data_ATD
# 
_chem_comp.id                                    ATD 
_chem_comp.name                                  "THYMIDINE-3'-PHOSPHATE" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H15 N2 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               DT 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     1999-09-29 
_chem_comp.pdbx_modified_date                    2011-06-04 
_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                        322.208 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     ATD 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1BX5 
_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 
ATD P      P    P 0 1 N N N -4.128 6.474  5.377 0.951  -0.076 -3.841 P      ATD 1  
ATD OP1    O1P  O 0 1 N N N -5.451 7.119  5.223 -0.299 -0.588 -4.444 OP1    ATD 2  
ATD OP2    O2P  O 0 1 N N N -3.469 6.422  6.699 1.690  0.901  -4.886 OP2    ATD 3  
ATD OP3    O3P  O 0 1 N Y N -3.117 7.102  4.296 1.920  -1.311 -3.485 OP3    ATD 4  
ATD "O5'"  O5*  O 0 1 N N N -8.444 3.779  6.545 -3.794 0.239  -1.511 "O5'"  ATD 5  
ATD "C5'"  C5*  C 0 1 N N N -7.678 4.212  5.448 -2.536 -0.278 -1.949 "C5'"  ATD 6  
ATD "C4'"  C4*  C 0 1 N N R -6.187 3.975  5.635 -1.408 0.375  -1.147 "C4'"  ATD 7  
ATD "O4'"  O4*  O 0 1 N N N -5.783 2.666  5.955 -1.553 0.057  0.242  "O4'"  ATD 8  
ATD "C3'"  C3*  C 0 1 N N S -5.399 4.357  4.403 -0.045 -0.177 -1.614 "C3'"  ATD 9  
ATD "O3'"  O3*  O 0 1 N N N -4.199 4.972  4.784 0.605  0.738  -2.497 "O3'"  ATD 10 
ATD "C2'"  C2*  C 0 1 N N N -5.170 3.029  3.693 0.734  -0.304 -0.277 "C2'"  ATD 11 
ATD "C1'"  C1*  C 0 1 N N S -5.233 2.014  4.824 -0.410 -0.685 0.695  "C1'"  ATD 12 
ATD N1     N1   N 0 1 N N N -3.846 1.540  5.049 -0.063 -0.300 2.065  N1     ATD 13 
ATD C2     C2   C 0 1 N N N -3.436 0.330  4.483 0.206  0.987  2.347  C2     ATD 14 
ATD O2     O2   O 0 1 N N N -4.154 -0.354 3.763 0.159  1.817  1.460  O2     ATD 15 
ATD N3     N3   N 0 1 N N N -2.161 -0.090 4.796 0.528  1.369  3.597  N3     ATD 16 
ATD C4     C4   C 0 1 N N N -1.272 0.568  5.625 0.580  0.461  4.593  C4     ATD 17 
ATD O4     O4   O 0 1 N N N -0.176 0.060  5.837 0.870  0.805  5.724  O4     ATD 18 
ATD C5     C5   C 0 1 N N N -1.758 1.852  6.133 0.302  -0.897 4.309  C5     ATD 19 
ATD C5M    C5M  C 0 1 N N N -0.943 2.715  7.070 0.358  -1.933 5.402  C5M    ATD 20 
ATD C6     C6   C 0 1 N N N -2.983 2.305  5.785 -0.017 -1.253 3.046  C6     ATD 21 
ATD HOP2   2HOP H 0 0 N N N -2.619 6.007  6.797 1.879  0.374  -5.675 HOP2   ATD 22 
ATD HOP3   3HOP H 0 0 N N N -2.267 6.687  4.394 2.722  -0.935 -3.095 HOP3   ATD 23 
ATD "HO'5" 5HO* H 0 0 N N N -9.375 3.927  6.428 -4.475 -0.197 -2.040 "HO'5" ATD 24 
ATD "H5'"  1H5* H 0 1 N N N -7.891 5.264  5.244 -2.402 -0.059 -3.009 "H5'"  ATD 25 
ATD "H5''" 2H5* H 0 0 N N N -7.964 3.642  4.597 -2.513 -1.356 -1.795 "H5''" ATD 26 
ATD "H4'"  H4*  H 0 1 N N N -5.884 4.580  6.437 -1.435 1.456  -1.285 "H4'"  ATD 27 
ATD "H3'"  H3*  H 0 1 N N N -5.933 5.047  3.795 -0.163 -1.152 -2.088 "H3'"  ATD 28 
ATD "H2'"  1H2* H 0 1 N N N -5.947 2.796  2.979 1.188  0.645  0.004  "H2'"  ATD 29 
ATD "H2''" 2H2* H 0 0 N N N -4.206 3.031  3.194 1.482  -1.094 -0.331 "H2''" ATD 30 
ATD "H1'"  H1*  H 0 1 N N N -5.897 1.167  4.639 -0.610 -1.755 0.643  "H1'"  ATD 31 
ATD H3     H3   H 0 1 N N N -1.896 -1.006 4.442 0.719  2.301  3.783  H3     ATD 32 
ATD H71    1H5M H 0 1 N N N -0.386 2.088  7.767 0.632  -1.454 6.342  H71    ATD 33 
ATD H72    2H5M H 0 1 N N N -0.279 3.337  6.490 -0.618 -2.404 5.506  H72    ATD 34 
ATD H73    3H5M H 0 1 N N N -1.592 3.380  7.637 1.101  -2.689 5.150  H73    ATD 35 
ATD H6     H6   H 0 1 N N N -3.314 3.282  6.093 -0.235 -2.284 2.811  H6     ATD 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 
ATD P     OP1    DOUB N N 1  
ATD P     OP2    SING N N 2  
ATD P     OP3    SING N N 3  
ATD P     "O3'"  SING N N 4  
ATD OP2   HOP2   SING N N 5  
ATD OP3   HOP3   SING N N 6  
ATD "O5'" "C5'"  SING N N 7  
ATD "O5'" "HO'5" SING N N 8  
ATD "C5'" "C4'"  SING N N 9  
ATD "C5'" "H5'"  SING N N 10 
ATD "C5'" "H5''" SING N N 11 
ATD "C4'" "O4'"  SING N N 12 
ATD "C4'" "C3'"  SING N N 13 
ATD "C4'" "H4'"  SING N N 14 
ATD "O4'" "C1'"  SING N N 15 
ATD "C3'" "O3'"  SING N N 16 
ATD "C3'" "C2'"  SING N N 17 
ATD "C3'" "H3'"  SING N N 18 
ATD "C2'" "C1'"  SING N N 19 
ATD "C2'" "H2'"  SING N N 20 
ATD "C2'" "H2''" SING N N 21 
ATD "C1'" N1     SING N N 22 
ATD "C1'" "H1'"  SING N N 23 
ATD N1    C2     SING N N 24 
ATD N1    C6     SING N N 25 
ATD C2    O2     DOUB N N 26 
ATD C2    N3     SING N N 27 
ATD N3    C4     SING N N 28 
ATD N3    H3     SING N N 29 
ATD C4    O4     DOUB N N 30 
ATD C4    C5     SING N N 31 
ATD C5    C5M    SING N N 32 
ATD C5    C6     DOUB N N 33 
ATD C5M   H71    SING N N 34 
ATD C5M   H72    SING N N 35 
ATD C5M   H73    SING N N 36 
ATD 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 
ATD SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(OP(=O)(O)O)C2)CO"                                                                                                      
ATD SMILES_CANONICAL CACTVS               3.341 "CC1=CN([C@@H]2C[C@H](O[P](O)(O)=O)[C@@H](CO)O2)C(=O)NC1=O"                                                                                      
ATD SMILES           CACTVS               3.341 "CC1=CN([CH]2C[CH](O[P](O)(O)=O)[CH](CO)O2)C(=O)NC1=O"                                                                                           
ATD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@@H]2C[C@@H]([C@H](O2)CO)OP(=O)(O)O"                                                                                        
ATD SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)CO)OP(=O)(O)O"                                                                                                      
ATD InChI            InChI                1.03  "InChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(7(4-13)19-8)20-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8-/m0/s1" 
ATD InChIKey         InChI                1.03  XXYIANZGUOSQHY-RNJXMRFFSA-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 
ATD "SYSTEMATIC NAME" ACDLabs              10.04 
;3'-thymidylic acid
;
ATD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5S)-2-(hydroxymethyl)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-3-yl] dihydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
ATD "Create component"  1999-09-29 RCSB 
ATD "Modify descriptor" 2011-06-04 RCSB 
# 
