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]phosphonamidic acid" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C15 H26 N5 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               DT 
_chem_comp.pdbx_synonyms                         "phosphoryl thymidine moiety, Rp-diastereomer" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2020-12-09 
_chem_comp.pdbx_modified_date                    2023-08-15 
_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                        419.370 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     T0N 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_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 N -8.675  -4.671 11.584 -2.495 1.335  0.656  P      T0N 1  
T0N OP1    O1  O 0 1 N N N -9.788  -5.262 10.803 -2.126 1.836  1.999  OP1    T0N 2  
T0N C6     C1  C 0 1 N N N -10.010 -1.189 8.079  4.801  -0.229 -1.406 C6     T0N 3  
T0N C5     C2  C 0 1 N N N -10.194 -1.412 6.752  5.939  0.468  -1.200 C5     T0N 4  
T0N C4     C3  C 0 1 N N N -10.062 -0.317 5.793  6.166  1.056  0.068  C4     T0N 5  
T0N N3     N1  N 0 1 N N N -9.787  0.911  6.349  5.244  0.909  1.041  N3     T0N 6  
T0N C2     C4  C 0 1 N N N -9.610  1.166  7.688  4.119  0.208  0.808  C2     T0N 7  
T0N N1     N2  N 0 1 N N N -9.703  0.070  8.558  3.891  -0.355 -0.392 N1     T0N 8  
T0N "C1'"  C5  C 0 1 N N R -9.463  0.294  10.011 2.654  -1.107 -0.618 "C1'"  T0N 9  
T0N "C2'"  C6  C 0 1 N N N -10.587 -0.221 10.906 2.585  -2.326 0.329  "C2'"  T0N 10 
T0N "C3'"  C7  C 0 1 N N S -9.866  -0.368 12.243 1.091  -2.418 0.713  "C3'"  T0N 11 
T0N "O3'"  O2  O 0 1 N N N -9.908  0.823  13.026 0.540  -3.665 0.283  "O3'"  T0N 12 
T0N "O4'"  O3  O 0 1 N N N -8.295  -0.386 10.430 1.506  -0.303 -0.268 "O4'"  T0N 13 
T0N "C4'"  C8  C 0 1 N N R -8.419  -0.677 11.817 0.434  -1.245 -0.047 "C4'"  T0N 14 
T0N "C5'"  C9  C 0 1 N N N -8.014  -2.137 12.078 -0.667 -0.609 0.803  "C5'"  T0N 15 
T0N "O5'"  O4  O 0 1 N N N -8.850  -3.077 11.401 -1.290 0.445  0.066  "O5'"  T0N 16 
T0N C7     C10 C 0 1 N N N -10.536 -2.813 6.271  6.953  0.618  -2.304 C7     T0N 17 
T0N O4     O5  O 0 1 N N N -10.155 -0.400 4.571  7.185  1.689  0.278  O4     T0N 18 
T0N O2     O6  O 0 1 N N N -9.387  2.320  8.053  3.296  0.083  1.695  O2     T0N 19 
T0N NP     N3  N 0 1 N N N -8.704  -5.102 13.102 -3.884 0.392  0.772  N2     T0N 20 
T0N CN     C11 C 0 1 N N N -7.470  -5.011 13.715 -4.281 -0.124 -0.545 CN     T0N 21 
T0N NC1    N4  N 0 1 N N N -7.344  -4.425 14.979 -5.124 -1.323 -0.378 NC1    T0N 22 
T0N NC2    N5  N 0 1 N N N -6.471  -5.990 13.576 -5.078 0.895  -1.263 NC2    T0N 23 
T0N C31    C12 C 0 1 N N N -6.188  -4.960 15.710 -6.432 -1.025 -1.007 C31    T0N 24 
T0N C32    C13 C 0 1 N N N -8.466  -3.860 15.759 -5.288 -1.658 1.043  C32    T0N 25 
T0N C33    C14 C 0 1 N N N -6.695  -7.305 12.935 -5.709 1.829  -0.321 C33    T0N 26 
T0N C34    C15 C 0 1 N N N -5.577  -5.988 14.749 -6.102 0.113  -2.006 C34    T0N 27 
T0N H6     H2  H 0 1 N N N -10.105 -2.011 8.773  4.608  -0.680 -2.368 H6     T0N 28 
T0N H3     H3  H 0 1 N N N -9.709  1.687  5.723  5.393  1.308  1.912  H3     T0N 29 
T0N "H1'"  H4  H 0 1 N N N -9.349  1.374  10.188 2.590  -1.428 -1.657 "H1'"  T0N 30 
T0N "H2'"  H5  H 0 1 N N N -11.412 0.503  10.972 2.903  -3.230 -0.189 "H2'"  T0N 31 
T0N "H2''" H6  H 0 0 N N N -10.974 -1.187 10.550 3.197  -2.156 1.215  "H2''" T0N 32 
T0N "H3'"  H7  H 0 1 N N N -10.279 -1.224 12.797 0.965  -2.297 1.789  "H3'"  T0N 33 
T0N "HO3'" H8  H 0 0 N Y N -9.448  0.681  13.845 0.958  -4.439 0.685  "HO3'" T0N 34 
T0N "H4'"  H9  H 0 1 N N N -7.746  -0.026 12.394 0.027  -1.588 -0.999 "H4'"  T0N 35 
T0N "H5'"  H10 H 0 1 N N N -8.074  -2.330 13.159 -1.412 -1.364 1.058  "H5'"  T0N 36 
T0N "H5''" H11 H 0 0 N N N -6.978  -2.280 11.737 -0.233 -0.205 1.718  "H5''" T0N 37 
T0N H73    H12 H 0 1 N N N -10.591 -3.494 7.133  6.729  1.513  -2.885 H73    T0N 38 
T0N H72    H13 H 0 1 N N N -11.507 -2.796 5.754  7.950  0.706  -1.872 H72    T0N 39 
T0N H71    H14 H 0 1 N N N -9.757  -3.163 5.577  6.915  -0.256 -2.954 H71    T0N 40 
T0N H5     H16 H 0 1 N N N -7.023  -4.213 13.103 -3.393 -0.375 -1.126 H5     T0N 41 
T0N H12    H19 H 0 1 N N N -6.507  -5.442 16.646 -6.813 -1.899 -1.534 H12    T0N 42 
T0N H11    H20 H 0 1 N N N -5.466  -4.161 15.937 -7.149 -0.686 -0.260 H11    T0N 43 
T0N H23    H21 H 0 1 N N N -8.088  -3.465 16.714 -5.646 -0.782 1.583  H23    T0N 44 
T0N H21    H22 H 0 1 N N N -8.937  -3.047 15.187 -6.010 -2.468 1.145  H21    T0N 45 
T0N H22    H23 H 0 1 N N N -9.208  -4.647 15.956 -4.329 -1.972 1.455  H22    T0N 46 
T0N H33    H24 H 0 1 N N N -5.761  -7.886 12.952 -4.938 2.334  0.261  H33    T0N 47 
T0N H31    H25 H 0 1 N N N -7.476  -7.852 13.483 -6.288 2.567  -0.876 H31    T0N 48 
T0N H32    H26 H 0 1 N N N -7.015  -7.155 11.893 -6.368 1.278  0.350  H32    T0N 49 
T0N H42    H27 H 0 1 N N N -5.548  -6.984 15.215 -6.985 0.721  -2.207 H42    T0N 50 
T0N H41    H28 H 0 1 N N N -4.559  -5.689 14.459 -5.689 -0.290 -2.931 H41    T0N 51 
T0N OP3    OP1 O 0 1 N Y N ?       ?      ?      -2.772 2.581  -0.325 OP3    T0N 52 
T0N HOP3   H29 H 0 0 N Y N ?       ?      ?      -3.019 2.326  -1.224 HOP3   T0N 53 
T0N HNP    H30 H 0 1 N N N -9.346  -4.509 13.589 -3.757 -0.360 1.432  H1     T0N 54 
# 
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      DOUB 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 C6    H6     SING N N 30 
T0N N3    H3     SING N N 31 
T0N "C1'" "H1'"  SING N N 32 
T0N "C2'" "H2'"  SING N N 33 
T0N "C2'" "H2''" SING N N 34 
T0N "C3'" "H3'"  SING N N 35 
T0N "O3'" "HO3'" SING N N 36 
T0N "C4'" "H4'"  SING N N 37 
T0N "C5'" "H5'"  SING N N 38 
T0N "C5'" "H5''" SING N N 39 
T0N C7    H73    SING N N 40 
T0N C7    H72    SING N N 41 
T0N C7    H71    SING N N 42 
T0N CN    H5     SING N N 43 
T0N C31   H12    SING N N 44 
T0N C31   H11    SING N N 45 
T0N C32   H23    SING N N 46 
T0N C32   H21    SING N N 47 
T0N C32   H22    SING N N 48 
T0N C33   H33    SING N N 49 
T0N C33   H31    SING N N 50 
T0N C33   H32    SING N N 51 
T0N C34   H42    SING N N 52 
T0N C34   H41    SING N N 53 
T0N P     OP3    SING N N 54 
T0N OP3   HOP3   SING N N 55 
T0N NP    HNP    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 
T0N InChI            InChI                1.06  "InChI=1S/C15H26N5O7P/c1-9-7-20(15(23)16-13(9)22)12-6-10(21)11(27-12)8-26-28(24,25)17-14-18(2)4-5-19(14)3/h7,10-12,14,21H,4-6,8H2,1-3H3,(H,16,22,23)(H2,17,24,25)/t10-,11+,12+/m0/s1" 
T0N InChIKey         InChI                1.06  NZONXHNEUWVHKC-QJPTWQEYSA-N                                                                                                                                                           
T0N SMILES_CANONICAL CACTVS               3.385 "CN1CCN(C)C1N[P](O)(=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)(=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(=O)(NC3N(CCN3C)C)O)O"                                                                                                                   
T0N SMILES           "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(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]phosphonamidic acid" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      T0N 
_pdbx_chem_comp_synonyms.name         "phosphoryl thymidine 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 
T0N "Modify leaving atom flag" 2023-08-15 PDBE 
T0N "Other modification"       2023-08-15 PDBE 
# 
