C4     H10    SING  N  N  34  
JMC  "C4'"  H11    SING  N  N  35  
JMC  C5     H12    SING  N  N  36  
JMC  "C5'"  H13    SING  N  N  37  
JMC  "C5'"  H14    SING  N  N  38  
JMC  C6     H15    SING  N  N  39  
JMC  N4     H16    SING  N  N  40  
JMC  N4     H17    SING  N  N  41  
JMC  "O3'"  H19    SING  N  N  42  
JMC  OP1    H20    SING  N  N  43  
JMC  O1     H21    SING  N  N  44  
#   #
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
JMC  InChI             InChI                 1.03   "InChI=1S/C11H20N3O8P/c1-13-7(12)3-4-14(11(13)16)10-9(20-2)8(15)6(22-10)5-21-23(17,18)19/h3-4,6-10,15H,5,12H2,1-2H3,(H2,17,18,19)/t6-,7-,8-,9-,10-/m1/s1"  
JMC  InChIKey          InChI                 1.03   BKSKIJTVQSZCSV-VVULQXIFSA-N  
JMC  SMILES_CANONICAL  CACTVS                3.385  "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C[C@H](N)N(C)C2=O"  
JMC  SMILES            CACTVS                3.385  "CO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C[CH](N)N(C)C2=O"  
JMC  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CN1C(C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OC)N"  
JMC  SMILES            "OpenEye OEToolkits"  2.0.7  "CN1C(C=CN(C1=O)C2C(C(C(O2)COP(=O)(O)O)O)OC)N"  
#
_pdbx_chem_comp_identifier.comp_id          JMC
_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-3-methyl-2-oxidanylidene-4~{H}-pyrimidin-1-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
JMC  "Create component"  2020-06-29  PDBE  
JMC  "Initial release"   2020-10-07  RCSB  
##
