data_JDL
#
_chem_comp.id JDL
_chem_comp.name 6-fluoranyl-10-methyl-1,10-diazatricyclo[6.3.1.0^{4,12}]dodeca-4,6,8(12)-trien-11-imine
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H12 F N3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-05-21
_chem_comp.pdbx_modified_date 2022-05-13
_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 205.231
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code JDL
_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 7EU5
_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
JDL C9 C1 C 0 1 Y N N N N N -5.852 6.195 8.055 -2.462 0.850 -0.150 C9 JDL 1
JDL C12 C2 C 0 1 Y N N N N N -6.739 7.558 6.260 -1.708 -1.422 0.191 C12 JDL 2
JDL C6 C3 C 0 1 Y N N N N N -5.989 5.090 7.282 -1.155 1.298 -0.114 C6 JDL 3
JDL C13 C4 C 0 1 Y N N N N N -6.872 6.416 5.503 -0.410 -0.983 0.226 C13 JDL 4
JDL C5 C5 C 0 1 Y N N N N N -6.482 5.232 6.055 -0.150 0.380 0.067 C5 JDL 5
JDL C10 C6 C 0 1 Y N N N N N -6.232 7.406 7.528 -2.733 -0.502 0.003 C10 JDL 6
JDL C3 C7 C 0 1 N N N N N N -6.788 3.985 4.105 2.233 0.134 0.193 C3 JDL 7
JDL C7 C8 C 0 1 N N N N N N -5.668 3.721 7.580 -0.514 2.661 -0.238 C7 JDL 8
JDL C14 C9 C 0 1 N N N N N N -7.408 6.391 4.110 0.788 -1.870 0.450 C14 JDL 9
JDL C8 C10 C 0 1 N N N N N N -5.918 3.050 6.257 1.004 2.397 -0.118 C8 JDL 10
JDL C1 C11 C 0 1 N N N N N N -7.235 5.257 1.989 2.939 -1.968 -0.902 C1 JDL 11
JDL N4 N1 N 0 1 N N N N N N -6.541 4.031 5.445 1.132 0.962 0.054 N4 JDL 12
JDL N2 N2 N 0 1 N N N N N N -7.011 5.195 3.414 1.992 -1.209 -0.082 N2 JDL 13
JDL N15 N3 N 0 1 N N N N N N -6.822 2.721 3.524 3.405 0.579 0.553 N15 JDL 14
JDL F11 F1 F 0 1 N N N N N N -6.080 8.475 8.312 -4.013 -0.931 -0.032 F11 JDL 15
JDL H1 H1 H 0 1 N N N N N N -5.455 6.126 9.057 -3.271 1.552 -0.292 H1 JDL 16
JDL H2 H2 H 0 1 N N N N N N -7.020 8.527 5.876 -1.933 -2.472 0.308 H2 JDL 17
JDL H4 H4 H 0 1 N N N N N N -6.325 3.317 8.364 -0.747 3.103 -1.207 H4 JDL 18
JDL H5 H5 H 0 1 N N N N N N -7.026 7.266 3.564 0.913 -2.049 1.518 H5 JDL 19
JDL H6 H6 H 0 1 N N N N N N -8.506 6.434 4.149 0.638 -2.820 -0.063 H6 JDL 20
JDL H7 H7 H 0 1 N N N N N N -6.580 2.181 6.386 1.515 2.715 -1.026 H7 JDL 21
JDL H8 H8 H 0 1 N N N N N N -7.383 6.304 1.686 3.761 -1.319 -1.203 H8 JDL 22
JDL H9 H9 H 0 1 N N N N N N -6.363 4.843 1.462 3.331 -2.806 -0.325 H9 JDL 23
JDL H10 H10 H 0 1 N N N N N N -8.130 4.671 1.733 2.431 -2.345 -1.790 H10 JDL 24
JDL H12 H12 H 0 1 N N N N N N -6.655 1.997 4.193 3.530 1.523 0.735 H12 JDL 25
JDL H3 H3 H 0 1 N N N N N N -4.618 3.615 7.891 -0.852 3.314 0.567 H3 JDL 26
JDL H15 H15 H 0 1 N N N N N N -4.969 2.724 5.806 1.411 2.920 0.747 H15 JDL 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
JDL C1 N2 SING N N 1
JDL N2 C3 SING N N 2
JDL N2 C14 SING N N 3
JDL N15 C3 DOUB N N 4
JDL C3 N4 SING N N 5
JDL C14 C13 SING N N 6
JDL N4 C5 SING N N 7
JDL N4 C8 SING N N 8
JDL C13 C5 DOUB Y N 9
JDL C13 C12 SING Y N 10
JDL C5 C6 SING Y N 11
JDL C8 C7 SING N N 12
JDL C12 C10 DOUB Y N 13
JDL C6 C7 SING N N 14
JDL C6 C9 DOUB Y N 15
JDL C10 C9 SING Y N 16
JDL C10 F11 SING N N 17
JDL C9 H1 SING N N 18
JDL C12 H2 SING N N 19
JDL C7 H4 SING N N 20
JDL C14 H5 SING N N 21
JDL C14 H6 SING N N 22
JDL C8 H7 SING N N 23
JDL C1 H8 SING N N 24
JDL C1 H9 SING N N 25
JDL C1 H10 SING N N 26
JDL N15 H12 SING N N 27
JDL C7 H3 SING N N 28
JDL C8 H15 SING N N 29
#
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
JDL InChI InChI 1.03 InChI=1S/C11H12FN3/c1-14-6-8-5-9(12)4-7-2-3-15(10(7)8)11(14)13/h4-5,13H,2-3,6H2,1H3/b13-11-
JDL InChIKey InChI 1.03 FHPIUPDPCMWKJY-QBFSEMIESA-N
JDL SMILES_CANONICAL CACTVS 3.385 CN1Cc2cc(F)cc3CCN(C1=N)c23
JDL SMILES CACTVS 3.385 CN1Cc2cc(F)cc3CCN(C1=N)c23
JDL SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C\1/N(Cc2cc(cc3c2N1CC3)F)C"
JDL SMILES "OpenEye OEToolkits" 2.0.7 CN1Cc2cc(cc3c2N(C1=N)CC3)F
#
_pdbx_chem_comp_identifier.comp_id JDL
_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
6-fluoranyl-10-methyl-1,10-diazatricyclo[6.3.1.0^{4,12}]dodeca-4,6,8(12)-trien-11-imine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
JDL 'Create component' 2021-05-21 PDBJ
JDL 'Initial release' 2022-05-18 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
JDL C9 C -2.757 0.715 1
JDL C12 C -1.694 -1.656 2
JDL C6 C -1.388 1.328 3
JDL C13 C -0.325 -1.042 4
JDL C5 C -0.172 0.450 5
JDL C10 C -2.910 -0.778 6
JDL C3 C 2.412 0.185 7
JDL C7 C -0.928 2.756 8
JDL C14 C 0.891 -1.921 9
JDL C8 C 0.571 2.760 10
JDL C1 C 3.476 -2.185 11
JDL N4 N 1.039 1.335 12
JDL N2 N 2.260 -1.307 13
JDL N15 N 3.802 0.750 14
JDL F11 F -4.278 -1.391 15
JDL H12 H 4.008 2.236 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
JDL C1 N2 SINGLE NONE 1
JDL N2 C3 SINGLE ENDDOWNRIGHT 2
JDL N2 C14 SINGLE NONE 3
JDL N15 C3 DOUBLE NONE 4
JDL C3 N4 SINGLE ENDDOWNRIGHT 5
JDL C14 C13 SINGLE NONE 6
JDL N4 C5 SINGLE NONE 7
JDL N4 C8 SINGLE NONE 8
JDL C13 C5 DOUBLE NONE 9
JDL C13 C12 SINGLE NONE 10
JDL C5 C6 SINGLE NONE 11
JDL C8 C7 SINGLE NONE 12
JDL C12 C10 DOUBLE NONE 13
JDL C6 C7 SINGLE NONE 14
JDL C6 C9 DOUBLE NONE 15
JDL C10 C9 SINGLE NONE 16
JDL C10 F11 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
JDL MurckoScaffold S1 scaffold N=C1NCc2cccc3c2N1CC3 InChI=1S/C10H11N3/c11-10-12-6-8-3-1-2-7-4-5-13(10)9(7)8/h1-3H,4-6H2,(H2,11,12) WGDXRDDBNPQEOY-UHFFFAOYSA-N
JDL 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
JDL C9 S1 1
JDL C12 S1 1
JDL C6 S1 1
JDL C13 S1 1
JDL C5 S1 1
JDL C10 S1 1
JDL C3 S1 1
JDL C7 S1 1
JDL C14 S1 1
JDL C8 S1 1
JDL N4 S1 1
JDL N2 S1 1
JDL N15 S1 1
JDL C9 F1 1
JDL C6 F1 1
JDL C5 F1 1
JDL C13 F1 1
JDL C12 F1 1
JDL C10 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id JDL
_pdbe_chem_comp_rdkit_properties.exactmw 205.102
_pdbe_chem_comp_rdkit_properties.amw 205.236
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_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 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 27
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.364
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_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 104.533
_pdbe_chem_comp_rdkit_properties.tpsa 30.330
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.078
_pdbe_chem_comp_rdkit_properties.CrippenMR 55.288
_pdbe_chem_comp_rdkit_properties.chi0v 7.220
_pdbe_chem_comp_rdkit_properties.chi1v 4.004
_pdbe_chem_comp_rdkit_properties.chi2v 2.083
_pdbe_chem_comp_rdkit_properties.chi3v 2.083
_pdbe_chem_comp_rdkit_properties.chi4v 1.469
_pdbe_chem_comp_rdkit_properties.chi0n 19.220
_pdbe_chem_comp_rdkit_properties.chi1n 9.951
_pdbe_chem_comp_rdkit_properties.chi2n 2.083
_pdbe_chem_comp_rdkit_properties.chi3n 2.083
_pdbe_chem_comp_rdkit_properties.chi4n 1.469
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.580
_pdbe_chem_comp_rdkit_properties.kappa1 2.753
_pdbe_chem_comp_rdkit_properties.kappa2 2.716
_pdbe_chem_comp_rdkit_properties.kappa3 1.075
_pdbe_chem_comp_rdkit_properties.Phi 0.499
#
_pdbe_chem_comp_external_mappings.comp_id JDL
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id JDL
#
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
JDL C9 -2.932 0.923 0.041 ETKDGv3 1
JDL C12 -1.029 2.438 -0.384 ETKDGv3 2
JDL C6 -2.080 -0.099 0.171 ETKDGv3 3
JDL C13 -0.114 1.273 -0.232 ETKDGv3 4
JDL C5 -0.674 0.096 0.031 ETKDGv3 5
JDL C10 -2.366 2.271 -0.255 ETKDGv3 6
JDL C3 1.448 -1.115 0.104 ETKDGv3 7
JDL C7 -2.341 -1.541 0.462 ETKDGv3 8
JDL C14 1.390 1.402 -0.366 ETKDGv3 9
JDL C8 -0.918 -2.186 0.479 ETKDGv3 10
JDL C1 3.589 0.149 -0.290 ETKDGv3 11
JDL N4 0.024 -1.098 0.205 ETKDGv3 12
JDL N2 2.129 0.129 -0.180 ETKDGv3 13
JDL N15 2.114 -2.216 0.263 ETKDGv3 14
JDL F11 -3.197 3.333 -0.394 ETKDGv3 15
JDL H1 -3.999 0.777 0.146 ETKDGv3 16
JDL H2 -0.623 3.418 -0.598 ETKDGv3 17
JDL H4 -2.837 -1.650 1.449 ETKDGv3 18
JDL H5 1.744 2.138 0.387 ETKDGv3 19
JDL H6 1.615 1.806 -1.376 ETKDGv3 20
JDL H7 -0.834 -2.965 -0.309 ETKDGv3 21
JDL H8 4.043 -0.190 0.665 ETKDGv3 22
JDL H9 3.913 -0.525 -1.112 ETKDGv3 23
JDL H10 3.960 1.173 -0.510 ETKDGv3 24
JDL H12 1.646 -3.126 0.468 ETKDGv3 25
JDL H3 -2.968 -1.987 -0.339 ETKDGv3 26
JDL H15 -0.704 -2.629 1.475 ETKDGv3 27
#