data_QME
#
_chem_comp.id QME
_chem_comp.name 2-[(2~{R})-piperidin-2-yl]-1~{H}-indole
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H16 N2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-06-30
_chem_comp.pdbx_modified_date 2020-08-14
_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 200.280
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code QME
_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 6ZLI
_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
QME C5 C1 C 0 1 N N N N N N -1.984 -17.747 28.307 -2.270 -0.147 1.255 C5 QME 1
QME C7 C2 C 0 1 Y N N N N N -5.463 -17.547 25.303 2.040 -0.756 -0.090 C7 QME 2
QME C8 C3 C 0 1 Y N N N N N -4.542 -16.632 24.755 1.827 0.626 0.066 C8 QME 3
QME C10 C4 C 0 1 N N N N N N -2.669 -15.516 30.062 -3.704 0.143 -1.245 C10 QME 4
QME C13 C5 C 0 1 N N N N N N -1.416 -16.358 30.331 -4.354 0.558 0.077 C13 QME 5
QME C15 C6 C 0 1 Y N N N N N -5.719 -16.773 22.685 4.198 0.958 0.128 C15 QME 6
QME C1 C7 C 0 1 Y N N N N N -3.953 -17.005 26.888 -0.184 -0.368 -0.067 C1 QME 7
QME C11 C8 C 0 1 Y N N N N N -6.504 -18.056 24.528 3.341 -1.259 -0.140 C11 QME 8
QME C12 C9 C 0 1 Y N N N N N -4.687 -16.252 23.425 2.922 1.476 0.175 C12 QME 9
QME C14 C10 C 0 1 Y N N N N N -6.634 -17.653 23.236 4.403 -0.406 -0.030 C14 QME 10
QME C2 C11 C 0 1 N N R N N N -3.258 -16.916 28.219 -1.680 -0.542 -0.101 C2 QME 11
QME C3 C12 C 0 1 Y N N N N N -5.053 -17.745 26.691 0.710 -1.364 -0.172 C3 QME 12
QME C9 C13 C 0 1 N N N N N N -1.575 -17.784 29.785 -3.793 -0.306 1.210 C9 QME 13
QME N4 N1 N 0 1 Y N N N N N -3.628 -16.318 25.745 0.465 0.828 0.076 N4 QME 14
QME N6 N2 N 0 1 N N N N N N -2.987 -15.539 28.626 -2.249 0.314 -1.151 N6 QME 15
QME H1 H1 H 0 1 N N N N N N -2.172 -18.767 27.941 -1.860 -0.792 2.032 H1 QME 16
QME H2 H2 H 0 1 N N N N N N -1.188 -17.283 27.706 -2.019 0.891 1.474 H2 QME 17
QME H3 H3 H 0 1 N N N N N N -2.487 -14.479 30.379 -3.934 -0.902 -1.451 H3 QME 18
QME H4 H4 H 0 1 N N N N N N -3.515 -15.929 30.630 -4.091 0.766 -2.051 H4 QME 19
QME H5 H5 H 0 1 N N N N N N -1.243 -16.407 31.416 -4.136 1.607 0.276 H5 QME 20
QME H6 H6 H 0 1 N N N N N N -0.553 -15.882 29.843 -5.433 0.417 0.012 H6 QME 21
QME H7 H7 H 0 1 N N N N N N -5.819 -16.489 21.648 5.048 1.620 0.213 H7 QME 22
QME H8 H8 H 0 1 N N N N N N -7.201 -18.764 24.950 3.509 -2.319 -0.265 H8 QME 23
QME H9 H9 H 0 1 N N N N N N -3.994 -15.554 22.979 2.773 2.538 0.298 H9 QME 24
QME H10 H10 H 0 1 N N N N N N -7.454 -18.021 22.638 5.410 -0.796 -0.065 H10 QME 25
QME H11 H11 H 0 1 N N N N N N -3.952 -17.338 28.961 -1.921 -1.584 -0.312 H11 QME 26
QME H12 H12 H 0 1 N N N N N N -5.544 -18.371 27.422 0.490 -2.414 -0.295 H12 QME 27
QME H13 H13 H 0 1 N N N N N N -2.350 -18.309 30.363 -4.045 -1.351 1.030 H13 QME 28
QME H14 H14 H 0 1 N N N N N N -0.619 -18.319 29.883 -4.221 0.015 2.159 H14 QME 29
QME H15 H15 H 0 1 N N N N N N -2.855 -15.691 25.644 0.031 1.690 0.171 H15 QME 30
QME H16 H16 H 0 1 N N N N N N -2.211 -15.182 28.105 -2.007 1.281 -0.999 H16 QME 31
#
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
QME C15 C14 DOUB Y N 1
QME C15 C12 SING Y N 2
QME C14 C11 SING Y N 3
QME C12 C8 DOUB Y N 4
QME C11 C7 DOUB Y N 5
QME C8 C7 SING Y N 6
QME C8 N4 SING Y N 7
QME C7 C3 SING Y N 8
QME N4 C1 SING Y N 9
QME C3 C1 DOUB Y N 10
QME C1 C2 SING N N 11
QME C2 C5 SING N N 12
QME C2 N6 SING N N 13
QME C5 C9 SING N N 14
QME N6 C10 SING N N 15
QME C9 C13 SING N N 16
QME C10 C13 SING N N 17
QME C5 H1 SING N N 18
QME C5 H2 SING N N 19
QME C10 H3 SING N N 20
QME C10 H4 SING N N 21
QME C13 H5 SING N N 22
QME C13 H6 SING N N 23
QME C15 H7 SING N N 24
QME C11 H8 SING N N 25
QME C12 H9 SING N N 26
QME C14 H10 SING N N 27
QME C2 H11 SING N N 28
QME C3 H12 SING N N 29
QME C9 H13 SING N N 30
QME C9 H14 SING N N 31
QME N4 H15 SING N N 32
QME N6 H16 SING N N 33
#
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
QME InChI InChI 1.03 InChI=1S/C13H16N2/c1-2-6-11-10(5-1)9-13(15-11)12-7-3-4-8-14-12/h1-2,5-6,9,12,14-15H,3-4,7-8H2/t12-/m1/s1
QME InChIKey InChI 1.03 BNKHEDZUOBHGMW-GFCCVEGCSA-N
QME SMILES_CANONICAL CACTVS 3.385 C1CC[C@@H](NC1)c2[nH]c3ccccc3c2
QME SMILES CACTVS 3.385 C1CC[CH](NC1)c2[nH]c3ccccc3c2
QME SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1ccc2c(c1)cc([nH]2)[C@H]3CCCCN3
QME SMILES "OpenEye OEToolkits" 2.0.7 c1ccc2c(c1)cc([nH]2)C3CCCCN3
#
_pdbx_chem_comp_identifier.comp_id QME
_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-[(2~{R})-piperidin-2-yl]-1~{H}-indole
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
QME 'Create component' 2020-06-30 PDBE
QME 'Initial release' 2020-08-19 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
QME C5 C 10.143 -0.997 1
QME C7 C 5.598 1.052 2
QME C8 C 5.598 -0.448 3
QME C10 C 11.643 1.601 4
QME C13 C 12.393 0.302 5
QME C15 C 3.000 -0.448 6
QME C1 C 7.893 0.302 7
QME C11 C 4.299 1.802 8
QME C12 C 4.299 -1.198 9
QME C14 C 3.000 1.052 10
QME C2 C 9.393 0.302 11
QME C3 C 7.018 1.509 12
QME C9 C 11.643 -0.997 13
QME N4 N 7.018 -0.905 14
QME N6 N 10.143 1.601 15
#
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
QME C15 C14 DOUBLE NONE 1
QME C15 C12 SINGLE NONE 2
QME C14 C11 SINGLE NONE 3
QME C12 C8 DOUBLE NONE 4
QME C11 C7 DOUBLE NONE 5
QME C8 C7 SINGLE NONE 6
QME C8 N4 SINGLE NONE 7
QME C7 C3 SINGLE NONE 8
QME N4 C1 SINGLE NONE 9
QME C3 C1 DOUBLE NONE 10
QME C2 C1 SINGLE BEGINDASH 11
QME C2 C5 SINGLE NONE 12
QME C2 N6 SINGLE NONE 13
QME C5 C9 SINGLE NONE 14
QME N6 C10 SINGLE NONE 15
QME C9 C13 SINGLE NONE 16
QME C10 C13 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
QME MurckoScaffold S1 scaffold 'c1ccc2[nH]c([C@H]3CCCCN3)cc2c1' InChI=1S/C13H16N2/c1-2-6-11-10(5-1)9-13(15-11)12-7-3-4-8-14-12/h1-2,5-6,9,12,14-15H,3-4,7-8H2/t12-/m1/s1 BNKHEDZUOBHGMW-GFCCVEGCSA-N
QME 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
QME phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
QME 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
QME C5 S1 1
QME C7 S1 1
QME C8 S1 1
QME C10 S1 1
QME C13 S1 1
QME C15 S1 1
QME C1 S1 1
QME C11 S1 1
QME C12 S1 1
QME C14 S1 1
QME C2 S1 1
QME C3 S1 1
QME C9 S1 1
QME N4 S1 1
QME N6 S1 1
QME C8 F1 1
QME C7 F1 1
QME C3 F1 1
QME C1 F1 1
QME N4 F1 1
QME C11 F1 1
QME C14 F1 1
QME C15 F1 1
QME C12 F1 1
QME C7 F2 1
QME C11 F2 1
QME C14 F2 1
QME C15 F2 1
QME C12 F2 1
QME C8 F2 1
QME C8 F3 1
QME C7 F3 1
QME C3 F3 1
QME C1 F3 1
QME N4 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id QME
_pdbe_chem_comp_rdkit_properties.exactmw 200.131
_pdbe_chem_comp_rdkit_properties.amw 200.285
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 1
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.385
_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 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 112.287
_pdbe_chem_comp_rdkit_properties.tpsa 27.820
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.499
_pdbe_chem_comp_rdkit_properties.CrippenMR 60.421
_pdbe_chem_comp_rdkit_properties.chi0v 7.394
_pdbe_chem_comp_rdkit_properties.chi1v 4.144
_pdbe_chem_comp_rdkit_properties.chi2v 1.826
_pdbe_chem_comp_rdkit_properties.chi3v 1.826
_pdbe_chem_comp_rdkit_properties.chi4v 1.193
_pdbe_chem_comp_rdkit_properties.chi0n 23.394
_pdbe_chem_comp_rdkit_properties.chi1n 12.039
_pdbe_chem_comp_rdkit_properties.chi2n 1.826
_pdbe_chem_comp_rdkit_properties.chi3n 1.826
_pdbe_chem_comp_rdkit_properties.chi4n 1.193
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.280
_pdbe_chem_comp_rdkit_properties.kappa1 2.206
_pdbe_chem_comp_rdkit_properties.kappa2 3.704
_pdbe_chem_comp_rdkit_properties.kappa3 1.655
_pdbe_chem_comp_rdkit_properties.Phi 0.545
#
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
QME UniChem PDBe QME
QME UniChem ZINC ZINC000001703729
QME UniChem PubChem 36690643
#
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
QME C5 -1.935 1.354 -0.189 ETKDGv3 1
QME C7 2.417 0.130 0.926 ETKDGv3 2
QME C8 2.173 -0.177 -0.456 ETKDGv3 3
QME C10 -2.572 -1.312 -0.544 ETKDGv3 4
QME C13 -3.703 -0.323 -0.876 ETKDGv3 5
QME C15 4.551 -0.431 -0.776 ETKDGv3 6
QME C1 0.192 0.212 0.555 ETKDGv3 7
QME C11 3.646 0.157 1.442 ETKDGv3 8
QME C12 3.161 -0.452 -1.309 ETKDGv3 9
QME C14 4.781 -0.143 0.526 ETKDGv3 10
QME C2 -1.299 0.330 0.784 ETKDGv3 11
QME C3 1.110 0.365 1.523 ETKDGv3 12
QME C9 -3.435 1.091 -0.329 ETKDGv3 13
QME N4 0.781 -0.135 -0.711 ETKDGv3 14
QME N6 -1.964 -0.995 0.754 ETKDGv3 15
QME H1 -1.771 2.385 0.193 ETKDGv3 16
QME H2 -1.472 1.293 -1.198 ETKDGv3 17
QME H3 -2.990 -2.342 -0.514 ETKDGv3 18
QME H4 -1.802 -1.292 -1.344 ETKDGv3 19
QME H5 -4.660 -0.696 -0.450 ETKDGv3 20
QME H6 -3.824 -0.278 -1.980 ETKDGv3 21
QME H7 5.381 -0.649 -1.436 ETKDGv3 22
QME H8 3.813 0.388 2.486 ETKDGv3 23
QME H9 2.961 -0.682 -2.347 ETKDGv3 24
QME H10 5.794 -0.130 0.907 ETKDGv3 25
QME H11 -1.457 0.736 1.808 ETKDGv3 26
QME H12 0.909 0.607 2.559 ETKDGv3 27
QME H13 -3.915 1.201 0.668 ETKDGv3 28
QME H14 -3.886 1.847 -1.007 ETKDGv3 29
QME H15 0.302 -0.305 -1.623 ETKDGv3 30
QME H16 -1.287 -1.754 1.005 ETKDGv3 31
#