data_96B
#
_chem_comp.id 96B
_chem_comp.name (2R)-2-phenylpyrrolidine
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H13 N"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-03-04
_chem_comp.pdbx_modified_date 2016-04-01
_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 147.217
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 96B
_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 4YJH
_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
96B N N1 N 0 1 N N N N N N -22.727 -14.635 10.821 -1.644 0.447 -1.101 N 96B 1
96B C3 C1 C 0 1 N N N N N N -22.299 -15.955 10.302 -2.730 0.934 -0.225 C3 96B 2
96B C C2 C 0 1 N N N N N N -23.562 -16.803 10.126 -3.057 -0.264 0.702 C 96B 3
96B C1 C3 C 0 1 N N N N N N -24.743 -15.904 10.500 -1.648 -0.868 0.942 C1 96B 4
96B C2 C4 C 0 1 N N R N N N -24.096 -14.832 11.352 -0.943 -0.652 -0.414 C2 96B 5
96B C4 C5 C 0 1 Y N N N N N -24.885 -13.600 11.584 0.500 -0.278 -0.188 C4 96B 6
96B C9 C6 C 0 1 Y N N N N N -24.245 -12.377 11.796 0.830 1.016 0.168 C9 96B 7
96B C5 C7 C 0 1 Y N N N N N -26.266 -13.680 11.733 1.491 -1.231 -0.330 C5 96B 8
96B C6 C8 C 0 1 Y N N N N N -27.007 -12.539 12.025 2.814 -0.888 -0.123 C6 96B 9
96B C7 C9 C 0 1 Y N N N N N -26.369 -11.318 12.203 3.145 0.408 0.227 C7 96B 10
96B C8 C10 C 0 1 Y N N N N N -24.985 -11.234 12.088 2.153 1.359 0.375 C8 96B 11
96B H1 H1 H 0 1 N N N N N N -22.112 -14.331 11.549 -2.007 0.143 -1.992 H1 96B 12
96B H3 H3 H 0 1 N N N N N N -21.617 -16.438 11.017 -2.391 1.787 0.363 H3 96B 13
96B H4 H4 H 0 1 N N N N N N -21.789 -15.833 9.335 -3.604 1.206 -0.817 H4 96B 14
96B H5 H5 H 0 1 N N N N N N -23.654 -17.136 9.082 -3.500 0.076 1.638 H5 96B 15
96B H6 H6 H 0 1 N N N N N N -23.527 -17.680 10.789 -3.709 -0.979 0.201 H6 96B 16
96B H7 H7 H 0 1 N N N N N N -25.209 -15.469 9.603 -1.129 -0.332 1.736 H7 96B 17
96B H8 H8 H 0 1 N N N N N N -25.499 -16.462 11.072 -1.719 -1.930 1.175 H8 96B 18
96B H9 H9 H 0 1 N N N N N N -23.965 -15.290 12.343 -1.003 -1.562 -1.012 H9 96B 19
96B H10 H10 H 0 1 N N N N N N -23.168 -12.317 11.733 0.055 1.759 0.283 H10 96B 20
96B H11 H11 H 0 1 N N N N N N -26.765 -14.631 11.622 1.232 -2.243 -0.604 H11 96B 21
96B H12 H12 H 0 1 N N N N N N -28.081 -12.603 12.114 3.589 -1.632 -0.234 H12 96B 22
96B H13 H13 H 0 1 N N N N N N -26.947 -10.434 12.431 4.179 0.676 0.389 H13 96B 23
96B H14 H14 H 0 1 N N N N N N -24.486 -10.286 12.225 2.412 2.370 0.653 H14 96B 24
#
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
96B C C3 SING N N 1
96B C C1 SING N N 2
96B C3 N SING N N 3
96B C1 C2 SING N N 4
96B N C2 SING N N 5
96B C2 C4 SING N N 6
96B C4 C5 DOUB Y N 7
96B C4 C9 SING Y N 8
96B C5 C6 SING Y N 9
96B C9 C8 DOUB Y N 10
96B C6 C7 DOUB Y N 11
96B C8 C7 SING Y N 12
96B N H1 SING N N 13
96B C3 H3 SING N N 14
96B C3 H4 SING N N 15
96B C H5 SING N N 16
96B C H6 SING N N 17
96B C1 H7 SING N N 18
96B C1 H8 SING N N 19
96B C2 H9 SING N N 20
96B C9 H10 SING N N 21
96B C5 H11 SING N N 22
96B C6 H12 SING N N 23
96B C7 H13 SING N N 24
96B C8 H14 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
96B SMILES ACDLabs 12.01 N1C(CCC1)c2ccccc2
96B InChI InChI 1.03 InChI=1S/C10H13N/c1-2-5-9(6-3-1)10-7-4-8-11-10/h1-3,5-6,10-11H,4,7-8H2/t10-/m1/s1
96B InChIKey InChI 1.03 JUTDHSGANMHVIC-SNVBAGLBSA-N
96B SMILES_CANONICAL CACTVS 3.385 C1CN[C@H](C1)c2ccccc2
96B SMILES CACTVS 3.385 C1CN[CH](C1)c2ccccc2
96B SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 c1ccc(cc1)[C@H]2CCCN2
96B SMILES "OpenEye OEToolkits" 1.9.2 c1ccc(cc1)C2CCCN2
#
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
96B "SYSTEMATIC NAME" ACDLabs 12.01 (2R)-2-phenylpyrrolidine
96B "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 (2R)-2-phenylpyrrolidine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
96B 'Create component' 2015-03-04 RCSB
96B 'Initial release' 2016-04-06 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
96B N N 3.884 1.978 1
96B C3 C 4.348 3.404 2
96B C C 5.848 3.404 3
96B C1 C 6.312 1.978 4
96B C2 C 5.098 1.096 5
96B C4 C 5.098 -0.404 6
96B C9 C 6.397 -1.154 7
96B C5 C 3.799 -1.154 8
96B C6 C 3.799 -2.654 9
96B C7 C 5.098 -3.404 10
96B C8 C 6.397 -2.654 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
96B C C3 SINGLE NONE 1
96B C C1 SINGLE NONE 2
96B C3 N SINGLE NONE 3
96B C1 C2 SINGLE NONE 4
96B N C2 SINGLE NONE 5
96B C2 C4 SINGLE BEGINDASH 6
96B C4 C5 SINGLE NONE 7
96B C4 C9 DOUBLE NONE 8
96B C5 C6 DOUBLE NONE 9
96B C9 C8 SINGLE NONE 10
96B C6 C7 SINGLE NONE 11
96B C8 C7 DOUBLE NONE 12
#
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
96B MurckoScaffold S1 scaffold 'c1ccc([C@H]2CCCN2)cc1' InChI=1S/C10H13N/c1-2-5-9(6-3-1)10-7-4-8-11-10/h1-3,5-6,10-11H,4,7-8H2/t10-/m1/s1 JUTDHSGANMHVIC-SNVBAGLBSA-N
96B phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-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
96B N S1 1
96B C3 S1 1
96B C S1 1
96B C1 S1 1
96B C2 S1 1
96B C4 S1 1
96B C9 S1 1
96B C5 S1 1
96B C6 S1 1
96B C7 S1 1
96B C8 S1 1
96B C4 F1 1
96B C5 F1 1
96B C6 F1 1
96B C7 F1 1
96B C8 F1 1
96B C9 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 96B
_pdbe_chem_comp_rdkit_properties.exactmw 147.105
_pdbe_chem_comp_rdkit_properties.amw 147.221
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 1
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 1
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 1
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.400
_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 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 85.758
_pdbe_chem_comp_rdkit_properties.tpsa 12.030
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.056
_pdbe_chem_comp_rdkit_properties.CrippenMR 46.154
_pdbe_chem_comp_rdkit_properties.chi0v 5.447
_pdbe_chem_comp_rdkit_properties.chi1v 2.947
_pdbe_chem_comp_rdkit_properties.chi2v 1.141
_pdbe_chem_comp_rdkit_properties.chi3v 1.141
_pdbe_chem_comp_rdkit_properties.chi4v 0.686
_pdbe_chem_comp_rdkit_properties.chi0n 18.447
_pdbe_chem_comp_rdkit_properties.chi1n 9.394
_pdbe_chem_comp_rdkit_properties.chi2n 1.141
_pdbe_chem_comp_rdkit_properties.chi3n 1.141
_pdbe_chem_comp_rdkit_properties.chi4n 0.686
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.820
_pdbe_chem_comp_rdkit_properties.kappa1 1.467
_pdbe_chem_comp_rdkit_properties.kappa2 3.055
_pdbe_chem_comp_rdkit_properties.kappa3 1.432
_pdbe_chem_comp_rdkit_properties.Phi 0.407
#
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
96B UniChem PDBe 96B
96B UniChem ZINC ZINC000001444851
96B UniChem eMolecules 36492306
96B UniChem SureChEMBL SCHEMBL167264
96B UniChem 'PubChem TPHARMA' 15946623
96B UniChem ACTor 1006-64-0
96B UniChem Nikkaji J574.146G
96B UniChem 'EPA CompTox Dashboard' DTXSID40364077
96B UniChem ChemicalBook CB8875433
96B UniChem PubChem 1520807
96B UniChem Mcule MCULE-5080918126
#
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
96B N 1.405 1.230 -0.233 ETKDGv3 1
96B C3 2.809 0.816 -0.256 ETKDGv3 2
96B C 2.863 -0.695 -0.052 ETKDGv3 3
96B C1 1.427 -1.121 0.177 ETKDGv3 4
96B C2 0.699 0.178 0.505 ETKDGv3 5
96B C4 -0.795 0.151 0.202 ETKDGv3 6
96B C9 -1.469 1.301 -0.013 ETKDGv3 7
96B C5 -1.570 -1.119 0.292 ETKDGv3 8
96B C6 -2.895 -1.124 0.095 ETKDGv3 9
96B C7 -3.605 0.135 -0.195 ETKDGv3 10
96B C8 -2.929 1.287 -0.241 ETKDGv3 11
96B H1 1.067 1.224 -1.226 ETKDGv3 12
96B H3 3.288 1.101 -1.220 ETKDGv3 13
96B H4 3.351 1.330 0.566 ETKDGv3 14
96B H5 3.485 -0.940 0.837 ETKDGv3 15
96B H6 3.287 -1.204 -0.946 ETKDGv3 16
96B H7 1.350 -1.855 1.008 ETKDGv3 17
96B H8 1.026 -1.566 -0.761 ETKDGv3 18
96B H9 0.814 0.380 1.594 ETKDGv3 19
96B H10 -0.958 2.255 -0.018 ETKDGv3 20
96B H11 -1.076 -2.053 0.526 ETKDGv3 21
96B H12 -3.450 -2.051 0.159 ETKDGv3 22
96B H13 -4.675 0.125 -0.359 ETKDGv3 23
96B H14 -3.450 2.215 -0.441 ETKDGv3 24
#