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               DT 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2002-09-10 
_chem_comp.pdbx_modified_date                    2018-03-14 
_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                        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        Corina 
_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  -5.261 0.738  -0.269 P      SMT 1  
SMT OP1    O1P    O 0 1 N N N 11.971 4.728  4.682  -5.124 0.303  -1.677 OP1    SMT 2  
SMT OP2    O2P    O 0 1 N N N 10.916 3.445  6.670  -5.796 2.256  -0.226 OP2    SMT 3  
SMT OP3    O3P    O 0 1 N Y N ?      ?      ?      -6.307 -0.221 0.490  OP3    SMT 4  
SMT "O5'"  "O5'"  O 0 1 N N N 9.743  5.400  5.717  -3.828 0.654  0.460  "O5'"  SMT 5  
SMT "C5'"  "C5'"  C 0 1 N N N 9.440  6.334  4.704  -2.661 1.311  -0.038 "C5'"  SMT 6  
SMT "C4'"  "C4'"  C 0 1 N N R 8.344  7.233  5.184  -1.479 1.024  0.890  "C4'"  SMT 7  
SMT "O4'"  "O4'"  O 0 1 N N N 7.136  6.429  5.377  -1.141 -0.372 0.834  "O4'"  SMT 8  
SMT "C3'"  "C3'"  C 0 1 N N R 8.503  7.870  6.523  -0.241 1.814  0.421  "C3'"  SMT 9  
SMT "O3'"  "O3'"  O 0 1 N N N 9.445  8.960  6.469  0.201  2.705  1.447  "O3'"  SMT 10 
SMT "C2'"  "C2'"  C 0 1 N N R 7.087  8.301  6.812  0.825  0.724  0.153  "C2'"  SMT 11 
SMT "O2'"  "O2'"  O 0 1 N N N 6.828  9.421  6.046  2.110  1.141  0.621  "O2'"  SMT 12 
SMT "C1'"  "C1'"  C 0 1 N N R 6.364  7.051  6.458  0.292  -0.466 0.990  "C1'"  SMT 13 
SMT N1     N1     N 0 1 N N N 6.251  6.036  7.511  0.787  -1.737 0.455  N1     SMT 14 
SMT C2     C2     C 0 1 N N N 5.185  6.193  8.395  0.483  -2.092 -0.806 C2     SMT 15 
SMT O2     O2     O 0 1 N N N 4.390  7.127  8.249  -0.200 -1.354 -1.489 O2     SMT 16 
SMT N3     N3     N 0 1 N N N 5.092  5.273  9.351  0.925  -3.254 -1.323 N3     SMT 17 
SMT C4     C4     C 0 1 N N N 6.000  4.226  9.620  1.684  -4.084 -0.579 C4     SMT 18 
SMT O4     O4     O 0 1 N N N 5.744  3.447  10.583 2.085  -5.135 -1.046 O4     SMT 19 
SMT C5     C5     C 0 1 N N N 7.097  4.084  8.664  2.011  -3.722 0.750  C5     SMT 20 
SMT C5A    C5A    C 0 1 N N N 8.129  3.062  8.827  2.858  -4.631 1.602  C5A    SMT 21 
SMT C6     C6     C 0 1 N N N 7.115  5.047  7.708  1.559  -2.548 1.241  C6     SMT 22 
SMT "CA'"  "CA'"  C 0 1 N N N 5.405  9.996  6.308  2.896  1.815  -0.364 "CA'"  SMT 23 
SMT CB     CB     C 0 1 N N N ?      ?      ?      4.242  2.214  0.244  CB     SMT 24 
SMT SC     SC     S 0 1 N N N ?      ?      ?      5.241  3.069  -1.005 SC     SMT 25 
SMT CD     CD     C 0 1 N N N ?      ?      ?      6.771  3.455  -0.111 CD     SMT 26 
SMT H2P    H2P    H 0 1 N N N 11.840 3.370  6.877  -5.909 2.608  0.667  H2P    SMT 27 
SMT H3P    H3P    H 0 1 N N N ?      ?      ?      -7.194 -0.220 0.104  H3P    SMT 28 
SMT "H5'"  "H5'"  H 0 1 N N N 10.334 6.932  4.474  -2.435 0.941  -1.039 "H5'"  SMT 29 
SMT "H5'2" "H5'2" H 0 0 N N N 9.112  5.803  3.798  -2.838 2.385  -0.079 "H5'2" SMT 30 
SMT "H4'"  "H4'"  H 0 1 N N N 8.156  8.011  4.430  -1.734 1.303  1.912  "H4'"  SMT 31 
SMT "H3'"  "H3'"  H 0 1 N N N 8.820  7.119  7.261  -0.464 2.365  -0.492 "H3'"  SMT 32 
SMT HO3    HO3    H 0 1 N Y N 9.529  9.349  7.332  -0.452 3.373  1.696  HO3    SMT 33 
SMT "H2'"  "H2'"  H 0 1 N N N 6.974  8.510  7.886  0.863  0.469  -0.906 "H2'"  SMT 34 
SMT "H1'"  "H1'"  H 0 1 N N N 5.360  7.308  6.089  0.571  -0.354 2.038  "H1'"  SMT 35 
SMT H3     H3     H 0 1 N N N 4.290  5.329  9.945  0.696  -3.495 -2.235 H3     SMT 36 
SMT H5A    H5A    H 0 1 N N N 8.851  3.134  8.000  3.126  -5.520 1.031  H5A    SMT 37 
SMT H5A1   H5A1   H 0 0 N N N 8.650  3.217  9.783  3.764  -4.106 1.904  H5A1   SMT 38 
SMT H5A2   H5A2   H 0 0 N N N 7.663  2.066  8.821  2.296  -4.925 2.489  H5A2   SMT 39 
SMT H6     H6     H 0 1 N N N 7.942  5.003  7.015  1.803  -2.253 2.251  H6     SMT 40 
SMT HA1    HA1    H 0 1 N N N 5.135  10.050 7.373  3.063  1.151  -1.212 HA1    SMT 41 
SMT HA2    HA2    H 0 1 N N N 5.224  10.972 5.834  2.370  2.709  -0.700 HA2    SMT 42 
SMT HB1    HB1    H 0 1 N N N ?      ?      ?      4.076  2.877  1.093  HB1    SMT 43 
SMT HB2    HB2    H 0 1 N N N ?      ?      ?      4.768  1.320  0.580  HB2    SMT 44 
SMT HD1    HD1    H 0 1 N N N ?      ?      ?      6.541  4.088  0.747  HD1    SMT 45 
SMT HD2    HD2    H 0 1 N N N ?      ?      ?      7.234  2.530  0.234  HD2    SMT 46 
SMT HD3    HD3    H 0 1 N N N ?      ?      ?      7.458  3.979  -0.775 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              12.01 "P(=O)(O)(O)OCC1OC(C(C1O)OCCSC)N2C(=O)NC(=O)C(C)=C2"                                                                                                                           
SMT InChI            InChI                1.03  "InChI=1S/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" 
SMT InChIKey         InChI                1.03  JQQIRBYIPIMLTK-DNRKLUKYSA-N                                                                                                                                                    
SMT SMILES_CANONICAL CACTVS               3.385 "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               3.385 "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" 1.7.6 "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" 1.7.6 "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              12.01 
;5-methyl-2'-O-[2-(methylsulfanyl)ethyl]uridine 5'-(dihydrogen phosphate)
;
SMT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3R,4R,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-(2-methylsulfanylethoxy)-3-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 
SMT "Create component"      2002-09-10 RCSB 
SMT "Modify descriptor"     2011-06-04 RCSB 
SMT "Modify parent residue" 2018-03-14 RCSB 
# 
