data_T0N
#

_chem_comp.id                                   T0N
_chem_comp.name                                 "~{N}-(1,3-dimethylimidazolidin-2-yl)-[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy]phosphonamidous acid"
_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C15 H26 N5 O6 P"
_chem_comp.mon_nstd_parent_comp_id              DG
_chem_comp.pdbx_synonyms                        "phosphoryl guanidine moiety, Rp-diastereomer"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-12-09
_chem_comp.pdbx_modified_date                   2021-07-29
_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                       403.371
_chem_comp.one_letter_code                      G
_chem_comp.three_letter_code                    T0N
_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       7B72
_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
T0N  P       P1   P  0  1  N  N  S   -8.675  -4.671  11.584  -2.956   1.160  -0.475  P       T0N   1  
T0N  OP1     O1   O  0  1  N  N  N   -9.788  -5.262  10.803  -3.723   2.475   0.047  OP1     T0N   2  
T0N  C6      C1   C  0  1  N  N  N  -10.010  -1.189   8.079   4.358  -0.770   1.171  C6      T0N   3  
T0N  C5      C2   C  0  1  N  N  N  -10.194  -1.412   6.752   5.116  -1.794   0.724  C5      T0N   4  
T0N  C4      C3   C  0  1  N  N  N  -10.062  -0.317   5.793   5.082  -2.126  -0.652  C4      T0N   5  
T0N  N3      N1   N  0  1  N  N  N   -9.787   0.911   6.349   4.295  -1.415  -1.485  N3      T0N   6  
T0N  C2      C4   C  0  1  N  N  N   -9.610   1.166   7.688   3.549  -0.400  -1.012  C2      T0N   7  
T0N  N1      N2   N  0  1  N  N  N   -9.703   0.070   8.558   3.572  -0.074   0.293  N1      T0N   8  
T0N  "C1'"   C5   C  0  1  N  N  R   -9.463   0.294  10.011   2.745   1.033   0.780  "C1'"   T0N   9  
T0N  "C2'"   C6   C  0  1  N  N  N  -10.587  -0.221  10.906   3.170   2.358   0.109  "C2'"   T0N  10  
T0N  "C3'"   C7   C  0  1  N  N  S   -9.866  -0.368  12.243   1.840   3.113  -0.107  "C3'"   T0N  11  
T0N  "O3'"   O2   O  0  1  N  N  N   -9.908   0.823  13.026   1.841   4.346   0.615  "O3'"   T0N  12  
T0N  "O4'"   O3   O  0  1  N  N  N   -8.295  -0.386  10.430   1.369   0.844   0.384  "O4'"   T0N  13  
T0N  "C4'"   C8   C  0  1  N  N  R   -8.419  -0.677  11.817   0.768   2.155   0.459  "C4'"   T0N  14  
T0N  "C5'"   C9   C  0  1  N  N  N   -8.014  -2.137  12.078  -0.500   2.209  -0.397  "C5'"   T0N  15  
T0N  "O5'"   O4   O  0  1  N  N  N   -8.850  -3.077  11.401  -1.492   1.350   0.167  "O5'"   T0N  16  
T0N  C7      C10  C  0  1  N  N  N  -10.536  -2.813   6.271   5.988  -2.572   1.675  C7      T0N  17  
T0N  O4      O5   O  0  1  N  N  N  -10.155  -0.400   4.571   5.758  -3.044  -1.080  O4      T0N  18  
T0N  O2      O6   O  0  1  N  N  N   -9.387   2.320   8.053   2.844   0.232  -1.775  O2      T0N  19  
T0N  NP      N3   N  0  1  N  N  N   -8.704  -5.102  13.102  -3.614  -0.041   0.502  NP      T0N  20  
T0N  CN      C11  C  0  1  N  N  N   -7.470  -5.011  13.715  -3.972  -1.226  -0.289  CN      T0N  21  
T0N  NC1     N4   N  0  1  N  N  N   -7.344  -4.425  14.979  -4.133  -2.391   0.602  NC1     T0N  22  
T0N  NC2     N5   N  0  1  N  N  N   -6.471  -5.990  13.576  -5.262  -0.999  -0.976  NC2     T0N  23  
T0N  C31     C12  C  0  1  N  N  N   -6.188  -4.960  15.710  -5.525  -2.871   0.442  C31     T0N  24  
T0N  C32     C13  C  0  1  N  N  N   -8.466  -3.860  15.759  -3.859  -2.027   1.999  C32     T0N  25  
T0N  C33     C14  C  0  1  N  N  N   -6.695  -7.305  12.935  -6.060   0.016  -0.276  C33     T0N  26  
T0N  C34     C15  C  0  1  N  N  N   -5.577  -5.988  14.749  -5.940  -2.323  -0.947  C34     T0N  27  
T0N  H1      H1   H  0  1  N  N  N   -9.750  -6.209  10.864  -3.468   3.288  -0.411  H1      T0N  28  
T0N  H6      H2   H  0  1  N  N  N  -10.105  -2.011   8.773   4.367  -0.505   2.218  H6      T0N  29  
T0N  H3      H3   H  0  1  N  N  N   -9.709   1.687   5.723   4.266  -1.636  -2.429  H3      T0N  30  
T0N  "H1'"   H4   H  0  1  N  N  N   -9.349   1.374  10.188   2.820   1.113   1.865  "H1'"   T0N  31  
T0N  "H2'"   H5   H  0  1  N  N  N  -11.412   0.503  10.972   3.829   2.924   0.767  "H2'"   T0N  32  
T0N  "H2''"  H6   H  0  0  N  N  N  -10.974  -1.187  10.550   3.659   2.163  -0.845  "H2''"  T0N  33  
T0N  "H3'"   H7   H  0  1  N  N  N  -10.279  -1.224  12.797   1.672   3.294  -1.169  "H3'"   T0N  34  
T0N  H2      H8   H  0  1  N  N  N   -9.448   0.681  13.845   2.534   4.962   0.342  H2      T0N  35  
T0N  "H4'"   H9   H  0  1  N  N  N   -7.746  -0.026  12.394   0.538   2.409   1.493  "H4'"   T0N  36  
T0N  "H5'"   H10  H  0  1  N  N  N   -8.074  -2.330  13.159  -0.877   3.232  -0.422  "H5'"   T0N  37  
T0N  "H5''"  H11  H  0  0  N  N  N   -6.978  -2.280  11.737  -0.268   1.882  -1.410  "H5''"  T0N  38  
T0N  H73     H12  H  0  1  N  N  N  -10.591  -3.494   7.133   5.423  -3.411   2.082  H73     T0N  39  
T0N  H72     H13  H  0  1  N  N  N  -11.507  -2.796   5.754   6.863  -2.945   1.144  H72     T0N  40  
T0N  H71     H14  H  0  1  N  N  N   -9.757  -3.163   5.577   6.308  -1.921   2.489  H71     T0N  41  
T0N  H4      H15  H  0  1  N  N  N   -9.346  -4.509  13.589  -2.984  -0.283   1.252  H4      T0N  42  
T0N  H5      H16  H  0  1  N  N  N   -7.023  -4.213  13.103  -3.192  -1.428  -1.023  H5      T0N  43  
T0N  H12     H19  H  0  1  N  N  N   -6.507  -5.442  16.646  -5.559  -3.960   0.450  H12     T0N  44  
T0N  H11     H20  H  0  1  N  N  N   -5.466  -4.161  15.937  -6.165  -2.462   1.224  H11     T0N  45  
T0N  H23     H21  H  0  1  N  N  N   -8.088  -3.465  16.714  -4.470  -1.168   2.277  H23     T0N  46  
T0N  H21     H22  H  0  1  N  N  N   -8.937  -3.047  15.187  -4.100  -2.870   2.648  H21     T0N  47  
T0N  H22     H23  H  0  1  N  N  N   -9.208  -4.647  15.956  -2.804  -1.774   2.109  H22     T0N  48  
T0N  H33     H24  H  0  1  N  N  N   -5.761  -7.886  12.952  -5.508   0.956  -0.248  H33     T0N  49  
T0N  H31     H25  H  0  1  N  N  N   -7.476  -7.852  13.483  -7.003   0.164  -0.802  H31     T0N  50  
T0N  H32     H26  H  0  1  N  N  N   -7.015  -7.155  11.893  -6.260  -0.317   0.742  H32     T0N  51  
T0N  H42     H27  H  0  1  N  N  N   -5.548  -6.984  15.215  -7.021  -2.207  -1.012  H42     T0N  52  
T0N  H41     H28  H  0  1  N  N  N   -4.559  -5.689  14.459  -5.569  -2.967  -1.745  H41     T0N  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
T0N  O4     C4      DOUB  N  N   1  
T0N  C4     N3      SING  N  N   2  
T0N  C4     C5      SING  N  N   3  
T0N  C7     C5      SING  N  N   4  
T0N  N3     C2      SING  N  N   5  
T0N  C5     C6      DOUB  N  N   6  
T0N  C2     O2      DOUB  N  N   7  
T0N  C2     N1      SING  N  N   8  
T0N  C6     N1      SING  N  N   9  
T0N  N1     "C1'"   SING  N  N  10  
T0N  "C1'"  "O4'"   SING  N  N  11  
T0N  "C1'"  "C2'"   SING  N  N  12  
T0N  "O4'"  "C4'"   SING  N  N  13  
T0N  OP1    P       SING  N  N  14  
T0N  "C2'"  "C3'"   SING  N  N  15  
T0N  "O5'"  P       SING  N  N  16  
T0N  "O5'"  "C5'"   SING  N  N  17  
T0N  P      NP      SING  N  N  18  
T0N  "C4'"  "C5'"   SING  N  N  19  
T0N  "C4'"  "C3'"   SING  N  N  20  
T0N  "C3'"  "O3'"   SING  N  N  21  
T0N  C33    NC2     SING  N  N  22  
T0N  NP     CN      SING  N  N  23  
T0N  NC2    CN      SING  N  N  24  
T0N  NC2    C34     SING  N  N  25  
T0N  CN     NC1     SING  N  N  26  
T0N  C34    C31     SING  N  N  27  
T0N  NC1    C31     SING  N  N  28  
T0N  NC1    C32     SING  N  N  29  
T0N  OP1    H1      SING  N  N  30  
T0N  C6     H6      SING  N  N  31  
T0N  N3     H3      SING  N  N  32  
T0N  "C1'"  "H1'"   SING  N  N  33  
T0N  "C2'"  "H2'"   SING  N  N  34  
T0N  "C2'"  "H2''"  SING  N  N  35  
T0N  "C3'"  "H3'"   SING  N  N  36  
T0N  "O3'"  H2      SING  N  N  37  
T0N  "C4'"  "H4'"   SING  N  N  38  
T0N  "C5'"  "H5'"   SING  N  N  39  
T0N  "C5'"  "H5''"  SING  N  N  40  
T0N  C7     H73     SING  N  N  41  
T0N  C7     H72     SING  N  N  42  
T0N  C7     H71     SING  N  N  43  
T0N  NP     H4      SING  N  N  44  
T0N  CN     H5      SING  N  N  45  
T0N  C31    H12     SING  N  N  46  
T0N  C31    H11     SING  N  N  47  
T0N  C32    H23     SING  N  N  48  
T0N  C32    H21     SING  N  N  49  
T0N  C32    H22     SING  N  N  50  
T0N  C33    H33     SING  N  N  51  
T0N  C33    H31     SING  N  N  52  
T0N  C33    H32     SING  N  N  53  
T0N  C34    H42     SING  N  N  54  
T0N  C34    H41     SING  N  N  55  
#   #
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
T0N  InChI             InChI                 1.03   "InChI=1S/C15H26N5O6P/c1-9-7-20(15(23)16-13(9)22)12-6-10(21)11(26-12)8-25-27(24)17-14-18(2)4-5-19(14)3/h7,10-12,14,17,21,24H,4-6,8H2,1-3H3,(H,16,22,23)/t10-,11+,12+,27-/m0/s1"  
T0N  InChIKey          InChI                 1.03   LHESFPBPMGZRQU-RTMXWMFYSA-N  
T0N  SMILES_CANONICAL  CACTVS                3.385  "CN1CCN(C)C1N[P@@](O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O"  
T0N  SMILES            CACTVS                3.385  "CN1CCN(C)C1N[P](O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O"  
T0N  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(NC3N(CCN3C)C)O)O"  
T0N  SMILES            "OpenEye OEToolkits"  2.0.7  "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(NC3N(CCN3C)C)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          T0N
_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       "~{N}-(1,3-dimethylimidazolidin-2-yl)-[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy]phosphonamidous acid"
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     T0N
_pdbx_chem_comp_synonyms.name        "phosphoryl guanidine moiety, Rp-diastereomer"
_pdbx_chem_comp_synonyms.provenance  PDB
_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
T0N  "Create component"    2020-12-09  PDBE  
T0N  "Initial release"     2021-01-13  RCSB  
T0N  "Modify synonyms"     2021-03-13  RCSB  
T0N  "Other modification"  2021-07-29  PDBE  
##
