data_S2M
# 
_chem_comp.id                                    S2M 
_chem_comp.name                                  "2'-O-[2-(METHOXY)ETHYL]-2-THIOTHYMIDINE-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                     2005-09-16 
_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                        412.353 
_chem_comp.one_letter_code                       T 
_chem_comp.three_letter_code                     S2M 
_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        2AXB 
_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 
S2M O4     O4   O 0 1 N N N 6.546  21.027 7.726 -2.087 5.250  -1.504 O4     S2M 1  
S2M C4     C4   C 0 1 N N N 6.134  20.649 6.649 -1.318 4.438  -0.998 C4     S2M 2  
S2M C5     C5   C 0 1 N N N 5.105  21.234 5.990 -0.491 3.525  -1.829 C5     S2M 3  
S2M C6     C6   C 0 1 N N N 4.712  20.787 4.866 0.317  2.655  -1.210 C6     S2M 4  
S2M C5M    C5M  C 0 1 N N N 4.432  22.417 6.607 -0.607 3.631  -3.316 C5M    S2M 5  
S2M N3     N3   N 0 1 N N N 6.726  19.602 6.086 -1.141 4.296  0.369  N3     S2M 6  
S2M S2     S2   S 0 1 N N N 7.138  17.755 4.270 -0.231 3.428  2.695  S2     S2M 7  
S2M C2     C2   C 0 1 N N N 6.384  19.087 4.924 -0.296 3.395  1.014  C2     S2M 8  
S2M "C5'"  C5*  C 0 1 N N N 2.000  21.272 2.305 2.282  -0.292 -1.921 "C5'"  S2M 9  
S2M "O5'"  O5*  O 0 1 N N N 2.127  21.864 3.590 3.063  0.476  -2.819 "O5'"  S2M 10 
S2M P      P    P 0 1 N N N 1.266  23.195 3.894 2.787  0.324  -4.407 P      S2M 11 
S2M OP2    O2P  O 0 1 N N N 1.608  23.735 5.251 1.198  0.588  -4.548 OP2    S2M 12 
S2M OP1    O1P  O 0 1 N N N -0.183 22.863 3.662 3.659  1.172  -5.286 OP1    S2M 13 
S2M "C4'"  C4*  C 0 1 N N R 2.760  19.949 2.258 2.725  0.023  -0.498 "C4'"  S2M 14 
S2M "O4'"  O4*  O 0 1 N N N 4.168  20.239 2.266 2.470  1.422  -0.246 "O4'"  S2M 15 
S2M "C1'"  C1*  C 0 1 N N R 4.844  19.244 3.051 1.373  1.543  0.675  "C1'"  S2M 16 
S2M N1     N1   N 0 1 N N N 5.333  19.783 4.319 0.452  2.524  0.177  N1     S2M 17 
S2M "C2'"  C2*  C 0 1 N N R 3.792  18.239 3.520 0.748  0.163  0.786  "C2'"  S2M 18 
S2M "C3'"  C3*  C 0 1 N N R 2.483  19.004 3.435 1.940  -0.742 0.560  "C3'"  S2M 19 
S2M "O3'"  O3*  O 0 1 N N N 1.376  18.157 3.164 2.742  -0.809 1.739  "O3'"  S2M 20 
S2M "O2'"  O2*  O 0 1 N N N 3.714  17.133 2.639 0.137  -0.058 2.041  "O2'"  S2M 21 
S2M "CA'"  CA*  C 0 1 N N N 4.812  16.207 2.491 -0.332 -1.396 2.174  "CA'"  S2M 22 
S2M "CB'"  CB*  C 0 1 N N N 5.420  16.081 1.312 -0.951 -1.569 3.547  "CB'"  S2M 23 
S2M "OC'"  OC*  O 0 1 N N N 6.599  16.867 1.000 0.039  -1.320 4.537  "OC'"  S2M 24 
S2M "CD'"  CD*  C 0 1 N N N 7.723  16.952 1.881 -0.494 -1.447 5.849  "CD'"  S2M 25 
S2M OP3    O3P  O 0 1 N Y N ?      ?      ?     2.921  -1.270 -4.647 OP3    S2M 26 
S2M H6     H6   H 0 1 N N N 3.846  21.262 4.373 0.934  1.978  -1.792 H6     S2M 27 
S2M H71    1H5M H 0 1 N N N 3.585  22.898 6.064 -0.945 2.681  -3.727 H71    S2M 28 
S2M H72    2H5M H 0 1 N N N 4.092  22.143 7.633 0.362  3.885  -3.744 H72    S2M 29 
S2M H73    3H5M H 0 1 N N N 5.201  23.191 6.832 -1.322 4.412  -3.574 H73    S2M 30 
S2M H3     H3   H 0 1 N N N 7.500  19.161 6.582 -1.684 4.915  0.964  H3     S2M 31 
S2M "H5'"  1H5* H 0 1 N N N 0.932  21.150 2.005 1.229  -0.035 -2.051 "H5'"  S2M 32 
S2M "H5''" 2H5* H 0 0 N N N 2.320  21.965 1.492 2.428  -1.352 -2.133 "H5''" S2M 33 
S2M HOP2   2HOP H 0 0 N N N 1.101  24.518 5.429 0.799  0.616  -5.443 HOP2   S2M 34 
S2M "H4'"  H4*  H 0 1 N N N 2.413  19.428 1.334 3.804  -0.139 -0.410 "H4'"  S2M 35 
S2M "H1'"  H1*  H 0 1 N N N 5.670  18.839 2.421 1.754  1.910  1.633  "H1'"  S2M 36 
S2M "H2'"  H2*  H 0 1 N N N 4.028  17.846 4.536 -0.000 0.004  -0.000 "H2'"  S2M 37 
S2M "H3'"  H3*  H 0 1 N N N 2.205  19.515 4.386 1.675  -1.764 0.277  "H3'"  S2M 38 
S2M "HO3'" H3T  H 0 0 N Y N 1.204  17.572 3.892 3.447  -0.153 1.628  "HO3'" S2M 39 
S2M "HA'1" 1HA* H 0 0 N N N 5.581  16.445 3.261 -1.066 -1.580 1.383  "HA'1" S2M 40 
S2M "HA'2" 2HA* H 0 0 N N N 4.470  15.198 2.822 0.520  -2.071 2.050  "HA'2" S2M 41 
S2M "HB'1" 1HB* H 0 0 N N N 5.669  15.004 1.161 -1.324 -2.588 3.686  "HB'1" S2M 42 
S2M "HB'2" 2HB* H 0 0 N N N 4.664  16.252 0.510 -1.768 -0.855 3.691  "HB'2" S2M 43 
S2M "HD'1" 1HD* H 0 0 N N N 8.629  17.556 1.641 -0.854 -0.474 6.192  "HD'1" S2M 44 
S2M "HD'2" 2HD* H 0 0 N N N 7.346  17.290 2.874 0.281  -1.819 6.523  "HD'2" S2M 45 
S2M "HD'3" 3HD* H 0 0 N N N 8.060  15.911 2.097 -1.326 -2.155 5.827  "HD'3" S2M 46 
S2M HOP3   3HOP H 0 0 N N N -0.506 0.783  0.178 2.886  -1.617 -5.563 HOP3   S2M 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 
S2M O4    C4     DOUB N N 1  
S2M C4    C5     SING N N 2  
S2M C4    N3     SING N N 3  
S2M C5    C6     DOUB N N 4  
S2M C5    C5M    SING N N 5  
S2M C6    N1     SING N N 6  
S2M C6    H6     SING N N 7  
S2M C5M   H71    SING N N 8  
S2M C5M   H72    SING N N 9  
S2M C5M   H73    SING N N 10 
S2M N3    C2     SING N N 11 
S2M N3    H3     SING N N 12 
S2M S2    C2     DOUB N N 13 
S2M C2    N1     SING N N 14 
S2M "C5'" "O5'"  SING N N 15 
S2M "C5'" "C4'"  SING N N 16 
S2M "C5'" "H5'"  SING N N 17 
S2M "C5'" "H5''" SING N N 18 
S2M "O5'" P      SING N N 19 
S2M P     OP2    SING N N 20 
S2M P     OP1    DOUB N N 21 
S2M P     OP3    SING N N 22 
S2M OP2   HOP2   SING N N 23 
S2M "C4'" "O4'"  SING N N 24 
S2M "C4'" "C3'"  SING N N 25 
S2M "C4'" "H4'"  SING N N 26 
S2M "O4'" "C1'"  SING N N 27 
S2M "C1'" N1     SING N N 28 
S2M "C1'" "C2'"  SING N N 29 
S2M "C1'" "H1'"  SING N N 30 
S2M "C2'" "C3'"  SING N N 31 
S2M "C2'" "O2'"  SING N N 32 
S2M "C2'" "H2'"  SING N N 33 
S2M "C3'" "O3'"  SING N N 34 
S2M "C3'" "H3'"  SING N N 35 
S2M "O3'" "HO3'" SING N N 36 
S2M "O2'" "CA'"  SING N N 37 
S2M "CA'" "CB'"  SING N N 38 
S2M "CA'" "HA'1" SING N N 39 
S2M "CA'" "HA'2" SING N N 40 
S2M "CB'" "OC'"  SING N N 41 
S2M "CB'" "HB'1" SING N N 42 
S2M "CB'" "HB'2" SING N N 43 
S2M "OC'" "CD'"  SING N N 44 
S2M "CD'" "HD'1" SING N N 45 
S2M "CD'" "HD'2" SING N N 46 
S2M "CD'" "HD'3" SING N N 47 
S2M OP3   HOP3   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 
S2M SMILES           ACDLabs              10.04 "O=C1NC(=S)N(C=C1C)C2OC(C(O)C2OCCOC)COP(=O)(O)O"                                                                                                                               
S2M SMILES_CANONICAL CACTVS               3.341 "COCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=S"                                                                                                           
S2M SMILES           CACTVS               3.341 "COCCO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=S"                                                                                                                 
S2M SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=S)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OCCOC"                                                                                                           
S2M SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=S)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)OCCOC"                                                                                                                             
S2M InChI            InChI                1.03  "InChI=1S/C13H21N2O9PS/c1-7-5-15(13(26)14-11(7)17)12-10(22-4-3-21-2)9(16)8(24-12)6-23-25(18,19)20/h5,8-10,12,16H,3-4,6H2,1-2H3,(H,14,17,26)(H2,18,19,20)/t8-,9-,10-,12-/m1/s1" 
S2M InChIKey         InChI                1.03  BCVUFQXUUOAMEV-DNRKLUKYSA-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 
S2M "SYSTEMATIC NAME" ACDLabs              10.04 "1-[2-O-(2-methoxyethyl)-5-O-phosphono-beta-D-ribofuranosyl]-5-methyl-2-thioxo-2,3-dihydropyrimidin-4(1H)-one"                          
S2M "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-3-hydroxy-4-(2-methoxyethoxy)-5-(5-methyl-4-oxo-2-sulfanylidene-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 
S2M "Create component"    2005-09-16 RCSB 
S2M "Modify linking type" 2011-06-04 RCSB 
S2M "Modify descriptor"   2011-06-04 RCSB 
# 
