data_F6X
#

_chem_comp.id                                   F6X
_chem_comp.name                                 "[(2R,3R)-3-[2-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)ethanoylamino]-4-oxidanyl-butan-2-yl] dihydrogen phosphate"
_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C10 H17 N4 O7 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-04-03
_chem_comp.pdbx_modified_date                   2020-11-20
_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                       336.238
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    F6X
_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       7BPF
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
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
F6X  "C1'"   C1   C  0  1  N  N  N  -25.542  -29.541  16.976  -1.249   2.899  -0.353  "C1'"  F6X   1  
F6X  N1      N1   N  0  1  N  N  N  -22.849  -24.581  15.626   2.877  -0.544   0.438  N1     F6X   2  
F6X  C6      C2   C  0  1  N  N  N  -23.354  -23.868  14.535   3.229  -1.557  -0.402  C6     F6X   3  
F6X  C5      C3   C  0  1  N  N  N  -23.394  -22.484  14.521   4.503  -1.630  -0.854  C5     F6X   4  
F6X  C4      C4   C  0  1  N  N  N  -22.921  -21.814  15.639   5.431  -0.652  -0.441  C4     F6X   5  
F6X  N3      N2   N  0  1  N  N  N  -22.437  -22.561  16.733   5.043   0.316   0.379  N3     F6X   6  
F6X  C2      C5   C  0  1  N  N  N  -22.401  -23.941  16.714   3.786   0.374   0.815  C2     F6X   7  
F6X  O2      O1   O  0  1  N  N  N  -21.969  -24.558  17.689   3.453   1.274   1.568  O2     F6X   8  
F6X  N4      N3   N  0  1  N  N  N  -22.936  -20.495  15.658   6.732  -0.702  -0.885  N4     F6X   9  
F6X  "C2'"   C6   C  0  1  N  N  R  -25.718  -28.439  15.948  -1.418   1.418  -0.697  "C2'"  F6X  10  
F6X  "C3'"   C7   C  0  1  N  N  R  -26.338  -28.992  14.677  -2.894   1.032  -0.576  "C3'"  F6X  11  
F6X  "O3'"   O2   O  0  1  N  N  N  -25.343  -29.766  14.048  -3.041  -0.368  -0.825  "O3'"  F6X  12  
F6X  OP1     O3   O  0  1  N  N  N  -27.249  -30.837  12.395  -5.143  -0.856   0.485  OP1    F6X  13  
F6X  P       P1   P  0  1  N  N  N  -25.687  -30.738  12.860  -3.784  -1.366   0.197  P      F6X  14  
F6X  OP2     O4   O  0  1  N  N  N  -24.616  -31.881  12.370  -3.889  -2.830  -0.465  OP2    F6X  15  
F6X  C3A     C8   C  0  1  N  N  N  -26.766  -27.829  13.765  -3.713   1.821  -1.599  C3A    F6X  16  
F6X  "O1'"   O5   O  0  1  N  N  N  -26.730  -29.532  17.789  -1.815   3.157   0.934  "O1'"  F6X  17  
F6X  "N2'"   N4   N  0  1  N  N  N  -24.432  -27.810  15.599  -0.623   0.608   0.228  "N2'"  F6X  18  
F6X  C2A     C9   C  0  1  N  N  N  -24.143  -26.584  16.041   0.682   0.384  -0.022  C2A    F6X  19  
F6X  O2A     O6   O  0  1  N  N  N  -24.866  -25.912  16.771   1.199   0.854  -1.014  O2A    F6X  20  
F6X  C2B     C10  C  0  1  N  N  N  -22.819  -26.050  15.564   1.500  -0.450   0.930  C2B    F6X  21  
F6X  H1      H1   H  0  1  N  N  N  -25.431  -30.514  16.475  -0.188   3.151  -0.340  H1     F6X  22  
F6X  H2      H2   H  0  1  N  N  N  -24.655  -29.345  17.596  -1.757   3.507  -1.101  H2     F6X  23  
F6X  H3      H3   H  0  1  N  N  N  -23.724  -24.412  13.678   2.499  -2.294  -0.704  H3     F6X  24  
F6X  H4      H4   H  0  1  N  N  N  -23.780  -21.945  13.669   4.804  -2.424  -1.521  H4     F6X  25  
F6X  H5      H5   H  0  1  N  N  N  -22.599  -20.003  16.461   7.014  -1.412  -1.484  H5     F6X  26  
F6X  H6      H6   H  0  1  N  N  N  -23.284  -19.988  14.870   7.369  -0.029  -0.599  H6     F6X  27  
F6X  H7      H7   H  0  1  N  N  N  -26.392  -27.676  16.364  -1.079   1.242  -1.718  H7     F6X  28  
F6X  H8      H8   H  0  1  N  N  N  -27.218  -29.602  14.929  -3.248   1.262   0.429  H8     F6X  29  
F6X  HOP2    H10  H  0  0  N  N  N  -25.062  -32.522  11.828  -4.327  -3.485   0.096  H10    F6X  30  
F6X  H11     H11  H  0  1  N  N  N  -27.542  -27.234  14.268  -4.764   1.546  -1.513  H11    F6X  31  
F6X  H12     H12  H  0  1  N  N  N  -25.896  -27.191  13.552  -3.601   2.888  -1.409  H12    F6X  32  
F6X  H13     H13  H  0  1  N  N  N  -27.166  -28.231  12.822  -3.359   1.591  -2.604  H13    F6X  33  
F6X  H14     H14  H  0  1  N  Y  N  -26.666  -30.210  18.452  -1.677   4.060   1.251  H14    F6X  34  
F6X  H15     H15  H  0  1  N  N  N  -23.774  -28.303  15.030  -1.036   0.232   1.021  H15    F6X  35  
F6X  H16     H16  H  0  1  N  N  N  -22.642  -26.373  14.527   1.070  -1.449   0.999  H16    F6X  36  
F6X  H17     H17  H  0  1  N  N  N  -22.013  -26.431  16.209   1.497   0.015   1.916  H17    F6X  37  
F6X  OP3     OP4  O  0  1  N  Y  N  -25.485  -29.782  11.743  -2.943  -1.456   1.566  OP4    F6X  38  
F6X  HOP3    H9   H  0  0  N  Y  N  -26.305  -29.658  11.279  -2.027  -1.742   1.447  H9     F6X  39  
#   #
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
F6X  OP2    P       SING  N  N   1  
F6X  OP1    P       DOUB  N  N   2  
F6X  P      "O3'"   SING  N  N   3  
F6X  C3A    "C3'"   SING  N  N   4  
F6X  "O3'"  "C3'"   SING  N  N   5  
F6X  C5     C6      DOUB  N  N   6  
F6X  C5     C4      SING  N  N   7  
F6X  C6     N1      SING  N  N   8  
F6X  "C3'"  "C2'"   SING  N  N   9  
F6X  C2B    N1      SING  N  N  10  
F6X  C2B    C2A     SING  N  N  11  
F6X  "N2'"  "C2'"   SING  N  N  12  
F6X  "N2'"  C2A     SING  N  N  13  
F6X  N1     C2      SING  N  N  14  
F6X  C4     N4      SING  N  N  15  
F6X  C4     N3      DOUB  N  N  16  
F6X  "C2'"  "C1'"   SING  N  N  17  
F6X  C2A    O2A     DOUB  N  N  18  
F6X  C2     N3      SING  N  N  19  
F6X  C2     O2      DOUB  N  N  20  
F6X  "C1'"  "O1'"   SING  N  N  21  
F6X  "C1'"  H1      SING  N  N  22  
F6X  "C1'"  H2      SING  N  N  23  
F6X  C6     H3      SING  N  N  24  
F6X  C5     H4      SING  N  N  25  
F6X  N4     H5      SING  N  N  26  
F6X  N4     H6      SING  N  N  27  
F6X  "C2'"  H7      SING  N  N  28  
F6X  "C3'"  H8      SING  N  N  29  
F6X  OP2    HOP2    SING  N  N  30  
F6X  C3A    H11     SING  N  N  31  
F6X  C3A    H12     SING  N  N  32  
F6X  C3A    H13     SING  N  N  33  
F6X  "O1'"  H14     SING  N  N  34  
F6X  "N2'"  H15     SING  N  N  35  
F6X  C2B    H16     SING  N  N  36  
F6X  C2B    H17     SING  N  N  37  
F6X  P      OP3     SING  N  N  38  
F6X  OP3    HOP3    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
F6X  InChI             InChI                 1.03   "InChI=1S/C10H17N4O7P/c1-6(21-22(18,19)20)7(5-15)12-9(16)4-14-3-2-8(11)13-10(14)17/h2-3,6-7,15H,4-5H2,1H3,(H,12,16)(H2,11,13,17)(H2,18,19,20)/t6-,7-/m1/s1"  
F6X  InChIKey          InChI                 1.03   BNPHLZWYYOHAKE-RNFRBKRXSA-N  
F6X  SMILES_CANONICAL  CACTVS                3.385  "C[C@@H](O[P](O)(O)=O)[C@@H](CO)NC(=O)CN1C=CC(=NC1=O)N"  
F6X  SMILES            CACTVS                3.385  "C[CH](O[P](O)(O)=O)[CH](CO)NC(=O)CN1C=CC(=NC1=O)N"  
F6X  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C[C@H]([C@@H](CO)NC(=O)CN1C=CC(=NC1=O)N)OP(=O)(O)O"  
F6X  SMILES            "OpenEye OEToolkits"  2.0.7  "CC(C(CO)NC(=O)CN1C=CC(=NC1=O)N)OP(=O)(O)O"  
#
_pdbx_chem_comp_identifier.comp_id          F6X
_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})-3-[2-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)ethanoylamino]-4-oxidanyl-butan-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
F6X  "Create component"          2020-04-03  PDBJ  
F6X  "Modify internal type"      2020-11-04  PDBJ  
F6X  "Modify linking type"       2020-11-04  PDBJ  
F6X  "Modify leaving atom flag"  2020-11-04  PDBJ  
F6X  "Modify linking type"       2020-11-18  PDBJ  
F6X  "Initial release"           2020-11-25  RCSB  
##
