data_8QR
#
_chem_comp.id 8QR
_chem_comp.name (3R)-3-aminopyrrolidin-2-one
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C4 H8 N2 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms (3R)-3-azanylpyrrolidin-2-one
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-10-28
_chem_comp.pdbx_modified_date 2022-11-04
_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 100.119
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 8QR
_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 7Q2L
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
8QR C02 C1 C 0 1 N N N N N N -19.418 -19.186 -17.101 -0.843 0.229 -0.099 C02 8QR 1
8QR C04 C2 C 0 1 N N N N N N -18.879 -16.873 -17.102 1.232 1.188 0.310 C04 8QR 2
8QR C05 C3 C 0 1 N N N N N N -18.561 -17.476 -18.502 1.507 -0.043 -0.580 C05 8QR 3
8QR C06 C4 C 0 1 N N R N N N -19.428 -18.743 -18.555 0.180 -0.827 -0.453 C06 8QR 4
8QR N03 N1 N 0 1 N N N N N N -19.106 -18.074 -16.306 -0.227 1.349 0.317 N03 8QR 5
8QR N07 N2 N 0 1 N N N N N N -18.927 -19.794 -19.389 0.276 -1.829 0.617 N07 8QR 6
8QR O01 O1 O 0 1 N N N N N N -19.630 -20.274 -16.640 -2.045 0.088 -0.184 O01 8QR 7
8QR H1 H1 H 0 1 N N N N N N -18.030 -16.290 -16.715 1.597 1.013 1.322 H1 8QR 8
8QR H2 H2 H 0 1 N N N N N N -19.776 -16.238 -17.134 1.707 2.073 -0.114 H2 8QR 9
8QR H3 H3 H 0 1 N N N N N N -17.493 -17.727 -18.588 1.686 0.255 -1.613 H3 8QR 10
8QR H4 H4 H 0 1 N N N N N N -18.839 -16.776 -19.304 2.343 -0.625 -0.193 H4 8QR 11
8QR H5 H5 H 0 1 N N N N N N -20.452 -18.469 -18.848 -0.074 -1.303 -1.401 H5 8QR 12
8QR H6 H6 H 0 1 N N N N N N -19.046 -18.101 -15.308 -0.687 2.159 0.586 H6 8QR 13
8QR H7 H7 H 0 1 N N N N N N -19.555 -20.572 -19.359 -0.586 -2.346 0.706 H7 8QR 14
8QR H8 H8 H 0 1 N N N N N N -18.849 -19.464 -20.330 1.056 -2.451 0.461 H8 8QR 15
#
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
8QR N07 C06 SING N N 1
8QR C06 C05 SING N N 2
8QR C06 C02 SING N N 3
8QR C05 C04 SING N N 4
8QR C04 N03 SING N N 5
8QR C02 O01 DOUB N N 6
8QR C02 N03 SING N N 7
8QR C04 H1 SING N N 8
8QR C04 H2 SING N N 9
8QR C05 H3 SING N N 10
8QR C05 H4 SING N N 11
8QR C06 H5 SING N N 12
8QR N03 H6 SING N N 13
8QR N07 H7 SING N N 14
8QR N07 H8 SING N N 15
#
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
8QR InChI InChI 1.06 InChI=1S/C4H8N2O/c5-3-1-2-6-4(3)7/h3H,1-2,5H2,(H,6,7)/t3-/m1/s1
8QR InChIKey InChI 1.06 YNDAMDVOGKACTP-GSVOUGTGSA-N
8QR SMILES_CANONICAL CACTVS 3.385 N[C@@H]1CCNC1=O
8QR SMILES CACTVS 3.385 N[CH]1CCNC1=O
8QR SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C1CNC(=O)[C@@H]1N
8QR SMILES "OpenEye OEToolkits" 2.0.7 C1CNC(=O)C1N
#
_pdbx_chem_comp_identifier.comp_id 8QR
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier (3~{R})-3-azanylpyrrolidin-2-one
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 8QR
_pdbx_chem_comp_synonyms.name (3R)-3-azanylpyrrolidin-2-one
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
8QR 'Create component' 2021-10-28 PDBE
8QR 'Modify descriptor' 2022-08-22 RCSB
8QR 'Initial release' 2022-11-09 RCSB
#
_pdbe_chem_comp_synonyms.comp_id 8QR
_pdbe_chem_comp_synonyms.name (3R)-3-azanylpyrrolidin-2-one
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
8QR C02 C 4.890 0.588 1
8QR C04 C 6.854 -0.839 2
8QR C05 C 5.640 -1.721 3
8QR C06 C 4.427 -0.839 4
8QR N03 N 6.390 0.588 5
8QR N07 N 3.000 -1.303 6
8QR O01 O 4.008 1.801 7
#
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
8QR C06 N07 SINGLE BEGINWEDGE 1
8QR C06 C05 SINGLE NONE 2
8QR C06 C02 SINGLE NONE 3
8QR C05 C04 SINGLE NONE 4
8QR C04 N03 SINGLE NONE 5
8QR C02 O01 DOUBLE NONE 6
8QR C02 N03 SINGLE NONE 7
#
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
8QR MurckoScaffold S1 scaffold O=C1CCCN1 InChI=1S/C4H7NO/c6-4-2-1-3-5-4/h1-3H2,(H,5,6) HNJBEVLQSNELDL-UHFFFAOYSA-N
8QR amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
8QR peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-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
8QR C02 S1 1
8QR C04 S1 1
8QR C05 S1 1
8QR C06 S1 1
8QR N03 S1 1
8QR O01 S1 1
8QR N03 F1 1
8QR C02 F1 1
8QR O01 F1 1
8QR C06 F1 1
8QR O01 F2 1
8QR C02 F2 1
8QR C06 F2 1
8QR N07 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 8QR
_pdbe_chem_comp_rdkit_properties.exactmw 100.064
_pdbe_chem_comp_rdkit_properties.amw 100.121
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 7
_pdbe_chem_comp_rdkit_properties.NumAtoms 15
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.750
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 53.293
_pdbe_chem_comp_rdkit_properties.tpsa 55.120
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.166
_pdbe_chem_comp_rdkit_properties.CrippenMR 25.602
_pdbe_chem_comp_rdkit_properties.chi0v 3.303
_pdbe_chem_comp_rdkit_properties.chi1v 1.625
_pdbe_chem_comp_rdkit_properties.chi2v 0.534
_pdbe_chem_comp_rdkit_properties.chi3v 0.534
_pdbe_chem_comp_rdkit_properties.chi4v 0.238
_pdbe_chem_comp_rdkit_properties.chi0n 11.303
_pdbe_chem_comp_rdkit_properties.chi1n 5.467
_pdbe_chem_comp_rdkit_properties.chi2n 0.534
_pdbe_chem_comp_rdkit_properties.chi3n 0.534
_pdbe_chem_comp_rdkit_properties.chi4n 0.238
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.570
_pdbe_chem_comp_rdkit_properties.kappa1 0.910
_pdbe_chem_comp_rdkit_properties.kappa2 1.500
_pdbe_chem_comp_rdkit_properties.kappa3 0.718
_pdbe_chem_comp_rdkit_properties.Phi 0.195
#
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
8QR UniChem PDBe 8QR
8QR UniChem ZINC ZINC000019737051
8QR UniChem eMolecules 28301618
8QR UniChem 'EPA CompTox Dashboard' DTXSID80620967
8QR UniChem ChemicalBook CB81292055
8QR UniChem SureChEMBL SCHEMBL4012275
8QR UniChem PubChem 21969418
#
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
8QR C02 0.236 1.225 -0.055 ETKDGv3 1
8QR C04 -1.512 -0.329 0.011 ETKDGv3 2
8QR C05 -0.251 -0.997 0.599 ETKDGv3 3
8QR C06 0.916 -0.006 0.414 ETKDGv3 4
8QR N03 -1.144 1.044 -0.274 ETKDGv3 5
8QR N07 1.873 -0.498 -0.579 ETKDGv3 6
8QR O01 0.817 2.326 -0.247 ETKDGv3 7
8QR H1 -2.352 -0.354 0.738 ETKDGv3 8
8QR H2 -1.815 -0.833 -0.931 ETKDGv3 9
8QR H3 -0.407 -1.188 1.683 ETKDGv3 10
8QR H4 -0.054 -1.971 0.099 ETKDGv3 11
8QR H5 1.432 0.180 1.382 ETKDGv3 12
8QR H6 -1.790 1.769 -0.658 ETKDGv3 13
8QR H7 2.646 0.201 -0.669 ETKDGv3 14
8QR H8 1.405 -0.568 -1.513 ETKDGv3 15
#