data_D0I # _chem_comp.id D0I _chem_comp.name "[(3~{R})-3-phenyl-1-(phenylmethyl)pyrrolidin-3-yl]methanol" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H21 N O" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-04-06 _chem_comp.pdbx_modified_date 2023-01-13 _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 267.365 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D0I _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 7XEF _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 D0I N N1 N 0 1 N N N N N N 17.067 8.350 12.240 -0.922 -0.197 0.376 N D0I 1 D0I C C1 C 0 1 N N N N N N 20.269 9.576 12.451 1.648 -2.152 0.128 C D0I 2 D0I O O1 O 0 1 N N N N N N 20.642 10.216 13.637 2.564 -2.595 -0.877 O D0I 3 D0I C1 C2 C 0 1 N N R N N N 18.807 9.975 12.119 1.395 -0.653 -0.038 C1 D0I 4 D0I C10 C3 C 0 1 N N N N N N 16.038 8.055 12.690 -1.878 0.686 1.057 C10 D0I 5 D0I C11 C4 C 0 1 Y N N N N N 15.075 9.209 13.121 -3.264 0.434 0.520 C11 D0I 6 D0I C12 C5 C 0 1 Y N N N N N 14.916 9.514 14.486 -4.073 -0.517 1.113 C12 D0I 7 D0I C13 C6 C 0 1 Y N N N N N 14.043 10.533 14.892 -5.344 -0.748 0.621 C13 D0I 8 D0I C14 C7 C 0 1 Y N N N N N 13.316 11.245 13.943 -5.806 -0.028 -0.465 C14 D0I 9 D0I C15 C8 C 0 1 Y N N N N N 13.461 10.941 12.586 -4.996 0.923 -1.059 C15 D0I 10 D0I C16 C9 C 0 1 Y N N N N N 14.331 9.921 12.183 -3.728 1.158 -0.563 C16 D0I 11 D0I C17 C10 C 0 1 N N N N N N 17.962 9.417 13.032 0.407 -0.153 1.038 C17 D0I 12 D0I C2 C11 C 0 1 Y N N N N N 18.669 11.624 12.104 2.693 0.109 0.049 C2 D0I 13 D0I C3 C12 C 0 1 Y N N N N N 18.923 12.341 10.940 2.714 1.468 -0.205 C3 D0I 14 D0I C4 C13 C 0 1 Y N N N N N 18.811 13.733 10.927 3.905 2.166 -0.126 C4 D0I 15 D0I C5 C14 C 0 1 Y N N N N N 18.451 14.416 12.086 5.073 1.506 0.207 C5 D0I 16 D0I C6 C15 C 0 1 Y N N N N N 18.209 13.711 13.250 5.051 0.148 0.461 C6 D0I 17 D0I C7 C16 C 0 1 Y N N N N N 18.319 12.324 13.262 3.860 -0.550 0.387 C7 D0I 18 D0I C8 C17 C 0 1 N N N N N N 18.456 9.374 10.781 0.696 -0.373 -1.384 C8 D0I 19 D0I C9 C18 C 0 1 N N N N N N 17.076 8.637 10.986 -0.656 0.272 -1.008 C9 D0I 20 D0I H2 H2 H 0 1 N N N N N N 20.337 8.486 12.580 0.707 -2.693 0.025 H2 D0I 21 D0I H3 H3 H 0 1 N N N N N N 20.935 9.890 11.634 2.071 -2.343 1.114 H3 D0I 22 D0I H4 H4 H 0 1 N N N N N N 21.536 9.982 13.856 2.771 -3.538 -0.832 H4 D0I 23 D0I H5 H5 H 0 1 N N N N N N 15.511 7.452 11.936 -1.862 0.483 2.128 H5 D0I 24 D0I H6 H6 H 0 1 N N N N N N 16.233 7.440 13.581 -1.603 1.725 0.879 H6 D0I 25 D0I H7 H7 H 0 1 N N N N N N 15.471 8.958 15.227 -3.712 -1.079 1.961 H7 D0I 26 D0I H8 H8 H 0 1 N N N N N N 13.935 10.765 15.941 -5.976 -1.491 1.084 H8 D0I 27 D0I H9 H9 H 0 1 N N N N N N 12.642 12.030 14.254 -6.798 -0.208 -0.850 H9 D0I 28 D0I H10 H10 H 0 1 N N N N N N 12.901 11.494 11.847 -5.357 1.485 -1.908 H10 D0I 29 D0I H11 H11 H 0 1 N N N N N N 14.426 9.684 11.134 -3.095 1.901 -1.026 H11 D0I 30 D0I H12 H12 H 0 1 N N N N N N 18.537 8.915 13.824 0.651 0.867 1.334 H12 D0I 31 D0I H13 H13 H 0 1 N N N N N N 17.322 10.192 13.479 0.423 -0.815 1.905 H13 D0I 32 D0I H14 H14 H 0 1 N N N N N N 19.209 11.818 10.040 1.802 1.984 -0.465 H14 D0I 33 D0I H15 H15 H 0 1 N N N N N N 19.004 14.281 10.016 3.922 3.228 -0.325 H15 D0I 34 D0I H16 H16 H 0 1 N N N N N N 18.361 15.492 12.075 6.003 2.052 0.268 H16 D0I 35 D0I H17 H17 H 0 1 N N N N N N 17.934 14.238 14.152 5.963 -0.368 0.721 H17 D0I 36 D0I H18 H18 H 0 1 N N N N N N 18.132 11.782 14.177 3.842 -1.611 0.589 H18 D0I 37 D0I H19 H19 H 0 1 N N N N N N 19.230 8.657 10.469 1.290 0.317 -1.984 H19 D0I 38 D0I H20 H20 H 0 1 N N N N N N 18.359 10.163 10.021 0.533 -1.304 -1.927 H20 D0I 39 D0I H21 H21 H 0 1 N N N N N N 16.236 9.299 10.729 -1.441 -0.069 -1.683 H21 D0I 40 D0I H22 H22 H 0 1 N N N N N N 17.024 7.724 10.374 -0.578 1.359 -1.033 H22 D0I 41 # 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 D0I C8 C9 SING N N 1 D0I C8 C1 SING N N 2 D0I C4 C3 DOUB Y N 3 D0I C4 C5 SING Y N 4 D0I C3 C2 SING Y N 5 D0I C9 N SING N N 6 D0I C5 C6 DOUB Y N 7 D0I C2 C1 SING N N 8 D0I C2 C7 DOUB Y N 9 D0I C1 C SING N N 10 D0I C1 C17 SING N N 11 D0I C16 C15 DOUB Y N 12 D0I C16 C11 SING Y N 13 D0I N C10 SING N N 14 D0I N C17 SING N N 15 D0I C O SING N N 16 D0I C15 C14 SING Y N 17 D0I C10 C11 SING N N 18 D0I C11 C12 DOUB Y N 19 D0I C6 C7 SING Y N 20 D0I C14 C13 DOUB Y N 21 D0I C12 C13 SING Y N 22 D0I C H2 SING N N 23 D0I C H3 SING N N 24 D0I O H4 SING N N 25 D0I C10 H5 SING N N 26 D0I C10 H6 SING N N 27 D0I C12 H7 SING N N 28 D0I C13 H8 SING N N 29 D0I C14 H9 SING N N 30 D0I C15 H10 SING N N 31 D0I C16 H11 SING N N 32 D0I C17 H12 SING N N 33 D0I C17 H13 SING N N 34 D0I C3 H14 SING N N 35 D0I C4 H15 SING N N 36 D0I C5 H16 SING N N 37 D0I C6 H17 SING N N 38 D0I C7 H18 SING N N 39 D0I C8 H19 SING N N 40 D0I C8 H20 SING N N 41 D0I C9 H21 SING N N 42 D0I C9 H22 SING N N 43 # 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 D0I InChI InChI 1.03 InChI=1S/C18H21NO/c20-15-18(17-9-5-2-6-10-17)11-12-19(14-18)13-16-7-3-1-4-8-16/h1-10,20H,11-15H2/t18-/m1/s1 D0I InChIKey InChI 1.03 SEKWWCPJXPJZKJ-GOSISDBHSA-N D0I SMILES_CANONICAL CACTVS 3.385 OC[C@]1(CCN(Cc2ccccc2)C1)c3ccccc3 D0I SMILES CACTVS 3.385 OC[C]1(CCN(Cc2ccccc2)C1)c3ccccc3 D0I SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1ccc(cc1)CN2CC[C@@](C2)(CO)c3ccccc3 D0I SMILES "OpenEye OEToolkits" 2.0.7 c1ccc(cc1)CN2CCC(C2)(CO)c3ccccc3 # _pdbx_chem_comp_identifier.comp_id D0I _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-phenyl-1-(phenylmethyl)pyrrolidin-3-yl]methanol" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site D0I 'Create component' 2022-04-06 PDBJ D0I 'Initial release' 2023-01-18 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 D0I N N 8.389 0.531 1 D0I C C 4.999 -1.359 2 D0I O O 3.884 -0.356 3 D0I C1 C 6.426 -0.896 4 D0I C10 C 9.816 0.994 5 D0I C11 C 10.128 2.462 6 D0I C12 C 9.013 3.465 7 D0I C13 C 9.325 4.932 8 D0I C14 C 10.752 5.396 9 D0I C15 C 11.866 4.392 10 D0I C16 C 11.554 2.925 11 D0I C17 C 7.926 -0.896 12 D0I C2 C 6.426 -2.396 13 D0I C3 C 5.127 -3.146 14 D0I C4 C 5.127 -4.646 15 D0I C5 C 6.426 -5.396 16 D0I C6 C 7.725 -4.646 17 D0I C7 C 7.725 -3.146 18 D0I C8 C 5.962 0.531 19 D0I C9 C 7.176 1.412 20 # 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 D0I C8 C9 SINGLE NONE 1 D0I C8 C1 SINGLE NONE 2 D0I C4 C3 DOUBLE NONE 3 D0I C4 C5 SINGLE NONE 4 D0I C3 C2 SINGLE NONE 5 D0I C9 N SINGLE NONE 6 D0I C5 C6 DOUBLE NONE 7 D0I C2 C1 SINGLE NONE 8 D0I C2 C7 DOUBLE NONE 9 D0I C1 C SINGLE BEGINWEDGE 10 D0I C1 C17 SINGLE NONE 11 D0I C16 C15 DOUBLE NONE 12 D0I C16 C11 SINGLE NONE 13 D0I N C10 SINGLE NONE 14 D0I N C17 SINGLE NONE 15 D0I C O SINGLE NONE 16 D0I C15 C14 SINGLE NONE 17 D0I C10 C11 SINGLE NONE 18 D0I C11 C12 DOUBLE NONE 19 D0I C6 C7 SINGLE NONE 20 D0I C14 C13 DOUBLE NONE 21 D0I C12 C13 SINGLE NONE 22 # 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 D0I MurckoScaffold S1 scaffold c1ccc(CN2CCC(c3ccccc3)C2)cc1 InChI=1S/C17H19N/c1-3-7-15(8-4-1)13-18-12-11-17(14-18)16-9-5-2-6-10-16/h1-10,17H,11-14H2 XGEZXIRZOJOBFI-UHFFFAOYSA-N D0I 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 D0I N S1 1 D0I C1 S1 1 D0I C10 S1 1 D0I C11 S1 1 D0I C12 S1 1 D0I C13 S1 1 D0I C14 S1 1 D0I C15 S1 1 D0I C16 S1 1 D0I C17 S1 1 D0I C2 S1 1 D0I C3 S1 1 D0I C4 S1 1 D0I C5 S1 1 D0I C6 S1 1 D0I C7 S1 1 D0I C8 S1 1 D0I C9 S1 1 D0I C11 F1 1 D0I C16 F1 1 D0I C15 F1 1 D0I C14 F1 1 D0I C13 F1 1 D0I C12 F1 1 D0I C2 F1 2 D0I C3 F1 2 D0I C4 F1 2 D0I C5 F1 2 D0I C6 F1 2 D0I C7 F1 2 # _pdbe_chem_comp_rdkit_properties.comp_id D0I _pdbe_chem_comp_rdkit_properties.exactmw 267.162 _pdbe_chem_comp_rdkit_properties.amw 267.372 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 2 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 1 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5 _pdbe_chem_comp_rdkit_properties.NumHBD 1 _pdbe_chem_comp_rdkit_properties.NumHBA 2 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20 _pdbe_chem_comp_rdkit_properties.NumAtoms 41 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 0 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.333 _pdbe_chem_comp_rdkit_properties.NumRings 3 _pdbe_chem_comp_rdkit_properties.NumAromaticRings 2 _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 149.817 _pdbe_chem_comp_rdkit_properties.tpsa 23.470 _pdbe_chem_comp_rdkit_properties.CrippenClogP 2.713 _pdbe_chem_comp_rdkit_properties.CrippenMR 81.010 _pdbe_chem_comp_rdkit_properties.chi0v 9.855 _pdbe_chem_comp_rdkit_properties.chi1v 5.375 _pdbe_chem_comp_rdkit_properties.chi2v 2.386 _pdbe_chem_comp_rdkit_properties.chi3v 2.386 _pdbe_chem_comp_rdkit_properties.chi4v 1.492 _pdbe_chem_comp_rdkit_properties.chi0n 30.855 _pdbe_chem_comp_rdkit_properties.chi1n 15.783 _pdbe_chem_comp_rdkit_properties.chi2n 2.386 _pdbe_chem_comp_rdkit_properties.chi3n 2.386 _pdbe_chem_comp_rdkit_properties.chi4n 1.492 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.640 _pdbe_chem_comp_rdkit_properties.kappa1 3.235 _pdbe_chem_comp_rdkit_properties.kappa2 5.777 _pdbe_chem_comp_rdkit_properties.kappa3 2.623 _pdbe_chem_comp_rdkit_properties.Phi 0.934 # _pdbe_chem_comp_external_mappings.comp_id D0I _pdbe_chem_comp_external_mappings.source UniChem _pdbe_chem_comp_external_mappings.resource PDBe _pdbe_chem_comp_external_mappings.resource_id D0I # 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 D0I N 0.786 -0.544 0.069 ETKDGv3 1 D0I C -1.446 1.806 1.203 ETKDGv3 2 D0I O -2.315 2.808 0.740 ETKDGv3 3 D0I C1 -1.385 0.605 0.208 ETKDGv3 4 D0I C10 1.847 0.192 0.791 ETKDGv3 5 D0I C11 3.200 -0.159 0.231 ETKDGv3 6 D0I C12 3.958 0.765 -0.387 ETKDGv3 7 D0I C13 5.279 0.395 -0.939 ETKDGv3 8 D0I C14 5.726 -0.862 -0.827 ETKDGv3 9 D0I C15 4.899 -1.882 -0.151 ETKDGv3 10 D0I C16 3.702 -1.551 0.351 ETKDGv3 11 D0I C17 -0.492 -0.514 0.798 ETKDGv3 12 D0I C2 -2.780 0.024 -0.129 ETKDGv3 13 D0I C3 -2.938 -0.895 -1.300 ETKDGv3 14 D0I C4 -4.119 -1.458 -1.582 ETKDGv3 15 D0I C5 -5.287 -1.196 -0.726 ETKDGv3 16 D0I C6 -5.161 -0.413 0.348 ETKDGv3 17 D0I C7 -3.858 0.203 0.673 ETKDGv3 18 D0I C8 -0.629 1.050 -1.065 ETKDGv3 19 D0I C9 0.505 0.055 -1.242 ETKDGv3 20 D0I H2 -0.430 2.228 1.381 ETKDGv3 21 D0I H3 -1.796 1.466 2.201 ETKDGv3 22 D0I H4 -1.786 3.404 0.150 ETKDGv3 23 D0I H5 1.666 1.290 0.759 ETKDGv3 24 D0I H6 1.861 -0.103 1.863 ETKDGv3 25 D0I H7 3.613 1.786 -0.494 ETKDGv3 26 D0I H8 5.883 1.144 -1.435 ETKDGv3 27 D0I H9 6.692 -1.133 -1.231 ETKDGv3 28 D0I H10 5.263 -2.897 -0.062 ETKDGv3 29 D0I H11 3.100 -2.303 0.845 ETKDGv3 30 D0I H12 -0.354 -0.410 1.899 ETKDGv3 31 D0I H13 -0.967 -1.512 0.667 ETKDGv3 32 D0I H14 -2.095 -1.133 -1.931 ETKDGv3 33 D0I H15 -4.216 -2.119 -2.433 ETKDGv3 34 D0I H16 -6.241 -1.649 -0.961 ETKDGv3 35 D0I H17 -6.016 -0.229 0.987 ETKDGv3 36 D0I H18 -3.814 0.794 1.574 ETKDGv3 37 D0I H19 -1.271 1.095 -1.972 ETKDGv3 38 D0I H20 -0.175 2.059 -0.953 ETKDGv3 39 D0I H21 0.195 -0.752 -1.939 ETKDGv3 40 D0I H22 1.396 0.544 -1.694 ETKDGv3 41 #