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  
##
