data_LVL
#
_chem_comp.id LVL
_chem_comp.name 2-[5-(trifluoromethyl)-1H-indol-3-yl]ethanenitrile
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H7 F3 N2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-07-14
_chem_comp.pdbx_modified_date 2022-10-07
_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 224.182
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code LVL
_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 8AEK
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
LVL C1 C1 C 0 1 Y N N N N N -106.336 -175.758 312.017 1.418 -0.252 -0.021 C1 LVL 1
LVL C2 C2 C 0 1 Y N N N N N -107.274 -176.640 312.553 1.485 -1.585 -0.406 C2 LVL 2
LVL C3 C3 C 0 1 Y N N N N N -108.567 -176.715 312.050 0.345 -2.354 -0.475 C3 LVL 3
LVL C4 C4 C 0 1 Y N N N N N -108.912 -175.868 310.994 -0.888 -1.793 -0.156 C4 LVL 4
LVL C5 C5 C 0 1 Y N N N N N -109.937 -174.751 309.351 -3.039 -1.299 0.264 C5 LVL 5
LVL C6 C6 C 0 1 Y N N N N N -108.669 -174.248 309.394 -2.364 -0.162 0.494 C6 LVL 6
LVL C7 C7 C 0 1 N N N N N N -108.071 -173.245 308.478 -2.949 1.153 0.940 C7 LVL 7
LVL C8 C8 C 0 1 N N N N N N -107.066 -173.890 307.645 -3.204 2.001 -0.236 C8 LVL 8
LVL N1 N1 N 0 1 N N N N N N -106.253 -174.448 307.072 -3.400 2.656 -1.143 N1 LVL 9
LVL N N2 N 0 1 Y N N N N N -110.089 -175.733 310.299 -2.174 -2.284 -0.127 N LVL 10
LVL C C9 C 0 1 N N N N N N -104.951 -175.682 312.579 2.678 0.571 0.046 C LVL 11
LVL C9 C10 C 0 1 Y N N N N N -107.991 -174.953 310.447 -0.951 -0.443 0.234 C9 LVL 12
LVL C10 C11 C 0 1 Y N N N N N -106.698 -174.916 310.965 0.217 0.320 0.291 C10 LVL 13
LVL F F1 F 0 1 N N N N N N -104.754 -176.472 313.624 2.859 1.041 1.351 F LVL 14
LVL F1 F2 F 0 1 N N N N N N -104.655 -174.483 313.008 3.772 -0.221 -0.320 F1 LVL 15
LVL F2 F3 F 0 1 N N N N N N -104.013 -175.993 311.683 2.574 1.656 -0.830 F2 LVL 16
LVL H1 H1 H 0 1 N N N N N N -106.989 -177.278 313.376 2.441 -2.022 -0.655 H1 LVL 17
LVL H2 H2 H 0 1 N N N N N N -109.285 -177.408 312.463 0.407 -3.390 -0.775 H2 LVL 18
LVL H3 H3 H 0 1 N N N N N N -110.709 -174.424 308.670 -4.108 -1.418 0.369 H3 LVL 19
LVL H4 H4 H 0 1 N N N N N N -107.600 -172.444 309.067 -3.886 0.974 1.468 H4 LVL 20
LVL H5 H5 H 0 1 N N N N N N -108.857 -172.816 307.839 -2.248 1.656 1.606 H5 LVL 21
LVL H6 H6 H 0 1 N N N N N N -110.922 -176.264 310.458 -2.429 -3.193 -0.350 H6 LVL 22
LVL H7 H7 H 0 1 N N N N N N -105.972 -174.232 310.550 0.172 1.359 0.582 H7 LVL 23
#
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
LVL N1 C8 TRIP N N 1
LVL C8 C7 SING N N 2
LVL C7 C6 SING N N 3
LVL C5 C6 DOUB Y N 4
LVL C5 N SING Y N 5
LVL C6 C9 SING Y N 6
LVL N C4 SING Y N 7
LVL C9 C10 SING Y N 8
LVL C9 C4 DOUB Y N 9
LVL C10 C1 DOUB Y N 10
LVL C4 C3 SING Y N 11
LVL F2 C SING N N 12
LVL C1 C2 SING Y N 13
LVL C1 C SING N N 14
LVL C3 C2 DOUB Y N 15
LVL C F1 SING N N 16
LVL C F SING N N 17
LVL C2 H1 SING N N 18
LVL C3 H2 SING N N 19
LVL C5 H3 SING N N 20
LVL C7 H4 SING N N 21
LVL C7 H5 SING N N 22
LVL N H6 SING N N 23
LVL C10 H7 SING N N 24
#
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
LVL InChI InChI 1.06 InChI=1S/C11H7F3N2/c12-11(13,14)8-1-2-10-9(5-8)7(3-4-15)6-16-10/h1-2,5-6,16H,3H2
LVL InChIKey InChI 1.06 RLNKXFUKNFUIHO-UHFFFAOYSA-N
LVL SMILES_CANONICAL CACTVS 3.385 "FC(F)(F)c1ccc2[nH]cc(CC#N)c2c1"
LVL SMILES CACTVS 3.385 "FC(F)(F)c1ccc2[nH]cc(CC#N)c2c1"
LVL SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc2c(cc1C(F)(F)F)c(c[nH]2)CC#N"
LVL SMILES "OpenEye OEToolkits" 2.0.7 "c1cc2c(cc1C(F)(F)F)c(c[nH]2)CC#N"
#
_pdbx_chem_comp_identifier.comp_id LVL
_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 2-[5-(trifluoromethyl)-1~{H}-indol-3-yl]ethanenitrile
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
LVL 'Create component' 2022-07-14 PDBE
LVL 'Modify descriptor' 2022-08-22 RCSB
LVL 'Initial release' 2022-10-12 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 '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
LVL C1 C 5.598 0.170 1
LVL C2 C 5.598 -1.330 2
LVL C3 C 6.897 -2.080 3
LVL C4 C 8.196 -1.330 4
LVL C5 C 10.491 -0.580 5
LVL C6 C 9.616 0.627 6
LVL C7 C 10.082 2.053 7
LVL C8 C 11.549 2.362 8
LVL N1 N 13.017 2.671 9
LVL N N 9.616 -1.787 10
LVL C C 4.299 0.920 11
LVL C9 C 8.196 0.170 12
LVL C10 C 6.897 0.920 13
LVL F F 5.049 2.219 14
LVL F1 F 3.549 -0.379 15
LVL F2 F 3.000 1.670 16
#
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
LVL N1 C8 TRIPLE NONE 1
LVL C8 C7 SINGLE NONE 2
LVL C7 C6 SINGLE NONE 3
LVL C5 C6 DOUBLE NONE 4
LVL C5 N SINGLE NONE 5
LVL C6 C9 SINGLE NONE 6
LVL N C4 SINGLE NONE 7
LVL C9 C10 SINGLE NONE 8
LVL C9 C4 DOUBLE NONE 9
LVL C10 C1 DOUBLE NONE 10
LVL C4 C3 SINGLE NONE 11
LVL F2 C SINGLE NONE 12
LVL C1 C2 SINGLE NONE 13
LVL C1 C SINGLE NONE 14
LVL C3 C2 DOUBLE NONE 15
LVL C F1 SINGLE NONE 16
LVL C F SINGLE NONE 17
#
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
LVL MurckoScaffold S1 scaffold 'c1ccc2[nH]ccc2c1' InChI=1S/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9H SIKJAQJRHWYJAI-UHFFFAOYSA-N
LVL indole F1 fragment 'c1ccc2[nH]ccc2c1' InChI=1S/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9H SIKJAQJRHWYJAI-UHFFFAOYSA-N
LVL phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
LVL pyrrole F3 fragment 'c1cc[nH]c1' InChI=1S/C4H5N/c1-2-4-5-3-1/h1-5H KAESVJOAVNADME-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
LVL C1 S1 1
LVL C2 S1 1
LVL C3 S1 1
LVL C4 S1 1
LVL C5 S1 1
LVL C6 S1 1
LVL N S1 1
LVL C9 S1 1
LVL C10 S1 1
LVL C4 F1 1
LVL C9 F1 1
LVL C6 F1 1
LVL C5 F1 1
LVL N F1 1
LVL C10 F1 1
LVL C1 F1 1
LVL C2 F1 1
LVL C3 F1 1
LVL C1 F2 1
LVL C10 F2 1
LVL C9 F2 1
LVL C4 F2 1
LVL C3 F2 1
LVL C2 F2 1
LVL C4 F3 1
LVL C9 F3 1
LVL C6 F3 1
LVL C5 F3 1
LVL N F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id LVL
_pdbe_chem_comp_rdkit_properties.exactmw 224.056
_pdbe_chem_comp_rdkit_properties.amw 224.185
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_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 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 23
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.182
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_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 99.199
_pdbe_chem_comp_rdkit_properties.tpsa 39.580
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.715
_pdbe_chem_comp_rdkit_properties.CrippenMR 49.880
_pdbe_chem_comp_rdkit_properties.chi0v 7.528
_pdbe_chem_comp_rdkit_properties.chi1v 3.988
_pdbe_chem_comp_rdkit_properties.chi2v 1.787
_pdbe_chem_comp_rdkit_properties.chi3v 1.787
_pdbe_chem_comp_rdkit_properties.chi4v 1.120
_pdbe_chem_comp_rdkit_properties.chi0n 14.528
_pdbe_chem_comp_rdkit_properties.chi1n 7.435
_pdbe_chem_comp_rdkit_properties.chi2n 1.787
_pdbe_chem_comp_rdkit_properties.chi3n 1.787
_pdbe_chem_comp_rdkit_properties.chi4n 1.120
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.960
_pdbe_chem_comp_rdkit_properties.kappa1 4.915
_pdbe_chem_comp_rdkit_properties.kappa2 3.561
_pdbe_chem_comp_rdkit_properties.kappa3 1.740
_pdbe_chem_comp_rdkit_properties.Phi 1.094
#
_pdbe_chem_comp_external_mappings.comp_id LVL
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 34175971
#
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
LVL C1 1.993 0.172 0.002 ETKDGv3 1
LVL C2 1.873 1.593 -0.468 ETKDGv3 2
LVL C3 0.670 2.126 -0.746 ETKDGv3 3
LVL C4 -0.520 1.278 -0.591 ETKDGv3 4
LVL C5 -2.606 0.458 -0.497 ETKDGv3 5
LVL C6 -1.776 -0.525 -0.144 ETKDGv3 6
LVL C7 -2.173 -1.890 0.322 ETKDGv3 7
LVL C8 -2.207 -1.927 1.786 ETKDGv3 8
LVL N1 -2.234 -1.956 2.943 ETKDGv3 9
LVL N -1.874 1.643 -0.811 ETKDGv3 10
LVL C 3.349 -0.430 0.264 ETKDGv3 11
LVL C9 -0.424 0.024 -0.199 ETKDGv3 12
LVL C10 0.879 -0.588 0.111 ETKDGv3 13
LVL F 3.297 -1.284 1.352 ETKDGv3 14
LVL F1 4.281 0.557 0.531 ETKDGv3 15
LVL F2 3.755 -1.141 -0.850 ETKDGv3 16
LVL H1 2.759 2.203 -0.589 ETKDGv3 17
LVL H2 0.579 3.151 -1.081 ETKDGv3 18
LVL H3 -3.685 0.385 -0.526 ETKDGv3 19
LVL H4 -1.439 -2.638 -0.045 ETKDGv3 20
LVL H5 -3.175 -2.157 -0.075 ETKDGv3 21
LVL H6 -2.251 2.572 -1.101 ETKDGv3 22
LVL H7 0.930 -1.626 0.414 ETKDGv3 23
#