data_Z6G
#
_chem_comp.id Z6G
_chem_comp.name 3-ammonio-2,3,6-trideoxy-alpha-L-arabino-hexopyranose
_chem_comp.type SACCHARIDE
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C6 H14 N O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2012-12-17
_chem_comp.pdbx_modified_date 2022-12-02
_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 148.180
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code Z6G
_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 1D54
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_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
Z6G O1 O1 O 0 1 N Y N N N N -13.189 10.250 6.124 1.921 0.959 -1.090 O1 Z6G 1
Z6G C1 C1 C 0 1 N N R N N N -12.292 9.154 6.071 1.618 0.825 0.300 C1 Z6G 2
Z6G C2 C2 C 0 1 N N N N N N -11.513 9.224 7.341 0.333 1.593 0.619 C2 Z6G 3
Z6G C3 C3 C 0 1 N N S N N N -12.410 8.930 8.564 -0.828 0.981 -0.171 C3 Z6G 4
Z6G C4 C4 C 0 1 N N R N N N -13.158 7.641 8.363 -0.938 -0.507 0.176 C4 Z6G 5
Z6G C5 C5 C 0 1 N N S N N N -13.912 7.661 7.061 0.396 -1.194 -0.126 C5 Z6G 6
Z6G C6 C6 C 0 1 N N N N N N -14.663 6.349 6.738 0.313 -2.668 0.274 C6 Z6G 7
Z6G O2 O2 O 0 1 N N N N N N -13.929 7.310 9.490 -1.972 -1.105 -0.609 O2 Z6G 8
Z6G O3 O3 O 0 1 N N N N N N -13.010 7.907 5.960 1.437 -0.557 0.617 O3 Z6G 9
Z6G N1 N1 N 1 1 N N N N N N -11.502 8.790 9.734 -2.079 1.663 0.186 N1 Z6G 10
Z6G H1O H1O H 0 1 N Y N N N N -13.720 10.263 5.337 2.725 0.497 -1.364 H1O Z6G 11
Z6G H11 H11 H 0 1 N N N N N N -11.605 9.266 5.219 2.440 1.229 0.891 H11 Z6G 12
Z6G H21 H21 H 0 1 N N N N N N -10.701 8.483 7.305 0.123 1.525 1.686 H21 Z6G 13
Z6G H22 H22 H 0 1 N N N N N N -11.085 10.232 7.444 0.454 2.639 0.337 H22 Z6G 14
Z6G H31 H31 H 0 1 N N N N N N -13.114 9.761 8.718 -0.641 1.093 -1.239 H31 Z6G 15
Z6G H41 H41 H 0 1 N N N N N N -12.391 6.860 8.256 -1.174 -0.618 1.235 H41 Z6G 16
Z6G H51 H51 H 0 1 N N N N N N -14.655 8.471 7.105 0.611 -1.118 -1.192 H51 Z6G 17
Z6G H61 H61 H 0 1 N N N N N N -15.183 6.452 5.774 -0.482 -3.154 -0.292 H61 Z6G 18
Z6G H62 H62 H 0 1 N N N N N N -13.943 5.519 6.679 1.263 -3.157 0.059 H62 Z6G 19
Z6G H63 H63 H 0 1 N N N N N N -15.397 6.142 7.531 0.098 -2.744 1.340 H63 Z6G 20
Z6G H2O H2O H 0 1 N N N N N N -14.388 6.493 9.332 -2.097 -2.049 -0.441 H2O Z6G 21
Z6G H11N H11N H 0 0 N N N N N N -12.041 8.598 10.554 -2.002 2.644 -0.036 H11N Z6G 22
Z6G H12N H12N H 0 0 N N N N N N -10.863 8.038 9.572 -2.843 1.259 -0.335 H12N Z6G 23
Z6G "HN'3" "HN'3" H 0 0 N N N N N N -10.991 9.640 9.863 -2.251 1.554 1.174 "HN'3" Z6G 24
#
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
Z6G O1 C1 SING N N 1
Z6G C1 C2 SING N N 2
Z6G C1 O3 SING N N 3
Z6G C1 H11 SING N N 4
Z6G C2 C3 SING N N 5
Z6G C2 H21 SING N N 6
Z6G C2 H22 SING N N 7
Z6G C3 C4 SING N N 8
Z6G C3 N1 SING N N 9
Z6G C3 H31 SING N N 10
Z6G C4 C5 SING N N 11
Z6G C4 O2 SING N N 12
Z6G C4 H41 SING N N 13
Z6G C5 C6 SING N N 14
Z6G C5 O3 SING N N 15
Z6G C5 H51 SING N N 16
Z6G C6 H61 SING N N 17
Z6G C6 H62 SING N N 18
Z6G C6 H63 SING N N 19
Z6G O2 H2O SING N N 20
Z6G N1 H11N SING N N 21
Z6G N1 H12N SING N N 22
Z6G N1 "HN'3" SING N N 23
Z6G H1O O1 SING N N 24
#
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
Z6G SMILES ACDLabs 12.01 OC1C(OC(O)CC1[NH3+])C
Z6G InChI InChI 1.03 InChI=1S/C6H13NO3/c1-3-6(9)4(7)2-5(8)10-3/h3-6,8-9H,2,7H2,1H3/p+1/t3-,4-,5+,6-/m0/s1
Z6G InChIKey InChI 1.03 BBMKQGIZNKEDOX-AZGQCCRYSA-O
Z6G SMILES_CANONICAL CACTVS 3.370 C[C@@H]1O[C@@H](O)C[C@H]([NH3+])[C@H]1O
Z6G SMILES CACTVS 3.370 C[CH]1O[CH](O)C[CH]([NH3+])[CH]1O
Z6G SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C[C@H]1[C@@H]([C@H](C[C@@H](O1)O)[NH3+])O
Z6G SMILES "OpenEye OEToolkits" 1.7.6 CC1C(C(CC(O1)O)[NH3+])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
Z6G "SYSTEMATIC NAME" ACDLabs 12.01 3-ammonio-2,3,6-trideoxy-alpha-L-arabino-hexopyranose
Z6G "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2S,3R,4S,6R)-2-methyl-3,6-bis(oxidanyl)oxan-4-yl]azanium"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
Z6G 'Create component' 2012-12-17 RCSB
Z6G 'Initial release' 2022-12-07 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
Z6G O1 O 9.002 2.250 1
Z6G C1 C 7.702 1.500 2
Z6G C2 C 6.404 2.250 3
Z6G C3 C 5.104 1.500 4
Z6G C4 C 5.104 0.000 5
Z6G C5 C 6.404 -0.750 6
Z6G C6 C 6.404 -2.250 7
Z6G O2 O 3.805 -0.750 8
Z6G O3 O 7.702 0.000 9
Z6G N1 N 3.805 2.250 10
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
Z6G C1 O1 SINGLE BEGINDASH 1
Z6G C1 C2 SINGLE NONE 2
Z6G C1 O3 SINGLE NONE 3
Z6G C2 C3 SINGLE NONE 4
Z6G C3 C4 SINGLE NONE 5
Z6G C3 N1 SINGLE BEGINWEDGE 6
Z6G C4 C5 SINGLE NONE 7
Z6G C4 O2 SINGLE BEGINDASH 8
Z6G C5 C6 SINGLE BEGINWEDGE 9
Z6G C5 O3 SINGLE NONE 10
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
Z6G MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
Z6G pyranose F1 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
Z6G C1 S1 1
Z6G C2 S1 1
Z6G C3 S1 1
Z6G C4 S1 1
Z6G C5 S1 1
Z6G O3 S1 1
Z6G C4 F1 1
Z6G C5 F1 1
Z6G O3 F1 1
Z6G C1 F1 1
Z6G C2 F1 1
Z6G C3 F1 1
Z6G O1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id Z6G
_pdbe_chem_comp_rdkit_properties.exactmw 148.097
_pdbe_chem_comp_rdkit_properties.amw 148.182
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 79.617
_pdbe_chem_comp_rdkit_properties.tpsa 77.330
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.915
_pdbe_chem_comp_rdkit_properties.CrippenMR 33.854
_pdbe_chem_comp_rdkit_properties.chi0v 4.672
_pdbe_chem_comp_rdkit_properties.chi1v 2.290
_pdbe_chem_comp_rdkit_properties.chi2v 0.837
_pdbe_chem_comp_rdkit_properties.chi3v 0.837
_pdbe_chem_comp_rdkit_properties.chi4v 0.426
_pdbe_chem_comp_rdkit_properties.chi0n 18.672
_pdbe_chem_comp_rdkit_properties.chi1n 8.948
_pdbe_chem_comp_rdkit_properties.chi2n 0.837
_pdbe_chem_comp_rdkit_properties.chi3n 0.837
_pdbe_chem_comp_rdkit_properties.chi4n 0.426
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.160
_pdbe_chem_comp_rdkit_properties.kappa1 1.353
_pdbe_chem_comp_rdkit_properties.kappa2 2.837
_pdbe_chem_comp_rdkit_properties.kappa3 1.462
_pdbe_chem_comp_rdkit_properties.Phi 0.384
#
_pdbe_chem_comp_external_mappings.comp_id Z6G
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id Z6G
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
Z6G O1 -0.923 2.957 -0.440 ETKDGv3 1
Z6G C1 -0.523 1.677 -0.028 ETKDGv3 2
Z6G C2 -1.263 0.619 -0.868 ETKDGv3 3
Z6G C3 -0.898 -0.807 -0.396 ETKDGv3 4
Z6G C4 0.506 -0.841 0.263 ETKDGv3 5
Z6G C5 1.404 0.274 -0.333 ETKDGv3 6
Z6G C6 2.808 0.224 0.273 ETKDGv3 7
Z6G O2 1.099 -2.096 0.044 ETKDGv3 8
Z6G O3 0.891 1.592 -0.148 ETKDGv3 9
Z6G N1 -1.916 -1.327 0.528 ETKDGv3 10
Z6G H1O -1.831 3.110 -0.069 ETKDGv3 11
Z6G H11 -0.789 1.544 1.047 ETKDGv3 12
Z6G H21 -2.361 0.786 -0.810 ETKDGv3 13
Z6G H22 -0.968 0.743 -1.933 ETKDGv3 14
Z6G H31 -0.883 -1.458 -1.300 ETKDGv3 15
Z6G H41 0.417 -0.650 1.360 ETKDGv3 16
Z6G H51 1.510 0.095 -1.427 ETKDGv3 17
Z6G H61 2.759 0.368 1.374 ETKDGv3 18
Z6G H62 3.299 -0.748 0.053 ETKDGv3 19
Z6G H63 3.434 1.032 -0.162 ETKDGv3 20
Z6G H2O 0.729 -2.714 0.727 ETKDGv3 21
Z6G H11N -2.840 -1.384 0.041 ETKDGv3 22
Z6G H12N -2.006 -0.706 1.364 ETKDGv3 23
Z6G "HN'3" -1.657 -2.291 0.840 ETKDGv3 24
#