data_MDU
# 
_chem_comp.id                                    MDU 
_chem_comp.name                                  
;3-(hydroxymethyl)thymidine 5'-(dihydrogen phosphate)
;
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C11 H17 N2 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2010-07-23 
_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                        352.234 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     MDU 
_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        3O1T 
_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 
MDU P      P      P 0 1 N N N 0.890  0.704  -0.990 -4.666 1.167  -0.167 P      MDU 1  
MDU N1     N1     N 0 1 N N N 0.158  -1.740 3.435  1.814  -0.545 -0.128 N1     MDU 2  
MDU C2     C2     C 0 1 N N N -0.447 -2.384 4.490  2.913  -0.380 -0.887 C2     MDU 3  
MDU O2     O2     O 0 1 N N N 0.280  -2.846 5.405  2.937  -0.832 -2.015 O2     MDU 4  
MDU N3     N3     N 0 1 N N N -1.814 -2.547 4.560  3.987  0.280  -0.414 N3     MDU 5  
MDU C4     C4     C 0 1 N N N -2.599 -2.064 3.539  3.977  0.789  0.835  C4     MDU 6  
MDU O4     O4     O 0 1 N N N -3.846 -2.216 3.564  4.948  1.386  1.263  O4     MDU 7  
MDU C5     C5     C 0 1 N N N -2.030 -1.389 2.434  2.827  0.621  1.643  C5     MDU 8  
MDU C6     C6     C 0 1 N N N -0.632 -1.230 2.443  1.764  -0.045 1.144  C6     MDU 9  
MDU "C1'"  "C1'"  C 0 1 N N R 1.613  -1.660 3.338  0.659  -1.263 -0.672 "C1'"  MDU 10 
MDU O1P    O1P    O 0 1 N N N 1.480  1.694  -1.969 -5.936 0.235  0.169  O1P    MDU 11 
MDU "C2'"  "C2'"  C 0 1 N N N 2.215  -3.009 2.880  0.432  -2.566 0.118  "C2'"  MDU 12 
MDU C21    C21    C 0 1 N N N -2.445 -3.241 5.675  5.171  0.447  -1.260 C21    MDU 13 
MDU O22    O22    O 0 1 N N N -3.327 -2.383 6.395  5.231  1.793  -1.737 O22    MDU 14 
MDU O2P    O2P    O 0 1 N N N -0.053 1.406  -0.095 -4.337 1.996  1.014  O2P    MDU 15 
MDU "C3'"  "C3'"  C 0 1 N N S 3.394  -2.621 1.979  -1.009 -2.430 0.669  "C3'"  MDU 16 
MDU "O3'"  "O3'"  O 0 1 N N N 4.616  -2.590 2.716  -1.711 -3.671 0.571  "O3'"  MDU 17 
MDU "C4'"  "C4'"  C 0 1 N N R 3.016  -1.204 1.494  -1.622 -1.372 -0.284 "C4'"  MDU 18 
MDU "O4'"  "O4'"  O 0 1 N N N 2.125  -0.636 2.467  -0.526 -0.463 -0.526 "O4'"  MDU 19 
MDU "C5'"  "C5'"  C 0 1 N N N 2.337  -1.159 0.100  -2.785 -0.646 0.395  "C5'"  MDU 20 
MDU "O5'"  "O5'"  O 0 1 N N N 2.023  0.117  -0.163 -3.404 0.239  -0.541 "O5'"  MDU 21 
MDU C5M    C5M    C 0 1 N N N -2.810 -0.868 1.278  2.790  1.179  3.043  C5M    MDU 22 
MDU H6     H6     H 0 1 N N N -0.166 -0.685 1.636  0.878  -0.182 1.747  H6     MDU 23 
MDU "H1'"  "H1'"  H 0 1 N N N 1.921  -1.397 4.361  0.827  -1.492 -1.724 "H1'"  MDU 24 
MDU "H2'"  "H2'"  H 0 1 N N N 2.553  -3.605 3.741  0.508  -3.431 -0.541 "H2'"  MDU 25 
MDU "H2'A" "H2'A" H 0 0 N N N 1.474  -3.607 2.328  1.147  -2.645 0.937  "H2'A" MDU 26 
MDU H21    H21    H 0 1 N N N -3.021 -4.092 5.282  6.067  0.228  -0.678 H21    MDU 27 
MDU "H3'"  "H3'"  H 0 1 N N N 3.558  -3.334 1.158  -1.000 -2.070 1.697  "H3'"  MDU 28 
MDU "HO3'" "HO3'" H 0 0 N N N 5.329  -2.348 2.137  -1.312 -4.390 1.080  "HO3'" MDU 29 
MDU "H4'"  "H4'"  H 0 1 N N N 3.952  -0.637 1.387  -1.948 -1.836 -1.214 "H4'"  MDU 30 
MDU "H5'"  "H5'"  H 0 1 N N N 3.026  -1.543 -0.667 -3.515 -1.375 0.743  "H5'"  MDU 31 
MDU "H5'A" "H5'A" H 0 0 N N N 1.427  -1.777 0.104  -2.410 -0.073 1.243  "H5'A" MDU 32 
MDU H5M    H5M    H 0 1 N N N -2.128 -0.388 0.561  3.734  1.678  3.260  H5M    MDU 33 
MDU H5MA   H5MA   H 0 0 N N N -3.334 -1.700 0.785  1.973  1.896  3.127  H5MA   MDU 34 
MDU H5MB   H5MB   H 0 0 N N N -3.545 -0.131 1.634  2.636  0.367  3.754  H5MB   MDU 35 
MDU O9     O9     O 0 1 N N N 0.156  -0.368 -1.759 -5.017 2.124  -1.413 O9     MDU 36 
MDU H14    H14    H 0 1 N N N 1.120  2.557  -1.802 -6.208 -0.336 -0.562 H14    MDU 37 
MDU H15    H15    H 0 1 N N N -0.760 -0.368 -1.507 -5.769 2.711  -1.259 H15    MDU 38 
MDU H16    H16    H 0 1 N N N -1.661 -3.598 6.359  5.112  -0.237 -2.107 H16    MDU 39 
MDU H17    H17    H 0 1 N N N -3.902 -1.936 5.785  5.991  1.975  -2.305 H17    MDU 40 
# 
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 
MDU P     O1P    SING N N 1  
MDU P     O2P    DOUB N N 2  
MDU P     "O5'"  SING N N 3  
MDU N1    C2     SING N N 4  
MDU N1    C6     SING N N 5  
MDU N1    "C1'"  SING N N 6  
MDU C2    O2     DOUB N N 7  
MDU C2    N3     SING N N 8  
MDU N3    C4     SING N N 9  
MDU N3    C21    SING N N 10 
MDU C4    O4     DOUB N N 11 
MDU C4    C5     SING N N 12 
MDU C5    C6     DOUB N N 13 
MDU C5    C5M    SING N N 14 
MDU C6    H6     SING N N 15 
MDU "C1'" "C2'"  SING N N 16 
MDU "C1'" "O4'"  SING N N 17 
MDU "C1'" "H1'"  SING N N 18 
MDU O1P   H14    SING N N 19 
MDU "C2'" "C3'"  SING N N 20 
MDU "C2'" "H2'"  SING N N 21 
MDU "C2'" "H2'A" SING N N 22 
MDU C21   O22    SING N N 23 
MDU C21   H21    SING N N 24 
MDU "C3'" "O3'"  SING N N 25 
MDU "C3'" "C4'"  SING N N 26 
MDU "C3'" "H3'"  SING N N 27 
MDU "O3'" "HO3'" SING N N 28 
MDU "C4'" "O4'"  SING N N 29 
MDU "C4'" "C5'"  SING N N 30 
MDU "C4'" "H4'"  SING N N 31 
MDU "C5'" "O5'"  SING N N 32 
MDU "C5'" "H5'"  SING N N 33 
MDU "C5'" "H5'A" SING N N 34 
MDU C5M   H5M    SING N N 35 
MDU C5M   H5MA   SING N N 36 
MDU C5M   H5MB   SING N N 37 
MDU O9    P      SING N N 38 
MDU O9    H15    SING N N 39 
MDU C21   H16    SING N N 40 
MDU O22   H17    SING N N 41 
# 
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 
MDU SMILES           ACDLabs              12.01 "O=P(O)(O)OCC2OC(N1C(=O)N(C(=O)C(=C1)C)CO)CC2O"                                                                                                 
MDU SMILES_CANONICAL CACTVS               3.370 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)N(CO)C1=O"                                                                                  
MDU SMILES           CACTVS               3.370 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)N(CO)C1=O"                                                                                      
MDU SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=O)N(C1=O)CO)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"                                                                                    
MDU SMILES           "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=O)N(C1=O)CO)C2CC(C(O2)COP(=O)(O)O)O"                                                                                                 
MDU InChI            InChI                1.03  "InChI=1S/C11H17N2O9P/c1-6-3-12(11(17)13(5-14)10(6)16)9-2-7(15)8(22-9)4-21-23(18,19)20/h3,7-9,14-15H,2,4-5H2,1H3,(H2,18,19,20)/t7-,8+,9+/m0/s1" 
MDU InChIKey         InChI                1.03  UGQLUWYICJLJKZ-DJLDLDEBSA-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 
MDU "SYSTEMATIC NAME" ACDLabs              12.01 
;3-(hydroxymethyl)thymidine 5'-(dihydrogen phosphate)
;
MDU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3S,5R)-3-hydroxy-5-[3-(hydroxymethyl)-5-methyl-2,4-dioxo-pyrimidin-1-yl]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 
MDU "Create component"  2010-07-23 RCSB 
MDU "Modify descriptor" 2011-06-04 RCSB 
# 
