data_HM0
#
_chem_comp.id HM0
_chem_comp.name "1-cyclobutylimidazole-2-carboxylic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H10 N2 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-01-19
_chem_comp.pdbx_modified_date 2022-01-14
_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 166.177
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code HM0
_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 7DUZ
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
HM0 C10 C1 C 0 1 N N N N N N 32.133 20.298 -12.211 3.149 -0.139 0.196 C10 HM0 1
HM0 C11 C2 C 0 1 N N N N N N 31.999 18.829 -12.603 2.158 -0.961 1.036 C11 HM0 2
HM0 O01 O1 O 0 1 N N N N N N 28.629 16.925 -8.258 -3.261 -0.623 0.048 O01 HM0 3
HM0 C02 C3 C 0 1 N N N N N N 29.278 17.465 -9.196 -1.924 -0.786 -0.014 C02 HM0 4
HM0 C03 C4 C 0 1 Y N N N N N 30.677 16.953 -9.524 -1.039 0.391 -0.009 C03 HM0 5
HM0 N04 N1 N 0 1 Y N N N N N 31.258 15.932 -8.917 -1.427 1.648 0.053 N04 HM0 6
HM0 C05 C5 C 0 1 Y N N N N N 32.462 15.764 -9.448 -0.354 2.435 0.036 C05 HM0 7
HM0 C06 C6 C 0 1 Y N N N N N 32.620 16.739 -10.419 0.750 1.652 -0.038 C06 HM0 8
HM0 N07 N2 N 0 1 Y N N N N N 31.506 17.449 -10.432 0.327 0.366 -0.061 N07 HM0 9
HM0 C08 C7 C 0 1 N N N N N N 31.223 18.578 -11.308 1.173 -0.827 -0.138 C08 HM0 10
HM0 C09 C8 C 0 1 N N N N N N 31.651 19.955 -10.803 2.402 -0.654 -1.046 C09 HM0 11
HM0 O12 O2 O 0 1 N N N N N N 28.769 18.418 -9.847 -1.450 -1.903 -0.073 O12 HM0 12
HM0 H1 H1 H 0 1 N N N N N N 33.162 20.684 -12.254 3.059 0.938 0.343 H1 HM0 13
HM0 H2 H2 H 0 1 N N N N N N 31.465 20.975 -12.764 4.178 -0.491 0.264 H2 HM0 14
HM0 H3 H3 H 0 1 N N N N N N 31.417 18.657 -13.520 2.484 -1.985 1.219 H3 HM0 15
HM0 H4 H4 H 0 1 N N N N N N 32.955 18.289 -12.669 1.828 -0.453 1.943 H4 HM0 16
HM0 H5 H5 H 0 1 N N N N N N 27.783 17.349 -8.172 -3.801 -1.426 0.042 H5 HM0 17
HM0 H6 H6 H 0 1 N N N N N N 33.184 15.009 -9.174 -0.362 3.515 0.075 H6 HM0 18
HM0 H7 H7 H 0 1 N N N N N N 33.487 16.890 -11.045 1.775 1.990 -0.069 H7 HM0 19
HM0 H8 H8 H 0 1 N N N N N N 30.147 18.607 -11.534 0.607 -1.737 -0.338 H8 HM0 20
HM0 H9 H9 H 0 1 N N N N N N 32.448 19.931 -10.045 2.269 0.101 -1.821 H9 HM0 21
HM0 H10 H10 H 0 1 N N N N N N 30.822 20.582 -10.443 2.795 -1.594 -1.433 H10 HM0 22
#
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
HM0 C11 C10 SING N N 1
HM0 C11 C08 SING N N 2
HM0 C10 C09 SING N N 3
HM0 C08 C09 SING N N 4
HM0 C08 N07 SING N N 5
HM0 N07 C06 SING Y N 6
HM0 N07 C03 SING Y N 7
HM0 C06 C05 DOUB Y N 8
HM0 O12 C02 DOUB N N 9
HM0 C03 C02 SING N N 10
HM0 C03 N04 DOUB Y N 11
HM0 C05 N04 SING Y N 12
HM0 C02 O01 SING N N 13
HM0 C10 H1 SING N N 14
HM0 C10 H2 SING N N 15
HM0 C11 H3 SING N N 16
HM0 C11 H4 SING N N 17
HM0 O01 H5 SING N N 18
HM0 C05 H6 SING N N 19
HM0 C06 H7 SING N N 20
HM0 C08 H8 SING N N 21
HM0 C09 H9 SING N N 22
HM0 C09 H10 SING N N 23
#
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
HM0 InChI InChI 1.03 InChI=1S/C8H10N2O2/c11-8(12)7-9-4-5-10(7)6-2-1-3-6/h4-6H,1-3H2,(H,11,12)
HM0 InChIKey InChI 1.03 NZCLFPVXVQMPNV-UHFFFAOYSA-N
HM0 SMILES_CANONICAL CACTVS 3.385 OC(=O)c1nccn1C2CCC2
HM0 SMILES CACTVS 3.385 OC(=O)c1nccn1C2CCC2
HM0 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1cn(c(n1)C(=O)O)C2CCC2
HM0 SMILES "OpenEye OEToolkits" 2.0.7 c1cn(c(n1)C(=O)O)C2CCC2
#
_pdbx_chem_comp_identifier.comp_id HM0
_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 "1-cyclobutylimidazole-2-carboxylic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
HM0 'Create component' 2021-01-19 PDBJ
HM0 'Initial release' 2022-01-19 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
HM0 C10 C 4.213 -2.965 1
HM0 C11 C 5.274 -1.904 2
HM0 O01 O 7.968 2.078 3
HM0 C02 C 6.854 1.075 4
HM0 C03 C 5.427 1.538 5
HM0 N04 N 4.963 2.965 6
HM0 C05 C 3.463 2.965 7
HM0 C06 C 3.000 1.538 8
HM0 N07 N 4.213 0.656 9
HM0 C08 C 4.213 -0.844 10
HM0 C09 C 3.153 -1.904 11
HM0 O12 O 7.165 -0.393 12
#
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
HM0 C11 C10 SINGLE NONE 1
HM0 C11 C08 SINGLE NONE 2
HM0 C10 C09 SINGLE NONE 3
HM0 C08 C09 SINGLE NONE 4
HM0 C08 N07 SINGLE NONE 5
HM0 N07 C06 SINGLE NONE 6
HM0 N07 C03 SINGLE NONE 7
HM0 C06 C05 DOUBLE NONE 8
HM0 O12 C02 DOUBLE NONE 9
HM0 C03 C02 SINGLE NONE 10
HM0 C03 N04 DOUBLE NONE 11
HM0 C05 N04 SINGLE NONE 12
HM0 C02 O01 SINGLE NONE 13
#
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
HM0 MurckoScaffold S1 scaffold c1cn(C2CCC2)cn1 InChI=1S/C7H10N2/c1-2-7(3-1)9-5-4-8-6-9/h4-7H,1-3H2 PVPOSMUWPZUTHQ-UHFFFAOYSA-N
HM0 cyclobutane F1 fragment C1CCC1 InChI=1S/C4H8/c1-2-4-3-1/h1-4H2 PMPVIKIVABFJJI-UHFFFAOYSA-N
HM0 imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-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
HM0 C10 S1 1
HM0 C11 S1 1
HM0 C03 S1 1
HM0 N04 S1 1
HM0 C05 S1 1
HM0 C06 S1 1
HM0 N07 S1 1
HM0 C08 S1 1
HM0 C09 S1 1
HM0 C10 F1 1
HM0 C11 F1 1
HM0 C08 F1 1
HM0 C09 F1 1
HM0 C05 F2 1
HM0 C06 F2 1
HM0 N07 F2 1
HM0 C03 F2 1
HM0 N04 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id HM0
_pdbe_chem_comp_rdkit_properties.exactmw 166.074
_pdbe_chem_comp_rdkit_properties.amw 166.180
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_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 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 83.981
_pdbe_chem_comp_rdkit_properties.tpsa 55.120
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.252
_pdbe_chem_comp_rdkit_properties.CrippenMR 41.808
_pdbe_chem_comp_rdkit_properties.chi0v 5.711
_pdbe_chem_comp_rdkit_properties.chi1v 3.026
_pdbe_chem_comp_rdkit_properties.chi2v 1.303
_pdbe_chem_comp_rdkit_properties.chi3v 1.303
_pdbe_chem_comp_rdkit_properties.chi4v 0.760
_pdbe_chem_comp_rdkit_properties.chi0n 15.711
_pdbe_chem_comp_rdkit_properties.chi1n 7.935
_pdbe_chem_comp_rdkit_properties.chi2n 1.303
_pdbe_chem_comp_rdkit_properties.chi3n 1.303
_pdbe_chem_comp_rdkit_properties.chi4n 0.760
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.320
_pdbe_chem_comp_rdkit_properties.kappa1 2.129
_pdbe_chem_comp_rdkit_properties.kappa2 2.621
_pdbe_chem_comp_rdkit_properties.kappa3 0.995
_pdbe_chem_comp_rdkit_properties.Phi 0.465
#
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
HM0 UniChem ChEMBL CHEMBL5181819
HM0 UniChem PDBe HM0
HM0 UniChem PubChem 83873455
#
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
HM0 C10 2.515 -0.314 0.404 ETKDGv3 1
HM0 C11 1.171 -0.851 0.869 ETKDGv3 2
HM0 O01 -1.495 -1.945 1.132 ETKDGv3 3
HM0 C02 -2.253 -0.782 1.059 ETKDGv3 4
HM0 C03 -1.816 0.359 0.234 ETKDGv3 5
HM0 N04 -2.632 1.316 -0.078 ETKDGv3 6
HM0 C05 -1.905 2.168 -0.956 ETKDGv3 7
HM0 C06 -0.689 1.691 -1.147 ETKDGv3 8
HM0 N07 -0.517 0.519 -0.354 ETKDGv3 9
HM0 C08 0.549 -0.487 -0.479 ETKDGv3 10
HM0 C09 1.901 0.076 -0.931 ETKDGv3 11
HM0 O12 -3.347 -0.718 1.681 ETKDGv3 12
HM0 H1 2.850 0.566 0.995 ETKDGv3 13
HM0 H2 3.283 -1.112 0.303 ETKDGv3 14
HM0 H3 0.761 -0.269 1.724 ETKDGv3 15
HM0 H4 1.199 -1.949 1.043 ETKDGv3 16
HM0 H5 -1.801 -2.732 1.690 ETKDGv3 17
HM0 H6 -2.315 3.046 -1.436 ETKDGv3 18
HM0 H7 0.040 2.113 -1.824 ETKDGv3 19
HM0 H8 0.227 -1.371 -1.072 ETKDGv3 20
HM0 H9 1.940 1.175 -1.077 ETKDGv3 21
HM0 H10 2.335 -0.498 -1.778 ETKDGv3 22
#