data_YYM # _chem_comp.id YYM _chem_comp.name alpha-D-ribopyranose _chem_comp.type "D-saccharide, alpha linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C5 H10 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "alpha-D-ribose; D-ribose; ribose" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-12-17 _chem_comp.pdbx_modified_date 2020-07-17 _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 150.130 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YYM _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 3MBV _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 YYM alpha-D-ribose PDB ? 2 YYM D-ribose PDB ? 3 YYM ribose PDB ? # # 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 YYM C1 C1 C 0 1 N N S 16.569 29.861 42.734 -1.452 -0.069 -0.524 C1 YYM 1 YYM C2 C2 C 0 1 N N R 17.676 29.314 41.786 -0.289 -1.030 -0.269 C2 YYM 2 YYM C3 C3 C 0 1 N N R 17.485 29.694 40.294 1.000 -0.422 -0.831 C3 YYM 3 YYM C4 C4 C 0 1 N N R 16.602 30.930 40.074 1.227 0.950 -0.187 C4 YYM 4 YYM C5 C5 C 0 1 N N N 16.534 31.801 41.323 0.005 1.835 -0.446 C5 YYM 5 YYM O1 O1 O 0 1 N Y N 17.116 30.152 44.031 -2.648 -0.604 0.047 O1 YYM 6 YYM O2 O2 O 0 1 N N N 19.010 29.627 42.252 -0.144 -1.241 1.137 O2 YYM 7 YYM O3 O3 O 0 1 N N N 18.758 29.896 39.708 2.103 -1.279 -0.532 O3 YYM 8 YYM O4 O4 O 0 1 N N N 17.059 31.677 38.959 1.412 0.791 1.221 O4 YYM 9 YYM O5 O5 O 0 1 N N N 15.799 30.979 42.234 -1.163 1.196 0.074 O5 YYM 10 YYM H1 H1 H 0 1 N N N 15.863 29.029 42.869 -1.588 0.060 -1.598 H1 YYM 11 YYM HO1 H1O H 0 1 N Y N 17.617 29.406 44.339 -3.427 -0.046 -0.076 HO1 YYM 12 YYM H2 H2 H 0 1 N N N 17.579 28.219 41.824 -0.488 -1.982 -0.762 H2 YYM 13 YYM HO2 H2O H 0 1 N Y N 19.649 29.274 41.644 -0.925 -1.621 1.561 HO2 YYM 14 YYM H3 H3 H 0 1 N N N 16.993 28.843 39.800 0.908 -0.308 -1.911 H3 YYM 15 YYM HO3 H3O H 0 1 N Y N 18.653 30.129 38.793 2.953 -0.954 -0.859 HO3 YYM 16 YYM H4 H4 H 0 1 N N N 15.583 30.571 39.867 2.112 1.414 -0.621 H4 YYM 17 YYM HO4 H4O H 0 1 N Y N 16.502 32.437 38.837 1.561 1.622 1.694 HO4 YYM 18 YYM H52 H51 H 0 1 N N N 16.004 32.744 41.122 0.142 2.798 0.046 H52 YYM 19 YYM H51 H52 H 0 1 N N N 17.540 32.021 41.709 -0.112 1.988 -1.519 H51 YYM 20 # # 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 YYM C1 O1 SING N N 1 YYM C1 O5 SING N N 2 YYM C1 C2 SING N N 3 YYM C1 H1 SING N N 4 YYM C2 C3 SING N N 5 YYM C2 O2 SING N N 6 YYM C2 H2 SING N N 7 YYM C3 O3 SING N N 8 YYM C3 H3 SING N N 9 YYM C3 C4 SING N N 10 YYM C4 O4 SING N N 11 YYM C4 H4 SING N N 12 YYM C4 C5 SING N N 13 YYM C5 H51 SING N N 14 YYM C5 H52 SING N N 15 YYM C5 O5 SING N N 16 YYM O1 HO1 SING N N 17 YYM O2 HO2 SING N N 18 YYM O3 HO3 SING N N 19 YYM O4 HO4 SING N N 20 # # 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 YYM SMILES ACDLabs 12.01 "OC1C(O)COC(O)C1O" YYM InChI InChI 1.03 "InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3-,4-,5+/m1/s1" YYM InChIKey InChI 1.03 SRBFZHDQGSBBOR-AIHAYLRMSA-N YYM SMILES_CANONICAL CACTVS 3.370 "O[C@@H]1CO[C@H](O)[C@H](O)[C@@H]1O" YYM SMILES CACTVS 3.370 "O[CH]1CO[CH](O)[CH](O)[CH]1O" YYM SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1[C@H]([C@H]([C@H]([C@H](O1)O)O)O)O" YYM SMILES "OpenEye OEToolkits" 1.7.6 "C1C(C(C(C(O1)O)O)O)O" # # 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 YYM "SYSTEMATIC NAME" ACDLabs 12.01 alpha-D-ribopyranose YYM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2S,3R,4R,5R)-oxane-2,3,4,5-tetrol" YYM "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML 1.0 DRibpa YYM "COMMON NAME" GMML 1.0 a-D-ribopyranose YYM "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 a-D-Ribp YYM "SNFG CARBOHYDRATE SYMBOL" GMML 1.0 Rib # # loop_ _pdbx_chem_comp_feature.comp_id _pdbx_chem_comp_feature.type _pdbx_chem_comp_feature.value _pdbx_chem_comp_feature.source _pdbx_chem_comp_feature.support YYM "CARBOHYDRATE ISOMER" D PDB ? YYM "CARBOHYDRATE RING" pyranose PDB ? YYM "CARBOHYDRATE ANOMER" alpha PDB ? YYM "CARBOHYDRATE PRIMARY CARBONYL GROUP" aldose PDB ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YYM "Create component" 2012-12-17 RCSB YYM "Modify atom id" 2013-02-12 RCSB YYM "Other modification" 2019-08-12 RCSB YYM "Other modification" 2019-12-19 RCSB YYM "Other modification" 2020-06-03 RCSB YYM "Other modification" 2020-06-10 RCSB YYM "Other modification" 2020-07-03 RCSB YYM "Modify atom id" 2020-07-17 RCSB YYM "Modify component atom id" 2020-07-17 RCSB YYM "Initial release" 2020-07-29 RCSB ##