data_2NJ
#
_chem_comp.id 2NJ
_chem_comp.name (4S)-1-methyl-4-phenyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C16 H16 N2 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2014-04-17
_chem_comp.pdbx_modified_date 2014-09-05
_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 252.311
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 2NJ
_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 4PCI
_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
2NJ O O1 O 0 1 N N N N N N 14.769 4.614 0.096 -2.036 -2.937 -0.406 O 2NJ 1
2NJ C9 C1 C 0 1 N N N N N N 13.769 5.322 0.201 -1.600 -1.805 -0.407 C9 2NJ 2
2NJ N N1 N 0 1 N N N N N N 12.600 4.948 -0.304 -2.416 -0.772 -0.104 N 2NJ 3
2NJ C C2 C 0 1 N N N N N N 12.473 3.717 -1.085 -3.841 -1.016 0.131 C 2NJ 4
2NJ C8 C3 C 0 1 N N N N N N 13.806 6.644 0.932 -0.152 -1.562 -0.741 C8 2NJ 5
2NJ C7 C4 C 0 1 N N S N N N 13.271 6.462 2.353 0.636 -1.247 0.532 C7 2NJ 6
2NJ C10 C5 C 0 1 Y N N N N N 13.321 7.772 3.074 1.959 -0.627 0.161 C10 2NJ 7
2NJ C15 C6 C 0 1 Y N N N N N 12.352 8.763 2.891 3.137 -1.295 0.438 C15 2NJ 8
2NJ C14 C7 C 0 1 Y N N N N N 12.434 9.980 3.574 4.350 -0.726 0.098 C14 2NJ 9
2NJ C13 C8 C 0 1 Y N N N N N 13.491 10.201 4.447 4.385 0.511 -0.518 C13 2NJ 10
2NJ C12 C9 C 0 1 Y N N N N N 14.468 9.227 4.625 3.207 1.178 -0.795 C12 2NJ 11
2NJ C11 C10 C 0 1 Y N N N N N 14.383 8.021 3.936 1.993 0.608 -0.460 C11 2NJ 12
2NJ N1 N2 N 0 1 N N N N N N 11.934 5.875 2.309 -0.122 -0.314 1.367 N1 2NJ 13
2NJ C6 C11 C 0 1 Y N N N N N 11.083 6.059 1.255 -0.771 0.764 0.754 C6 2NJ 14
2NJ C1 C12 C 0 1 Y N N N N N 11.401 5.640 -0.034 -1.910 0.531 -0.010 C1 2NJ 15
2NJ C5 C13 C 0 1 Y N N N N N 9.857 6.683 1.474 -0.279 2.052 0.886 C5 2NJ 16
2NJ C4 C14 C 0 1 Y N N N N N 8.949 6.877 0.435 -0.912 3.100 0.244 C4 2NJ 17
2NJ C3 C15 C 0 1 Y N N N N N 9.270 6.460 -0.848 -2.031 2.866 -0.535 C3 2NJ 18
2NJ C2 C16 C 0 1 Y N N N N N 10.494 5.842 -1.077 -2.533 1.585 -0.656 C2 2NJ 19
2NJ H1 H1 H 0 1 N N N N N N 13.468 3.270 -1.230 -4.384 -0.931 -0.811 H1 2NJ 20
2NJ H2 H2 H 0 1 N N N N N N 11.827 3.007 -0.548 -3.976 -2.017 0.539 H2 2NJ 21
2NJ H3 H3 H 0 1 N N N N N N 12.029 3.948 -2.064 -4.224 -0.280 0.838 H3 2NJ 22
2NJ H4 H4 H 0 1 N N N N N N 14.843 7.009 0.976 0.265 -2.452 -1.213 H4 2NJ 23
2NJ H5 H5 H 0 1 N N N N N N 13.182 7.375 0.397 -0.076 -0.721 -1.430 H5 2NJ 24
2NJ H6 H6 H 0 1 N N N N N N 13.941 5.762 2.873 0.811 -2.169 1.087 H6 2NJ 25
2NJ H7 H7 H 0 1 N N N N N N 11.530 8.586 2.213 3.109 -2.261 0.919 H7 2NJ 26
2NJ H8 H8 H 0 1 N N N N N N 11.682 10.741 3.424 5.271 -1.248 0.315 H8 2NJ 27
2NJ H9 H9 H 0 1 N N N N N N 13.555 11.133 4.990 5.333 0.955 -0.783 H9 2NJ 28
2NJ H10 H10 H 0 1 N N N N N N 15.293 9.407 5.298 3.234 2.145 -1.276 H10 2NJ 29
2NJ H11 H11 H 0 1 N N N N N N 15.149 7.272 4.072 1.073 1.128 -0.679 H11 2NJ 30
2NJ H12 H12 H 0 1 N N N N N N 11.454 6.218 3.116 -0.173 -0.441 2.327 H12 2NJ 31
2NJ H13 H13 H 0 1 N N N N N N 9.605 7.023 2.468 0.598 2.237 1.490 H13 2NJ 32
2NJ H14 H14 H 0 1 N N N N N N 7.998 7.351 0.628 -0.532 4.105 0.351 H14 2NJ 33
2NJ H15 H15 H 0 1 N N N N N N 8.576 6.614 -1.661 -2.515 3.688 -1.042 H15 2NJ 34
2NJ H16 H16 H 0 1 N N N N N N 10.747 5.514 -2.074 -3.406 1.400 -1.265 H16 2NJ 35
#
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
2NJ C N SING N N 1
2NJ C2 C3 DOUB Y N 2
2NJ C2 C1 SING Y N 3
2NJ C3 C4 SING Y N 4
2NJ N C1 SING N N 5
2NJ N C9 SING N N 6
2NJ C1 C6 DOUB Y N 7
2NJ O C9 DOUB N N 8
2NJ C9 C8 SING N N 9
2NJ C4 C5 DOUB Y N 10
2NJ C8 C7 SING N N 11
2NJ C6 C5 SING Y N 12
2NJ C6 N1 SING N N 13
2NJ N1 C7 SING N N 14
2NJ C7 C10 SING N N 15
2NJ C15 C10 DOUB Y N 16
2NJ C15 C14 SING Y N 17
2NJ C10 C11 SING Y N 18
2NJ C14 C13 DOUB Y N 19
2NJ C11 C12 DOUB Y N 20
2NJ C13 C12 SING Y N 21
2NJ C H1 SING N N 22
2NJ C H2 SING N N 23
2NJ C H3 SING N N 24
2NJ C8 H4 SING N N 25
2NJ C8 H5 SING N N 26
2NJ C7 H6 SING N N 27
2NJ C15 H7 SING N N 28
2NJ C14 H8 SING N N 29
2NJ C13 H9 SING N N 30
2NJ C12 H10 SING N N 31
2NJ C11 H11 SING N N 32
2NJ N1 H12 SING N N 33
2NJ C5 H13 SING N N 34
2NJ C4 H14 SING N N 35
2NJ C3 H15 SING N N 36
2NJ C2 H16 SING N N 37
#
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
2NJ SMILES ACDLabs 12.01 O=C3N(c1ccccc1NC(c2ccccc2)C3)C
2NJ InChI InChI 1.03 InChI=1S/C16H16N2O/c1-18-15-10-6-5-9-13(15)17-14(11-16(18)19)12-7-3-2-4-8-12/h2-10,14,17H,11H2,1H3/t14-/m0/s1
2NJ InChIKey InChI 1.03 FHOSJKIPIAZPJP-AWEZNQCLSA-N
2NJ SMILES_CANONICAL CACTVS 3.385 CN1C(=O)C[C@H](Nc2ccccc12)c3ccccc3
2NJ SMILES CACTVS 3.385 CN1C(=O)C[CH](Nc2ccccc12)c3ccccc3
2NJ SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 CN1c2ccccc2N[C@@H](CC1=O)c3ccccc3
2NJ SMILES "OpenEye OEToolkits" 1.9.2 CN1c2ccccc2NC(CC1=O)c3ccccc3
#
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
2NJ "SYSTEMATIC NAME" ACDLabs 12.01 (4S)-1-methyl-4-phenyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one
2NJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 (2S)-5-methyl-2-phenyl-2,3-dihydro-1H-1,5-benzodiazepin-4-one
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
2NJ 'Create component' 2014-04-17 RCSB
2NJ 'Initial release' 2014-05-14 RCSB
2NJ 'Modify descriptor' 2014-09-05 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
2NJ O O 5.418 -3.497 1
2NJ C9 C 6.354 -2.324 2
2NJ N N 7.816 -2.658 3
2NJ C C 8.150 -4.120 4
2NJ C8 C 5.703 -0.973 5
2NJ C7 C 6.354 0.379 6
2NJ C10 C 5.418 1.551 7
2NJ C15 C 5.966 2.948 8
2NJ C14 C 5.031 4.120 9
2NJ C13 C 3.548 3.897 10
2NJ C12 C 3.000 2.501 11
2NJ C11 C 3.935 1.328 12
2NJ N1 N 7.816 0.712 13
2NJ C6 C 8.989 -0.223 14
2NJ C1 C 8.989 -1.723 15
2NJ C5 C 10.330 0.579 16
2NJ C4 C 11.689 -0.192 17
2NJ C3 C 11.689 -1.754 18
2NJ C2 C 10.330 -2.525 19
#
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
2NJ C N SINGLE NONE 1
2NJ C2 C3 SINGLE NONE 2
2NJ C2 C1 DOUBLE NONE 3
2NJ C3 C4 DOUBLE NONE 4
2NJ N C1 SINGLE NONE 5
2NJ N C9 SINGLE NONE 6
2NJ C1 C6 SINGLE NONE 7
2NJ O C9 DOUBLE NONE 8
2NJ C9 C8 SINGLE NONE 9
2NJ C4 C5 SINGLE NONE 10
2NJ C8 C7 SINGLE NONE 11
2NJ C6 C5 DOUBLE NONE 12
2NJ C6 N1 SINGLE NONE 13
2NJ N1 C7 SINGLE NONE 14
2NJ C7 C10 SINGLE BEGINWEDGE 15
2NJ C15 C10 DOUBLE NONE 16
2NJ C15 C14 SINGLE NONE 17
2NJ C10 C11 SINGLE NONE 18
2NJ C14 C13 DOUBLE NONE 19
2NJ C11 C12 DOUBLE NONE 20
2NJ C13 C12 SINGLE NONE 21
#
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
2NJ MurckoScaffold S1 scaffold 'O=C1C[C@@H](c2ccccc2)Nc2ccccc2N1' InChI=1S/C15H14N2O/c18-15-10-14(11-6-2-1-3-7-11)16-12-8-4-5-9-13(12)17-15/h1-9,14,16H,10H2,(H,17,18)/t14-/m0/s1 BPBSKHLEGJWMBO-AWEZNQCLSA-N
2NJ amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
2NJ phenyl F2 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
2NJ O S1 1
2NJ C9 S1 1
2NJ N S1 1
2NJ C8 S1 1
2NJ C7 S1 1
2NJ C10 S1 1
2NJ C15 S1 1
2NJ C14 S1 1
2NJ C13 S1 1
2NJ C12 S1 1
2NJ C11 S1 1
2NJ N1 S1 1
2NJ C6 S1 1
2NJ C1 S1 1
2NJ C5 S1 1
2NJ C4 S1 1
2NJ C3 S1 1
2NJ C2 S1 1
2NJ N F1 1
2NJ C9 F1 1
2NJ O F1 1
2NJ C8 F1 1
2NJ C10 F2 1
2NJ C15 F2 1
2NJ C14 F2 1
2NJ C13 F2 1
2NJ C12 F2 1
2NJ C11 F2 1
2NJ C6 F2 2
2NJ C1 F2 2
2NJ C2 F2 2
2NJ C3 F2 2
2NJ C4 F2 2
2NJ C5 F2 2
#
_pdbe_chem_comp_rdkit_properties.comp_id 2NJ
_pdbe_chem_comp_rdkit_properties.exactmw 252.126
_pdbe_chem_comp_rdkit_properties.amw 252.317
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 35
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.188
_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 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_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 134.951
_pdbe_chem_comp_rdkit_properties.tpsa 32.340
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.390
_pdbe_chem_comp_rdkit_properties.CrippenMR 75.361
_pdbe_chem_comp_rdkit_properties.chi0v 9.303
_pdbe_chem_comp_rdkit_properties.chi1v 5.072
_pdbe_chem_comp_rdkit_properties.chi2v 2.261
_pdbe_chem_comp_rdkit_properties.chi3v 2.261
_pdbe_chem_comp_rdkit_properties.chi4v 1.427
_pdbe_chem_comp_rdkit_properties.chi0n 25.303
_pdbe_chem_comp_rdkit_properties.chi1n 13.019
_pdbe_chem_comp_rdkit_properties.chi2n 2.261
_pdbe_chem_comp_rdkit_properties.chi3n 2.261
_pdbe_chem_comp_rdkit_properties.chi4n 1.427
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.290
_pdbe_chem_comp_rdkit_properties.kappa1 3.423
_pdbe_chem_comp_rdkit_properties.kappa2 4.765
_pdbe_chem_comp_rdkit_properties.kappa3 2.191
_pdbe_chem_comp_rdkit_properties.Phi 0.858
#
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
2NJ UniChem ZINC ZINC000000173231
2NJ UniChem PubChem 738782
#
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
2NJ O -0.764 -0.359 -3.550 ETKDGv3 1
2NJ C9 -0.871 -0.196 -2.303 ETKDGv3 2
2NJ N -2.044 -0.665 -1.609 ETKDGv3 3
2NJ C -3.145 -1.257 -2.377 ETKDGv3 4
2NJ C8 0.248 0.473 -1.563 ETKDGv3 5
2NJ C7 1.034 -0.553 -0.728 ETKDGv3 6
2NJ C10 2.186 0.121 -0.014 ETKDGv3 7
2NJ C15 1.972 0.979 1.004 ETKDGv3 8
2NJ C14 3.110 1.636 1.680 ETKDGv3 9
2NJ C13 4.363 1.388 1.281 ETKDGv3 10
2NJ C12 4.609 0.457 0.161 ETKDGv3 11
2NJ C11 3.582 -0.142 -0.454 ETKDGv3 12
2NJ N1 0.198 -1.278 0.240 ETKDGv3 13
2NJ C6 -1.058 -0.793 0.742 ETKDGv3 14
2NJ C1 -2.183 -0.464 -0.186 ETKDGv3 15
2NJ C5 -1.239 -0.689 2.069 ETKDGv3 16
2NJ C4 -2.518 -0.194 2.613 ETKDGv3 17
2NJ C3 -3.514 0.135 1.787 ETKDGv3 18
2NJ C2 -3.344 -0.013 0.328 ETKDGv3 19
2NJ H1 -2.750 -1.936 -3.162 ETKDGv3 20
2NJ H2 -3.805 -1.862 -1.719 ETKDGv3 21
2NJ H3 -3.743 -0.452 -2.854 ETKDGv3 22
2NJ H4 -0.165 1.279 -0.919 ETKDGv3 23
2NJ H5 0.936 0.956 -2.291 ETKDGv3 24
2NJ H6 1.448 -1.307 -1.435 ETKDGv3 25
2NJ H7 0.968 1.204 1.339 ETKDGv3 26
2NJ H8 2.927 2.319 2.499 ETKDGv3 27
2NJ H9 5.197 1.869 1.775 ETKDGv3 28
2NJ H10 5.624 0.263 -0.162 ETKDGv3 29
2NJ H11 3.776 -0.820 -1.275 ETKDGv3 30
2NJ H12 0.670 -2.038 0.781 ETKDGv3 31
2NJ H13 -0.439 -0.944 2.753 ETKDGv3 32
2NJ H14 -2.644 -0.094 3.684 ETKDGv3 33
2NJ H15 -4.452 0.501 2.185 ETKDGv3 34
2NJ H16 -4.172 0.246 -0.320 ETKDGv3 35
#