data_TCJ
#

_chem_comp.id                                   TCJ
_chem_comp.name                                 "[(1~{S},2~{R},4~{R},6~{S},8~{R})-8-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-6-oxidanyl-9-oxatricyclo[4.3.0.0^{2,4}]nonan-2-yl] dihydrogen phosphate"
_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C13 H18 N3 O7 P"
_chem_comp.mon_nstd_parent_comp_id              DC
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2018-03-12
_chem_comp.pdbx_modified_date                   2019-05-06
_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                       359.272
_chem_comp.one_letter_code                      C
_chem_comp.three_letter_code                    TCJ
_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       6FW6
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 EBI
#   #
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
TCJ  P       P1   P  0  1  N  N  N  -3.913  -4.784  16.470   3.080   1.596   0.396  P       TCJ   1  
TCJ  O1P     O1   O  0  1  N  N  N  -3.281  -5.938  15.792   1.909   1.638   1.299  O1P     TCJ   2  
TCJ  O2P     O2   O  0  1  N  N  N  -4.601  -4.986  17.764   4.327   0.928   1.164  O2P     TCJ   3  
TCJ  "O5'"   O3   O  0  1  N  N  N  -2.782  -3.652  16.680   2.721   0.722  -0.908  "O5'"   TCJ   4  
TCJ  "C5'"   C1   C  0  1  N  N  R  -1.607  -3.974  17.395   2.238  -0.621  -0.835  "C5'"   TCJ   5  
TCJ  "C4'"   C2   C  0  1  N  N  S  -0.454  -4.630  16.653   1.392  -1.001   0.394  "C4'"   TCJ   6  
TCJ  "O4'"   O4   O  0  1  N  N  N  -0.375  -4.110  15.320   0.340  -0.032   0.558  "O4'"   TCJ   7  
TCJ  "C1'"   C3   C  0  1  N  N  R   0.923  -3.544  15.083  -0.788  -0.706   1.136  "C1'"   TCJ   8  
TCJ  N1      N1   N  0  1  N  N  N   0.828  -2.050  14.947  -2.031  -0.139   0.608  N1      TCJ   9  
TCJ  C6      C4   C  0  1  N  N  N  -0.329  -1.347  15.265  -2.035   0.470  -0.611  C6      TCJ  10  
TCJ  C5      C5   C  0  1  N  N  N  -0.386   0.011  15.146  -3.190   0.991  -1.088  C5      TCJ  11  
TCJ  C7      C6   C  0  1  N  N  N  -1.643   0.794  15.488  -3.226   1.669  -2.433  C7      TCJ  12  
TCJ  C4      C7   C  0  1  N  N  N   0.809   0.687  14.674  -4.359   0.888  -0.306  C4      TCJ  13  
TCJ  N4      N2   N  0  1  N  N  N   0.823   2.022  14.534  -5.547   1.408  -0.767  N4      TCJ  14  
TCJ  N3      N3   N  0  1  N  N  N   1.928  -0.007  14.367  -4.308   0.287   0.875  N3      TCJ  15  
TCJ  C2      C8   C  0  1  N  N  N   1.980  -1.376  14.488  -3.165  -0.226   1.328  C2      TCJ  16  
TCJ  O2      O5   O  0  1  N  N  N   3.004  -2.000  14.208  -3.143  -0.774   2.417  O2      TCJ  17  
TCJ  "C3'"   C9   C  0  1  N  N  S   0.837  -4.279  17.376   0.643  -2.299  -0.036  "C3'"   TCJ  18  
TCJ  "C2'"   C10  C  0  1  N  N  N   1.815  -3.914  16.267  -0.685  -2.192   0.746  "C2'"   TCJ  19  
TCJ  "C7'"   C11  C  0  1  N  N  N   0.493  -3.092  18.313   0.375  -2.067  -1.539  "C7'"   TCJ  20  
TCJ  "C6'"   C12  C  0  1  N  N  S  -1.025  -3.011  18.397   1.590  -1.297  -2.054  "C6'"   TCJ  21  
TCJ  "C8'"   C13  C  0  1  N  N  N  -1.723  -4.251  18.866   2.984  -1.723  -1.591  "C8'"   TCJ  22  
TCJ  "O3'"   O6   O  0  1  N  N  N   1.310  -5.391  18.121   1.369  -3.500   0.235  "O3'"   TCJ  23  
TCJ  H2      H2   H  0  1  N  N  N  -4.545  -5.901  18.014   5.131   0.867   0.630  H2      TCJ  24  
TCJ  "H4'"   H3   H  0  1  N  N  N  -0.590  -5.721  16.644   1.994  -1.137   1.293  "H4'"   TCJ  25  
TCJ  "H1'"   H4   H  0  1  N  N  N   1.358  -3.964  14.164  -0.764  -0.605   2.221  "H1'"   TCJ  26  
TCJ  H6      H5   H  0  1  N  N  N  -1.198  -1.886  15.612  -1.126   0.536  -1.191  H6      TCJ  27  
TCJ  H73     H6   H  0  1  N  N  N  -2.428   0.100  15.824  -3.455   0.934  -3.205  H73     TCJ  28  
TCJ  H71     H7   H  0  1  N  N  N  -1.420   1.512  16.291  -3.993   2.443  -2.429  H71     TCJ  29  
TCJ  H72     H8   H  0  1  N  N  N  -1.991   1.337  14.597  -2.255   2.121  -2.638  H72     TCJ  30  
TCJ  H41     H9   H  0  1  N  N  N   1.649   2.482  14.209  -5.582   1.847  -1.631  H41     TCJ  31  
TCJ  H42     H10  H  0  1  N  N  N   0.007   2.556  14.755  -6.350   1.336  -0.227  H42     TCJ  32  
TCJ  "H2'"   H11  H  0  1  N  N  N   2.458  -4.771  16.017  -0.652  -2.818   1.638  "H2'"   TCJ  33  
TCJ  "H2''"  H12  H  0  0  N  N  N   2.441  -3.060  16.565  -1.524  -2.478   0.111  "H2''"  TCJ  34  
TCJ  "H7'"   H13  H  0  1  N  N  N   0.917  -3.266  19.313   0.268  -3.020  -2.058  "H7'"   TCJ  35  
TCJ  "H7''"  H14  H  0  0  N  N  N   0.898  -2.156  17.900  -0.518  -1.457  -1.676  "H7''"  TCJ  36  
TCJ  "H6'"   H15  H  0  1  N  N  N  -1.501  -2.030  18.544   1.474  -0.761  -2.997  "H6'"   TCJ  37  
TCJ  "H8'"   H16  H  0  1  N  N  N  -2.701  -4.176  19.364   3.832  -1.424  -2.207  "H8'"   TCJ  38  
TCJ  "H8''"  H17  H  0  0  N  N  N  -1.144  -5.070  19.318   3.077  -2.694  -1.103  "H8''"  TCJ  39  
TCJ  H3T     H18  H  0  1  N  N  N   0.687  -5.602  18.806   0.907  -4.307  -0.031  H3T     TCJ  40  
TCJ  OP3     OP3  O  0  1  N  Y  N  -5.097  -4.261  15.336   3.466   3.094  -0.053  OP3     TCJ  41  
TCJ  H1      H1   H  0  1  N  N  N  -5.067  -4.818  14.567   3.694   3.678   0.683  H1      TCJ  42  
#   #
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
TCJ  O2     C2      DOUB  N  N   1  
TCJ  N3     C2      SING  N  N   2  
TCJ  N3     C4      DOUB  N  N   3  
TCJ  C2     N1      SING  N  N   4  
TCJ  N4     C4      SING  N  N   5  
TCJ  C4     C5      SING  N  N   6  
TCJ  N1     "C1'"   SING  N  N   7  
TCJ  N1     C6      SING  N  N   8  
TCJ  "C1'"  "O4'"   SING  N  N   9  
TCJ  "C1'"  "C2'"   SING  N  N  10  
TCJ  C5     C6      DOUB  N  N  11  
TCJ  C5     C7      SING  N  N  12  
TCJ  "O4'"  "C4'"   SING  N  N  13  
TCJ  O1P    P       DOUB  N  N  14  
TCJ  "C2'"  "C3'"   SING  N  N  15  
TCJ  P      "O5'"   SING  N  N  16  
TCJ  P      O2P     SING  N  N  17  
TCJ  "C4'"  "C3'"   SING  N  N  18  
TCJ  "C4'"  "C5'"   SING  N  N  19  
TCJ  "O5'"  "C5'"   SING  N  N  20  
TCJ  "C3'"  "O3'"   SING  N  N  21  
TCJ  "C3'"  "C7'"   SING  N  N  22  
TCJ  "C5'"  "C6'"   SING  N  N  23  
TCJ  "C5'"  "C8'"   SING  N  N  24  
TCJ  "C7'"  "C6'"   SING  N  N  25  
TCJ  "C6'"  "C8'"   SING  N  N  26  
TCJ  O2P    H2      SING  N  N  27  
TCJ  "C4'"  "H4'"   SING  N  N  28  
TCJ  "C1'"  "H1'"   SING  N  N  29  
TCJ  C6     H6      SING  N  N  30  
TCJ  C7     H73     SING  N  N  31  
TCJ  C7     H71     SING  N  N  32  
TCJ  C7     H72     SING  N  N  33  
TCJ  N4     H41     SING  N  N  34  
TCJ  N4     H42     SING  N  N  35  
TCJ  "C2'"  "H2'"   SING  N  N  36  
TCJ  "C2'"  "H2''"  SING  N  N  37  
TCJ  "C7'"  "H7'"   SING  N  N  38  
TCJ  "C7'"  "H7''"  SING  N  N  39  
TCJ  "C6'"  "H6'"   SING  N  N  40  
TCJ  "C8'"  "H8'"   SING  N  N  41  
TCJ  "C8'"  "H8''"  SING  N  N  42  
TCJ  "O3'"  H3T     SING  N  N  43  
TCJ  P      OP3     SING  N  N  44  
TCJ  OP3    H1      SING  N  N  45  
#   #
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
TCJ  InChI             InChI                 1.03   "InChI=1S/C13H18N3O7P/c1-6-5-16(11(17)15-9(6)14)8-4-12(18)2-7-3-13(7,10(12)22-8)23-24(19,20)21/h5,7-8,10,18H,2-4H2,1H3,(H2,14,15,17)(H2,19,20,21)/t7-,8-,10+,12+,13-/m1/s1"  
TCJ  InChIKey          InChI                 1.03   QNNOIYJQVYUYLR-ZIDZYHNGSA-N  
TCJ  SMILES_CANONICAL  CACTVS                3.385  "CC1=CN([C@H]2C[C@@]3(O)C[C@@H]4C[C@]4(O[P](O)(O)=O)[C@H]3O2)C(=O)N=C1N"  
TCJ  SMILES            CACTVS                3.385  "CC1=CN([CH]2C[C]3(O)C[CH]4C[C]4(O[P](O)(O)=O)[CH]3O2)C(=O)N=C1N"  
TCJ  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "CC1=CN(C(=O)N=C1N)[C@H]2C[C@]3(C[C@@H]4C[C@@]4([C@H]3O2)OP(=O)(O)O)O"  
TCJ  SMILES            "OpenEye OEToolkits"  2.0.6  "CC1=CN(C(=O)N=C1N)C2CC3(CC4CC4(C3O2)OP(=O)(O)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          TCJ
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.6
_pdbx_chem_comp_identifier.identifier       "[(1~{S},2~{R},4~{R},6~{S},8~{R})-8-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-6-oxidanyl-9-oxatricyclo[4.3.0.0^{2,4}]nonan-2-yl] 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
TCJ  "Create component"        2018-03-12  EBI   
TCJ  "Initial release"         2018-06-06  RCSB  
TCJ  "Modify one letter code"  2019-05-06  EBI   
##
