data_NGO
#
_chem_comp.id NGO
_chem_comp.name 2-METHYL-4,5-DIHYDRO-(1,2-DIDEOXY-ALPHA-D-GLUCOPYRANOSO)[2,1-D]-1,3-OXAZOLE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H14 N O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "N-ACETYLGLUCOSAMINE-OXAZOLINIUM ION INTERMEDIATE"
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2000-08-25
_chem_comp.pdbx_modified_date 2021-03-01
_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 204.200
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code NGO
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1E6Z
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
NGO C1 C1 C 0 1 N N R N N N 42.891 74.324 51.785 0.638 -0.769 -1.015 C1 NGO 1
NGO C2 C2 C 0 1 N N R N N N 42.663 75.706 52.506 1.101 0.673 -0.823 C2 NGO 2
NGO C3 C3 C 0 1 N N R N N N 43.746 76.733 52.135 0.219 1.495 0.104 C3 NGO 3
NGO C4 C4 C 0 1 N N S N N N 45.129 76.048 52.325 -1.254 1.132 -0.057 C4 NGO 4
NGO C5 C5 C 0 1 N N R N N N 45.245 74.745 51.491 -1.392 -0.387 0.084 C5 NGO 5
NGO C6 C6 C 0 1 N N N N N N 45.694 73.515 52.248 -2.873 -0.771 0.095 C6 NGO 6
NGO C7 C7 C 0 1 N N N N N N 40.863 75.130 51.372 2.436 -0.735 0.313 C7 NGO 7
NGO C8 C8 C 0 1 N N N N N N 39.464 75.196 50.822 3.613 -1.300 1.066 C8 NGO 8
NGO N2 N2 N 1 1 N N N N N N 41.378 76.111 52.145 2.406 0.469 -0.144 N2 NGO 9
NGO O1 O1 O 0 1 N N N N N N 41.683 74.076 51.114 1.319 -1.448 0.052 O1 NGO 10
NGO O3 O3 O 0 1 N N N N N N 43.626 77.880 52.981 0.393 2.882 -0.195 O3 NGO 11
NGO O4 O4 O 0 1 N N N N N N 46.162 76.939 51.940 -2.024 1.783 0.955 O4 NGO 12
NGO O5 O5 O 0 1 N N N N N N 43.991 74.414 50.861 -0.743 -1.002 -1.020 O5 NGO 13
NGO O6 O6 O 0 1 N N N N N N 47.103 73.354 52.192 -3.001 -2.172 0.343 O6 NGO 14
NGO HC1 HC1 H 0 1 N N N N N N 43.149 73.504 52.495 1.049 -1.137 -1.956 HC1 NGO 15
NGO HC2 HC2 H 0 1 N N N N N N 42.746 75.612 53.613 1.231 1.173 -1.783 HC2 NGO 16
NGO HC3 HC3 H 0 1 N N N N N N 43.633 77.071 51.078 0.520 1.313 1.136 HC3 NGO 17
NGO HC4 HC4 H 0 1 N N N N N N 45.228 75.782 53.403 -1.603 1.444 -1.042 HC4 NGO 18
NGO HC5 HC5 H 0 1 N N N N N N 46.041 74.994 50.751 -0.922 -0.713 1.012 HC5 NGO 19
NGO HC61 1HC6 H 0 0 N N N N N N 45.326 73.527 53.300 -3.387 -0.215 0.879 HC61 NGO 20
NGO HC62 2HC6 H 0 0 N N N N N N 45.164 72.600 51.891 -3.317 -0.531 -0.871 HC62 NGO 21
NGO HC81 1HC8 H 0 0 N N N N N N 39.039 74.386 50.184 3.487 -1.110 2.132 HC81 NGO 22
NGO HC82 2HC8 H 0 0 N N N N N N 38.769 75.351 51.680 3.674 -2.374 0.893 HC82 NGO 23
NGO HC83 3HC8 H 0 0 N N N N N N 39.364 76.155 50.263 4.529 -0.823 0.718 HC83 NGO 24
NGO HN HN H 0 1 N N N N N N 40.898 76.974 52.401 3.113 1.128 -0.060 HN NGO 25
NGO HO3 HO3 H 0 1 N N N N N N 44.295 78.514 52.751 -0.180 3.372 0.411 HO3 NGO 26
NGO HO4 HO4 H 0 1 N N N N N N 47.006 76.520 52.056 -2.946 1.526 0.814 HO4 NGO 27
NGO HO6 HO6 H 0 1 N N N N N N 47.385 72.581 52.667 -3.947 -2.371 0.341 HO6 NGO 28
#
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
NGO C1 C2 SING N N 1
NGO C1 O1 SING N N 2
NGO C1 O5 SING N N 3
NGO C1 HC1 SING N N 4
NGO C2 C3 SING N N 5
NGO C2 N2 SING N N 6
NGO C2 HC2 SING N N 7
NGO C3 C4 SING N N 8
NGO C3 O3 SING N N 9
NGO C3 HC3 SING N N 10
NGO C4 C5 SING N N 11
NGO C4 O4 SING N N 12
NGO C4 HC4 SING N N 13
NGO C5 C6 SING N N 14
NGO C5 O5 SING N N 15
NGO C5 HC5 SING N N 16
NGO C6 O6 SING N N 17
NGO C6 HC61 SING N N 18
NGO C6 HC62 SING N N 19
NGO C7 C8 SING N N 20
NGO C7 N2 DOUB N N 21
NGO C7 O1 SING N N 22
NGO C8 HC81 SING N N 23
NGO C8 HC82 SING N N 24
NGO C8 HC83 SING N N 25
NGO N2 HN SING N N 26
NGO O3 HO3 SING N N 27
NGO O4 HO4 SING N N 28
NGO O6 HO6 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
NGO SMILES ACDLabs 10.04 O1C(=[NH+]C2C(O)C(O)C(OC12)CO)C
NGO SMILES_CANONICAL CACTVS 3.341 CC1=[NH+][C@@H]2[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]2O1
NGO SMILES CACTVS 3.341 CC1=[NH+][CH]2[CH](O)[CH](O)[CH](CO)O[CH]2O1
NGO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC1=[NH+][C@@H]2[C@H]([C@@H]([C@H](O[C@@H]2O1)CO)O)O
NGO SMILES "OpenEye OEToolkits" 1.5.0 CC1=[NH+]C2C(C(C(OC2O1)CO)O)O
NGO InChI InChI 1.03 InChI=1S/C8H13NO5/c1-3-9-5-7(12)6(11)4(2-10)14-8(5)13-3/h4-8,10-12H,2H2,1H3/p+1/t4-,5-,6-,7-,8+/m1/s1
NGO InChIKey InChI 1.03 PDBSWNMXMILYCQ-PVFLNQBWSA-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
NGO "SYSTEMATIC NAME" ACDLabs 10.04 (3aR,5R,6S,7R,7aR)-6,7-dihydroxy-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]oxazol-1-ium
NGO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (3aR,5R,6S,7R,7aR)-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[5,6-d][1,3]oxazol-1-ium-6,7-diol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
NGO 'Create component' 2000-08-25 EBI
NGO 'Modify descriptor' 2011-06-04 RCSB
NGO 'Modify synonyms' 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id NGO
_pdbx_chem_comp_synonyms.name "N-ACETYLGLUCOSAMINE-OXAZOLINIUM ION INTERMEDIATE"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id NGO
_pdbe_chem_comp_synonyms.name 'N-ACETYLGLUCOSAMINE-OXAZOLINIUM ION INTERMEDIATE'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
NGO C1 C 7.702 -0.750 1
NGO C2 C 7.702 0.750 2
NGO C3 C 6.404 1.500 3
NGO C4 C 5.104 0.750 4
NGO C5 C 5.104 -0.750 5
NGO C6 C 3.805 -1.500 6
NGO C7 C 9.997 0.000 7
NGO C8 C 11.497 0.000 8
NGO N2 N 9.122 1.207 9
NGO O1 O 9.122 -1.207 10
NGO O3 O 6.404 3.000 11
NGO O4 O 3.805 1.500 12
NGO O5 O 6.404 -1.500 13
NGO O6 O 3.805 -3.000 14
#
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
NGO C1 C2 SINGLE NONE 1
NGO C1 O1 SINGLE NONE 2
NGO C1 O5 SINGLE NONE 3
NGO C2 C3 SINGLE NONE 4
NGO C2 N2 SINGLE NONE 5
NGO C3 C4 SINGLE NONE 6
NGO C3 O3 SINGLE BEGINDASH 7
NGO C4 C5 SINGLE NONE 8
NGO C4 O4 SINGLE BEGINWEDGE 9
NGO C5 C6 SINGLE BEGINDASH 10
NGO C5 O5 SINGLE NONE 11
NGO C6 O6 SINGLE NONE 12
NGO C7 C8 SINGLE NONE 13
NGO C7 N2 DOUBLE NONE 14
NGO C7 O1 SINGLE NONE 15
#
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
NGO MurckoScaffold S1 scaffold 'C1=[NH+][C@@H]2CCCO[C@@H]2O1' InChI=1S/C6H9NO2/c1-2-5-6(8-3-1)9-4-7-5/h4-6H,1-3H2/p+1/t5-,6-/m1/s1 KQDAGTONRHUHJF-PHDIDXHHSA-O
NGO 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
NGO C1 S1 1
NGO C2 S1 1
NGO C3 S1 1
NGO C4 S1 1
NGO C5 S1 1
NGO C7 S1 1
NGO N2 S1 1
NGO O1 S1 1
NGO O5 S1 1
NGO C4 F1 1
NGO C5 F1 1
NGO O5 F1 1
NGO C1 F1 1
NGO C2 F1 1
NGO C3 F1 1
NGO O1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id NGO
_pdbe_chem_comp_rdkit_properties.exactmw 204.087
_pdbe_chem_comp_rdkit_properties.amw 204.202
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.875
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 5
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 100.775
_pdbe_chem_comp_rdkit_properties.tpsa 93.120
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.677
_pdbe_chem_comp_rdkit_properties.CrippenMR 44.277
_pdbe_chem_comp_rdkit_properties.chi0v 6.488
_pdbe_chem_comp_rdkit_properties.chi1v 3.376
_pdbe_chem_comp_rdkit_properties.chi2v 1.511
_pdbe_chem_comp_rdkit_properties.chi3v 1.511
_pdbe_chem_comp_rdkit_properties.chi4v 0.936
_pdbe_chem_comp_rdkit_properties.chi0n 20.488
_pdbe_chem_comp_rdkit_properties.chi1n 10.048
_pdbe_chem_comp_rdkit_properties.chi2n 1.511
_pdbe_chem_comp_rdkit_properties.chi3n 1.511
_pdbe_chem_comp_rdkit_properties.chi4n 0.936
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.690
_pdbe_chem_comp_rdkit_properties.kappa1 2.517
_pdbe_chem_comp_rdkit_properties.kappa2 3.467
_pdbe_chem_comp_rdkit_properties.kappa3 1.399
_pdbe_chem_comp_rdkit_properties.Phi 0.623
#
_pdbe_chem_comp_external_mappings.comp_id NGO
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 5289020
#
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
NGO C1 0.348 0.776 0.556 ETKDGv3 1
NGO C2 0.905 -0.610 0.137 ETKDGv3 2
NGO C3 0.033 -1.266 -0.943 ETKDGv3 3
NGO C4 -1.437 -1.166 -0.514 ETKDGv3 4
NGO C5 -1.826 0.325 -0.265 ETKDGv3 5
NGO C6 -2.684 0.499 1.003 ETKDGv3 6
NGO C7 2.504 0.927 -0.199 ETKDGv3 7
NGO C8 3.812 1.543 -0.567 ETKDGv3 8
NGO N2 2.241 -0.322 -0.363 ETKDGv3 9
NGO O1 1.460 1.637 0.361 ETKDGv3 10
NGO O3 0.415 -2.603 -1.158 ETKDGv3 11
NGO O4 -2.250 -1.726 -1.512 ETKDGv3 12
NGO O5 -0.715 1.217 -0.272 ETKDGv3 13
NGO O6 -2.993 1.851 1.208 ETKDGv3 14
NGO HC1 0.061 0.796 1.629 ETKDGv3 15
NGO HC2 0.980 -1.266 1.033 ETKDGv3 16
NGO HC3 0.162 -0.715 -1.902 ETKDGv3 17
NGO HC4 -1.556 -1.754 0.428 ETKDGv3 18
NGO HC5 -2.468 0.643 -1.117 ETKDGv3 19
NGO HC61 -2.140 0.120 1.893 ETKDGv3 20
NGO HC62 -3.620 -0.098 0.911 ETKDGv3 21
NGO HC81 4.019 1.366 -1.643 ETKDGv3 22
NGO HC82 4.622 1.092 0.043 ETKDGv3 23
NGO HC83 3.781 2.636 -0.379 ETKDGv3 24
NGO HN 2.908 -1.027 -0.750 ETKDGv3 25
NGO HO3 0.278 -3.099 -0.309 ETKDGv3 26
NGO HO4 -3.145 -1.864 -1.105 ETKDGv3 27
NGO HO6 -3.694 2.086 0.546 ETKDGv3 28
#