data_SMT
# 
_chem_comp.id                                    SMT 
_chem_comp.name                                  "2'-[(METHYLTHIO)ETHYLOXY]-THYMIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type                                  "RNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C13 H21 N2 O9 P S" 
_chem_comp.mon_nstd_parent_comp_id               T 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2002-09-10 
_chem_comp.pdbx_modified_date                    2009-01-07 
_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                        412.353 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     SMT 
_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        1MLX 
_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 
SMT P      P      P 0 1 N N N 10.751 4.213  5.406  2.787  0.324  -4.407 P      SMT 1  
SMT OP1    O1P    O 0 1 N N N 11.971 4.728  4.682  3.659  1.172  -5.286 OP1    SMT 2  
SMT OP2    O2P    O 0 1 N N N 10.916 3.445  6.670  1.198  0.588  -4.548 OP2    SMT 3  
SMT OP3    O3P    O 0 1 N Y N ?      ?      ?      2.921  -1.270 -4.647 OP3    SMT 4  
SMT "O5'"  "O5'"  O 0 1 N N N 9.743  5.400  5.717  3.063  0.476  -2.819 "O5'"  SMT 5  
SMT "C5'"  "C5'"  C 0 1 N N N 9.440  6.334  4.704  2.282  -0.292 -1.921 "C5'"  SMT 6  
SMT "C4'"  "C4'"  C 0 1 N N R 8.344  7.233  5.184  2.725  0.023  -0.498 "C4'"  SMT 7  
SMT "O4'"  "O4'"  O 0 1 N N N 7.136  6.429  5.377  2.470  1.422  -0.246 "O4'"  SMT 8  
SMT "C3'"  "C3'"  C 0 1 N N R 8.503  7.870  6.523  1.940  -0.742 0.560  "C3'"  SMT 9  
SMT "O3'"  "O3'"  O 0 1 N N N 9.445  8.960  6.469  2.742  -0.809 1.739  "O3'"  SMT 10 
SMT "C2'"  "C2'"  C 0 1 N N R 7.087  8.301  6.812  0.748  0.163  0.786  "C2'"  SMT 11 
SMT "O2'"  "O2'"  O 0 1 N N N 6.828  9.421  6.046  0.137  -0.058 2.041  "O2'"  SMT 12 
SMT "C1'"  "C1'"  C 0 1 N N R 6.364  7.051  6.458  1.373  1.543  0.675  "C1'"  SMT 13 
SMT N1     N1     N 0 1 N N N 6.251  6.036  7.511  0.452  2.524  0.177  N1     SMT 14 
SMT C2     C2     C 0 1 N N N 5.185  6.193  8.395  -0.300 3.336  1.055  C2     SMT 15 
SMT O2     O2     O 0 1 N N N 4.390  7.127  8.249  -0.225 3.269  2.283  O2     SMT 16 
SMT N3     N3     N 0 1 N N N 5.092  5.273  9.351  -1.159 4.248  0.431  N3     SMT 17 
SMT C4     C4     C 0 1 N N N 6.000  4.226  9.620  -1.338 4.427  -0.932 C4     SMT 18 
SMT O4     O4     O 0 1 N N N 5.744  3.447  10.583 -2.112 5.251  -1.413 O4     SMT 19 
SMT C5     C5     C 0 1 N N N 7.097  4.084  8.664  -0.514 3.537  -1.792 C5     SMT 20 
SMT C5A    C5A    C 0 1 N N N 8.129  3.062  8.827  -0.651 3.669  -3.275 C5A    SMT 21 
SMT C6     C6     C 0 1 N N N 7.115  5.047  7.708  0.309  2.663  -1.199 C6     SMT 22 
SMT "CA'"  "CA'"  C 0 1 N N N 5.405  9.996  6.308  -0.332 -1.396 2.174  "CA'"  SMT 23 
SMT CB     CB     C 0 1 N N N ?      ?      ?      -0.903 -1.612 3.566  CB     SMT 24 
SMT SC     SC     S 0 1 N N N ?      ?      ?      -2.290 -0.484 3.898  SC     SMT 25 
SMT CD     CD     C 0 1 N N N ?      ?      ?      -2.704 -1.063 5.559  CD     SMT 26 
SMT H2P    H2P    H 0 1 N N N 10.951 2.516  6.474  0.799  0.616  -5.443 H2P    SMT 27 
SMT H3P    H3P    H 0 1 N N N ?      ?      ?      2.886  -1.617 -5.563 H3P    SMT 28 
SMT "H5'"  "H5'"  H 0 1 N N N 10.334 6.932  4.473  1.229  -0.035 -2.051 "H5'"  SMT 29 
SMT "H5'2" "2H5'" H 0 0 N N N 9.116  5.805  3.795  2.428  -1.352 -2.133 "H5'2" SMT 30 
SMT "H4'"  "H4'"  H 0 1 N N N 8.329  8.018  4.414  3.804  -0.139 -0.410 "H4'"  SMT 31 
SMT "H3'"  "H3'"  H 0 1 N N N 8.917  7.221  7.308  1.675  -1.764 0.277  "H3'"  SMT 32 
SMT HO3    HO3    H 0 1 N Y N 9.652  9.244  7.352  3.447  -0.153 1.628  HO3    SMT 33 
SMT "H2'"  "H2'"  H 0 1 N N N 6.814  8.626  7.827  -0.000 0.004  -0.000 "H2'"  SMT 34 
SMT "H1'"  "H1'"  H 0 1 N N N 5.334  7.354  6.217  1.754  1.910  1.633  "H1'"  SMT 35 
SMT H3     H3     H 0 1 N N N 4.290  5.329  9.945  -1.709 4.843  1.045  H3     SMT 36 
SMT H5A    H5A    H 0 1 N N N 8.550  2.805  7.844  -1.057 2.748  -3.690 H5A    SMT 37 
SMT H5A1   1H5A   H 0 0 N N N 8.927  3.448  9.478  0.324  3.866  -3.719 H5A1   SMT 38 
SMT H5A2   2H5A   H 0 0 N N N 7.686  2.164  9.282  -1.320 4.497  -3.510 H5A2   SMT 39 
SMT H6     H6     H 0 1 N N N 7.942  5.003  7.015  0.928  1.995  -1.790 H6     SMT 40 
SMT HA1    1HA    H 0 1 N N N 5.117  10.119 7.362  -1.069 -1.599 1.390  HA1    SMT 41 
SMT HA2    2HA    H 0 1 N N N 5.168  11.026 6.002  0.523  -2.064 2.022  HA2    SMT 42 
SMT HB1    1HB    H 0 1 N N N ?      ?      ?      -0.138 -1.433 4.328  HB1    SMT 43 
SMT HB2    2HB    H 0 1 N N N ?      ?      ?      -1.268 -2.639 3.669  HB2    SMT 44 
SMT HD1    1HD    H 0 1 N N N ?      ?      ?      -2.493 -2.132 5.643  HD1    SMT 45 
SMT HD2    2HD    H 0 1 N N N ?      ?      ?      -3.765 -0.891 5.758  HD2    SMT 46 
SMT HD3    3HD    H 0 1 N N N ?      ?      ?      -2.109 -0.522 6.299  HD3    SMT 47 
# 
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 
SMT P     OP1    DOUB N N 1  
SMT P     OP2    SING N N 2  
SMT P     OP3    SING N N 3  
SMT P     "O5'"  SING N N 4  
SMT OP2   H2P    SING N N 5  
SMT OP3   H3P    SING N N 6  
SMT "O5'" "C5'"  SING N N 7  
SMT "C5'" "C4'"  SING N N 8  
SMT "C5'" "H5'"  SING N N 9  
SMT "C5'" "H5'2" SING N N 10 
SMT "C4'" "O4'"  SING N N 11 
SMT "C4'" "C3'"  SING N N 12 
SMT "C4'" "H4'"  SING N N 13 
SMT "O4'" "C1'"  SING N N 14 
SMT "C3'" "O3'"  SING N N 15 
SMT "C3'" "C2'"  SING N N 16 
SMT "C3'" "H3'"  SING N N 17 
SMT "O3'" HO3    SING N N 18 
SMT "C2'" "O2'"  SING N N 19 
SMT "C2'" "C1'"  SING N N 20 
SMT "C2'" "H2'"  SING N N 21 
SMT "O2'" "CA'"  SING N N 22 
SMT "C1'" N1     SING N N 23 
SMT "C1'" "H1'"  SING N N 24 
SMT N1    C2     SING N N 25 
SMT N1    C6     SING N N 26 
SMT C2    O2     DOUB N N 27 
SMT C2    N3     SING N N 28 
SMT N3    C4     SING N N 29 
SMT N3    H3     SING N N 30 
SMT C4    O4     DOUB N N 31 
SMT C4    C5     SING N N 32 
SMT C5    C5A    SING N N 33 
SMT C5    C6     DOUB N N 34 
SMT C5A   H5A    SING N N 35 
SMT C5A   H5A1   SING N N 36 
SMT C5A   H5A2   SING N N 37 
SMT C6    H6     SING N N 38 
SMT "CA'" CB     SING N N 39 
SMT "CA'" HA1    SING N N 40 
SMT "CA'" HA2    SING N N 41 
SMT CB    SC     SING N N 42 
SMT CB    HB1    SING N N 43 
SMT CB    HB2    SING N N 44 
SMT SC    CD     SING N N 45 
SMT CD    HD1    SING N N 46 
SMT CD    HD2    SING N N 47 
SMT CD    HD3    SING N N 48 
# 
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 
SMT SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(O)C2OCCSC)COP(=O)(O)O"                                                                                                                                           
SMT InChI            InChI                1.02b "InChI=1/C13H21N2O9PS/c1-7-5-15(13(18)14-11(7)17)12-10(22-3-4-26-2)9(16)8(24-12)6-23-25(19,20)21/h5,8-10,12,16H,3-4,6H2,1-2H3,(H,14,17,18)(H2,19,20,21)/t8-,9-,10-,12-/m1/s1/f/h14,19-20H" 
SMT InChIKey         InChI                1.02b JQQIRBYIPIMLTK-IHXBBRRKDM                                                                                                                                                                  
SMT SMILES_CANONICAL CACTVS               3.341 "CSCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O"                                                                                                                       
SMT SMILES           CACTVS               3.341 "CSCCO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O"                                                                                                                             
SMT SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OCCSC"                                                                                                                       
SMT SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OCCSC"                                                                                                                                         
# 
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 
SMT "SYSTEMATIC NAME" ACDLabs              10.04 
;5-methyl-2'-O-[2-(methylsulfanyl)ethyl]uridine 5'-(dihydrogen phosphate)
;
SMT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-4-(2-methylsulfanylethoxy)oxolan-2-yl]methyl dihydrogen phosphate" 
# 
