data_L5E
#
_chem_comp.id L5E
_chem_comp.name "[(7~{S})-1,4-bis(bromanyl)-6,6-bis(oxidanyl)-5,7,8,9-tetrahydrobenzo[7]annulen-7-yl]azanium"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H14 Br2 N O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2019-07-22
_chem_comp.pdbx_modified_date 2020-03-20
_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 352.042
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code L5E
_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 6SBR
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
L5E N1 N1 N 1 1 N N N N N N 88.756 122.800 123.473 -0.638 4.190 0.565 N1 L5E 1
L5E C2 C1 C 0 1 Y N N N N N 93.065 117.811 124.386 1.272 -2.099 0.485 C2 L5E 2
L5E C4 C2 C 0 1 Y N N N N N 93.076 119.137 122.414 -0.967 -1.407 -0.015 C4 L5E 3
L5E C5 C3 C 0 1 Y N N N N N 92.582 120.249 123.100 -0.481 -0.195 -0.477 C5 L5E 4
L5E C6 C4 C 0 1 Y N N N N N 92.338 120.129 124.476 0.864 0.065 -0.453 C6 L5E 5
L5E C8 C5 C 0 1 N N N N N N 92.319 121.568 122.408 -1.447 0.845 -1.005 C8 L5E 6
L5E C9 C6 C 0 1 N N N N N N 90.365 121.656 124.882 0.989 2.484 0.031 C9 L5E 7
L5E C11 C7 C 0 1 N N S N N N 90.267 122.597 123.684 -0.397 3.001 -0.264 C11 L5E 8
L5E C1 C8 C 0 1 Y N N N N N 92.591 118.902 125.084 1.752 -0.886 0.023 C1 L5E 9
L5E C10 C9 C 0 1 N N N N N N 90.853 121.962 122.364 -1.507 2.002 -0.004 C10 L5E 10
L5E C3 C10 C 0 1 Y N N N N N 93.315 117.932 123.038 -0.086 -2.359 0.466 C3 L5E 11
L5E C7 C11 C 0 1 N N N N N N 91.807 121.309 125.257 1.393 1.390 -0.961 C7 L5E 12
L5E O1 O1 O 0 1 N N N N N N 90.554 122.879 121.348 -2.770 2.661 -0.124 O1 L5E 13
L5E O2 O2 O 0 1 N N N N N N 90.073 120.828 122.122 -1.373 1.484 1.321 O2 L5E 14
L5E BR1 BR1 BR 0 0 N N N N N N 92.303 118.685 126.937 3.609 -0.529 0.041 BR1 L5E 15
L5E BR2 BR2 BR 0 0 N N N N N N 93.451 119.239 120.563 -2.825 -1.758 -0.043 BR2 L5E 16
L5E H10 H1 H 0 1 N N N N N N 88.355 123.203 124.296 0.047 4.897 0.346 H10 L5E 17
L5E H11 H2 H 0 1 N N N N N N 88.607 123.412 122.696 -1.563 4.548 0.379 H11 L5E 18
L5E H14 H3 H 0 1 N N N N N N 88.324 121.917 123.289 -0.564 3.940 1.540 H14 L5E 19
L5E H1 H4 H 0 1 N N N N N N 93.238 116.872 124.891 1.959 -2.845 0.857 H1 L5E 20
L5E H6 H5 H 0 1 N N N N N N 92.689 121.496 121.375 -1.098 1.213 -1.970 H6 L5E 21
L5E H5 H6 H 0 1 N N N N N N 92.873 122.355 122.942 -2.436 0.402 -1.117 H5 L5E 22
L5E H8 H7 H 0 1 N N N N N N 89.885 122.139 125.746 1.700 3.308 -0.036 H8 L5E 23
L5E H7 H8 H 0 1 N N N N N N 89.833 120.724 124.640 1.009 2.076 1.042 H7 L5E 24
L5E H9 H9 H 0 1 N N N N N N 90.763 123.556 123.897 -0.440 3.298 -1.312 H9 L5E 25
L5E H2 H10 H 0 1 N N N N N N 93.694 117.092 122.476 -0.459 -3.306 0.828 H2 L5E 26
L5E H3 H11 H 0 1 N N N N N N 91.845 121.068 126.330 2.479 1.347 -1.037 H3 L5E 27
L5E H4 H12 H 0 1 N N N N N N 92.444 122.182 125.054 0.962 1.606 -1.939 H4 L5E 28
L5E H12 H13 H 0 1 N N N N N N 91.065 123.670 121.474 -3.530 2.089 0.051 H12 L5E 29
L5E H13 H14 H 0 1 N N N N N N 90.245 120.176 122.791 -2.062 0.853 1.569 H13 L5E 30
#
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
L5E BR2 C4 SING N N 1
L5E O1 C10 SING N N 2
L5E O2 C10 SING N N 3
L5E C10 C8 SING N N 4
L5E C10 C11 SING N N 5
L5E C8 C5 SING N N 6
L5E C4 C3 DOUB Y N 7
L5E C4 C5 SING Y N 8
L5E C3 C2 SING Y N 9
L5E C5 C6 DOUB Y N 10
L5E N1 C11 SING N N 11
L5E C11 C9 SING N N 12
L5E C2 C1 DOUB Y N 13
L5E C6 C1 SING Y N 14
L5E C6 C7 SING N N 15
L5E C9 C7 SING N N 16
L5E C1 BR1 SING N N 17
L5E N1 H10 SING N N 18
L5E N1 H11 SING N N 19
L5E N1 H14 SING N N 20
L5E C2 H1 SING N N 21
L5E C8 H6 SING N N 22
L5E C8 H5 SING N N 23
L5E C9 H8 SING N N 24
L5E C9 H7 SING N N 25
L5E C11 H9 SING N N 26
L5E C3 H2 SING N N 27
L5E C7 H3 SING N N 28
L5E C7 H4 SING N N 29
L5E O1 H12 SING N N 30
L5E O2 H13 SING N N 31
#
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
L5E InChI InChI 1.03 InChI=1S/C11H13Br2NO2/c12-8-2-3-9(13)7-5-11(15,16)10(14)4-1-6(7)8/h2-3,10,15-16H,1,4-5,14H2/p+1/t10-/m0/s1
L5E InChIKey InChI 1.03 JKSZJUHJLDPZJQ-JTQLQIEISA-O
L5E SMILES_CANONICAL CACTVS 3.385 "[NH3+][C@H]1CCc2c(Br)ccc(Br)c2CC1(O)O"
L5E SMILES CACTVS 3.385 "[NH3+][CH]1CCc2c(Br)ccc(Br)c2CC1(O)O"
L5E SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1cc(c2c(c1Br)CC[C@@H](C(C2)(O)O)[NH3+])Br
L5E SMILES "OpenEye OEToolkits" 2.0.7 c1cc(c2c(c1Br)CCC(C(C2)(O)O)[NH3+])Br
#
_pdbx_chem_comp_identifier.comp_id L5E
_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
"[(7~{S})-1,4-bis(bromanyl)-6,6-bis(oxidanyl)-5,7,8,9-tetrahydrobenzo[7]annulen-7-yl]azanium"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
L5E 'Create component' 2019-07-22 EBI
L5E 'Other modification' 2019-07-22 EBI
L5E 'Initial release' 2020-03-25 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
L5E N1 N 3.930 -0.197 1
L5E C2 C 11.416 -0.979 2
L5E C4 C 10.057 1.355 3
L5E C5 C 8.716 0.553 4
L5E C6 C 8.716 -0.947 5
L5E C8 C 7.543 1.488 6
L5E C9 C 6.081 -1.549 7
L5E C11 C 5.430 -0.197 8
L5E C1 C 10.057 -1.749 9
L5E C10 C 6.081 1.154 10
L5E C3 C 11.416 0.584 11
L5E C7 C 7.543 -1.883 12
L5E O1 O 4.729 1.805 13
L5E O2 O 5.747 2.617 14
L5E BR1 Br 10.040 -3.249 15
L5E BR2 Br 10.040 2.855 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
L5E BR2 C4 SINGLE NONE 1
L5E O1 C10 SINGLE NONE 2
L5E O2 C10 SINGLE NONE 3
L5E C10 C8 SINGLE NONE 4
L5E C10 C11 SINGLE NONE 5
L5E C8 C5 SINGLE NONE 6
L5E C4 C3 SINGLE NONE 7
L5E C4 C5 DOUBLE NONE 8
L5E C3 C2 DOUBLE NONE 9
L5E C5 C6 SINGLE NONE 10
L5E C11 N1 SINGLE BEGINDASH 11
L5E C11 C9 SINGLE NONE 12
L5E C2 C1 SINGLE NONE 13
L5E C6 C1 DOUBLE NONE 14
L5E C6 C7 SINGLE NONE 15
L5E C9 C7 SINGLE NONE 16
L5E C1 BR1 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
L5E MurckoScaffold S1 scaffold c1ccc2c(c1)CCCCC2 InChI=1S/C11H14/c1-2-6-10-8-4-5-9-11(10)7-3-1/h4-5,8-9H,1-3,6-7H2 HEOQXHNKRXRCTO-UHFFFAOYSA-N
L5E phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
L5E Z419084966 F2 fragment NCC(O)Cc1ccccc1 InChI=1S/C9H13NO/c10-7-9(11)6-8-4-2-1-3-5-8/h1-5,9,11H,6-7,10H2 JIIXMZQZEAAIJX-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
L5E C2 S1 1
L5E C4 S1 1
L5E C5 S1 1
L5E C6 S1 1
L5E C8 S1 1
L5E C9 S1 1
L5E C11 S1 1
L5E C1 S1 1
L5E C10 S1 1
L5E C3 S1 1
L5E C7 S1 1
L5E C2 F1 1
L5E C3 F1 1
L5E C4 F1 1
L5E C5 F1 1
L5E C6 F1 1
L5E C1 F1 1
L5E N1 F2 1
L5E C11 F2 1
L5E C10 F2 1
L5E O1 F2 1
L5E C8 F2 1
L5E C5 F2 1
L5E C4 F2 1
L5E C3 F2 1
L5E C2 F2 1
L5E C1 F2 1
L5E C6 F2 1
L5E N1 F2 2
L5E C11 F2 2
L5E C10 F2 2
L5E O2 F2 2
L5E C8 F2 2
L5E C5 F2 2
L5E C4 F2 2
L5E C3 F2 2
L5E C2 F2 2
L5E C1 F2 2
L5E C6 F2 2
#
_pdbe_chem_comp_rdkit_properties.comp_id L5E
_pdbe_chem_comp_rdkit_properties.exactmw 349.939
_pdbe_chem_comp_rdkit_properties.amw 352.046
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 30
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.455
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 130.931
_pdbe_chem_comp_rdkit_properties.tpsa 68.100
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.882
_pdbe_chem_comp_rdkit_properties.CrippenMR 67.180
_pdbe_chem_comp_rdkit_properties.chi0v 10.692
_pdbe_chem_comp_rdkit_properties.chi1v 5.596
_pdbe_chem_comp_rdkit_properties.chi2v 3.068
_pdbe_chem_comp_rdkit_properties.chi3v 3.068
_pdbe_chem_comp_rdkit_properties.chi4v 1.910
_pdbe_chem_comp_rdkit_properties.chi0n 21.520
_pdbe_chem_comp_rdkit_properties.chi1n 10.668
_pdbe_chem_comp_rdkit_properties.chi2n 1.878
_pdbe_chem_comp_rdkit_properties.chi3n 1.878
_pdbe_chem_comp_rdkit_properties.chi4n 1.117
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.060
_pdbe_chem_comp_rdkit_properties.kappa1 3.776
_pdbe_chem_comp_rdkit_properties.kappa2 4.384
_pdbe_chem_comp_rdkit_properties.kappa3 2.194
_pdbe_chem_comp_rdkit_properties.Phi 1.034
#
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
L5E UniChem PDBe L5E
L5E UniChem PubChem 145998274
#
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
L5E N1 -2.725 -0.119 -1.261 ETKDGv3 1
L5E C2 3.533 -0.738 0.628 ETKDGv3 2
L5E C4 2.210 1.308 0.619 ETKDGv3 3
L5E C5 1.186 0.702 -0.032 ETKDGv3 4
L5E C6 1.300 -0.752 -0.385 ETKDGv3 5
L5E C8 -0.099 1.443 -0.361 ETKDGv3 6
L5E C9 -1.060 -1.558 -0.067 ETKDGv3 7
L5E C11 -1.988 -0.318 0.000 ETKDGv3 8
L5E C1 2.424 -1.433 -0.048 ETKDGv3 9
L5E C10 -1.301 0.991 0.515 ETKDGv3 10
L5E C3 3.433 0.552 0.943 ETKDGv3 11
L5E C7 0.122 -1.439 -1.043 ETKDGv3 12
L5E O1 -0.866 0.775 1.840 ETKDGv3 13
L5E O2 -2.250 2.034 0.508 ETKDGv3 14
L5E BR1 2.677 -3.311 -0.373 ETKDGv3 15
L5E BR2 2.178 3.143 1.196 ETKDGv3 16
L5E H10 -3.179 -1.015 -1.553 ETKDGv3 17
L5E H11 -2.108 0.208 -2.034 ETKDGv3 18
L5E H14 -3.487 0.584 -1.123 ETKDGv3 19
L5E H1 4.435 -1.281 0.881 ETKDGv3 20
L5E H6 0.030 2.537 -0.241 ETKDGv3 21
L5E H5 -0.317 1.335 -1.440 ETKDGv3 22
L5E H8 -0.684 -1.797 0.953 ETKDGv3 23
L5E H7 -1.676 -2.433 -0.373 ETKDGv3 24
L5E H9 -2.751 -0.579 0.771 ETKDGv3 25
L5E H2 4.254 1.044 1.448 ETKDGv3 26
L5E H3 0.380 -2.455 -1.396 ETKDGv3 27
L5E H4 -0.161 -0.899 -1.967 ETKDGv3 28
L5E H12 -0.571 1.652 2.203 ETKDGv3 29
L5E H13 -2.937 1.818 1.193 ETKDGv3 30
#