data_HD4
#

_chem_comp.id                                   HD4
_chem_comp.name                                 4-O-[2-acetamido-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol
_chem_comp.type                                 D-saccharide
_chem_comp.pdbx_type                            ATOMS
_chem_comp.formula                              "C13 H26 N O13 P"
_chem_comp.mon_nstd_parent_comp_id              NAG
_chem_comp.pdbx_synonyms                        
;4-O-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol;
4-O-[2-acetamido-2-deoxy-beta-D-glucosyl]-1-O-phosphono-D-ribitol;
4-O-[2-acetamido-2-deoxy-D-glucosyl]-1-O-phosphono-D-ribitol; 4-O-[2-acetamido-2-deoxy-glucosyl]-1-O-phosphono-D-ribitol
;

_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2018-06-26
_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                       435.318
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    HD4
_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       6DW2
_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  HD4  "4-O-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol"  PDB  ?  
2  HD4  4-O-[2-acetamido-2-deoxy-beta-D-glucosyl]-1-O-phosphono-D-ribitol              PDB  ?  
3  HD4  4-O-[2-acetamido-2-deoxy-D-glucosyl]-1-O-phosphono-D-ribitol                   PDB  ?  
4  HD4  4-O-[2-acetamido-2-deoxy-glucosyl]-1-O-phosphono-D-ribitol                     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
HD4  C1   C14  C  0  1  N  N  S  -2.695  46.590  38.627   2.170  -0.120   0.485  C1   HD4   1  
HD4  C2   C5   C  0  1  N  N  R  -3.731  46.975  37.567   2.907  -0.265  -0.849  C2   HD4   2  
HD4  C5   C11  C  0  1  N  N  R  -2.579  44.279  37.931   2.808   2.184   0.673  C5   HD4   3  
HD4  C3   C7   C  0  1  N  N  R  -4.507  45.706  37.135   4.090   0.707  -0.878  C3   HD4   4  
HD4  C4   C9   C  0  1  N  N  S  -3.575  44.520  36.775   3.571   2.131  -0.653  C4   HD4   5  
HD4  C8   C1   C  0  1  N  N  N  -5.809  50.030  38.683   3.095  -4.009  -1.625  C8   HD4   6  
HD4  C7   C2   C  0  1  N  N  N  -4.783  49.225  37.930   2.589  -2.597  -1.480  C7   HD4   7  
HD4  O7   O3   O  0  1  N  N  N  -4.051  49.798  37.146   1.453  -2.324  -1.806  O7   HD4   8  
HD4  N2   N4   N  0  1  N  N  N  -4.702  47.897  38.186   3.399  -1.638  -0.989  N2   HD4   9  
HD4  O5   O13  O  0  1  N  N  N  -1.875  45.496  38.170   1.741   1.234   0.646  O5   HD4  10  
HD4  O1   O16  O  0  1  N  N  N  -1.802  47.683  38.904   1.032  -0.984   0.497  O1   HD4  11  
HD4  C17  C17  C  0  1  N  N  R  -1.053  47.592  40.132   0.335  -1.009   1.744  C17  HD4  12  
HD4  C19  C19  C  0  1  N  N  N  -0.919  49.000  40.721   0.919  -2.109   2.634  C19  HD4  13  
HD4  O20  O20  O  0  1  N  N  N  -2.231  49.529  40.916   0.674  -3.384   2.038  O20  HD4  14  
HD4  C21  C21  C  0  1  N  N  S   0.307  46.864  40.008  -1.148  -1.291   1.494  C21  HD4  15  
HD4  C23  C23  C  0  1  N  N  S   0.993  47.061  38.647  -1.733  -0.191   0.604  C23  HD4  16  
HD4  C25  C25  C  0  1  N  N  N   2.300  46.275  38.585  -3.216  -0.472   0.354  C25  HD4  17  
HD4  O26  O26  O  0  1  N  N  N   2.863  46.515  37.296  -3.789   0.612  -0.378  O26  HD4  18  
HD4  P27  P27  P  0  1  N  N  N   4.063  45.648  36.673  -5.338   0.652  -0.817  P27  HD4  19  
HD4  O28  O28  O  0  1  N  N  N   3.459  44.365  36.248  -5.629  -0.533  -1.867  O28  HD4  20  
HD4  O29  O29  O  0  1  N  N  N   4.672  46.427  35.400  -6.194   0.475   0.377  O29  HD4  21  
HD4  O30  O30  O  0  1  N  N  N   5.202  45.413  37.782  -5.664   2.071  -1.506  O30  HD4  22  
HD4  O31  O31  O  0  1  N  N  N   1.283  48.445  38.419  -1.035  -0.166  -0.642  O31  HD4  23  
HD4  O32  O32  O  0  1  N  N  N   0.098  45.451  40.239  -1.846  -1.316   2.741  O32  HD4  24  
HD4  C6   C33  C  0  1  N  N  N  -1.534  43.214  37.594   2.236   3.588   0.877  C6   HD4  25  
HD4  O6   O34  O  0  1  N  N  N  -0.442  43.242  38.535   1.624   3.671   2.166  O6   HD4  26  
HD4  O4   O35  O  0  1  N  N  N  -4.369  43.327  36.617   4.674   3.039  -0.607  O4   HD4  27  
HD4  O3   O36  O  0  1  N  N  N  -5.351  46.079  36.039   4.741   0.629  -2.148  O3   HD4  28  
HD4  H1   H1   H  0  1  N  N  N  -3.225  46.299  39.546   2.839  -0.389   1.302  H1   HD4  29  
HD4  H2   H2   H  0  1  N  N  N  -3.240  47.436  36.697   2.226  -0.037  -1.668  H2   HD4  30  
HD4  H5   H3   H  0  1  N  N  N  -3.137  43.969  38.827   3.487   1.946   1.492  H5   HD4  31  
HD4  H3   H4   H  0  1  N  N  N  -5.134  45.393  37.983   4.796   0.447  -0.090  H3   HD4  32  
HD4  H4   H5   H  0  1  N  N  N  -3.022  44.753  35.853   2.904   2.409  -1.469  H4   HD4  33  
HD4  H81  H6   H  0  1  N  N  N  -5.735  51.087  38.388   3.392  -4.391  -0.648  H81  HD4  34  
HD4  H82  H7   H  0  1  N  N  N  -6.815  49.654  38.447   2.305  -4.638  -2.035  H82  HD4  35  
HD4  H83  H8   H  0  1  N  N  N  -5.627  49.937  39.764   3.954  -4.021  -2.296  H83  HD4  36  
HD4  HN2  H9   H  0  1  N  N  N  -5.349  47.513  38.844   4.307  -1.857  -0.728  HN2  HD4  37  
HD4  H10  H10  H  0  1  N  N  N  -1.653  47.009  40.846   0.443  -0.045   2.240  H10  HD4  38  
HD4  H11  H11  H  0  1  N  N  N  -0.390  48.952  41.684   1.993  -1.957   2.739  H11  HD4  39  
HD4  H12  H12  H  0  1  N  N  N  -0.358  49.642  40.026   0.448  -2.070   3.616  H12  HD4  40  
HD4  H13  H13  H  0  1  N  N  N  -2.169  50.404  41.281   1.018  -4.129   2.549  H13  HD4  41  
HD4  H14  H14  H  0  1  N  N  N   0.975  47.262  40.786  -1.257  -2.255   0.998  H14  HD4  42  
HD4  H15  H15  H  0  1  N  N  N   0.321  46.686  37.861  -1.625   0.773   1.101  H15  HD4  43  
HD4  H16  H16  H  0  1  N  N  N   2.103  45.201  38.719  -3.319  -1.393  -0.220  H16  HD4  44  
HD4  H17  H17  H  0  1  N  N  N   2.988  46.622  39.370  -3.731  -0.580   1.308  H17  HD4  45  
HD4  H18  H18  H  0  1  N  N  N   3.555  44.265  35.308  -5.101  -0.481  -2.676  H18  HD4  46  
HD4  H19  H19  H  0  1  N  N  N   6.023  45.780  37.476  -6.581   2.165  -1.797  H19  HD4  47  
HD4  H20  H20  H  0  1  N  N  N   0.478  48.948  38.455  -1.089  -0.994  -1.140  H20  HD4  48  
HD4  H21  H21  H  0  1  N  N  N  -0.326  45.326  41.080  -1.792  -0.488   3.238  H21  HD4  49  
HD4  H61  H22  H  0  1  N  N  N  -2.009  42.222  37.624   3.040   4.322   0.809  H61  HD4  50  
HD4  H62  H23  H  0  1  N  N  N  -1.142  43.402  36.583   1.492   3.793   0.108  H62  HD4  51  
HD4  HO6  H24  H  0  1  N  Y  N   0.192  42.573  38.305   1.239   4.535   2.364  HO6  HD4  52  
HD4  HO4  H25  H  0  1  N  Y  N  -3.803  42.596  36.396   4.418   3.961  -0.466  HO4  HD4  53  
HD4  HO3  H26  H  0  1  N  Y  N  -5.905  46.806  36.298   5.501   1.221  -2.237  HO3  HD4  54  
#   #
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
HD4  O29  P27  DOUB  N  N   1  
HD4  O3   C3   SING  N  N   2  
HD4  O28  P27  SING  N  N   3  
HD4  O4   C4   SING  N  N   4  
HD4  P27  O26  SING  N  N   5  
HD4  P27  O30  SING  N  N   6  
HD4  C4   C3   SING  N  N   7  
HD4  C4   C5   SING  N  N   8  
HD4  C3   C2   SING  N  N   9  
HD4  O7   C7   DOUB  N  N  10  
HD4  O26  C25  SING  N  N  11  
HD4  C2   N2   SING  N  N  12  
HD4  C2   C1   SING  N  N  13  
HD4  C6   C5   SING  N  N  14  
HD4  C6   O6   SING  N  N  15  
HD4  C7   N2   SING  N  N  16  
HD4  C7   C8   SING  N  N  17  
HD4  C5   O5   SING  N  N  18  
HD4  O5   C1   SING  N  N  19  
HD4  O31  C23  SING  N  N  20  
HD4  C25  C23  SING  N  N  21  
HD4  C1   O1   SING  N  N  22  
HD4  C23  C21  SING  N  N  23  
HD4  O1   C17  SING  N  N  24  
HD4  C21  C17  SING  N  N  25  
HD4  C21  O32  SING  N  N  26  
HD4  C17  C19  SING  N  N  27  
HD4  C19  O20  SING  N  N  28  
HD4  C1   H1   SING  N  N  29  
HD4  C2   H2   SING  N  N  30  
HD4  C5   H5   SING  N  N  31  
HD4  C3   H3   SING  N  N  32  
HD4  C4   H4   SING  N  N  33  
HD4  C8   H81  SING  N  N  34  
HD4  C8   H82  SING  N  N  35  
HD4  C8   H83  SING  N  N  36  
HD4  N2   HN2  SING  N  N  37  
HD4  C17  H10  SING  N  N  38  
HD4  C19  H11  SING  N  N  39  
HD4  C19  H12  SING  N  N  40  
HD4  O20  H13  SING  N  N  41  
HD4  C21  H14  SING  N  N  42  
HD4  C23  H15  SING  N  N  43  
HD4  C25  H16  SING  N  N  44  
HD4  C25  H17  SING  N  N  45  
HD4  O28  H18  SING  N  N  46  
HD4  O30  H19  SING  N  N  47  
HD4  O31  H20  SING  N  N  48  
HD4  O32  H21  SING  N  N  49  
HD4  C6   H61  SING  N  N  50  
HD4  C6   H62  SING  N  N  51  
HD4  O6   HO6  SING  N  N  52  
HD4  O4   HO4  SING  N  N  53  
HD4  O3   HO3  SING  N  N  54  
#   #
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
HD4  SMILES            ACDLabs               12.01  "C1(OC(CO)C(O)C(COP(O)(O)=O)O)C(NC(C)=O)C(C(C(O1)CO)O)O"  
HD4  InChI             InChI                 1.03   "InChI=1S/C13H26NO13P/c1-5(17)14-9-12(21)11(20)8(3-16)27-13(9)26-7(2-15)10(19)6(18)4-25-28(22,23)24/h6-13,15-16,18-21H,2-4H2,1H3,(H,14,17)(H2,22,23,24)/t6-,7+,8+,9+,10-,11+,12+,13+/m0/s1"  
HD4  InChIKey          InChI                 1.03   UTDJSTSCOBYMHN-SKCKNYEVSA-N  
HD4  SMILES_CANONICAL  CACTVS                3.385  "CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@H]1O[C@H](CO)[C@@H](O)[C@@H](O)CO[P](O)(O)=O"  
HD4  SMILES            CACTVS                3.385  "CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1O[CH](CO)[CH](O)[CH](O)CO[P](O)(O)=O"  
HD4  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1O[C@H](CO)[C@H]([C@H](COP(=O)(O)O)O)O)CO)O)O"  
HD4  SMILES            "OpenEye OEToolkits"  2.0.6  "CC(=O)NC1C(C(C(OC1OC(CO)C(C(COP(=O)(O)O)O)O)CO)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
HD4  "SYSTEMATIC NAME"  ACDLabs               12.01  "4-O-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol"  
HD4  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  
;[(2~{S},3~{S},4~{R})-4-[(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-2,
3,5-tris(oxidanyl)pentyl] dihydrogen phosphate
;
  
#
_pdbx_chem_comp_related.comp_id            HD4
_pdbx_chem_comp_related.related_comp_id    NAG
_pdbx_chem_comp_related.relationship_type  "Carbohydrate core"
_pdbx_chem_comp_related.details            ?
#   #
loop_
_pdbx_chem_comp_atom_related.ordinal
_pdbx_chem_comp_atom_related.comp_id
_pdbx_chem_comp_atom_related.atom_id
_pdbx_chem_comp_atom_related.related_comp_id
_pdbx_chem_comp_atom_related.related_atom_id
_pdbx_chem_comp_atom_related.related_type
 1  HD4  C8   NAG  C8   "Carbohydrate core"  
 2  HD4  C5   NAG  C5   "Carbohydrate core"  
 3  HD4  C1   NAG  C1   "Carbohydrate core"  
 4  HD4  C7   NAG  C7   "Carbohydrate core"  
 5  HD4  C6   NAG  C6   "Carbohydrate core"  
 6  HD4  C2   NAG  C2   "Carbohydrate core"  
 7  HD4  C3   NAG  C3   "Carbohydrate core"  
 8  HD4  C4   NAG  C4   "Carbohydrate core"  
 9  HD4  N2   NAG  N2   "Carbohydrate core"  
10  HD4  O5   NAG  O5   "Carbohydrate core"  
11  HD4  O1   NAG  O1   "Carbohydrate core"  
12  HD4  O7   NAG  O7   "Carbohydrate core"  
13  HD4  O6   NAG  O6   "Carbohydrate core"  
14  HD4  O4   NAG  O4   "Carbohydrate core"  
15  HD4  O3   NAG  O3   "Carbohydrate core"  
16  HD4  H1   NAG  H1   "Carbohydrate core"  
17  HD4  H2   NAG  H2   "Carbohydrate core"  
18  HD4  H61  NAG  H61  "Carbohydrate core"  
19  HD4  H62  NAG  H62  "Carbohydrate core"  
20  HD4  HO6  NAG  HO6  "Carbohydrate core"  
21  HD4  HO4  NAG  HO4  "Carbohydrate core"  
22  HD4  HO3  NAG  HO3  "Carbohydrate core"  
23  HD4  H5   NAG  H5   "Carbohydrate core"  
24  HD4  H3   NAG  H3   "Carbohydrate core"  
25  HD4  H4   NAG  H4   "Carbohydrate core"  
26  HD4  H81  NAG  H81  "Carbohydrate core"  
27  HD4  H82  NAG  H82  "Carbohydrate core"  
28  HD4  H83  NAG  H83  "Carbohydrate core"  
29  HD4  HN2  NAG  HN2  "Carbohydrate core"  
#   #
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
HD4  "CARBOHYDRATE ISOMER"                  D         PDB  ?  
HD4  "CARBOHYDRATE RING"                    pyranose  PDB  ?  
HD4  "CARBOHYDRATE ANOMER"                  beta      PDB  ?  
HD4  "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
HD4  "Create component"          2018-06-26  RCSB  
HD4  "Initial release"           2018-08-29  RCSB  
HD4  "Other modification"        2020-07-03  RCSB  
HD4  "Modify parent residue"     2020-07-17  RCSB  
HD4  "Modify name"               2020-07-17  RCSB  
HD4  "Modify synonyms"           2020-07-17  RCSB  
HD4  "Modify internal type"      2020-07-17  RCSB  
HD4  "Modify linking type"       2020-07-17  RCSB  
HD4  "Modify atom id"            2020-07-17  RCSB  
HD4  "Modify component atom id"  2020-07-17  RCSB  
HD4  "Modify leaving atom flag"  2020-07-17  RCSB  
##
