data_XRF
#

_chem_comp.id                                   XRF
_chem_comp.name                                 "1-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C10 H17 N2 O14 P3"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-03-09
_chem_comp.pdbx_modified_date                   2022-02-18
_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                       482.168
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    XRF
_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       7LSK
_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
XRF  N    N1   N  0  1  N  N  N  -0.045  -45.710  132.178  -4.804   0.457  -0.498  N    XRF   1  
XRF  C    C1   C  0  1  N  N  N  -2.770  -43.408  133.440  -4.333   3.597   1.477  C    XRF   2  
XRF  O    O1   O  0  1  N  N  N   0.020  -47.988  131.993  -6.602  -0.356  -1.501  O    XRF   3  
XRF  C1   C2   C  0  1  N  N  N  -2.000  -44.635  133.050  -4.958   2.501   0.653  C1   XRF   4  
XRF  C2   C3   C  0  1  N  N  N  -0.755  -44.590  132.552  -4.221   1.444   0.250  C2   XRF   5  
XRF  C3   C4   C  0  1  N  N  N  -0.583  -46.973  132.305  -6.104   0.532  -0.836  C3   XRF   6  
XRF  C4   C5   C  0  1  N  N  N  -2.624  -45.930  133.209  -6.325   2.567   0.289  C4   XRF   7  
XRF  C5   C6   C  0  1  N  N  S   1.318  -45.588  131.619  -4.004  -0.687  -0.940  C5   XRF   8  
XRF  C6   C7   C  0  1  N  N  N   2.339  -45.029  132.596  -4.597  -2.003  -0.390  C6   XRF   9  
XRF  C7   C8   C  0  1  N  N  R   3.222  -44.132  131.737  -3.358  -2.864  -0.058  C7   XRF  10  
XRF  C8   C9   C  0  1  N  N  S   2.272  -43.669  130.641  -2.162  -1.967  -0.447  C8   XRF  11  
XRF  C9   C10  C  0  1  N  N  N   1.609  -42.350  130.932  -1.013  -2.151   0.546  C9   XRF  12  
XRF  N1   N2   N  0  1  N  N  N  -1.854  -47.007  132.818  -6.862   1.575  -0.449  N1   XRF  13  
XRF  O1   O2   O  0  1  N  N  N  -3.751  -46.115  133.664  -7.009   3.511   0.640  O1   XRF  14  
XRF  O10  O3   O  0  1  N  N  N  -0.038  -36.473  126.364   6.046   2.792  -1.852  O10  XRF  15  
XRF  O11  O4   O  0  1  N  N  N   0.289  -38.933  125.906   7.199   0.753  -0.912  O11  XRF  16  
XRF  O12  O5   O  0  1  N  N  N   1.524  -37.861  127.782   6.320   2.448   0.739  O12  XRF  17  
XRF  O13  O6   O  0  1  N  N  N   4.338  -44.824  131.180  -3.360  -4.064  -0.834  O13  XRF  18  
XRF  O2   O7   O  0  1  N  N  N   1.265  -44.696  130.516  -2.675  -0.618  -0.378  O2   XRF  19  
XRF  O3   O8   O  0  1  N  N  N   0.719  -42.069  129.843   0.122  -1.404   0.105  O3   XRF  20  
XRF  O4   O9   O  0  1  N  N  N   1.128  -42.530  127.375   2.000  -2.750   1.120  O4   XRF  21  
XRF  O5   O10  O  0  1  N  N  N   2.261  -40.550  128.589   1.291  -0.655   2.337  O5   XRF  22  
XRF  O6   O11  O  0  1  N  N  N  -0.230  -40.577  128.301   2.604  -0.539   0.062  O6   XRF  23  
XRF  O7   O12  O  0  1  N  N  N   0.405  -38.917  130.105   4.810  -1.726  -0.736  O7   XRF  24  
XRF  O8   O13  O  0  1  N  N  N  -2.048  -39.624  129.745   4.699  -0.506   1.470  O8   XRF  25  
XRF  O9   O14  O  0  1  N  N  N  -0.868  -38.234  128.015   4.695   0.898  -0.627  O9   XRF  26  
XRF  P    P1   P  0  1  N  N  N   1.066  -41.488  128.423   1.515  -1.367   0.910  P    XRF  27  
XRF  P1   P2   P  0  1  N  N  N  -0.671  -39.316  129.164   4.213  -0.469   0.073  P1   XRF  28  
XRF  P2   P3   P  0  1  N  N  N   0.241  -37.812  126.952   6.090   1.702  -0.668  P2   XRF  29  
XRF  H1   H1   H  0  1  N  N  N  -3.760  -43.701  133.819  -5.083   4.356   1.701  H1   XRF  30  
XRF  H2   H2   H  0  1  N  N  N  -2.223  -42.866  134.225  -3.951   3.179   2.408  H2   XRF  31  
XRF  H3   H3   H  0  1  N  N  N  -2.892  -42.757  132.562  -3.514   4.050   0.919  H3   XRF  32  
XRF  H4   H4   H  0  1  N  N  N  -0.284  -43.625  132.438  -3.177   1.376   0.518  H4   XRF  33  
XRF  H5   H5   H  0  1  N  N  N   1.660  -46.578  131.284  -3.956  -0.718  -2.028  H5   XRF  34  
XRF  H6   H6   H  0  1  N  N  N   1.844  -44.447  133.388  -5.181  -1.812   0.511  H6   XRF  35  
XRF  H7   H7   H  0  1  N  N  N   2.929  -45.839  133.050  -5.212  -2.490  -1.146  H7   XRF  36  
XRF  H8   H8   H  0  1  N  N  N   3.552  -43.265  132.329  -3.330  -3.099   1.006  H8   XRF  37  
XRF  H9   H9   H  0  1  N  N  N   2.835  -43.585  129.700  -1.829  -2.197  -1.459  H9   XRF  38  
XRF  H10  H10  H  0  1  N  N  N   2.367  -41.557  131.012  -1.322  -1.797   1.529  H10  XRF  39  
XRF  H11  H11  H  0  1  N  N  N   1.043  -42.413  131.873  -0.751  -3.208   0.606  H11  XRF  40  
XRF  H12  H12  H  0  1  N  N  N  -2.269  -47.911  132.920  -7.798   1.612  -0.701  H12  XRF  41  
XRF  H13  H13  H  0  1  N  N  N  -0.139  -36.555  125.423   6.855   3.315  -1.936  H13  XRF  42  
XRF  H14  H14  H  0  1  N  N  N   2.074  -38.572  127.474   5.630   3.086   0.965  H14  XRF  43  
XRF  H15  H15  H  0  1  N  N  N   4.918  -45.104  131.878  -4.123  -4.637  -0.671  H15  XRF  44  
XRF  H16  H16  H  0  1  N  N  N   2.931  -40.775  127.954   0.973   0.255   2.276  H16  XRF  45  
XRF  H17  H17  H  0  1  N  N  N   0.064  -38.909  130.992   4.532  -1.766  -1.662  H17  XRF  46  
#   #
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
XRF  O11  P2   DOUB  N  N   1  
XRF  O10  P2   SING  N  N   2  
XRF  P2   O12  SING  N  N   3  
XRF  P2   O9   SING  N  N   4  
XRF  O4   P    DOUB  N  N   5  
XRF  O9   P1   SING  N  N   6  
XRF  O6   P    SING  N  N   7  
XRF  O6   P1   SING  N  N   8  
XRF  P    O5   SING  N  N   9  
XRF  P    O3   SING  N  N  10  
XRF  P1   O8   DOUB  N  N  11  
XRF  P1   O7   SING  N  N  12  
XRF  O3   C9   SING  N  N  13  
XRF  O2   C8   SING  N  N  14  
XRF  O2   C5   SING  N  N  15  
XRF  C8   C9   SING  N  N  16  
XRF  C8   C7   SING  N  N  17  
XRF  O13  C7   SING  N  N  18  
XRF  C5   N    SING  N  N  19  
XRF  C5   C6   SING  N  N  20  
XRF  C7   C6   SING  N  N  21  
XRF  O    C3   DOUB  N  N  22  
XRF  N    C3   SING  N  N  23  
XRF  N    C2   SING  N  N  24  
XRF  C3   N1   SING  N  N  25  
XRF  C2   C1   DOUB  N  N  26  
XRF  N1   C4   SING  N  N  27  
XRF  C1   C4   SING  N  N  28  
XRF  C1   C    SING  N  N  29  
XRF  C4   O1   DOUB  N  N  30  
XRF  C    H1   SING  N  N  31  
XRF  C    H2   SING  N  N  32  
XRF  C    H3   SING  N  N  33  
XRF  C2   H4   SING  N  N  34  
XRF  C5   H5   SING  N  N  35  
XRF  C6   H6   SING  N  N  36  
XRF  C6   H7   SING  N  N  37  
XRF  C7   H8   SING  N  N  38  
XRF  C8   H9   SING  N  N  39  
XRF  C9   H10  SING  N  N  40  
XRF  C9   H11  SING  N  N  41  
XRF  N1   H12  SING  N  N  42  
XRF  O10  H13  SING  N  N  43  
XRF  O12  H14  SING  N  N  44  
XRF  O13  H15  SING  N  N  45  
XRF  O5   H16  SING  N  N  46  
XRF  O7   H17  SING  N  N  47  
#   #
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
XRF  SMILES            ACDLabs               12.01  "O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC1OC(CC1O)N1C=C(C)C(=O)NC1=O"  
XRF  InChI             InChI                 1.03   "InChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m1/s1"  
XRF  InChIKey          InChI                 1.03   NHVNXKFIZYSCEB-CSMHCCOUSA-N  
XRF  SMILES_CANONICAL  CACTVS                3.385  "CC1=CN([C@@H]2C[C@@H](O)[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O"  
XRF  SMILES            CACTVS                3.385  "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O"  
XRF  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CC1=CN(C(=O)NC1=O)[C@@H]2C[C@H]([C@@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O"  
XRF  SMILES            "OpenEye OEToolkits"  2.0.7  "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)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
XRF  "SYSTEMATIC NAME"  ACDLabs               12.01  "1-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione"  
XRF  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[[(2~{S},3~{R},5~{S})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate"  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     XRF
_pdbx_chem_comp_synonyms.name        L-dTTP
_pdbx_chem_comp_synonyms.provenance  AUTHOR
_pdbx_chem_comp_synonyms.type        ?
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
XRF  "Create component"  2021-03-09  RCSB  
XRF  "Initial release"   2022-02-23  RCSB  
##
