data_3TD
# 
_chem_comp.id                                    3TD 
_chem_comp.name                                  "(1S)-1,4-anhydro-1-(3-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-ribitol" 
_chem_comp.type                                  "RNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H15 N2 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               U 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2011-01-18 
_chem_comp.pdbx_modified_date                    2011-12-14 
_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                        338.208 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     3TD 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        3IZT 
_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 
3TD P      P      P 0 1 N N N -0.106 0.017  -0.147 4.263  -1.099 -0.157 P      3TD 1  
3TD N1     N1     N 0 1 N N N 5.169  0.693  5.003  -4.373 -0.595 -1.385 N1     3TD 2  
3TD C2     C2     C 0 1 N N N 6.482  0.820  5.302  -4.459 -1.339 -0.266 C2     3TD 3  
3TD O2     O2     O 0 1 N N N 6.745  1.369  6.398  -5.427 -2.054 -0.095 O2     3TD 4  
3TD N3     N3     N 0 1 N N N 7.452  0.374  4.438  -3.488 -1.302 0.665  N3     3TD 5  
3TD C4     C4     C 0 1 N N N 7.064  -0.184 3.239  -2.408 -0.515 0.490  C4     3TD 6  
3TD O4     O4     O 0 1 N N N 7.926  -0.582 2.418  -1.528 -0.481 1.332  O4     3TD 7  
3TD C5     C5     C 0 1 N N N 5.694  -0.330 2.897  -2.305 0.273  -0.682 C5     3TD 8  
3TD C6     C6     C 0 1 N N N 4.759  0.133  3.844  -3.294 0.217  -1.600 C6     3TD 9  
3TD "C1'"  "C1'"  C 0 1 N N S 5.237  -0.968 1.625  -1.108 1.162  -0.902 "C1'"  3TD 10 
3TD C10    C10    C 0 1 N N N 8.853  0.516  4.782  -3.605 -2.121 1.874  C10    3TD 11 
3TD "C2'"  "C2'"  C 0 1 N N R 5.038  -2.488 1.767  -1.078 2.274  0.164  "C2'"  3TD 12 
3TD "O2'"  "O2'"  O 0 1 N N N 6.269  -3.208 1.718  -1.145 3.561  -0.453 "O2'"  3TD 13 
3TD "C3'"  "C3'"  C 0 1 N N S 4.090  -2.826 0.604  0.284  2.082  0.874  "C3'"  3TD 14 
3TD "O3'"  "O3'"  O 0 1 N N N 4.789  -3.371 -0.517 0.904  3.343  1.136  "O3'"  3TD 15 
3TD "C4'"  "C4'"  C 0 1 N N R 3.441  -1.459 0.246  1.089  1.279  -0.179 "C4'"  3TD 16 
3TD "O4'"  "O4'"  O 0 1 N N N 3.950  -0.502 1.189  0.101  0.399  -0.758 "O4'"  3TD 17 
3TD "C5'"  "C5'"  C 0 1 N N N 1.894  -1.492 0.280  2.201  0.472  0.493  "C5'"  3TD 18 
3TD "O5'"  "O5'"  O 0 1 N N N 1.380  -0.299 -0.044 2.999  -0.166 -0.507 "O5'"  3TD 19 
3TD OP1    OP1    O 0 1 N N N -0.722 -0.855 -1.217 5.410  -0.210 0.540  OP1    3TD 20 
3TD OP2    OP2    O 0 1 N N N -0.768 -0.240 1.149  3.841  -2.174 0.768  OP2    3TD 21 
3TD HN1    HN1    H 0 1 N N N 4.486  1.021  5.655  -5.082 -0.639 -2.046 HN1    3TD 22 
3TD H6     H6     H 0 1 N N N 3.702  0.039  3.641  -3.232 0.810  -2.500 H6     3TD 23 
3TD "H1'"  "H1'"  H 0 1 N N N 5.987  -0.785 0.841  -1.153 1.604  -1.898 "H1'"  3TD 24 
3TD H10    H10    H 0 1 N N N 9.473  0.104  3.973  -4.537 -2.686 1.841  H10    3TD 25 
3TD H10A   H10A   H 0 0 N N N 9.090  1.581  4.920  -2.763 -2.811 1.929  H10A   3TD 26 
3TD H10B   H10B   H 0 0 N N N 9.058  -0.029 5.715  -3.603 -1.475 2.752  H10B   3TD 27 
3TD "H2'"  "H2'"  H 0 1 N N N 4.518  -2.688 2.715  -1.899 2.147  0.870  "H2'"  3TD 28 
3TD "HO2'" "HO2'" H 0 0 N N N 6.096  -4.138 1.809  -1.129 4.298  0.173  "HO2'" 3TD 29 
3TD "H3'"  "H3'"  H 0 1 N N N 3.310  -3.517 0.956  0.167  1.510  1.794  "H3'"  3TD 30 
3TD "HO3'" "HO3'" H 0 0 N Y N 4.171  -3.566 -1.212 0.392  3.919  1.720  "HO3'" 3TD 31 
3TD "H4'"  "H4'"  H 0 1 N N N 3.758  -1.184 -0.771 1.500  1.945  -0.938 "H4'"  3TD 32 
3TD "H5'"  "H5'"  H 0 1 N N N 1.535  -2.245 -0.437 2.827  1.140  1.085  "H5'"  3TD 33 
3TD "H5'A" "H5'A" H 0 0 N N N 1.562  -1.763 1.293  1.760  -0.284 1.143  "H5'A" 3TD 34 
3TD O9     O9     O 0 1 N Y N -0.287 1.468  -0.527 4.839  -1.751 -1.512 O9     3TD 35 
3TD H14    H14    H 0 1 N N N -1.408 -1.389 -0.835 5.734  0.516  -0.010 H14    3TD 36 
3TD H15    H15    H 0 1 N N N -0.789 1.912  0.147  5.604  -2.327 -1.376 H15    3TD 37 
# 
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 
3TD P     "O5'"  SING N N 1  
3TD P     OP1    SING N N 2  
3TD P     OP2    DOUB N N 3  
3TD N1    C2     SING N N 4  
3TD N1    C6     SING N N 5  
3TD N1    HN1    SING N N 6  
3TD C2    O2     DOUB N N 7  
3TD C2    N3     SING N N 8  
3TD N3    C4     SING N N 9  
3TD N3    C10    SING N N 10 
3TD C4    O4     DOUB N N 11 
3TD C4    C5     SING N N 12 
3TD C5    C6     DOUB N N 13 
3TD C5    "C1'"  SING N N 14 
3TD C6    H6     SING N N 15 
3TD "C1'" "C2'"  SING N N 16 
3TD "C1'" "O4'"  SING N N 17 
3TD "C1'" "H1'"  SING N N 18 
3TD C10   H10    SING N N 19 
3TD C10   H10A   SING N N 20 
3TD C10   H10B   SING N N 21 
3TD "C2'" "O2'"  SING N N 22 
3TD "C2'" "C3'"  SING N N 23 
3TD "C2'" "H2'"  SING N N 24 
3TD "O2'" "HO2'" SING N N 25 
3TD "C3'" "O3'"  SING N N 26 
3TD "C3'" "C4'"  SING N N 27 
3TD "C3'" "H3'"  SING N N 28 
3TD "O3'" "HO3'" SING N N 29 
3TD "C4'" "O4'"  SING N N 30 
3TD "C4'" "C5'"  SING N N 31 
3TD "C4'" "H4'"  SING N N 32 
3TD "C5'" "O5'"  SING N N 33 
3TD "C5'" "H5'"  SING N N 34 
3TD "C5'" "H5'A" SING N N 35 
3TD P     O9     SING N N 36 
3TD OP1   H14    SING N N 37 
3TD O9    H15    SING N N 38 
# 
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 
3TD SMILES           ACDLabs              12.01 "O=C1NC=C(C(=O)N1C)C2OC(COP(=O)(O)O)C(O)C2O"                                                                                                          
3TD InChI            InChI                1.03  "InChI=1S/C10H15N2O9P/c1-12-9(15)4(2-11-10(12)16)8-7(14)6(13)5(21-8)3-20-22(17,18)19/h2,5-8,13-14H,3H2,1H3,(H,11,16)(H2,17,18,19)/t5-,6-,7-,8+/m1/s1" 
3TD InChIKey         InChI                1.03  XBPGZENOIJPXSD-XUTVFYLZSA-N                                                                                                                           
3TD SMILES_CANONICAL CACTVS               3.370 "CN1C(=O)NC=C([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C1=O"                                                                                      
3TD SMILES           CACTVS               3.370 "CN1C(=O)NC=C([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C1=O"                                                                                            
3TD SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CN1C(=O)C(=CNC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O"                                                                                      
3TD SMILES           "OpenEye OEToolkits" 1.7.6 "CN1C(=O)C(=CNC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O"                                                                                                        
# 
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 
3TD "SYSTEMATIC NAME" ACDLabs              12.01 "(1S)-1,4-anhydro-1-(3-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-ribitol"                              
3TD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4R,5S)-5-[3-methyl-2,4-bis(oxidanylidene)-1H-pyrimidin-5-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl 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 
3TD "Create component"         2011-01-18 RCSB 
3TD "Modify descriptor"        2011-06-04 RCSB 
3TD "Modify leaving atom flag" 2011-12-14 RCSB 
# 
