data_T0Q
# 
_chem_comp.id                                    T0Q 
_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, Sp-diastereomer" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2020-12-09 
_chem_comp.pdbx_modified_date                    2023-09-22 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   OBS 
_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                     T0Q 
_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        7B71 
_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 
T0Q "O5'"  O1  O 0 1 N N N -6.063 6.499 2.915  1.278  0.484  0.089  "O5'"  T0Q 1  
T0Q "C5'"  C1  C 0 1 N N N -5.210 7.602 3.205  0.596  -0.512 -0.676 "C5'"  T0Q 2  
T0Q "C4'"  C2  C 0 1 N N R -3.796 7.413 2.634  -0.459 -1.193 0.197  "C4'"  T0Q 3  
T0Q "O4'"  O2  O 0 1 N N N -3.216 6.234 3.188  -1.505 -0.262 0.550  "O4'"  T0Q 4  
T0Q "C3'"  C3  C 0 1 N N S -3.777 7.274 1.101  -1.207 -2.289 -0.604 "C3'"  T0Q 5  
T0Q "O3'"  O3  O 0 1 N N N -2.761 8.113 0.558  -0.502 -3.531 -0.550 "O3'"  T0Q 6  
T0Q "C2'"  C4  C 0 1 N N N -3.485 5.791 0.912  -2.553 -2.384 0.153  "C2'"  T0Q 7  
T0Q "C1'"  C5  C 0 1 N N R -2.631 5.482 2.140  -2.659 -1.042 0.904  "C1'"  T0Q 8  
T0Q C5     C6  C 0 1 N N N -3.694 1.983 2.985  -5.996 0.526  1.038  C5     T0Q 9  
T0Q C6     C7  C 0 1 N N N -3.737 3.297 2.645  -4.873 -0.122 1.413  C6     T0Q 10 
T0Q N1     N1  N 0 1 N N N -2.578 4.038 2.507  -3.879 -0.339 0.498  N1     T0Q 11 
T0Q C2     C8  C 0 1 N N N -1.320 3.449 2.711  -4.011 0.088  -0.771 C2     T0Q 12 
T0Q N3     N2  N 0 1 N N N -1.307 2.115 3.049  -5.120 0.737  -1.171 N3     T0Q 13 
T0Q C4     C9  C 0 1 N N N -2.416 1.321 3.226  -6.124 0.966  -0.301 C4     T0Q 14 
T0Q P      P1  P 0 1 N N N -7.545 6.400 3.533  2.456  1.400  -0.515 P      T0Q 15 
T0Q OP1    O4  O 0 1 N N N -8.285 7.682 3.462  2.012  1.994  -1.795 OP1    T0Q 16 
T0Q C7     C10 C 0 1 N N N -4.988 1.202 3.118  -7.102 0.774  2.032  C7     T0Q 17 
T0Q O4     O5  O 0 1 N N N -2.256 0.157 3.581  -7.131 1.548  -0.664 O4     T0Q 18 
T0Q O2     O6  O 0 1 N N N -0.250 4.048 2.604  -3.115 -0.116 -1.568 O2     T0Q 19 
T0Q NP     N3  N 0 1 N N N -8.451 5.191 3.080  3.822  0.454  -0.779 N2     T0Q 20 
T0Q CN     C11 C 0 1 N N N -7.919 4.399 2.079  4.293  -0.154 0.473  CN     T0Q 21 
T0Q NC1    N4  N 0 1 N N N -8.155 3.027 2.037  5.063  -1.376 0.177  NC1    T0Q 22 
T0Q NC2    N5  N 0 1 N N N -7.495 4.832 0.811  5.188  0.788  1.181  NC2    T0Q 23 
T0Q C31    C12 C 0 1 N N N -7.409 3.682 -0.112 6.228  -0.078 1.799  C31    T0Q 24 
T0Q C32    C13 C 0 1 N N N -7.860 6.139 0.214  5.789  1.747  0.245  C32    T0Q 25 
T0Q C33    C14 C 0 1 N N N -8.971 2.264 3.004  5.103  -1.636 -1.269 C33    T0Q 26 
T0Q C34    C15 C 0 1 N N N -7.891 2.472 0.704  6.427  -1.171 0.717  C34    T0Q 27 
T0Q "H5''" H1  H 0 0 N N N -5.138 7.716 4.297  0.112  -0.043 -1.533 "H5''" T0Q 28 
T0Q "H5'"  H2  H 0 1 N N N -5.648 8.512 2.770  1.313  -1.255 -1.026 "H5'"  T0Q 29 
T0Q "H4'"  H3  H 0 1 N N N -3.192 8.290 2.909  -0.001 -1.614 1.092  "H4'"  T0Q 30 
T0Q "H3'"  H4  H 0 1 N N N -4.767 7.520 0.690  -1.362 -1.977 -1.637 "H3'"  T0Q 31 
T0Q "HO3'" H5  H 0 0 N Y N -2.991 9.023 0.702  -0.930 -4.248 -1.037 "HO3'" T0Q 32 
T0Q "H2''" H6  H 0 0 N N N -4.411 5.198 0.909  -3.379 -2.494 -0.549 "H2''" T0Q 33 
T0Q "H2'"  H7  H 0 1 N N N -2.929 5.608 -0.019 -2.537 -3.215 0.858  "H2'"  T0Q 34 
T0Q "H1'"  H8  H 0 1 N N N -1.608 5.838 1.950  -2.674 -1.219 1.979  "H1'"  T0Q 35 
T0Q H6     H9  H 0 1 N N N -4.693 3.771 2.480  -4.759 -0.467 2.430  H6     T0Q 36 
T0Q H3     H10 H 0 1 N N N -0.413 1.685 3.177  -5.199 1.038  -2.090 H3     T0Q 37 
T0Q H71    H12 H 0 1 N N N -4.762 0.162 3.397  -7.919 1.303  1.542  H71    T0Q 38 
T0Q H73    H13 H 0 1 N N N -5.616 1.662 3.895  -7.465 -0.179 2.417  H73    T0Q 39 
T0Q H72    H14 H 0 1 N N N -5.525 1.216 2.158  -6.721 1.377  2.856  H72    T0Q 40 
T0Q H5     H16 H 0 1 N N N -6.912 4.327 2.515  3.440  -0.399 1.107  H5     T0Q 41 
T0Q H11    H19 H 0 1 N N N -6.372 3.533 -0.447 7.150  0.479  1.962  H11    T0Q 42 
T0Q H12    H20 H 0 1 N N N -8.057 3.840 -0.987 5.866  -0.515 2.730  H12    T0Q 43 
T0Q H23    H21 H 0 1 N N N -7.890 6.907 1.001  5.012  2.392  -0.164 H23    T0Q 44 
T0Q H21    H22 H 0 1 N N N -7.112 6.418 -0.542 6.527  2.354  0.770  H21    T0Q 45 
T0Q H22    H23 H 0 1 N N N -8.850 6.062 -0.260 6.276  1.206  -0.567 H22    T0Q 46 
T0Q H31    H24 H 0 1 N N N -9.060 2.834 3.940  5.575  -0.794 -1.776 H31    T0Q 47 
T0Q H32    H25 H 0 1 N N N -9.973 2.092 2.583  5.677  -2.542 -1.459 H32    T0Q 48 
T0Q H33    H26 H 0 1 N N N -8.488 1.297 3.208  4.088  -1.763 -1.643 H33    T0Q 49 
T0Q H42    H27 H 0 1 N N N -8.807 2.047 0.269  6.805  -2.090 1.165  H42    T0Q 50 
T0Q H41    H28 H 0 1 N N N -7.113 1.696 0.750  7.101  -0.818 -0.064 H41    T0Q 51 
T0Q OP3    O7  O 0 1 N Y N ?      ?     ?      2.810  2.575  0.528  OP3    T0Q 52 
T0Q HOP3   H29 H 0 0 N Y N ?      ?     ?      3.109  2.258  1.391  HOP3   T0Q 53 
T0Q HNP    H30 H 0 1 N N N -9.320 5.562 2.752  4.555  0.991  -1.218 HN1    T0Q 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 
T0Q C31   C34    SING N N 1  
T0Q C31   NC2    SING N N 2  
T0Q C32   NC2    SING N N 3  
T0Q "O3'" "C3'"  SING N N 4  
T0Q C34   NC1    SING N N 5  
T0Q NC2   CN     SING N N 6  
T0Q "C2'" "C3'"  SING N N 7  
T0Q "C2'" "C1'"  SING N N 8  
T0Q "C3'" "C4'"  SING N N 9  
T0Q NC1   CN     SING N N 10 
T0Q NC1   C33    SING N N 11 
T0Q CN    NP     SING N N 12 
T0Q "C1'" N1     SING N N 13 
T0Q "C1'" "O4'"  SING N N 14 
T0Q N1    C6     SING N N 15 
T0Q N1    C2     SING N N 16 
T0Q O2    C2     DOUB N N 17 
T0Q "C4'" "O4'"  SING N N 18 
T0Q "C4'" "C5'"  SING N N 19 
T0Q C6    C5     DOUB N N 20 
T0Q C2    N3     SING N N 21 
T0Q "O5'" "C5'"  SING N N 22 
T0Q "O5'" P      SING N N 23 
T0Q C5    C7     SING N N 24 
T0Q C5    C4     SING N N 25 
T0Q N3    C4     SING N N 26 
T0Q NP    P      SING N N 27 
T0Q C4    O4     DOUB N N 28 
T0Q OP1   P      DOUB N N 29 
T0Q "C5'" "H5''" SING N N 30 
T0Q "C5'" "H5'"  SING N N 31 
T0Q "C4'" "H4'"  SING N N 32 
T0Q "C3'" "H3'"  SING N N 33 
T0Q "O3'" "HO3'" SING N N 34 
T0Q "C2'" "H2''" SING N N 35 
T0Q "C2'" "H2'"  SING N N 36 
T0Q "C1'" "H1'"  SING N N 37 
T0Q C6    H6     SING N N 38 
T0Q N3    H3     SING N N 39 
T0Q C7    H71    SING N N 40 
T0Q C7    H73    SING N N 41 
T0Q C7    H72    SING N N 42 
T0Q CN    H5     SING N N 43 
T0Q C31   H11    SING N N 44 
T0Q C31   H12    SING N N 45 
T0Q C32   H23    SING N N 46 
T0Q C32   H21    SING N N 47 
T0Q C32   H22    SING N N 48 
T0Q C33   H31    SING N N 49 
T0Q C33   H32    SING N N 50 
T0Q C33   H33    SING N N 51 
T0Q C34   H42    SING N N 52 
T0Q C34   H41    SING N N 53 
T0Q P     OP3    SING N N 54 
T0Q OP3   HOP3   SING N N 55 
T0Q 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 
T0Q 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" 
T0Q InChIKey         InChI                1.06  NZONXHNEUWVHKC-QJPTWQEYSA-N                                                                                                                                                           
T0Q 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"                                                                                                                   
T0Q SMILES           CACTVS               3.385 "CN1CCN(C)C1N[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O"                                                                                                                       
T0Q 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"                                                                                                                   
T0Q 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           T0Q 
_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      T0Q 
_pdbx_chem_comp_synonyms.name         "phosphoryl thymidine moiety, Sp-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 
T0Q "Create component"         2020-12-09 PDBE 
T0Q "Initial release"          2021-01-13 RCSB 
T0Q "Modify synonyms"          2021-03-13 RCSB 
T0Q "Other modification"       2021-07-29 PDBE 
T0Q "Modify leaving atom flag" 2023-08-15 PDBE 
T0Q "Other modification"       2023-08-15 PDBE 
T0Q "Obsolete component"       2023-09-22 PDBE 
# 
