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 #