data_G63
#
_chem_comp.id G63
_chem_comp.name " mannose-alpha-1,3-2-aminodeoxymannojirimycin"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H14 N2 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-12-15
_chem_comp.pdbx_modified_date 2018-03-16
_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 162.187
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code G63
_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 6FAM
_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
G63 O3 O1 O 0 1 N N N N N N 3.008 23.027 6.171 -2.504 -1.222 0.038 O3 G63 1
G63 C3 C1 C 0 1 N N R N N N 3.415 23.059 4.785 -1.393 -0.467 0.524 C3 G63 2
G63 C2 C2 C 0 1 N N R N N N 4.907 23.351 4.803 -1.636 1.023 0.268 C2 G63 3
G63 N2 N1 N 0 1 N N N N N N 5.156 24.645 5.501 -1.847 1.246 -1.168 N2 G63 4
G63 C4 C3 C 0 1 N N R N N N 2.641 24.168 4.082 -0.120 -0.901 -0.207 C4 G63 5
G63 O4 O2 O 0 1 N N N N N N 1.251 23.788 4.083 0.145 -2.277 0.073 O4 G63 6
G63 C5 C4 C 0 1 N N R N N N 3.112 24.388 2.644 1.055 -0.047 0.274 C5 G63 7
G63 C6 C5 C 0 1 N N N N N N 2.530 25.640 1.982 2.326 -0.464 -0.469 C6 G63 8
G63 O6 O3 O 0 1 N N N N N N 2.842 26.823 2.764 3.444 0.250 0.062 O6 G63 9
G63 N7 N2 N 0 1 N N N N N N 4.585 24.572 2.720 0.775 1.369 0.006 N7 G63 10
G63 C1 C6 C 0 1 N N N N N N 5.362 23.491 3.386 -0.417 1.821 0.735 C1 G63 11
G63 H1 H1 H 0 1 N N N N N N 3.482 22.340 6.625 -3.347 -0.995 0.455 H1 G63 12
G63 H2 H2 H 0 1 N N N N N N 3.224 22.094 4.292 -1.276 -0.638 1.594 H2 G63 13
G63 H3 H3 H 0 1 N N N N N N 5.447 22.533 5.302 -2.518 1.348 0.820 H3 G63 14
G63 H4 H4 H 0 1 N N N N N N 4.858 24.574 6.453 -2.010 2.222 -1.363 H4 G63 15
G63 H5 H5 H 0 1 N N N N N N 6.133 24.856 5.473 -1.070 0.894 -1.707 H5 G63 16
G63 H7 H7 H 0 1 N N N N N N 2.774 25.104 4.644 -0.253 -0.767 -1.280 H7 G63 17
G63 H8 H8 H 0 1 N N N N N N 0.960 23.652 4.977 -0.561 -2.878 -0.203 H8 G63 18
G63 H9 H9 H 0 1 N N N N N N 2.870 23.503 2.037 1.196 -0.193 1.345 H9 G63 19
G63 H10 H10 H 0 1 N N N N N N 2.959 25.749 0.975 2.486 -1.535 -0.343 H10 G63 20
G63 H11 H11 H 0 1 N N N N N N 1.438 25.534 1.906 2.219 -0.235 -1.529 H11 G63 21
G63 H12 H12 H 0 1 N N N N N N 2.474 27.589 2.340 4.286 0.035 -0.363 H12 G63 22
G63 H13 H13 H 0 1 N N N N N N 4.928 24.659 1.785 1.574 1.944 0.227 H13 G63 23
G63 H15 H15 H 0 1 N N N N N N 5.201 22.542 2.854 -0.581 2.882 0.541 H15 G63 24
G63 H16 H16 H 0 1 N N N N N N 6.432 23.744 3.368 -0.269 1.667 1.804 H16 G63 25
#
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
G63 C6 C5 SING N N 1
G63 C6 O6 SING N N 2
G63 C5 N7 SING N N 3
G63 C5 C4 SING N N 4
G63 N7 C1 SING N N 5
G63 C1 C2 SING N N 6
G63 C4 O4 SING N N 7
G63 C4 C3 SING N N 8
G63 C3 C2 SING N N 9
G63 C3 O3 SING N N 10
G63 C2 N2 SING N N 11
G63 O3 H1 SING N N 12
G63 C3 H2 SING N N 13
G63 C2 H3 SING N N 14
G63 N2 H4 SING N N 15
G63 N2 H5 SING N N 16
G63 C4 H7 SING N N 17
G63 O4 H8 SING N N 18
G63 C5 H9 SING N N 19
G63 C6 H10 SING N N 20
G63 C6 H11 SING N N 21
G63 O6 H12 SING N N 22
G63 N7 H13 SING N N 23
G63 C1 H15 SING N N 24
G63 C1 H16 SING N N 25
#
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
G63 InChI InChI 1.03 InChI=1S/C6H14N2O3/c7-3-1-8-4(2-9)6(11)5(3)10/h3-6,8-11H,1-2,7H2/t3-,4-,5-,6-/m1/s1
G63 InChIKey InChI 1.03 GFTGLZPGRKFGDU-KVTDHHQDSA-N
G63 SMILES_CANONICAL CACTVS 3.385 N[C@@H]1CN[C@H](CO)[C@@H](O)[C@@H]1O
G63 SMILES CACTVS 3.385 N[CH]1CN[CH](CO)[CH](O)[CH]1O
G63 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 C1[C@H]([C@H]([C@@H]([C@H](N1)CO)O)O)N
G63 SMILES "OpenEye OEToolkits" 2.0.6 C1C(C(C(C(N1)CO)O)O)N
#
_pdbx_chem_comp_identifier.comp_id G63
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.6
_pdbx_chem_comp_identifier.identifier (2~{R},3~{R},4~{R},5~{R})-5-azanyl-2-(hydroxymethyl)piperidine-3,4-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
G63 'Create component' 2017-12-15 RCSB
G63 'Initial release' 2018-03-21 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
G63 O3 O 6.404 3.000 1
G63 C3 C 6.404 1.500 2
G63 C2 C 5.104 0.750 3
G63 N2 N 3.805 1.500 4
G63 C4 C 7.702 0.750 5
G63 O4 O 9.002 1.500 6
G63 C5 C 7.702 -0.750 7
G63 C6 C 9.002 -1.500 8
G63 O6 O 9.002 -3.000 9
G63 N7 N 6.404 -1.500 10
G63 C1 C 5.104 -0.750 11
#
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
G63 C5 C6 SINGLE BEGINWEDGE 1
G63 C6 O6 SINGLE NONE 2
G63 C5 N7 SINGLE NONE 3
G63 C5 C4 SINGLE NONE 4
G63 N7 C1 SINGLE NONE 5
G63 C1 C2 SINGLE NONE 6
G63 C4 O4 SINGLE BEGINDASH 7
G63 C4 C3 SINGLE NONE 8
G63 C3 C2 SINGLE NONE 9
G63 C3 O3 SINGLE BEGINWEDGE 10
G63 C2 N2 SINGLE BEGINWEDGE 11
#
_pdbe_chem_comp_substructure.comp_id G63
_pdbe_chem_comp_substructure.substructure_name MurckoScaffold
_pdbe_chem_comp_substructure.id S1
_pdbe_chem_comp_substructure.substructure_type scaffold
_pdbe_chem_comp_substructure.substructure_smiles C1CCNCC1
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C5H11N/c1-2-4-6-5-3-1/h6H,1-5H2
_pdbe_chem_comp_substructure.substructure_inchikeys NQRYJNQNLNOLGT-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
G63 C3 S1 1
G63 C2 S1 1
G63 C4 S1 1
G63 C5 S1 1
G63 N7 S1 1
G63 C1 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id G63
_pdbe_chem_comp_rdkit_properties.exactmw 162.100
_pdbe_chem_comp_rdkit_properties.amw 162.189
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 25
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_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 84.934
_pdbe_chem_comp_rdkit_properties.tpsa 98.740
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.000
_pdbe_chem_comp_rdkit_properties.CrippenMR 38.866
_pdbe_chem_comp_rdkit_properties.chi0v 5.119
_pdbe_chem_comp_rdkit_properties.chi1v 2.533
_pdbe_chem_comp_rdkit_properties.chi2v 1.007
_pdbe_chem_comp_rdkit_properties.chi3v 1.007
_pdbe_chem_comp_rdkit_properties.chi4v 0.495
_pdbe_chem_comp_rdkit_properties.chi0n 19.119
_pdbe_chem_comp_rdkit_properties.chi1n 9.100
_pdbe_chem_comp_rdkit_properties.chi2n 1.007
_pdbe_chem_comp_rdkit_properties.chi3n 1.007
_pdbe_chem_comp_rdkit_properties.chi4n 0.495
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.200
_pdbe_chem_comp_rdkit_properties.kappa1 1.686
_pdbe_chem_comp_rdkit_properties.kappa2 3.465
_pdbe_chem_comp_rdkit_properties.kappa3 1.687
_pdbe_chem_comp_rdkit_properties.Phi 0.531
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
G63 UniChem PDBe G63
G63 UniChem SureChEMBL SCHEMBL10574705
G63 UniChem PubChem 18635119
G63 UniChem Nikkaji J3.543.318J
G63 UniChem BRENDA 138361
#
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
G63 O3 0.350 -0.833 -1.715 ETKDGv3 1
G63 C3 0.875 0.260 -1.004 ETKDGv3 2
G63 C2 1.683 -0.214 0.227 ETKDGv3 3
G63 N2 2.729 -1.172 -0.139 ETKDGv3 4
G63 C4 -0.271 1.198 -0.572 ETKDGv3 5
G63 O4 0.281 2.427 -0.172 ETKDGv3 6
G63 C5 -1.119 0.611 0.592 ETKDGv3 7
G63 C6 -2.123 -0.480 0.144 ETKDGv3 8
G63 O6 -3.021 0.028 -0.806 ETKDGv3 9
G63 N7 -0.259 0.158 1.704 ETKDGv3 10
G63 C1 0.755 -0.820 1.288 ETKDGv3 11
G63 H1 1.024 -1.093 -2.397 ETKDGv3 12
G63 H2 1.555 0.846 -1.669 ETKDGv3 13
G63 H3 2.180 0.673 0.681 ETKDGv3 14
G63 H4 3.338 -0.744 -0.874 ETKDGv3 15
G63 H5 2.297 -2.033 -0.546 ETKDGv3 16
G63 H7 -0.923 1.372 -1.461 ETKDGv3 17
G63 H8 -0.445 3.103 -0.224 ETKDGv3 18
G63 H9 -1.741 1.445 0.989 ETKDGv3 19
G63 H10 -1.605 -1.351 -0.299 ETKDGv3 20
G63 H11 -2.687 -0.858 1.027 ETKDGv3 21
G63 H12 -3.663 0.603 -0.313 ETKDGv3 22
G63 H13 -0.853 -0.275 2.450 ETKDGv3 23
G63 H15 0.279 -1.753 0.915 ETKDGv3 24
G63 H16 1.365 -1.097 2.175 ETKDGv3 25
#