data_YO5 # _chem_comp.id YO5 _chem_comp.name "(1R)-1,5-anhydro-1-(phosphonomethyl)-D-glucitol" _chem_comp.type D-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C7 H15 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "Beta-1 phosphonomethylene-D-glucopyranose" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-09-09 _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 258.163 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YO5 _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 4C4R _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id YO5 _pdbx_chem_comp_synonyms.name "Beta-1 phosphonomethylene-D-glucopyranose" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # # 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 YO5 C2 C2 C 0 1 N N R -13.787 -9.582 -13.011 1.010 -1.636 -0.342 C2 YO5 1 YO5 C3 C3 C 0 1 N N S -12.324 -9.456 -12.610 2.331 -1.149 0.260 C3 YO5 2 YO5 C4 C4 C 0 1 N N S -11.804 -8.065 -12.899 2.596 0.285 -0.210 C4 YO5 3 YO5 C5 C5 C 0 1 N N R -12.698 -7.035 -12.221 1.414 1.171 0.191 C5 YO5 4 YO5 C1 C1 C 0 1 N N R -14.606 -8.442 -12.430 -0.112 -0.676 0.062 C1 YO5 5 YO5 C6 C6 C 0 1 N N N -12.241 -5.617 -12.440 1.643 2.592 -0.327 C6 YO5 6 YO5 C7 C7 C 0 1 N N N -16.019 -8.342 -12.979 -1.425 -1.120 -0.585 C7 YO5 7 YO5 O2 O2 O 0 1 N N N -14.325 -10.825 -12.616 0.716 -2.946 0.147 O2 YO5 8 YO5 O3 O3 O 0 1 N N N -11.546 -10.443 -13.252 3.396 -1.998 -0.174 O3 YO5 9 YO5 O4 O4 O 0 1 N N N -10.488 -7.917 -12.465 3.790 0.776 0.403 O4 YO5 10 YO5 O5 O5 O 0 1 N N N -13.992 -7.190 -12.689 0.212 0.645 -0.376 O5 YO5 11 YO5 O6 O6 O 0 1 N N N -13.005 -4.641 -11.776 0.598 3.446 0.145 O6 YO5 12 YO5 P P P 0 1 N N N -17.294 -9.082 -11.886 -2.786 -0.065 0.015 P YO5 13 YO5 O2P O2P O 0 1 N N N -17.111 -8.575 -10.468 -4.143 -0.447 -0.763 O2P YO5 14 YO5 O3P O3P O 0 1 N N N -17.054 -10.581 -11.969 -2.990 -0.299 1.595 O3P YO5 15 YO5 O1P O1P O 0 1 N N N -18.672 -8.707 -12.485 -2.456 1.355 -0.236 O1P YO5 16 YO5 H3P H3P H 0 1 N N N -17.803 -11.000 -12.376 -3.209 -1.210 1.833 H3P YO5 17 YO5 H2P H2P H 0 1 N N N -17.892 -8.108 -10.195 -4.911 0.076 -0.494 H2P YO5 18 YO5 H71C H71C H 0 0 N N N -16.051 -8.860 -13.949 -1.345 -1.029 -1.668 H71C YO5 19 YO5 H72C H72C H 0 0 N N N -16.261 -7.279 -13.123 -1.627 -2.158 -0.321 H72C YO5 20 YO5 H1 H1 H 0 1 N N N -14.675 -8.594 -11.343 -0.221 -0.682 1.147 H1 YO5 21 YO5 H2 H2 H 0 1 N N N -13.838 -9.502 -14.107 1.092 -1.663 -1.429 H2 YO5 22 YO5 H5 H5 H 0 1 N N N -12.674 -7.233 -11.139 1.325 1.190 1.277 H5 YO5 23 YO5 H61C H61C H 0 0 N N N -11.202 -5.535 -12.089 2.603 2.960 0.034 H61C YO5 24 YO5 H62C H62C H 0 0 N N N -12.282 -5.407 -13.519 1.642 2.586 -1.417 H62C YO5 25 YO5 H4 H4 H 0 1 N N N -11.858 -7.899 -13.985 2.711 0.298 -1.294 H4 YO5 26 YO5 HA HA H 0 1 N N N -9.938 -8.563 -12.893 4.019 1.680 0.150 HA YO5 27 YO5 H3 H3 H 0 1 N N N -12.267 -9.611 -11.523 2.267 -1.172 1.348 H3 YO5 28 YO5 HB HB H 0 1 N N N -11.897 -11.303 -13.052 4.264 -1.747 0.170 HB YO5 29 YO5 HC HC H 0 1 N N N -13.804 -11.528 -12.986 1.387 -3.607 -0.072 HC YO5 30 YO5 H6O H6O H 0 1 N N N -12.653 -3.779 -11.965 0.680 4.365 -0.146 H6O YO5 31 # # 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 YO5 O1P P DOUB N N 1 YO5 P O2P SING N N 2 YO5 P O3P SING N N 3 YO5 P C7 SING N N 4 YO5 C7 C1 SING N N 5 YO5 C1 O5 SING N N 6 YO5 C1 C2 SING N N 7 YO5 O5 C5 SING N N 8 YO5 C5 C6 SING N N 9 YO5 C5 C4 SING N N 10 YO5 C6 O6 SING N N 11 YO5 C4 O4 SING N N 12 YO5 C4 C3 SING N N 13 YO5 C3 O3 SING N N 14 YO5 C3 C2 SING N N 15 YO5 C2 O2 SING N N 16 YO5 O6 H6O SING N N 17 YO5 O3P H3P SING N N 18 YO5 O2P H2P SING N N 19 YO5 C7 H71C SING N N 20 YO5 C7 H72C SING N N 21 YO5 C1 H1 SING N N 22 YO5 C2 H2 SING N N 23 YO5 C5 H5 SING N N 24 YO5 C6 H61C SING N N 25 YO5 C6 H62C SING N N 26 YO5 C4 H4 SING N N 27 YO5 O4 HA SING N N 28 YO5 C3 H3 SING N N 29 YO5 O3 HB SING N N 30 YO5 O2 HC SING N N 31 # # 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 YO5 SMILES ACDLabs 12.01 "O=P(O)(O)CC1OC(C(O)C(O)C1O)CO" YO5 InChI InChI 1.03 "InChI=1S/C7H15O8P/c8-1-3-5(9)7(11)6(10)4(15-3)2-16(12,13)14/h3-11H,1-2H2,(H2,12,13,14)/t3-,4+,5-,6+,7+/m1/s1" YO5 InChIKey InChI 1.03 XRMRHVWWWWFMKR-UOYQFSTFSA-N YO5 SMILES_CANONICAL CACTVS 3.385 "OC[C@H]1O[C@@H](C[P](O)(O)=O)[C@H](O)[C@@H](O)[C@@H]1O" YO5 SMILES CACTVS 3.385 "OC[CH]1O[CH](C[P](O)(O)=O)[CH](O)[CH](O)[CH]1O" YO5 SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)CP(=O)(O)O)O)O)O)O" YO5 SMILES "OpenEye OEToolkits" 1.9.2 "C(C1C(C(C(C(O1)CP(=O)(O)O)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 YO5 "SYSTEMATIC NAME" ACDLabs 12.01 "(1R)-1,5-anhydro-1-(phosphonomethyl)-D-glucitol" YO5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(2R,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]methylphosphonic acid" # # 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 YO5 "CARBOHYDRATE ISOMER" D PDB ? YO5 "CARBOHYDRATE RING" pyranose 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 YO5 "Create component" 2013-09-09 EBI YO5 "Initial release" 2014-07-16 RCSB YO5 "Modify descriptor" 2014-09-05 RCSB YO5 "Other modification" 2020-07-03 RCSB YO5 "Modify name" 2020-07-17 RCSB YO5 "Modify synonyms" 2020-07-17 RCSB YO5 "Modify linking type" 2020-07-17 RCSB ##