data_WUH
# 
_chem_comp.id                                    WUH 
_chem_comp.name                                  "Thymine dimer" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C20 H28 N4 O15 P2" 
_chem_comp.mon_nstd_parent_comp_id               TTD 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    -2 
_chem_comp.pdbx_initial_date                     2023-05-18 
_chem_comp.pdbx_modified_date                    2023-11-17 
_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                        626.402 
_chem_comp.one_letter_code                       TT 
_chem_comp.three_letter_code                     WUH 
_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        8OY4 
_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.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
WUH C1R    C1  C 0  1 N N R N N N 26.699 12.954 4.456  0.386  0.374  -0.530 C1R    WUH 1  
WUH C1     C2  C 0  1 N N R N N N 23.047 11.682 6.053  -3.292 0.216  -0.710 C1     WUH 2  
WUH C2T    C3  C 0  1 N N N N N N 25.180 14.746 4.021  1.280  -1.902 -0.371 C2T    WUH 3  
WUH C2R    C4  C 0  1 N N N N N N 26.966 11.466 4.448  0.318  1.343  0.657  C2R    WUH 4  
WUH C3     C5  C 0  1 N N N N N N 22.885 10.186 6.200  -4.699 0.885  -0.581 C3     WUH 5  
WUH C7     C6  C 0  1 N N N N N N 21.977 13.382 4.721  -4.435 -1.764 0.005  C7     WUH 6  
WUH "C3'"  C7  C 0  1 N N S N N N 23.553 9.947  7.565  -4.396 2.379  -0.883 "C3'"  WUH 7  
WUH C3R    C8  C 0  1 N N S N N N 28.455 11.444 4.796  1.578  2.214  0.556  C3R    WUH 8  
WUH C4T    C9  C 0  1 N N N N N N 23.755 14.752 2.099  0.755  -3.111 1.665  C4T    WUH 9  
WUH "C4'"  C10 C 0  1 N N R N N N 24.400 11.208 7.790  -2.864 2.500  -0.804 "C4'"  WUH 10 
WUH C4R    C11 C 0  1 N N R N N N 28.988 12.683 4.080  2.432  1.547  -0.536 C4R    WUH 11 
WUH C2     C12 C 0  1 N N N N N N 21.381 12.797 2.412  -3.241 -3.795 -0.609 C2     WUH 12 
WUH C5T    C13 C 0  1 N N N N N N 24.263 13.493 1.759  -0.389 -2.465 1.949  C5T    WUH 13 
WUH C5R    C14 C 0  1 N N N N N N 29.694 12.402 2.779  3.613  0.815  0.102  C5R    WUH 14 
WUH C5A    C15 C 0  1 N N N N N N 24.394 12.988 0.350  -1.155 -2.695 3.232  C5A    WUH 15 
WUH C5M    C16 C 0  1 N N N N N N 22.157 10.651 1.565  -0.774 -4.014 -1.024 C5M    WUH 16 
WUH C4     C17 C 0  1 N N N N N N 25.831 10.988 8.208  -2.481 3.635  0.126  C4     WUH 17 
WUH C8     C18 C 0  1 N N N N N N 22.303 11.741 2.494  -1.985 -3.293 -0.503 C8     WUH 18 
WUH C6T    C19 C 0  1 N N R N N N 24.686 12.595 2.901  -0.798 -1.445 0.832  C6T    WUH 19 
WUH C5     C20 C 0  1 N N S N N N 23.453 11.784 3.514  -2.057 -1.943 0.232  C5     WUH 20 
WUH N1T    N1  N 0  1 N N N N N N 25.489 13.438 3.802  0.301  -1.007 -0.045 N1T    WUH 21 
WUH N2     N2  N 0  1 N N N N N N 22.833 12.307 4.744  -3.206 -1.104 -0.163 N2     WUH 22 
WUH N3T    N3  N 0  1 N N N N N N 24.069 15.221 3.367  1.506  -2.888 0.526  N3T    WUH 23 
WUH N1     N4  N 0  1 N N N N N N 21.431 13.653 3.499  -4.357 -3.097 -0.195 N1     WUH 24 
WUH O2T    O1  O 0  1 N N N N N N 25.860 15.472 4.729  1.954  -1.801 -1.378 O2T    WUH 25 
WUH O1     O2  O 0  1 N N N N N N 21.681 14.032 5.712  -5.494 -1.235 0.252  O1     WUH 26 
WUH "O3'"  O3  O 0  1 N N N N N N 22.574 9.906  8.599  -4.853 2.719  -2.194 "O3'"  WUH 27 
WUH O3R    O4  O 0  1 N N N N N N 28.656 11.401 6.254  1.259  3.560  0.182  O3R    WUH 28 
WUH O4T    O5  O -1 1 N N N N N N 23.044 15.471 1.360  1.199  -4.040 2.553  O4T    WUH 29 
WUH O4R    O6  O 0  1 N N N N N N 27.834 13.524 3.829  1.597  0.620  -1.230 O4R    WUH 30 
WUH O5P    O7  O 0  1 N N N N N N 28.385 8.819  6.506  -0.387 3.760  2.095  O5P    WUH 31 
WUH O2     O8  O 0  1 N N N N N N 24.346 11.925 6.539  -2.367 1.236  -0.301 O2     WUH 32 
WUH O3     O9  O -1 1 N N N N N N 20.555 12.979 1.516  -3.396 -5.033 -1.144 O3     WUH 33 
WUH O5R    O10 O 0  1 N N N N N N 30.847 11.586 3.034  4.463  0.298  -0.923 O5R    WUH 34 
WUH O4P    O11 O 0  1 N N N N N N 28.443 10.339 8.561  0.366  5.901  0.989  O4P    WUH 35 
WUH O4     O12 O 0  1 N N N N N N 26.502 10.381 7.085  -1.234 4.214  -0.250 O4     WUH 36 
WUH OP1    O13 O 0  1 N N N N N N 32.531 12.455 1.337  6.685  0.264  0.275  OP1    WUH 37 
WUH OP2    O14 O 0  1 N N N N N N 32.437 13.429 3.671  5.426  -1.918 0.115  OP2    WUH 38 
WUH PB     P1  P 0  1 N N N N N N 32.335 12.186 2.811  5.807  -0.532 -0.611 PB     WUH 39 
WUH P1     P2  P 0  1 N N N N N N 28.075 10.125 7.149  -0.007 4.346  0.792  P1     WUH 40 
WUH H1R    H1  H 0  1 N N N N N N 26.675 13.280 5.506  -0.466 0.513  -1.193 H1R    WUH 41 
WUH H2     H2  H 0  1 N N N N N N 22.334 12.144 6.752  -3.170 0.099  -1.826 H2     WUH 42 
WUH H2R1   H3  H 0  0 N N N N N N 26.365 10.942 5.206  -0.576 1.958  0.590  H2R1   WUH 43 
WUH H2R2   H4  H 0  0 N N N N N N 26.774 11.025 3.459  0.325  0.788  1.597  H2R2   WUH 44 
WUH H3     H5  H 0  1 N N N N N N 21.824 9.895  6.213  -5.393 0.481  -1.312 H3     WUH 45 
WUH H4     H6  H 0  1 N N N N N N 23.404 9.643  5.396  -5.083 0.785  0.435  H4     WUH 46 
WUH H1     H7  H 0  1 N N N N N N 24.185 9.047  7.542  -4.869 3.019  -0.140 H1     WUH 47 
WUH H3R    H8  H 0  1 N N N N N N 28.909 10.552 4.339  2.120  2.241  1.498  H3R    WUH 48 
WUH "H4'"  H9  H 0  1 N N N N N N 23.906 11.809 8.567  -2.473 2.661  -1.814 "H4'"  WUH 49 
WUH H4R    H10 H 0  1 N N N N N N 29.683 13.204 4.755  2.798  2.307  -1.226 H4R    WUH 50 
WUH H5R1   H12 H 0  0 N N N N N N 30.009 13.350 2.319  4.176  1.510  0.726  H5R1   WUH 51 
WUH H5R2   H13 H 0  0 N N N N N N 29.012 11.873 2.097  3.243  -0.006 0.716  H5R2   WUH 52 
WUH H5A1   H14 H 0  0 N N N N N N 24.820 11.974 0.362  -0.634 -3.435 3.839  H5A1   WUH 53 
WUH H5A2   H15 H 0  0 N N N N N N 23.402 12.964 -0.124 -1.227 -1.758 3.784  H5A2   WUH 54 
WUH H5A3   H16 H 0  0 N N N N N N 25.056 13.657 -0.219 -2.156 -3.057 2.997  H5A3   WUH 55 
WUH H71    H17 H 0  1 N N N N N N 22.944 9.905  1.748  -1.079 -4.958 -1.474 H71    WUH 56 
WUH H72    H18 H 0  1 N N N N N N 21.170 10.184 1.700  -0.278 -3.397 -1.773 H72    WUH 57 
WUH H73    H19 H 0  1 N N N N N N 22.245 11.032 0.537  -0.086 -4.209 -0.201 H73    WUH 58 
WUH H5     H20 H 0  1 N N N N N N 25.873 10.320 9.081  -3.254 4.404  0.083  H5     WUH 59 
WUH H7     H21 H 0  1 N N N N N N 26.305 11.949 8.459  -2.414 3.256  1.146  H7     WUH 60 
WUH H6T    H23 H 0  1 N N N N N N 25.361 11.838 2.475  -1.021 -0.545 1.442  H6T    WUH 61 
WUH H8     H24 H 0  1 N N N N N N 23.792 10.753 3.694  -2.581 -2.372 1.158  H8     WUH 62 
WUH HN3    H25 H 0  1 N N N N N N 23.486 15.905 3.805  2.255  -3.484 0.355  HN3    WUH 63 
WUH HT     H26 H 0  1 N N N N N N 21.027 14.560 3.377  -5.166 -3.605 -0.028 HT     WUH 64 
WUH "HO3'" H27 H 0  0 N Y N N N N 23.001 9.758  9.435  -5.806 2.616  -2.318 "HO3'" WUH 65 
WUH H4P    H28 H 0  1 N N N N N N 28.861 9.557  8.902  -0.354 6.435  1.354  H4P    WUH 66 
WUH HOP2   H30 H 0  0 N N N N N N 32.611 14.183 3.120  4.852  -2.492 -0.410 HOP2   WUH 67 
WUH OP3    O15 O 0  1 N Y N N N N ?      ?      ?      6.578  -0.843 -1.990 OP3    WUH 68 
WUH HOP3   H31 H 0  0 N N N N N N ?      ?      ?      7.399  -1.342 -1.879 HOP3   WUH 69 
# 
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 
WUH C5A   C5T    SING N N 1  
WUH OP1   PB     DOUB N N 2  
WUH O4T   C4T    SING N N 3  
WUH O3    C2     SING N N 4  
WUH C5M   C8     SING N N 5  
WUH C5T   C4T    DOUB N N 6  
WUH C5T   C6T    SING N N 7  
WUH C4T   N3T    SING N N 8  
WUH C2    C8     DOUB N N 9  
WUH C2    N1     SING N N 10 
WUH C8    C5     SING N N 11 
WUH C5R   O5R    SING N N 12 
WUH C5R   C4R    SING N N 13 
WUH PB    O5R    SING N N 14 
WUH PB    OP2    SING N N 15 
WUH C6T   C5     SING N N 16 
WUH C6T   N1T    SING N N 17 
WUH N3T   C2T    SING N N 18 
WUH N1    C7     SING N N 19 
WUH C5    N2     SING N N 20 
WUH N1T   C2T    SING N N 21 
WUH N1T   C1R    SING N N 22 
WUH O4R   C4R    SING N N 23 
WUH O4R   C1R    SING N N 24 
WUH C2T   O2T    DOUB N N 25 
WUH C4R   C3R    SING N N 26 
WUH C2R   C1R    SING N N 27 
WUH C2R   C3R    SING N N 28 
WUH C7    N2     SING N N 29 
WUH C7    O1     DOUB N N 30 
WUH N2    C1     SING N N 31 
WUH C3R   O3R    SING N N 32 
WUH C1    C3     SING N N 33 
WUH C1    O2     SING N N 34 
WUH C3    "C3'"  SING N N 35 
WUH O3R   P1     SING N N 36 
WUH O5P   P1     DOUB N N 37 
WUH O2    "C4'"  SING N N 38 
WUH O4    P1     SING N N 39 
WUH O4    C4     SING N N 40 
WUH P1    O4P    SING N N 41 
WUH "C3'" "C4'"  SING N N 42 
WUH "C3'" "O3'"  SING N N 43 
WUH "C4'" C4     SING N N 44 
WUH C1R   H1R    SING N N 45 
WUH C1    H2     SING N N 46 
WUH C2R   H2R1   SING N N 47 
WUH C2R   H2R2   SING N N 48 
WUH C3    H3     SING N N 49 
WUH C3    H4     SING N N 50 
WUH "C3'" H1     SING N N 51 
WUH C3R   H3R    SING N N 52 
WUH "C4'" "H4'"  SING N N 53 
WUH C4R   H4R    SING N N 54 
WUH C5R   H5R1   SING N N 55 
WUH C5R   H5R2   SING N N 56 
WUH C5A   H5A1   SING N N 57 
WUH C5A   H5A2   SING N N 58 
WUH C5A   H5A3   SING N N 59 
WUH C5M   H71    SING N N 60 
WUH C5M   H72    SING N N 61 
WUH C5M   H73    SING N N 62 
WUH C4    H5     SING N N 63 
WUH C4    H7     SING N N 64 
WUH C6T   H6T    SING N N 65 
WUH C5    H8     SING N N 66 
WUH N3T   HN3    SING N N 67 
WUH N1    HT     SING N N 68 
WUH "O3'" "HO3'" SING N N 69 
WUH O4P   H4P    SING N N 70 
WUH OP2   HOP2   SING N N 71 
WUH PB    OP3    SING N N 72 
WUH OP3   HOP3   SING N N 73 
# 
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 
WUH InChI            InChI                1.06  "InChI=1S/C20H30N4O15P2/c1-7-15-16-8(2)18(27)22-20(29)24(16)14-4-10(12(38-14)6-35-40(30,31)32)39-41(33,34)36-5-11-9(25)3-13(37-11)23(15)19(28)21-17(7)26/h9-16,25-27H,3-6H2,1-2H3,(H,21,28)(H,22,29)(H,33,34)(H2,30,31,32)/p-2/t9-,10-,11+,12+,13+,14+,15-,16+/m0/s1" 
WUH InChIKey         InChI                1.06  MLKSHAMOXDJESO-BIELKLQGSA-L                                                                                                                                                                                                                                           
WUH SMILES_CANONICAL CACTVS               3.385 "CC1=C([O-])NC(=O)N2[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[C@H]4C[C@@H](O[C@@H]4CO[P](O)(O)=O)N5[C@@H]([C@H]12)C(=C([O-])NC5=O)C)O3"                                                                                                                                     
WUH SMILES           CACTVS               3.385 "CC1=C([O-])NC(=O)N2[CH]3C[CH](O)[CH](CO[P](O)(=O)O[CH]4C[CH](O[CH]4CO[P](O)(O)=O)N5[CH]([CH]12)C(=C([O-])NC5=O)C)O3"                                                                                                                                                 
WUH SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=C(NC(=O)N2[C@@H]1[C@H]3C(=C(NC(=O)N3[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)OP(=O)(OC[C@@H]5[C@H](C[C@H]2O5)O)O)[O-])C)[O-]"                                                                                                                                          
WUH SMILES           "OpenEye OEToolkits" 2.0.7 "CC1=C(NC(=O)N2C1C3C(=C(NC(=O)N3C4CC(C(O4)COP(=O)(O)O)OP(=O)(OCC5C(CC2O5)O)O)[O-])C)[O-]"                                                                                                                                                                             
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
WUH "Create component"     2023-05-18 PDBE 
WUH "Modify aromatic_flag" 2023-05-19 PDBE 
WUH "Modify aromatic_flag" 2023-05-22 PDBE 
WUH "Initial release"      2023-11-22 RCSB 
# 
