data_60L
#
_chem_comp.id 60L
_chem_comp.name ~{N}-methyl-1-(3-thiophen-2-ylphenyl)methanamine
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H13 N S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2016-01-10
_chem_comp.pdbx_modified_date 2017-12-22
_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 203.303
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 60L
_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 5HEF
_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
60L S8 S1 S 0 1 Y N N N N N 18.029 -11.424 5.707 -2.214 -1.531 0.189 S8 60L 1
60L C14 C1 C 0 1 N N N N N N 21.019 -5.973 1.132 4.797 -1.855 -0.396 C14 60L 2
60L N13 N1 N 0 1 N N N N N N 20.892 -7.429 1.465 3.645 -0.973 -0.626 N13 60L 3
60L C12 C2 C 0 1 N N N N N N 19.555 -7.718 1.891 3.101 -0.475 0.644 C12 60L 4
60L C2 C3 C 0 1 Y N N N N N 19.099 -9.132 1.842 1.924 0.424 0.368 C2 60L 5
60L C3 C4 C 0 1 Y N N N N N 19.040 -9.753 0.635 2.121 1.781 0.180 C3 60L 6
60L C4 C5 C 0 1 Y N N N N N 18.619 -11.085 0.558 1.046 2.614 -0.074 C4 60L 7
60L C5 C6 C 0 1 Y N N N N N 18.266 -11.759 1.708 -0.231 2.095 -0.143 C5 60L 8
60L C6 C7 C 0 1 Y N N N N N 18.314 -11.157 2.907 -0.437 0.728 0.045 C6 60L 9
60L C1 C8 C 0 1 Y N N N N N 18.741 -9.814 2.990 0.653 -0.108 0.297 C1 60L 10
60L C7 C9 C 0 1 Y N N N N N 17.900 -11.951 4.156 -1.802 0.166 -0.026 C7 60L 11
60L C11 C10 C 0 1 Y N N N N N 17.343 -13.261 4.157 -2.924 0.873 -0.266 C11 60L 12
60L C10 C11 C 0 1 Y N N N N N 17.071 -13.713 5.592 -4.084 0.127 -0.285 C10 60L 13
60L C9 C12 C 0 1 Y N N N N N 17.466 -12.660 6.525 -3.919 -1.181 -0.063 C9 60L 14
60L H1 H1 H 0 1 N N N N N N 22.048 -5.759 0.806 5.578 -1.304 0.127 H1 60L 15
60L H2 H2 H 0 1 N N N N N N 20.318 -5.720 0.323 4.487 -2.707 0.210 H2 60L 16
60L H3 H3 H 0 1 N N N N N N 20.784 -5.371 2.023 5.181 -2.210 -1.352 H3 60L 17
60L H4 H4 H 0 1 N N N N N N 21.107 -7.974 0.655 3.892 -0.210 -1.238 H4 60L 18
60L H6 H6 H 0 1 N N N N N N 19.463 -7.380 2.934 2.779 -1.317 1.256 H6 60L 19
60L H7 H7 H 0 1 N N N N N N 18.875 -7.132 1.255 3.871 0.086 1.174 H7 60L 20
60L H8 H8 H 0 1 N N N N N N 19.317 -9.220 -0.262 3.118 2.192 0.232 H8 60L 21
60L H9 H9 H 0 1 N N N N N N 18.571 -11.584 -0.399 1.206 3.672 -0.219 H9 60L 22
60L H10 H10 H 0 1 N N N N N N 17.946 -12.788 1.643 -1.070 2.746 -0.341 H10 60L 23
60L H11 H11 H 0 1 N N N N N N 18.788 -9.320 3.949 0.501 -1.167 0.440 H11 60L 24
60L H12 H12 H 0 1 N N N N N N 17.142 -13.849 3.274 -2.915 1.941 -0.430 H12 60L 25
60L H13 H13 H 0 1 N N N N N N 16.650 -14.667 5.874 -5.054 0.567 -0.466 H13 60L 26
60L H14 H14 H 0 1 N N N N N N 17.387 -12.715 7.601 -4.714 -1.912 -0.043 H14 60L 27
#
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
60L C4 C3 DOUB Y N 1
60L C4 C5 SING Y N 2
60L C3 C2 SING Y N 3
60L C14 N13 SING N N 4
60L N13 C12 SING N N 5
60L C5 C6 DOUB Y N 6
60L C2 C12 SING N N 7
60L C2 C1 DOUB Y N 8
60L C6 C1 SING Y N 9
60L C6 C7 SING N N 10
60L C7 C11 DOUB Y N 11
60L C7 S8 SING Y N 12
60L C11 C10 SING Y N 13
60L C10 C9 DOUB Y N 14
60L S8 C9 SING Y N 15
60L C14 H1 SING N N 16
60L C14 H2 SING N N 17
60L C14 H3 SING N N 18
60L N13 H4 SING N N 19
60L C12 H6 SING N N 20
60L C12 H7 SING N N 21
60L C3 H8 SING N N 22
60L C4 H9 SING N N 23
60L C5 H10 SING N N 24
60L C1 H11 SING N N 25
60L C11 H12 SING N N 26
60L C10 H13 SING N N 27
60L C9 H14 SING N N 28
#
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
60L InChI InChI 1.03 InChI=1S/C12H13NS/c1-13-9-10-4-2-5-11(8-10)12-6-3-7-14-12/h2-8,13H,9H2,1H3
60L InChIKey InChI 1.03 BIULJOFRQMLCQK-UHFFFAOYSA-N
60L SMILES_CANONICAL CACTVS 3.385 CNCc1cccc(c1)c2sccc2
60L SMILES CACTVS 3.385 CNCc1cccc(c1)c2sccc2
60L SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 CNCc1cccc(c1)c2cccs2
60L SMILES "OpenEye OEToolkits" 2.0.4 CNCc1cccc(c1)c2cccs2
#
_pdbx_chem_comp_identifier.comp_id 60L
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.4
_pdbx_chem_comp_identifier.identifier ~{N}-methyl-1-(3-thiophen-2-ylphenyl)methanamine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
60L 'Create component' 2016-01-10 RCSB
60L 'Initial release' 2017-12-27 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
60L S8 S 8.111 3.103 1
60L C14 C 3.000 -4.529 2
60L N13 N 4.299 -3.779 3
60L C12 C 4.299 -2.279 4
60L C2 C 5.598 -1.529 5
60L C3 C 6.897 -2.279 6
60L C4 C 8.196 -1.529 7
60L C5 C 8.196 -0.029 8
60L C6 C 6.897 0.721 9
60L C1 C 5.598 -0.029 10
60L C7 C 6.897 2.221 11
60L C11 C 5.684 3.103 12
60L C10 C 6.147 4.529 13
60L C9 C 7.647 4.529 14
#
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
60L C4 C3 SINGLE NONE 1
60L C4 C5 DOUBLE NONE 2
60L C3 C2 DOUBLE NONE 3
60L C14 N13 SINGLE NONE 4
60L N13 C12 SINGLE NONE 5
60L C5 C6 SINGLE NONE 6
60L C2 C12 SINGLE NONE 7
60L C2 C1 SINGLE NONE 8
60L C6 C1 DOUBLE NONE 9
60L C6 C7 SINGLE NONE 10
60L C7 C11 DOUBLE NONE 11
60L C7 S8 SINGLE NONE 12
60L C11 C10 SINGLE NONE 13
60L C10 C9 DOUBLE NONE 14
60L S8 C9 SINGLE NONE 15
#
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
60L MurckoScaffold S1 scaffold c1ccc(-c2cccs2)cc1 InChI=1S/C10H8S/c1-2-5-9(6-3-1)10-7-4-8-11-10/h1-8H PJRGDKFLFAYRBV-UHFFFAOYSA-N
60L phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
60L thiophen F2 fragment c1ccsc1 InChI=1S/C4H4S/c1-2-4-5-3-1/h1-4H YTPLMLYBLZKORZ-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
60L S8 S1 1
60L C2 S1 1
60L C3 S1 1
60L C4 S1 1
60L C5 S1 1
60L C6 S1 1
60L C1 S1 1
60L C7 S1 1
60L C11 S1 1
60L C10 S1 1
60L C9 S1 1
60L C2 F1 1
60L C3 F1 1
60L C4 F1 1
60L C5 F1 1
60L C6 F1 1
60L C1 F1 1
60L C7 F2 1
60L C11 F2 1
60L C10 F2 1
60L C9 F2 1
60L S8 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 60L
_pdbe_chem_comp_rdkit_properties.exactmw 203.077
_pdbe_chem_comp_rdkit_properties.amw 203.310
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 1
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 27
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.167
_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 106.731
_pdbe_chem_comp_rdkit_properties.tpsa 12.030
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.700
_pdbe_chem_comp_rdkit_properties.CrippenMR 60.931
_pdbe_chem_comp_rdkit_properties.chi0v 7.672
_pdbe_chem_comp_rdkit_properties.chi1v 4.422
_pdbe_chem_comp_rdkit_properties.chi2v 2.114
_pdbe_chem_comp_rdkit_properties.chi3v 2.114
_pdbe_chem_comp_rdkit_properties.chi4v 1.377
_pdbe_chem_comp_rdkit_properties.chi0n 19.855
_pdbe_chem_comp_rdkit_properties.chi1n 10.053
_pdbe_chem_comp_rdkit_properties.chi2n 1.400
_pdbe_chem_comp_rdkit_properties.chi3n 1.400
_pdbe_chem_comp_rdkit_properties.chi4n 0.867
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.120
_pdbe_chem_comp_rdkit_properties.kappa1 2.516
_pdbe_chem_comp_rdkit_properties.kappa2 4.399
_pdbe_chem_comp_rdkit_properties.kappa3 2.029
_pdbe_chem_comp_rdkit_properties.Phi 0.790
#
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
60L UniChem ZINC ZINC000012370292
60L UniChem eMolecules 5849614
60L UniChem PubChem 18525772
60L UniChem BindingDb 50158370
60L UniChem 'EPA CompTox Dashboard' DTXSID00594530
#
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
60L S8 4.035 -0.048 -1.244 ETKDGv3 1
60L C14 -3.972 0.604 1.792 ETKDGv3 2
60L N13 -2.926 0.627 0.768 ETKDGv3 3
60L C12 -2.358 -0.714 0.592 ETKDGv3 4
60L C2 -1.208 -0.653 -0.376 ETKDGv3 5
60L C3 -1.404 -0.869 -1.687 ETKDGv3 6
60L C4 -0.275 -0.772 -2.631 ETKDGv3 7
60L C5 0.946 -0.450 -2.190 ETKDGv3 8
60L C6 1.182 -0.180 -0.747 ETKDGv3 9
60L C1 0.144 -0.283 0.110 ETKDGv3 10
60L C7 2.548 0.179 -0.286 ETKDGv3 11
60L C11 2.874 0.738 0.887 ETKDGv3 12
60L C10 4.322 0.994 1.059 ETKDGv3 13
60L C9 5.074 0.635 0.023 ETKDGv3 14
60L H1 -4.408 1.621 1.894 ETKDGv3 15
60L H2 -3.543 0.315 2.776 ETKDGv3 16
60L H3 -4.785 -0.102 1.514 ETKDGv3 17
60L H4 -3.377 0.910 -0.134 ETKDGv3 18
60L H6 -3.136 -1.422 0.225 ETKDGv3 19
60L H7 -1.983 -1.102 1.566 ETKDGv3 20
60L H8 -2.388 -1.115 -2.067 ETKDGv3 21
60L H9 -0.440 -0.959 -3.684 ETKDGv3 22
60L H10 1.757 -0.377 -2.902 ETKDGv3 23
60L H11 0.278 -0.116 1.170 ETKDGv3 24
60L H12 2.157 1.009 1.648 ETKDGv3 25
60L H13 4.737 1.441 1.953 ETKDGv3 26
60L H14 6.149 0.749 -0.029 ETKDGv3 27
#