data_SVJ
#
_chem_comp.id SVJ
_chem_comp.name (1~{S},5~{R})-8-methyl-8-azabicyclo[3.2.1]octan-3-amine
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H16 N2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-03-11
_chem_comp.pdbx_modified_date 2020-07-17
_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 140.226
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SVJ
_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 5RA5
_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
SVJ N1 N1 N 0 1 N N N N N N 31.011 112.572 23.454 -2.049 -0.001 0.733 N1 SVJ 1
SVJ C4 C1 C 0 1 N N R N N N 27.879 112.609 24.746 0.533 1.163 -0.112 C4 SVJ 2
SVJ C5 C2 C 0 1 N N N N N N 28.964 111.581 24.454 -0.768 1.268 -0.924 C5 SVJ 3
SVJ C6 C3 C 0 1 N N R N N N 29.749 111.841 23.138 -1.613 0.017 -0.669 C6 SVJ 4
SVJ C7 C4 C 0 1 N N N N N N 28.992 112.707 22.112 -0.784 -1.236 -0.962 C7 SVJ 5
SVJ N N2 N 0 1 N N N N N N 27.066 112.746 23.503 1.304 0.005 -0.638 N SVJ 6
SVJ C C5 C 0 1 N N N N N N 25.725 113.374 23.736 2.676 0.004 -0.112 C SVJ 7
SVJ C1 C6 C 0 1 N N S N N N 27.967 113.652 22.715 0.518 -1.172 -0.148 C1 SVJ 8
SVJ C2 C7 C 0 1 N N N N N N 28.589 114.659 23.706 0.149 -0.795 1.306 C2 SVJ 9
SVJ C3 C8 C 0 1 N N N N N N 28.501 113.976 25.023 0.159 0.747 1.329 C3 SVJ 10
SVJ H1 H1 H 0 1 N N N N N N 31.542 112.048 24.120 -2.576 0.829 0.960 H1 SVJ 11
SVJ H2 H2 H 0 1 N N N N N N 31.547 112.688 22.618 -2.582 -0.834 0.936 H2 SVJ 12
SVJ H4 H4 H 0 1 N N N N N N 27.257 112.287 25.594 1.109 2.088 -0.138 H4 SVJ 13
SVJ H5 H5 H 0 1 N N N N N N 28.491 110.590 24.384 -1.322 2.153 -0.612 H5 SVJ 14
SVJ H6 H6 H 0 1 N N N N N N 29.679 111.587 25.290 -0.531 1.341 -1.985 H6 SVJ 15
SVJ H7 H7 H 0 1 N N N N N N 29.992 110.873 22.675 -2.488 0.032 -1.320 H7 SVJ 16
SVJ H8 H8 H 0 1 N N N N N N 28.470 112.035 21.414 -1.349 -2.124 -0.677 H8 SVJ 17
SVJ H9 H9 H 0 1 N N N N N N 29.730 113.308 21.560 -0.548 -1.277 -2.025 H9 SVJ 18
SVJ H11 H11 H 0 1 N N N N N N 25.092 112.685 24.315 2.648 -0.060 0.975 H11 SVJ 19
SVJ H12 H12 H 0 1 N N N N N N 25.852 114.312 24.296 3.218 -0.854 -0.513 H12 SVJ 20
SVJ H13 H13 H 0 1 N N N N N N 25.247 113.586 22.768 3.180 0.923 -0.410 H13 SVJ 21
SVJ H14 H14 H 0 1 N N N N N N 27.409 114.180 21.928 1.088 -2.099 -0.211 H14 SVJ 22
SVJ H15 H15 H 0 1 N N N N N N 29.637 114.868 23.444 -0.843 -1.172 1.555 H15 SVJ 23
SVJ H16 H16 H 0 1 N N N N N N 28.019 115.600 23.716 0.891 -1.190 2.000 H16 SVJ 24
SVJ H17 H17 H 0 1 N N N N N N 29.503 113.858 25.461 0.900 1.121 2.036 H17 SVJ 25
SVJ H18 H18 H 0 1 N N N N N N 27.866 114.553 25.711 -0.833 1.120 1.586 H18 SVJ 26
#
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
SVJ C7 C1 SING N N 1
SVJ C7 C6 SING N N 2
SVJ C1 N SING N N 3
SVJ C1 C2 SING N N 4
SVJ C6 N1 SING N N 5
SVJ C6 C5 SING N N 6
SVJ N C SING N N 7
SVJ N C4 SING N N 8
SVJ C2 C3 SING N N 9
SVJ C5 C4 SING N N 10
SVJ C4 C3 SING N N 11
SVJ N1 H1 SING N N 12
SVJ N1 H2 SING N N 13
SVJ C4 H4 SING N N 14
SVJ C5 H5 SING N N 15
SVJ C5 H6 SING N N 16
SVJ C6 H7 SING N N 17
SVJ C7 H8 SING N N 18
SVJ C7 H9 SING N N 19
SVJ C H11 SING N N 20
SVJ C H12 SING N N 21
SVJ C H13 SING N N 22
SVJ C1 H14 SING N N 23
SVJ C2 H15 SING N N 24
SVJ C2 H16 SING N N 25
SVJ C3 H17 SING N N 26
SVJ C3 H18 SING N N 27
#
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
SVJ InChI InChI 1.03 InChI=1S/C8H16N2/c1-10-7-2-3-8(10)5-6(9)4-7/h6-8H,2-5,9H2,1H3/t6-,7+,8-
SVJ InChIKey InChI 1.03 HJGMRAKQWLKWMH-RNLVFQAGSA-N
SVJ SMILES_CANONICAL CACTVS 3.385 CN1[C@H]2CC[C@@H]1C[C@H](N)C2
SVJ SMILES CACTVS 3.385 CN1[CH]2CC[CH]1C[CH](N)C2
SVJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 CN1[C@@H]2CC[C@H]1CC(C2)N
SVJ SMILES "OpenEye OEToolkits" 2.0.6 CN1C2CCC1CC(C2)N
#
_pdbx_chem_comp_identifier.comp_id SVJ
_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 (1~{S},5~{R})-8-methyl-8-azabicyclo[3.2.1]octan-3-amine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
SVJ 'Create component' 2020-03-11 RCSB
SVJ 'Initial release' 2020-07-22 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
SVJ N1 N -3.082 0.013 1
SVJ C4 C 0.735 1.021 2
SVJ C5 C -0.531 1.524 3
SVJ C6 C -1.583 0.007 4
SVJ C7 C -0.545 -1.519 5
SVJ N N 0.356 -0.001 6
SVJ C C -0.501 0.002 7
SVJ C1 C 0.726 -1.027 8
SVJ C2 C 2.209 -0.769 9
SVJ C3 C 2.216 0.750 10
#
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
SVJ C7 C1 SINGLE NONE 1
SVJ C7 C6 SINGLE NONE 2
SVJ C1 N SINGLE NONE 3
SVJ C1 C2 SINGLE NONE 4
SVJ C6 N1 SINGLE BEGINWEDGE 5
SVJ C6 C5 SINGLE NONE 6
SVJ N C SINGLE NONE 7
SVJ N C4 SINGLE NONE 8
SVJ C2 C3 SINGLE NONE 9
SVJ C5 C4 SINGLE NONE 10
SVJ C4 C3 SINGLE NONE 11
#
_pdbe_chem_comp_substructure.comp_id SVJ
_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 'C1C[C@@H]2CC[C@H](C1)N2'
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C7H13N/c1-2-6-4-5-7(3-1)8-6/h6-8H,1-5H2/t6-,7+
_pdbe_chem_comp_substructure.substructure_inchikeys DGGKXQQCVPAUEA-KNVOCYPGSA-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
SVJ C4 S1 1
SVJ C5 S1 1
SVJ C6 S1 1
SVJ C7 S1 1
SVJ N S1 1
SVJ C1 S1 1
SVJ C2 S1 1
SVJ C3 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id SVJ
_pdbe_chem_comp_rdkit_properties.exactmw 140.131
_pdbe_chem_comp_rdkit_properties.amw 140.230
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 26
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_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 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 2
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 84.978
_pdbe_chem_comp_rdkit_properties.tpsa 29.260
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.570
_pdbe_chem_comp_rdkit_properties.CrippenMR 41.782
_pdbe_chem_comp_rdkit_properties.chi0v 4.894
_pdbe_chem_comp_rdkit_properties.chi1v 2.644
_pdbe_chem_comp_rdkit_properties.chi2v 1.220
_pdbe_chem_comp_rdkit_properties.chi3v 1.220
_pdbe_chem_comp_rdkit_properties.chi4v 0.772
_pdbe_chem_comp_rdkit_properties.chi0n 20.894
_pdbe_chem_comp_rdkit_properties.chi1n 10.539
_pdbe_chem_comp_rdkit_properties.chi2n 1.220
_pdbe_chem_comp_rdkit_properties.chi3n 1.220
_pdbe_chem_comp_rdkit_properties.chi4n 0.772
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.080
_pdbe_chem_comp_rdkit_properties.kappa1 1.089
_pdbe_chem_comp_rdkit_properties.kappa2 2.208
_pdbe_chem_comp_rdkit_properties.kappa3 0.867
_pdbe_chem_comp_rdkit_properties.Phi 0.240
#
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
SVJ UniChem ChEMBL CHEMBL3084978
SVJ UniChem PDBe SVJ
SVJ UniChem ZINC ZINC000100013524
SVJ UniChem eMolecules 36413660
SVJ UniChem 'PubChem TPHARMA' 15585885
SVJ UniChem ChemicalBook CB81120930
SVJ UniChem Nikkaji J949.854K
SVJ UniChem SureChEMBL SCHEMBL852253
SVJ UniChem Mcule MCULE-2572102810
SVJ UniChem Nikkaji J1.238.852G
#
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
SVJ N1 2.391 0.749 0.594 ETKDGv3 1
SVJ C4 -0.588 -0.721 0.859 ETKDGv3 2
SVJ C5 0.881 -1.205 0.876 ETKDGv3 3
SVJ C6 1.795 -0.397 -0.099 ETKDGv3 4
SVJ C7 1.040 0.077 -1.381 ETKDGv3 5
SVJ N -1.042 -0.805 -0.531 ETKDGv3 6
SVJ C -2.512 -0.817 -0.642 ETKDGv3 7
SVJ C1 -0.448 0.400 -1.114 ETKDGv3 8
SVJ C2 -0.597 1.511 -0.063 ETKDGv3 9
SVJ C3 -0.691 0.759 1.262 ETKDGv3 10
SVJ H1 3.068 1.213 -0.053 ETKDGv3 11
SVJ H2 2.966 0.392 1.392 ETKDGv3 12
SVJ H4 -1.195 -1.365 1.535 ETKDGv3 13
SVJ H5 0.892 -2.273 0.564 ETKDGv3 14
SVJ H6 1.278 -1.173 1.913 ETKDGv3 15
SVJ H7 2.624 -1.068 -0.421 ETKDGv3 16
SVJ H8 1.544 0.957 -1.837 ETKDGv3 17
SVJ H9 1.083 -0.739 -2.136 ETKDGv3 18
SVJ H11 -2.917 -1.731 -0.158 ETKDGv3 19
SVJ H12 -2.978 0.074 -0.168 ETKDGv3 20
SVJ H13 -2.807 -0.848 -1.712 ETKDGv3 21
SVJ H14 -0.939 0.685 -2.073 ETKDGv3 22
SVJ H15 -1.535 2.081 -0.245 ETKDGv3 23
SVJ H16 0.253 2.227 -0.075 ETKDGv3 24
SVJ H17 0.108 1.065 1.971 ETKDGv3 25
SVJ H18 -1.675 0.953 1.741 ETKDGv3 26
#