data_T2S
# 
_chem_comp.id                                    T2S 
_chem_comp.name                                  "THYMIDINE-5'-DITHIOPHOSPHORATE" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H15 N2 O6 P S2" 
_chem_comp.mon_nstd_parent_comp_id               DT 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2001-11-02 
_chem_comp.pdbx_modified_date                    2022-06-13 
_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                        354.340 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     T2S 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        ? 
_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 
T2S OP3    O3P  O 0 1 N Y N ?      ?      ?       -4.058 -2.262 4.783  OP3    T2S 1  
T2S P      P    P 0 1 N N S 7.847  -5.172 -10.280 -4.096 -1.131 3.606  P      T2S 2  
T2S S1P    S1P  S 0 1 N N N 8.276  -5.779 -12.112 -4.869 0.537  4.277  S1P    T2S 3  
T2S S2P    S2P  S 0 1 N N N 8.999  -6.135 -8.994  -5.000 -2.081 1.942  S2P    T2S 4  
T2S "O5'"  O5*  O 0 1 N N N 8.109  -3.588 -10.143 -2.493 -1.028 3.315  "O5'"  T2S 5  
T2S "C5'"  C5*  C 0 1 N N N 7.466  -2.661 -11.002 -2.005 -0.136 2.327  "C5'"  T2S 6  
T2S "C4'"  C4*  C 0 1 N N R 7.721  -1.214 -10.559 -0.611 0.328  2.728  "C4'"  T2S 7  
T2S "O4'"  O4*  O 0 1 N N N 7.224  -1.048 -9.237  0.247  -0.829 2.764  "O4'"  T2S 8  
T2S "C3'"  C3*  C 0 1 N N S 9.204  -0.817 -10.572 0.008  1.286  1.720  "C3'"  T2S 9  
T2S "O3'"  O3*  O 0 1 N N N 9.329  0.478  -11.145 0.965  2.121  2.368  "O3'"  T2S 10 
T2S "C2'"  C2*  C 0 1 N N N 9.562  -0.845 -9.091  0.710  0.360  0.754  "C2'"  T2S 11 
T2S "C1'"  C1*  C 0 1 N N R 8.231  -0.463 -8.435  1.157  -0.778 1.657  "C1'"  T2S 12 
T2S N1     N1   N 0 1 N N N 8.089  -0.940 -7.030  1.164  -2.047 0.989  N1     T2S 13 
T2S C2     C2   C 0 1 N N N 7.694  -0.013 -6.055  2.333  -2.544 0.374  C2     T2S 14 
T2S O2     O2   O 0 1 N N N 7.462  1.168  -6.289  3.410  -1.945 0.363  O2     T2S 15 
T2S N3     N3   N 0 1 N N N 7.598  -0.479 -4.762  2.194  -3.793 -0.240 N3     T2S 16 
T2S C4     C4   C 0 1 N N N 7.864  -1.765 -4.344  1.047  -4.570 -0.300 C4     T2S 17 
T2S O4     O4   O 0 1 N N N 7.756  -2.039 -3.154  0.995  -5.663 -0.857 O4     T2S 18 
T2S C5     C5   C 0 1 N N N 8.264  -2.683 -5.405  -0.143 -3.980 0.369  C5     T2S 19 
T2S C5M    C5M  C 0 1 N N N 8.598  -4.126 -5.067  -1.420 -4.757 0.347  C5M    T2S 20 
T2S C6     C6   C 0 1 N N N 8.353  -2.254 -6.692  -0.013 -2.784 0.958  C6     T2S 21 
T2S HOP3   3HOP H 0 0 N N N -0.206 0.292  0.880   -3.741 -1.998 5.673  HOP3   T2S 22 
T2S HOP2   2HOP H 0 0 N N N 10.165 -6.346 -9.529  -5.372 -3.212 2.558  HOP2   T2S 23 
T2S "H5'"  1H5* H 0 1 N N N 6.383  -2.849 -10.965 -1.971 -0.654 1.366  "H5'"  T2S 24 
T2S "H5''" 2H5* H 0 0 N N N 7.856  -2.793 -12.022 -2.683 0.718  2.254  "H5''" T2S 25 
T2S "H4'"  H4*  H 0 1 N N N 7.206  -0.565 -11.282 -0.644 0.753  3.736  "H4'"  T2S 26 
T2S "H3'"  H3*  H 0 1 N N N 9.864  -1.468 -11.164 -0.722 1.941  1.236  "H3'"  T2S 27 
T2S "HO3'" H3T  H 0 0 N Y N 8.466  0.853  -11.273 0.743  3.042  2.146  "HO3'" T2S 28 
T2S "H2'"  1H2* H 0 1 N N N 10.393 -0.175 -8.826  -0.003 -0.001 0.003  "H2'"  T2S 29 
T2S "H2''" 2H2* H 0 0 N N N 9.911  -1.837 -8.769  1.556  0.818  0.232  "H2''" T2S 30 
T2S "H1'"  H1*  H 0 1 N N N 8.163  0.633  -8.376  2.163  -0.604 2.054  "H1'"  T2S 31 
T2S H3     H3   H 0 1 N N N 7.309  0.175  -4.063  3.023  -4.171 -0.689 H3     T2S 32 
T2S H71    1H5M H 0 1 N N N 8.219  -4.786 -5.861  -1.735 -4.916 -0.683 H71    T2S 33 
T2S H72    2H5M H 0 1 N N N 8.128  -4.396 -4.110  -2.195 -4.208 0.881  H72    T2S 34 
T2S H73    3H5M H 0 1 N N N 9.689  -4.241 -4.985  -1.272 -5.721 0.833  H73    T2S 35 
T2S H6     H6   H 0 1 N N N 8.635  -2.953 -7.465  -0.857 -2.318 1.458  H6     T2S 36 
# 
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 
T2S OP3   P      SING N N 1  
T2S OP3   HOP3   SING N N 2  
T2S P     S1P    DOUB N N 3  
T2S P     S2P    SING N N 4  
T2S P     "O5'"  SING N N 5  
T2S S2P   HOP2   SING N N 6  
T2S "O5'" "C5'"  SING N N 7  
T2S "C5'" "C4'"  SING N N 8  
T2S "C5'" "H5'"  SING N N 9  
T2S "C5'" "H5''" SING N N 10 
T2S "C4'" "O4'"  SING N N 11 
T2S "C4'" "C3'"  SING N N 12 
T2S "C4'" "H4'"  SING N N 13 
T2S "O4'" "C1'"  SING N N 14 
T2S "C3'" "O3'"  SING N N 15 
T2S "C3'" "C2'"  SING N N 16 
T2S "C3'" "H3'"  SING N N 17 
T2S "O3'" "HO3'" SING N N 18 
T2S "C2'" "C1'"  SING N N 19 
T2S "C2'" "H2'"  SING N N 20 
T2S "C2'" "H2''" SING N N 21 
T2S "C1'" N1     SING N N 22 
T2S "C1'" "H1'"  SING N N 23 
T2S N1    C2     SING N N 24 
T2S N1    C6     SING N N 25 
T2S C2    O2     DOUB N N 26 
T2S C2    N3     SING N N 27 
T2S N3    C4     SING N N 28 
T2S N3    H3     SING N N 29 
T2S C4    O4     DOUB N N 30 
T2S C4    C5     SING N N 31 
T2S C5    C5M    SING N N 32 
T2S C5    C6     DOUB N N 33 
T2S C5M   H71    SING N N 34 
T2S C5M   H72    SING N N 35 
T2S C5M   H73    SING N N 36 
T2S C6    H6     SING N N 37 
# 
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 
T2S SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)COP(=S)(O)S"                                                                                                        
T2S SMILES_CANONICAL CACTVS               3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@](O)(S)=S)O2)C(=O)NC1=O"                                                                                        
T2S SMILES           CACTVS               3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(S)=S)O2)C(=O)NC1=O"                                                                                             
T2S SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=S)(O)S)O"                                                                                        
T2S SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=S)(O)S)O"                                                                                                        
T2S InChI            InChI                1.03  "InChI=1S/C10H15N2O6PS2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(18-8)4-17-19(16,20)21/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,20,21)/t6-,7+,8+/m0/s1" 
T2S InChIKey         InChI                1.03  KMPXQZWMYQHTNT-XLPZGREQSA-N                                                                                                                        
# 
loop_
_pdbx_chem_comp_identifier.comp_id 
_pdbx_chem_comp_identifier.type 
_pdbx_chem_comp_identifier.program 
_pdbx_chem_comp_identifier.program_version 
_pdbx_chem_comp_identifier.identifier 
T2S "SYSTEMATIC NAME" ACDLabs              10.04 "5'-O-[(dithiophosphono)]thymidine"                                                                                 
T2S "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "1-[(2R,4S,5R)-4-hydroxy-5-[(hydroxy-sulfanyl-phosphinothioyl)oxymethyl]oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
T2S "Create component"      2001-11-02 RCSB 
T2S "Modify descriptor"     2011-06-04 RCSB 
T2S "Other modification"    2018-03-14 EBI  
T2S "Modify parent residue" 2022-06-13 RCSB 
# 
