data_T0P
#

_chem_comp.id                                   T0P
_chem_comp.name                                 "[(2~{R},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-7-phenacyl-1~{H}-purin-9-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate"
_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C18 H20 F N5 O8 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-03-16
_chem_comp.pdbx_modified_date                   2022-02-04
_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                       484.352
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    ?
_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  Y
_chem_comp.pdbx_model_coordinates_db_code       7LCD
_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
T0P  N    N1   N  0  1  Y  N  N  -56.958  -5.307  -19.390  ?  ?  ?  N    T0P   1  
T0P  CA   C1   C  0  1  N  N  N  -55.618  -5.342  -18.744  ?  ?  ?  CA   T0P   2  
T0P  C    C2   C  0  1  N  N  N  -54.474  -5.163  -19.747  ?  ?  ?  C    T0P   3  
T0P  O    O1   O  0  1  N  N  N  -54.652  -4.968  -20.955  ?  ?  ?  O    T0P   4  
T0P  CAA  C3   C  0  1  Y  N  N  -57.535  -4.327  -20.096  ?  ?  ?  CAA  T0P   5  
T0P  CAB  C4   C  0  1  Y  N  N  -58.755  -4.763  -20.455  ?  ?  ?  CAB  T0P   6  
T0P  CAD  C5   C  0  1  N  N  N  -59.212  -2.779  -21.574  ?  ?  ?  CAD  T0P   7  
T0P  CAF  C6   C  0  1  N  N  N  -57.122  -3.104  -20.465  ?  ?  ?  CAF  T0P   8  
T0P  CAH  C7   C  0  1  Y  N  N  -57.819  -6.323  -19.306  ?  ?  ?  CAH  T0P   9  
T0P  CAK  C8   C  0  1  N  N  R  -60.137  -6.875  -20.124  ?  ?  ?  CAK  T0P  10  
T0P  CAN  C9   C  0  1  N  N  R  -61.651  -8.011  -21.365  ?  ?  ?  CAN  T0P  11  
T0P  CAO  C10  C  0  1  N  N  R  -62.307  -7.490  -20.081  ?  ?  ?  CAO  T0P  12  
T0P  CAP  C11  C  0  1  N  N  S  -61.471  -6.264  -19.787  ?  ?  ?  CAP  T0P  13  
T0P  CAS  C12  C  0  1  N  N  N  -62.586  -7.837  -22.563  ?  ?  ?  CAS  T0P  14  
T0P  CAW  C13  C  0  1  Y  N  N  -53.200  -5.238  -19.197  ?  ?  ?  CAW  T0P  15  
T0P  CAY  C14  C  0  1  Y  N  N  -53.017  -5.769  -17.924  ?  ?  ?  CAY  T0P  16  
T0P  CAZ  C15  C  0  1  Y  N  N  -51.729  -5.847  -17.385  ?  ?  ?  CAZ  T0P  17  
T0P  CBA  C16  C  0  1  Y  N  N  -50.626  -5.394  -18.101  ?  ?  ?  CBA  T0P  18  
T0P  CBB  C17  C  0  1  Y  N  N  -50.824  -4.862  -19.374  ?  ?  ?  CBB  T0P  19  
T0P  CBC  C18  C  0  1  Y  N  N  -52.104  -4.785  -19.923  ?  ?  ?  CBC  T0P  20  
T0P  FAQ  F1   F  0  1  N  N  N  -61.705  -5.284  -20.709  ?  ?  ?  FAQ  T0P  21  
T0P  NAC  N2   N  0  1  N  N  N  -59.581  -4.000  -21.183  ?  ?  ?  NAC  T0P  22  
T0P  NAE  N3   N  0  1  N  N  N  -57.960  -2.296  -21.223  ?  ?  ?  NAE  T0P  23  
T0P  NAI  N4   N  0  1  Y  N  N  -58.932  -5.987  -19.964  ?  ?  ?  NAI  T0P  24  
T0P  NAL  N5   N  0  1  N  N  N  -60.042  -2.034  -22.297  ?  ?  ?  NAL  T0P  25  
T0P  OAJ  O2   O  0  1  N  N  N  -56.020  -2.656  -20.160  ?  ?  ?  OAJ  T0P  26  
T0P  OAM  O3   O  0  1  N  N  N  -60.427  -7.211  -21.494  ?  ?  ?  OAM  T0P  27  
T0P  OAR  O4   O  0  1  N  N  N  -62.050  -8.444  -19.076  ?  ?  ?  OAR  T0P  28  
T0P  OAT  O5   O  0  1  N  N  N  -62.854  -6.439  -22.721  ?  ?  ?  OAT  T0P  29  
T0P  OBE  O6   O  0  1  N  N  N  -63.845  -4.437  -23.900  ?  ?  ?  OBE  T0P  30  
T0P  OBF  O7   O  0  1  N  N  N  -65.379  -6.251  -22.918  ?  ?  ?  OBF  T0P  31  
T0P  PBD  P1   P  0  1  N  N  N  -64.113  -5.871  -23.604  ?  ?  ?  PBD  T0P  32  
T0P  O1   O8   O  0  1  N  Y  N  -64.141  -6.303  -25.109  ?  ?  ?  O1   T0P  33  
T0P  H1   H1   H  0  1  N  N  N  -55.496  -6.312  -18.240  ?  ?  ?  H1   T0P  34  
T0P  H2   H2   H  0  1  N  N  N  -55.564  -4.533  -18.001  ?  ?  ?  H2   T0P  35  
T0P  H3   H3   H  0  1  N  N  N  -57.646  -7.258  -18.793  ?  ?  ?  H3   T0P  36  
T0P  H4   H4   H  0  1  N  N  N  -59.996  -7.790  -19.530  ?  ?  ?  H4   T0P  37  
T0P  H5   H5   H  0  1  N  N  N  -61.402  -9.076  -21.244  ?  ?  ?  H5   T0P  38  
T0P  H6   H6   H  0  1  N  N  N  -63.372  -7.253  -20.222  ?  ?  ?  H6   T0P  39  
T0P  H7   H7   H  0  1  N  N  N  -61.540  -5.946  -18.736  ?  ?  ?  H7   T0P  40  
T0P  H8   H8   H  0  1  N  N  N  -63.526  -8.379  -22.383  ?  ?  ?  H8   T0P  41  
T0P  H9   H9   H  0  1  N  N  N  -62.105  -8.229  -23.471  ?  ?  ?  H9   T0P  42  
T0P  H10  H10  H  0  1  N  N  N  -53.866  -6.119  -17.355  ?  ?  ?  H10  T0P  43  
T0P  H11  H11  H  0  1  N  N  N  -51.589  -6.265  -16.399  ?  ?  ?  H11  T0P  44  
T0P  H12  H12  H  0  1  N  N  N  -49.634  -5.453  -17.678  ?  ?  ?  H12  T0P  45  
T0P  H13  H13  H  0  1  N  N  N  -49.977  -4.505  -19.942  ?  ?  ?  H13  T0P  46  
T0P  H14  H14  H  0  1  N  N  N  -52.244  -4.374  -20.912  ?  ?  ?  H14  T0P  47  
T0P  H15  H15  H  0  1  N  N  N  -57.666  -1.384  -21.510  ?  ?  ?  H15  T0P  48  
T0P  H16  H16  H  0  1  N  N  N  -60.943  -2.389  -22.548  ?  ?  ?  H16  T0P  49  
T0P  H17  H17  H  0  1  N  N  N  -59.766  -1.119  -22.590  ?  ?  ?  H17  T0P  50  
T0P  H18  H18  H  0  1  N  N  N  -62.442  -8.158  -18.259  ?  ?  ?  H18  T0P  51  
T0P  H19  H19  H  0  1  N  N  N  -65.892  -5.471  -22.744  ?  ?  ?  H19  T0P  52  
T0P  H20  H20  H  0  1  N  N  N  -63.986  -5.544  -25.660  ?  ?  ?  H20  T0P  53  
#   #
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
T0P  OBE  PBD  DOUB  N  N   1  
T0P  PBD  OBF  SING  N  N   2  
T0P  PBD  OAT  SING  N  N   3  
T0P  OAT  CAS  SING  N  N   4  
T0P  CAS  CAN  SING  N  N   5  
T0P  NAL  CAD  SING  N  N   6  
T0P  CAD  NAE  SING  N  N   7  
T0P  CAD  NAC  DOUB  N  N   8  
T0P  OAM  CAN  SING  N  N   9  
T0P  OAM  CAK  SING  N  N  10  
T0P  CAN  CAO  SING  N  N  11  
T0P  NAE  CAF  SING  N  N  12  
T0P  NAC  CAB  SING  N  N  13  
T0P  O    C    DOUB  N  N  14  
T0P  FAQ  CAP  SING  N  N  15  
T0P  CAF  OAJ  DOUB  N  N  16  
T0P  CAF  CAA  SING  N  N  17  
T0P  CAB  CAA  DOUB  Y  N  18  
T0P  CAB  NAI  SING  Y  N  19  
T0P  CAK  NAI  SING  N  N  20  
T0P  CAK  CAP  SING  N  N  21  
T0P  CAA  N    SING  Y  N  22  
T0P  CAO  CAP  SING  N  N  23  
T0P  CAO  OAR  SING  N  N  24  
T0P  NAI  CAH  DOUB  Y  N  25  
T0P  CBC  CBB  DOUB  Y  N  26  
T0P  CBC  CAW  SING  Y  N  27  
T0P  C    CAW  SING  N  N  28  
T0P  C    CA   SING  N  N  29  
T0P  N    CAH  SING  Y  N  30  
T0P  N    CA   SING  N  N  31  
T0P  CBB  CBA  SING  Y  N  32  
T0P  CAW  CAY  DOUB  Y  N  33  
T0P  CBA  CAZ  DOUB  Y  N  34  
T0P  CAY  CAZ  SING  Y  N  35  
T0P  PBD  O1   SING  N  N  36  
T0P  CA   H1   SING  N  N  37  
T0P  CA   H2   SING  N  N  38  
T0P  CAH  H3   SING  N  N  39  
T0P  CAK  H4   SING  N  N  40  
T0P  CAN  H5   SING  N  N  41  
T0P  CAO  H6   SING  N  N  42  
T0P  CAP  H7   SING  N  N  43  
T0P  CAS  H8   SING  N  N  44  
T0P  CAS  H9   SING  N  N  45  
T0P  CAY  H10  SING  N  N  46  
T0P  CAZ  H11  SING  N  N  47  
T0P  CBA  H12  SING  N  N  48  
T0P  CBB  H13  SING  N  N  49  
T0P  CBC  H14  SING  N  N  50  
T0P  NAE  H15  SING  N  N  51  
T0P  NAL  H16  SING  N  N  52  
T0P  NAL  H17  SING  N  N  53  
T0P  OAR  H18  SING  N  N  54  
T0P  OBF  H19  SING  N  N  55  
T0P  O1   H20  SING  N  N  56  
#   #
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
T0P  InChI             InChI                 1.03   "InChI=1S/C18H20FN5O8P/c19-12-14(26)11(7-31-33(28,29)30)32-17(12)24-8-23(6-10(25)9-4-2-1-3-5-9)13-15(24)21-18(20)22-16(13)27/h1-5,8,11-12,14,17,26H,6-7H2,(H2,28,29,30)(H3,20,21,22,27)/t11-,12+,14-,17-/m1/s1"  
T0P  InChIKey          InChI                 1.03   RRUAIQFWCYLDFU-DMVWFOPNSA-N  
T0P  SMILES_CANONICAL  CACTVS                3.385  "NC1=Nc2c(n(CC(=O)c3ccccc3)c[n]2[C@@H]4O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@@H]4F)C(=O)N1"  
T0P  SMILES            CACTVS                3.385  "NC1=Nc2c(n(CC(=O)c3ccccc3)c[n]2[CH]4O[CH](CO[P](O)(O)=O)[CH](O)[CH]4F)C(=O)N1"  
T0P  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1ccc(cc1)C(=O)CN2C=[N](C3=C2C(=O)NC(=N3)N)[C@H]4[C@H]([C@@H]([C@H](O4)COP(=O)(O)O)O)F"  
T0P  SMILES            "OpenEye OEToolkits"  2.0.7  "c1ccc(cc1)C(=O)CN2C=[N](C3=C2C(=O)NC(=N3)N)C4C(C(C(O4)COP(=O)(O)O)O)F"  
#
_pdbx_chem_comp_identifier.comp_id          T0P
_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~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-7-phenacyl-1~{H}-purin-9-yl)-4-fluoranyl-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
T0P  "Create component"               2020-03-16  RCSB  
T0P  "Modify model coordinates code"  2021-12-08  RCSB  
T0P  "Initial release"                2022-02-09  RCSB  
##
