data_2IM
#
_chem_comp.id 2IM
_chem_comp.name PIPERIDIN-2-IMINE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H10 N2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2005-09-12
_chem_comp.pdbx_modified_date 2011-06-04
_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 98.146
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 2IM
_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 2AS2
_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
2IM N2 N2 N 0 1 N N N N N N -16.355 -4.393 -7.249 2.261 -0.069 0.289 N2 2IM 1
2IM C1 C1 C 0 1 N N N N N N -16.349 -3.491 -6.264 1.029 -0.043 -0.103 C1 2IM 2
2IM N1 N1 N 0 1 N N N N N N -15.199 -3.150 -5.676 0.365 1.151 -0.302 N1 2IM 3
2IM C4 C4 C 0 1 N N N N N N -15.132 -2.275 -4.470 -0.983 1.289 0.260 C4 2IM 4
2IM C5 C5 C 0 1 N N N N N N -16.329 -2.464 -3.563 -1.812 0.064 -0.137 C5 2IM 5
2IM C3 C3 C 0 1 N N N N N N -17.618 -2.267 -4.380 -1.106 -1.208 0.340 C3 2IM 6
2IM C2 C2 C 0 1 N N N N N N -17.664 -3.263 -5.555 0.257 -1.321 -0.354 C2 2IM 7
2IM HN2 HN2 H 0 1 N N N N N N -17.284 -4.757 -7.323 2.738 0.761 0.445 HN2 2IM 8
2IM HN1 HN1 H 0 1 N N N N N N -14.344 -3.497 -6.062 0.778 1.873 -0.801 HN1 2IM 9
2IM H41 1H4 H 0 1 N N N N N N -15.123 -1.228 -4.809 -1.454 2.191 -0.132 H41 2IM 10
2IM H42 2H4 H 0 1 N N N N N N -14.221 -2.524 -3.906 -0.919 1.351 1.346 H42 2IM 11
2IM H51 1H5 H 0 1 N N N N N N -16.293 -1.729 -2.746 -1.920 0.034 -1.221 H51 2IM 12
2IM H52 2H5 H 0 1 N N N N N N -16.313 -3.479 -3.139 -2.798 0.127 0.325 H52 2IM 13
2IM H31 1H3 H 0 1 N N N N N N -17.636 -1.242 -4.778 -1.714 -2.077 0.092 H31 2IM 14
2IM H32 2H3 H 0 1 N N N N N N -18.488 -2.436 -3.729 -0.961 -1.160 1.420 H32 2IM 15
2IM H21 1H2 H 0 1 N N N N N N -17.951 -4.233 -5.123 0.112 -1.457 -1.426 H21 2IM 16
2IM H22 2H2 H 0 1 N N N N N N -18.376 -2.869 -6.295 0.807 -2.168 0.054 H22 2IM 17
#
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
2IM N2 C1 DOUB N N 1
2IM N2 HN2 SING N N 2
2IM C1 N1 SING N N 3
2IM C1 C2 SING N N 4
2IM N1 C4 SING N N 5
2IM N1 HN1 SING N N 6
2IM C4 C5 SING N N 7
2IM C4 H41 SING N N 8
2IM C4 H42 SING N N 9
2IM C5 C3 SING N N 10
2IM C5 H51 SING N N 11
2IM C5 H52 SING N N 12
2IM C3 C2 SING N N 13
2IM C3 H31 SING N N 14
2IM C3 H32 SING N N 15
2IM C2 H21 SING N N 16
2IM C2 H22 SING N N 17
#
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
2IM SMILES ACDLabs 10.04 "[N@H]=C1NCCCC1"
2IM SMILES_CANONICAL CACTVS 3.341 N=C1CCCCN1
2IM SMILES CACTVS 3.341 N=C1CCCCN1
2IM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1CCNC(=N)C1
2IM SMILES "OpenEye OEToolkits" 1.5.0 C1CCNC(=N)C1
2IM InChI InChI 1.03 InChI=1S/C5H10N2/c6-5-3-1-2-4-7-5/h1-4H2,(H2,6,7)
2IM InChIKey InChI 1.03 DHGUMNJVFYRSIG-UHFFFAOYSA-N
#
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
2IM "SYSTEMATIC NAME" ACDLabs 10.04 (2E)-piperidin-2-imine
2IM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 piperidin-2-imine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
2IM 'Create component' 2005-09-12 RCSB
2IM 'Modify descriptor' 2011-06-04 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
2IM N2 N 3.805 -1.035 1
2IM C1 C 5.104 -0.285 2
2IM N1 N 6.404 -1.035 3
2IM C4 C 7.702 -0.285 4
2IM C5 C 7.702 1.215 5
2IM C3 C 6.404 1.965 6
2IM C2 C 5.104 1.215 7
2IM HN2 H 3.805 -2.535 8
#
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
2IM N2 C1 DOUBLE NONE 1
2IM C1 N1 SINGLE ENDUPRIGHT 2
2IM C1 C2 SINGLE ENDDOWNRIGHT 3
2IM N1 C4 SINGLE NONE 4
2IM C4 C5 SINGLE NONE 5
2IM C5 C3 SINGLE NONE 6
2IM C3 C2 SINGLE NONE 7
#
_pdbe_chem_comp_substructure.comp_id 2IM
_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 N=C1CCCCN1
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C5H10N2/c6-5-3-1-2-4-7-5/h1-4H2,(H2,6,7)
_pdbe_chem_comp_substructure.substructure_inchikeys DHGUMNJVFYRSIG-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
2IM N2 S1 1
2IM C1 S1 1
2IM N1 S1 1
2IM C4 S1 1
2IM C5 S1 1
2IM C3 S1 1
2IM C2 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 2IM
_pdbe_chem_comp_rdkit_properties.exactmw 98.084
_pdbe_chem_comp_rdkit_properties.amw 98.149
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 0
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 1
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 7
_pdbe_chem_comp_rdkit_properties.NumAtoms 17
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.800
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 57.594
_pdbe_chem_comp_rdkit_properties.tpsa 35.880
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.737
_pdbe_chem_comp_rdkit_properties.CrippenMR 29.580
_pdbe_chem_comp_rdkit_properties.chi0v 3.394
_pdbe_chem_comp_rdkit_properties.chi1v 1.671
_pdbe_chem_comp_rdkit_properties.chi2v 0.455
_pdbe_chem_comp_rdkit_properties.chi3v 0.455
_pdbe_chem_comp_rdkit_properties.chi4v 0.224
_pdbe_chem_comp_rdkit_properties.chi0n 13.394
_pdbe_chem_comp_rdkit_properties.chi1n 6.565
_pdbe_chem_comp_rdkit_properties.chi2n 0.455
_pdbe_chem_comp_rdkit_properties.chi3n 0.455
_pdbe_chem_comp_rdkit_properties.chi4n 0.224
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.530
_pdbe_chem_comp_rdkit_properties.kappa1 0.714
_pdbe_chem_comp_rdkit_properties.kappa2 1.959
_pdbe_chem_comp_rdkit_properties.kappa3 1.180
_pdbe_chem_comp_rdkit_properties.Phi 0.200
#
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
2IM UniChem ChEMBL CHEMBL269058
2IM UniChem PDBe 2IM
2IM UniChem ZINC ZINC000002141055
2IM UniChem eMolecules 31226601
2IM UniChem SureChEMBL SCHEMBL224913
2IM UniChem HMDB HMDB0256574
2IM UniChem 'PubChem TPHARMA' 15170440
2IM UniChem Nikkaji J221.238B
2IM UniChem BindingDb 50049255
2IM UniChem 'EPA CompTox Dashboard' DTXSID40275816
2IM UniChem 'Probes And Drugs' PD070966
2IM UniChem 'PubChem TPHARMA' 16019579
2IM UniChem PubChem 85237
2IM UniChem Mcule MCULE-9735306041
#
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
2IM N2 1.844 1.410 -1.313 ETKDGv3 1
2IM C1 0.937 0.771 -0.646 ETKDGv3 2
2IM N1 -0.255 1.460 -0.242 ETKDGv3 3
2IM C4 -1.431 0.752 0.263 ETKDGv3 4
2IM C5 -1.039 -0.537 0.989 ETKDGv3 5
2IM C3 -0.115 -1.383 0.110 ETKDGv3 6
2IM C2 1.192 -0.641 -0.183 ETKDGv3 7
2IM HN2 2.748 0.962 -1.587 ETKDGv3 8
2IM HN1 -0.367 2.465 -0.505 ETKDGv3 9
2IM H41 -1.987 1.412 0.963 ETKDGv3 10
2IM H42 -2.102 0.510 -0.590 ETKDGv3 11
2IM H51 -1.955 -1.118 1.229 ETKDGv3 12
2IM H52 -0.526 -0.289 1.945 ETKDGv3 13
2IM H31 -0.628 -1.629 -0.846 ETKDGv3 14
2IM H32 0.116 -2.338 0.629 ETKDGv3 15
2IM H21 1.758 -1.201 -0.958 ETKDGv3 16
2IM H22 1.810 -0.604 0.740 ETKDGv3 17
#