data_6YR
#

_chem_comp.id                                   6YR
_chem_comp.name                                 "methyl 1-seleno-2-O-methyl-beta-L-fucopyranoside"
_chem_comp.type                                 L-saccharide
_chem_comp.pdbx_type                            ATOMS
_chem_comp.formula                              "C8 H16 O4 Se"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        
;2-O-methyl-methyl-seleno-L-fucopyranoside; methyl 1-seleno-2-O-methyl-beta-L-fucoside; methyl
1-seleno-2-O-methyl-L-fucoside; methyl 1-seleno-2-O-methyl-fucoside
;

_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2016-01-04
_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                       255.170
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    6YR
_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       5FSB
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 EBI
#   #
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  6YR  2-O-methyl-methyl-seleno-L-fucopyranoside     PDB  ?  
2  6YR  "methyl 1-seleno-2-O-methyl-beta-L-fucoside"  PDB  ?  
3  6YR  "methyl 1-seleno-2-O-methyl-L-fucoside"       PDB  ?  
4  6YR  "methyl 1-seleno-2-O-methyl-fucoside"         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
6YR  O4    O4    O   0  1  N  N  N  3.758  -17.900   6.202   2.571   0.677   1.309  O4    6YR   1  
6YR  C4    C4    C   0  1  N  N  S  5.171  -17.769   6.095   2.480   0.689  -0.117  C4    6YR   2  
6YR  C3    C3    C   0  1  N  N  R  5.575  -16.548   6.904   1.998  -0.678  -0.611  C3    6YR   3  
6YR  O3    O3    O   0  1  N  N  N  4.821  -15.434   6.540   2.885  -1.696  -0.143  O3    6YR   4  
6YR  C2    C2    C   0  1  N  N  S  5.596  -16.881   8.411   0.589  -0.937  -0.069  C2    6YR   5  
6YR  O2    O2    O   0  1  N  N  N  6.180  -15.773   9.024   0.100  -2.177  -0.582  O2    6YR   6  
6YR  C7    C7    C   0  1  N  N  N  5.515  -15.242  10.138   0.308  -3.290   0.290  C7    6YR   7  
6YR  C5    C5    C   0  1  N  N  S  5.861  -19.020   6.585   1.482   1.764  -0.557  C5    6YR   8  
6YR  C6    C6    C   0  1  N  N  N  5.326  -20.172   5.766   1.926   3.124  -0.016  C6    6YR   9  
6YR  O5    O5    O   0  1  N  N  N  5.697  -19.226   7.992   0.186   1.446  -0.045  O5    6YR  10  
6YR  C1    C1    C   0  1  N  N  R  6.351  -18.181   8.652  -0.336   0.200  -0.510  C1    6YR  11  
6YR  SE    SE    SE  0  1  N  N  N  6.280  -18.636  10.539  -2.123  -0.081   0.243  SE    6YR  12  
6YR  C8    C8    C   0  1  N  N  N  8.120  -19.030  10.682  -3.077   1.478  -0.463  C8    6YR  13  
6YR  HO4   HO4   H   0  1  N  Y  N  3.471  -18.657   5.705   2.872   1.513   1.691  HO4   6YR  14  
6YR  H4    H4    H   0  1  N  N  N  5.452  -17.601   5.045   3.460   0.906  -0.543  H4    6YR  15  
6YR  H3    H3    H   0  1  N  N  N  6.620  -16.340   6.632   1.977  -0.685  -1.701  H3    6YR  16  
6YR  H5    H5    H   0  1  N  N  N  6.934  -18.921   6.364   1.444   1.800  -1.646  H5    6YR  17  
6YR  HO3   HO3   H   0  1  N  Y  N  5.091  -14.685   7.058   3.798  -1.590  -0.444  HO3   6YR  18  
6YR  H2    H2    H   0  1  N  N  N  4.558  -17.008   8.753   0.621  -0.980   1.020  H2    6YR  19  
6YR  H1    H1    H   0  1  N  N  N  7.415  -18.088   8.387  -0.399   0.216  -1.598  H1    6YR  20  
6YR  H71C  H71C  H   0  0  N  N  N  6.077  -14.378  10.524   1.377  -3.474   0.396  H71C  6YR  21  
6YR  H72C  H72C  H   0  0  N  N  N  4.505  -14.921   9.843  -0.121  -3.070   1.268  H72C  6YR  22  
6YR  H73C  H73C  H   0  0  N  N  N  5.441  -16.011  10.921  -0.173  -4.174  -0.128  H73C  6YR  23  
6YR  H61   H61C  H   0  1  N  N  N  5.804  -21.107   6.092   2.914   3.366  -0.407  H61   6YR  24  
6YR  H62   H62C  H   0  1  N  N  N  4.238  -20.248   5.908   1.215   3.889  -0.329  H62   6YR  25  
6YR  H63   H63C  H   0  1  N  N  N  5.546  -19.999   4.702   1.964   3.088   1.072  H63   6YR  26  
6YR  H81C  H81C  H   0  0  N  N  N  8.352  -19.332  11.714  -2.595   2.390  -0.110  H81C  6YR  27  
6YR  H82C  H82C  H   0  0  N  N  N  8.374  -19.850   9.995  -3.056   1.454  -1.553  H82C  6YR  28  
6YR  H83C  H83C  H   0  0  N  N  N  8.707  -18.138  10.420  -4.111   1.458  -0.120  H83C  6YR  29  
#   #
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
6YR  O4  C4    SING  N  N   1  
6YR  C4  C3    SING  N  N   2  
6YR  C4  C5    SING  N  N   3  
6YR  C3  O3    SING  N  N   4  
6YR  C3  C2    SING  N  N   5  
6YR  C2  O2    SING  N  N   6  
6YR  C2  C1    SING  N  N   7  
6YR  O2  C7    SING  N  N   8  
6YR  C5  C6    SING  N  N   9  
6YR  C5  O5    SING  N  N  10  
6YR  O5  C1    SING  N  N  11  
6YR  C1  SE    SING  N  N  12  
6YR  SE  C8    SING  N  N  13  
6YR  O4  HO4   SING  N  N  14  
6YR  C4  H4    SING  N  N  15  
6YR  C3  H3    SING  N  N  16  
6YR  C5  H5    SING  N  N  17  
6YR  O3  HO3   SING  N  N  18  
6YR  C2  H2    SING  N  N  19  
6YR  C1  H1    SING  N  N  20  
6YR  C7  H71C  SING  N  N  21  
6YR  C7  H72C  SING  N  N  22  
6YR  C7  H73C  SING  N  N  23  
6YR  C6  H61   SING  N  N  24  
6YR  C6  H62   SING  N  N  25  
6YR  C6  H63   SING  N  N  26  
6YR  C8  H81C  SING  N  N  27  
6YR  C8  H82C  SING  N  N  28  
6YR  C8  H83C  SING  N  N  29  
#   #
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
6YR  InChI             InChI                 1.03   "InChI=1S/C8H16O4Se/c1-4-5(9)6(10)7(11-2)8(12-4)13-3/h4-10H,1-3H3/t4-,5+,6+,7-,8+/m0/s1"  
6YR  InChIKey          InChI                 1.03   JGCHFCAEXBTPJU-FMGWEMOISA-N  
6YR  SMILES_CANONICAL  CACTVS                3.385  "CO[C@H]1[C@H](O)[C@H](O)[C@H](C)O[C@@H]1[Se]C"  
6YR  SMILES            CACTVS                3.385  "CO[CH]1[CH](O)[CH](O)[CH](C)O[CH]1[Se]C"  
6YR  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "C[C@H]1[C@H]([C@H]([C@@H]([C@H](O1)[Se]C)OC)O)O"  
6YR  SMILES            "OpenEye OEToolkits"  1.7.6  "CC1C(C(C(C(O1)[Se]C)OC)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          6YR
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  1.7.6
_pdbx_chem_comp_identifier.identifier       "(2S,3S,4R,5S,6R)-5-methoxy-2-methyl-6-methylselanyl-oxane-3,4-diol"
#   #
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
6YR  "CARBOHYDRATE ISOMER"                  L         PDB  ?  
6YR  "CARBOHYDRATE RING"                    pyranose  PDB  ?  
6YR  "CARBOHYDRATE ANOMER"                  beta      PDB  ?  
6YR  "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
6YR  "Create component"          2016-01-04  EBI   
6YR  "Modify atom id"            2016-02-22  EBI   
6YR  "Other modification"        2016-03-03  EBI   
6YR  "Initial release"           2017-03-29  RCSB  
6YR  "Other modification"        2020-07-03  RCSB  
6YR  "Modify name"               2020-07-17  RCSB  
6YR  "Modify synonyms"           2020-07-17  RCSB  
6YR  "Modify linking type"       2020-07-17  RCSB  
6YR  "Modify atom id"            2020-07-17  RCSB  
6YR  "Modify component atom id"  2020-07-17  RCSB  
6YR  "Modify leaving atom flag"  2020-07-17  RCSB  
##
