data_LJL
#
_chem_comp.id LJL
_chem_comp.name (1R,2S)-1,2-bis(3-methoxy-4-oxidanyl-phenyl)propane-1,3-diol
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C17 H20 O6"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-07-05
_chem_comp.pdbx_modified_date 2023-01-27
_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 320.337
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code LJL
_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 8ABV
_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
LJL C7 C1 C 0 1 Y N N N N N 20.070 13.944 27.950 -1.907 0.273 -0.179 C7 LJL 1
LJL C8 C2 C 0 1 Y N N N N N 21.125 14.138 28.847 -2.210 1.545 0.270 C8 LJL 2
LJL C9 C3 C 0 1 Y N N N N N 20.914 14.097 30.219 -3.522 1.898 0.523 C9 LJL 3
LJL O1 O1 O 0 1 N N N N N N 21.999 12.574 26.406 -0.196 -0.813 1.848 O1 LJL 4
LJL C1 C4 C 0 1 Y N N N N N 21.098 13.705 22.254 4.042 0.297 0.114 C1 LJL 5
LJL O5 O2 O 0 1 N N N N N N 22.431 14.308 20.389 5.702 -1.392 -0.163 O5 LJL 6
LJL C5 C5 C 0 1 N N S N N N 20.249 14.107 26.452 -0.474 -0.108 -0.447 C5 LJL 7
LJL C6 C6 C 0 1 N N N N N N 19.932 15.530 26.011 0.104 0.808 -1.528 C6 LJL 8
LJL C4 C7 C 0 1 N N R N N N 21.689 13.905 25.977 0.343 0.042 0.838 C4 LJL 9
LJL O4 O3 O 0 1 N N N N N N 17.377 13.440 30.386 -5.225 -1.214 -0.318 O4 LJL 10
LJL C3 C8 C 0 1 Y N N N N N 21.879 14.100 24.485 1.776 -0.339 0.570 C3 LJL 11
LJL O3 O4 O 0 1 N N N N N N 19.345 13.827 32.021 -5.829 1.320 0.575 O3 LJL 12
LJL C2 C9 C 0 1 Y N N N N N 20.911 13.645 23.612 2.724 0.646 0.360 C2 LJL 13
LJL C16 C10 C 0 1 Y N N N N N 22.254 14.265 21.742 4.409 -1.045 0.078 C16 LJL 14
LJL O O5 O 0 1 N N N N N N 20.187 13.268 21.325 4.975 1.264 -0.099 O LJL 15
LJL C C11 C 0 1 N N N N N N 19.568 12.007 21.552 4.525 2.620 -0.054 C LJL 16
LJL C15 C12 C 0 1 Y N N N N N 23.225 14.749 22.598 3.454 -2.026 0.289 C15 LJL 17
LJL C14 C13 C 0 1 Y N N N N N 23.049 14.633 23.964 2.141 -1.672 0.535 C14 LJL 18
LJL O2 O6 O 0 1 N N N N N N 21.045 16.257 26.297 1.423 0.374 -1.865 O2 LJL 19
LJL C13 C14 C 0 1 Y N N N N N 18.802 13.737 28.444 -2.915 -0.652 -0.376 C13 LJL 20
LJL C11 C15 C 0 1 Y N N N N N 18.585 13.675 29.808 -4.232 -0.305 -0.124 C11 LJL 21
LJL C12 C16 C 0 1 N N N N N N 16.353 12.911 29.544 -4.838 -2.509 -0.783 C12 LJL 22
LJL C10 C17 C 0 1 Y N N N N N 19.639 13.866 30.699 -4.538 0.975 0.327 C10 LJL 23
LJL H1 H1 H 0 1 N N N N N N 22.119 14.323 28.467 -1.419 2.265 0.423 H1 LJL 24
LJL H2 H2 H 0 1 N N N N N N 21.737 14.244 30.903 -3.757 2.892 0.873 H2 LJL 25
LJL H3 H3 H 0 1 N N N N N N 21.865 12.504 27.344 -0.189 -1.751 1.614 H3 LJL 26
LJL H4 H4 H 0 1 N N N N N N 23.265 14.718 20.191 6.243 -1.469 0.635 H4 LJL 27
LJL H5 H5 H 0 1 N N N N N N 19.588 13.404 25.924 -0.430 -1.143 -0.786 H5 LJL 28
LJL H6 H6 H 0 1 N N N N N N 19.066 15.920 26.565 -0.530 0.768 -2.414 H6 LJL 29
LJL H7 H7 H 0 1 N N N N N N 19.721 15.560 24.932 0.142 1.831 -1.155 H7 LJL 30
LJL H8 H8 H 0 1 N N N N N N 22.332 14.623 26.507 0.300 1.077 1.178 H8 LJL 31
LJL H9 H9 H 0 1 N N N N N N 20.137 13.969 32.526 -6.290 1.694 -0.189 H9 LJL 32
LJL H10 H10 H 0 1 N N N N N N 19.992 13.235 24.004 2.437 1.686 0.388 H10 LJL 33
LJL H11 H11 H 0 1 N N N N N N 18.867 11.789 20.732 3.763 2.776 -0.817 H11 LJL 34
LJL H12 H12 H 0 1 N N N N N N 20.338 11.223 21.594 4.103 2.830 0.929 H12 LJL 35
LJL H13 H13 H 0 1 N N N N N N 19.020 12.034 22.505 5.366 3.288 -0.239 H13 LJL 36
LJL H14 H14 H 0 1 N N N N N N 24.115 15.215 22.202 3.736 -3.069 0.262 H14 LJL 37
LJL H15 H15 H 0 1 N N N N N N 23.831 14.961 24.633 1.398 -2.438 0.700 H15 LJL 38
LJL H16 H16 H 0 1 N N N N N N 20.907 17.162 26.042 1.851 0.910 -2.547 H16 LJL 39
LJL H17 H17 H 0 1 N N N N N N 17.972 13.622 27.762 -2.675 -1.645 -0.727 H17 LJL 40
LJL H18 H18 H 0 1 N N N N N N 15.433 12.768 30.130 -5.723 -3.134 -0.896 H18 LJL 41
LJL H19 H19 H 0 1 N N N N N N 16.157 13.613 28.720 -4.336 -2.414 -1.746 H19 LJL 42
LJL H20 H20 H 0 1 N N N N N N 16.679 11.944 29.133 -4.160 -2.966 -0.063 H20 LJL 43
#
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
LJL O5 C16 SING N N 1
LJL O C SING N N 2
LJL O C1 SING N N 3
LJL C16 C1 DOUB Y N 4
LJL C16 C15 SING Y N 5
LJL C1 C2 SING Y N 6
LJL C15 C14 DOUB Y N 7
LJL C2 C3 DOUB Y N 8
LJL C14 C3 SING Y N 9
LJL C3 C4 SING N N 10
LJL C4 O1 SING N N 11
LJL C4 C5 SING N N 12
LJL C6 O2 SING N N 13
LJL C6 C5 SING N N 14
LJL C5 C7 SING N N 15
LJL C7 C13 DOUB Y N 16
LJL C7 C8 SING Y N 17
LJL C13 C11 SING Y N 18
LJL C8 C9 DOUB Y N 19
LJL C12 O4 SING N N 20
LJL C11 O4 SING N N 21
LJL C11 C10 DOUB Y N 22
LJL C9 C10 SING Y N 23
LJL C10 O3 SING N N 24
LJL C8 H1 SING N N 25
LJL C9 H2 SING N N 26
LJL O1 H3 SING N N 27
LJL O5 H4 SING N N 28
LJL C5 H5 SING N N 29
LJL C6 H6 SING N N 30
LJL C6 H7 SING N N 31
LJL C4 H8 SING N N 32
LJL O3 H9 SING N N 33
LJL C2 H10 SING N N 34
LJL C H11 SING N N 35
LJL C H12 SING N N 36
LJL C H13 SING N N 37
LJL C15 H14 SING N N 38
LJL C14 H15 SING N N 39
LJL O2 H16 SING N N 40
LJL C13 H17 SING N N 41
LJL C12 H18 SING N N 42
LJL C12 H19 SING N N 43
LJL C12 H20 SING N N 44
#
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
LJL InChI InChI 1.06 InChI=1S/C17H20O6/c1-22-15-7-10(3-5-13(15)19)12(9-18)17(21)11-4-6-14(20)16(8-11)23-2/h3-8,12,17-21H,9H2,1-2H3/t12-,17+/m1/s1
LJL InChIKey InChI 1.06 DFUOJBWSSSODTR-PXAZEXFGSA-N
LJL SMILES_CANONICAL CACTVS 3.385 COc1cc(ccc1O)[C@H](O)[C@H](CO)c2ccc(O)c(OC)c2
LJL SMILES CACTVS 3.385 COc1cc(ccc1O)[CH](O)[CH](CO)c2ccc(O)c(OC)c2
LJL SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 COc1cc(ccc1O)[C@@H](CO)[C@H](c2ccc(c(c2)OC)O)O
LJL SMILES "OpenEye OEToolkits" 2.0.7 COc1cc(ccc1O)C(CO)C(c2ccc(c(c2)OC)O)O
#
_pdbx_chem_comp_identifier.comp_id LJL
_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 (1~{R},2~{S})-1,2-bis(3-methoxy-4-oxidanyl-phenyl)propane-1,3-diol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
LJL 'Create component' 2022-07-05 PDBE
LJL 'Modify name' 2022-07-13 PDBE
LJL 'Modify descriptor' 2022-08-22 RCSB
LJL 'Initial release' 2023-02-01 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
LJL C7 C 6.897 -1.875 1
LJL C8 C 8.196 -2.625 2
LJL C9 C 8.196 -4.125 3
LJL O1 O 9.495 -0.375 4
LJL C1 C 9.495 4.125 5
LJL O5 O 8.196 6.375 6
LJL C5 C 6.897 -0.375 7
LJL C6 C 5.598 0.375 8
LJL C4 C 8.196 0.375 9
LJL O4 O 4.299 -4.875 10
LJL C3 C 8.196 1.875 11
LJL O3 O 6.897 -6.375 12
LJL C2 C 9.495 2.625 13
LJL C16 C 8.196 4.875 14
LJL O O 10.794 4.875 15
LJL C C 12.093 4.125 16
LJL C15 C 6.897 4.125 17
LJL C14 C 6.897 2.625 18
LJL O2 O 4.299 -0.375 19
LJL C13 C 5.598 -2.625 20
LJL C11 C 5.598 -4.125 21
LJL C12 C 3.000 -4.125 22
LJL C10 C 6.897 -4.875 23
#
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
LJL O5 C16 SINGLE NONE 1
LJL O C SINGLE NONE 2
LJL O C1 SINGLE NONE 3
LJL C16 C1 DOUBLE NONE 4
LJL C16 C15 SINGLE NONE 5
LJL C1 C2 SINGLE NONE 6
LJL C15 C14 DOUBLE NONE 7
LJL C2 C3 DOUBLE NONE 8
LJL C14 C3 SINGLE NONE 9
LJL C3 C4 SINGLE NONE 10
LJL C4 O1 SINGLE BEGINDASH 11
LJL C4 C5 SINGLE NONE 12
LJL C6 O2 SINGLE NONE 13
LJL C5 C6 SINGLE BEGINWEDGE 14
LJL C5 C7 SINGLE NONE 15
LJL C7 C13 SINGLE NONE 16
LJL C7 C8 DOUBLE NONE 17
LJL C13 C11 DOUBLE NONE 18
LJL C8 C9 SINGLE NONE 19
LJL C12 O4 SINGLE NONE 20
LJL C11 O4 SINGLE NONE 21
LJL C11 C10 SINGLE NONE 22
LJL C9 C10 DOUBLE NONE 23
LJL C10 O3 SINGLE NONE 24
#
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
LJL MurckoScaffold S1 scaffold c1ccc(CCc2ccccc2)cc1 InChI=1S/C14H14/c1-3-7-13(8-4-1)11-12-14-9-5-2-6-10-14/h1-10H,11-12H2 QWUWMCYKGHVNAV-UHFFFAOYSA-N
LJL 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
LJL C7 S1 1
LJL C8 S1 1
LJL C9 S1 1
LJL C1 S1 1
LJL C5 S1 1
LJL C4 S1 1
LJL C3 S1 1
LJL C2 S1 1
LJL C16 S1 1
LJL C15 S1 1
LJL C14 S1 1
LJL C13 S1 1
LJL C11 S1 1
LJL C10 S1 1
LJL C7 F1 1
LJL C13 F1 1
LJL C11 F1 1
LJL C10 F1 1
LJL C9 F1 1
LJL C8 F1 1
LJL C1 F1 2
LJL C16 F1 2
LJL C15 F1 2
LJL C14 F1 2
LJL C3 F1 2
LJL C2 F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id LJL
_pdbe_chem_comp_rdkit_properties.exactmw 320.126
_pdbe_chem_comp_rdkit_properties.amw 320.341
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 12
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 23
_pdbe_chem_comp_rdkit_properties.NumAtoms 43
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.294
_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 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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 162.163
_pdbe_chem_comp_rdkit_properties.tpsa 99.380
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.035
_pdbe_chem_comp_rdkit_properties.CrippenMR 81.132
_pdbe_chem_comp_rdkit_properties.chi0v 10.949
_pdbe_chem_comp_rdkit_properties.chi1v 5.633
_pdbe_chem_comp_rdkit_properties.chi2v 2.502
_pdbe_chem_comp_rdkit_properties.chi3v 2.502
_pdbe_chem_comp_rdkit_properties.chi4v 1.473
_pdbe_chem_comp_rdkit_properties.chi0n 30.949
_pdbe_chem_comp_rdkit_properties.chi1n 15.266
_pdbe_chem_comp_rdkit_properties.chi2n 2.502
_pdbe_chem_comp_rdkit_properties.chi3n 2.502
_pdbe_chem_comp_rdkit_properties.chi4n 1.473
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.440
_pdbe_chem_comp_rdkit_properties.kappa1 4.554
_pdbe_chem_comp_rdkit_properties.kappa2 7.215
_pdbe_chem_comp_rdkit_properties.kappa3 3.492
_pdbe_chem_comp_rdkit_properties.Phi 1.429
#
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
LJL UniChem PDBe LJL
LJL UniChem PubChem 12468618
LJL UniChem Nikkaji J1.927.054H
#
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
LJL C7 -1.806 0.748 -0.166 ETKDGv3 1
LJL C8 -2.853 0.388 -0.934 ETKDGv3 2
LJL C9 -3.360 -0.996 -0.917 ETKDGv3 3
LJL O1 0.348 3.649 -1.322 ETKDGv3 4
LJL C1 2.283 -0.751 -0.971 ETKDGv3 5
LJL O5 4.366 -1.075 0.161 ETKDGv3 6
LJL C5 -1.265 2.174 -0.247 ETKDGv3 7
LJL C6 -1.041 2.822 1.139 ETKDGv3 8
LJL C4 -0.069 2.309 -1.238 ETKDGv3 9
LJL O4 -0.972 -2.585 1.413 ETKDGv3 10
LJL C3 1.118 1.423 -0.903 ETKDGv3 11
LJL O3 -3.235 -3.239 -0.145 ETKDGv3 12
LJL C2 1.162 0.152 -1.347 ETKDGv3 13
LJL C16 3.290 -0.270 -0.217 ETKDGv3 14
LJL O 2.308 -2.095 -1.371 ETKDGv3 15
LJL C 1.263 -2.730 -2.100 ETKDGv3 16
LJL C15 3.267 1.135 0.237 ETKDGv3 17
LJL C14 2.245 1.935 -0.083 ETKDGv3 18
LJL O2 0.063 2.280 1.806 ETKDGv3 19
LJL C13 -1.152 -0.293 0.676 ETKDGv3 20
LJL C11 -1.593 -1.567 0.669 ETKDGv3 21
LJL C12 0.208 -2.417 2.194 ETKDGv3 22
LJL C10 -2.764 -1.926 -0.158 ETKDGv3 23
LJL H1 -3.338 1.105 -1.585 ETKDGv3 24
LJL H2 -4.214 -1.254 -1.531 ETKDGv3 25
LJL H3 -0.357 4.144 -1.815 ETKDGv3 26
LJL H4 4.442 -2.047 -0.113 ETKDGv3 27
LJL H5 -2.074 2.799 -0.691 ETKDGv3 28
LJL H6 -1.956 2.681 1.758 ETKDGv3 29
LJL H7 -0.889 3.917 1.010 ETKDGv3 30
LJL H8 -0.439 2.004 -2.247 ETKDGv3 31
LJL H9 -4.033 -3.526 -0.700 ETKDGv3 32
LJL H10 0.351 -0.227 -1.955 ETKDGv3 33
LJL H11 1.528 -3.795 -2.259 ETKDGv3 34
LJL H12 0.314 -2.682 -1.525 ETKDGv3 35
LJL H13 1.137 -2.243 -3.089 ETKDGv3 36
LJL H14 4.082 1.518 0.839 ETKDGv3 37
LJL H15 2.245 2.959 0.269 ETKDGv3 38
LJL H16 0.122 2.754 2.675 ETKDGv3 39
LJL H17 -0.286 -0.031 1.261 ETKDGv3 40
LJL H18 0.028 -1.682 3.007 ETKDGv3 41
LJL H19 0.482 -3.390 2.650 ETKDGv3 42
LJL H20 1.047 -2.078 1.550 ETKDGv3 43
#