data_LKZ
#
_chem_comp.id LKZ
_chem_comp.name 3,5,7,9,11-pentakis(oxidanylidene)dodecanal
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H14 O6"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-08-22
_chem_comp.pdbx_modified_date 2020-05-22
_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 254.236
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code LKZ
_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 6SMO
_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
LKZ C4 C1 C 0 1 N N N N N N -22.737 77.739 -5.324 4.757 0.756 0.089 C4 LKZ 1
LKZ C5 C2 C 0 1 N N N N N N -23.545 78.167 -6.523 3.307 0.352 0.036 C5 LKZ 2
LKZ C6 C3 C 0 1 N N N N N N -24.744 77.295 -6.909 2.229 1.404 0.075 C6 LKZ 3
LKZ C7 C4 C 0 1 N N N N N N -26.016 78.061 -6.618 0.877 0.741 0.009 C7 LKZ 4
LKZ C8 C5 C 0 1 N N N N N N -27.373 77.454 -6.994 -0.375 1.579 0.032 C8 LKZ 5
LKZ C10 C6 C 0 1 N N N N N N -31.314 78.593 -3.753 -5.459 0.506 -0.132 C10 LKZ 6
LKZ C22 C7 C 0 1 N N N N N N -21.510 77.006 -5.829 5.625 -0.475 0.036 C22 LKZ 7
LKZ C11 C8 C 0 1 N N N N N N -31.460 77.101 -3.593 -6.262 -0.766 -0.222 C11 LKZ 8
LKZ O19 O1 O 0 1 N N N N N N -31.222 76.530 -2.544 -7.109 -1.005 0.606 O19 LKZ 9
LKZ C3 C9 C 0 1 N N N N N N -30.536 78.739 -5.047 -3.989 0.173 -0.122 C3 LKZ 10
LKZ O23 O2 O 0 1 N N N N N N -30.961 79.442 -5.947 -3.631 -0.979 -0.181 O23 LKZ 11
LKZ C2 C10 C 0 1 N N N N N N -29.284 77.868 -5.217 -2.967 1.277 -0.038 C2 LKZ 12
LKZ C9 C11 C 0 1 N N N N N N -28.449 78.366 -6.398 -1.583 0.681 -0.044 C9 LKZ 13
LKZ O20 O3 O 0 1 N N N N N N -28.567 79.502 -6.814 -1.441 -0.517 -0.110 O20 LKZ 14
LKZ O21 O4 O 0 1 N N N N N N -25.955 79.125 -6.042 0.797 -0.462 -0.061 O21 LKZ 15
LKZ O22 O5 O 0 1 N N N N N N -23.219 79.156 -7.159 3.008 -0.816 -0.037 O22 LKZ 16
LKZ O24 O6 O 0 1 N N N N N N -20.432 77.562 -5.979 5.117 -1.568 -0.037 O24 LKZ 17
LKZ C23 C12 C 0 1 N N N N N N -21.701 75.533 -6.134 7.125 -0.342 0.074 C23 LKZ 18
LKZ H1 H1 H 0 1 N N N N N N -22.433 78.622 -4.743 4.986 1.399 -0.761 H1 LKZ 19
LKZ H2 H2 H 0 1 N N N N N N -23.336 77.071 -4.688 4.950 1.297 1.015 H2 LKZ 20
LKZ H3 H3 H 0 1 N N N N N N -24.730 76.365 -6.322 2.310 1.973 1.001 H3 LKZ 21
LKZ H4 H4 H 0 1 N N N N N N -24.695 77.052 -7.981 2.346 2.075 -0.776 H4 LKZ 22
LKZ H5 H5 H 0 1 N N N N N N -27.478 77.410 -8.088 -0.409 2.157 0.956 H5 LKZ 23
LKZ H6 H6 H 0 1 N N N N N N -27.463 76.440 -6.576 -0.373 2.259 -0.821 H6 LKZ 24
LKZ H7 H7 H 0 1 N N N N N N -30.757 79.026 -2.909 -5.682 1.138 -0.992 H7 LKZ 25
LKZ H8 H8 H 0 1 N N N N N N -32.298 79.078 -3.830 -5.718 1.036 0.784 H8 LKZ 26
LKZ H9 H9 H 0 1 N N N N N N -31.788 76.517 -4.440 -6.081 -1.464 -1.026 H9 LKZ 27
LKZ H10 H10 H 0 1 N N N N N N -29.588 76.827 -5.401 -3.080 1.942 -0.893 H10 LKZ 28
LKZ H11 H11 H 0 1 N N N N N N -28.680 77.917 -4.299 -3.116 1.840 0.883 H11 LKZ 29
LKZ H12 H12 H 0 1 N N N N N N -20.751 75.105 -6.488 7.466 -0.368 1.109 H12 LKZ 30
LKZ H13 H13 H 0 1 N N N N N N -22.022 75.009 -5.222 7.577 -1.165 -0.479 H13 LKZ 31
LKZ H14 H14 H 0 1 N N N N N N -22.468 75.417 -6.914 7.418 0.605 -0.381 H14 LKZ 32
#
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
LKZ O22 C5 DOUB N N 1
LKZ C8 C7 SING N N 2
LKZ C8 C9 SING N N 3
LKZ C6 C7 SING N N 4
LKZ C6 C5 SING N N 5
LKZ O20 C9 DOUB N N 6
LKZ C7 O21 DOUB N N 7
LKZ C5 C4 SING N N 8
LKZ C9 C2 SING N N 9
LKZ C23 C22 SING N N 10
LKZ O24 C22 DOUB N N 11
LKZ O23 C3 DOUB N N 12
LKZ C22 C4 SING N N 13
LKZ C2 C3 SING N N 14
LKZ C3 C10 SING N N 15
LKZ C10 C11 SING N N 16
LKZ C11 O19 DOUB N N 17
LKZ C4 H1 SING N N 18
LKZ C4 H2 SING N N 19
LKZ C6 H3 SING N N 20
LKZ C6 H4 SING N N 21
LKZ C8 H5 SING N N 22
LKZ C8 H6 SING N N 23
LKZ C10 H7 SING N N 24
LKZ C10 H8 SING N N 25
LKZ C11 H9 SING N N 26
LKZ C2 H10 SING N N 27
LKZ C2 H11 SING N N 28
LKZ C23 H12 SING N N 29
LKZ C23 H13 SING N N 30
LKZ C23 H14 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
LKZ InChI InChI 1.03 InChI=1S/C12H14O6/c1-8(14)4-10(16)6-12(18)7-11(17)5-9(15)2-3-13/h3H,2,4-7H2,1H3
LKZ InChIKey InChI 1.03 PTGARLKYUIIZKU-UHFFFAOYSA-N
LKZ SMILES_CANONICAL CACTVS 3.385 CC(=O)CC(=O)CC(=O)CC(=O)CC(=O)CC=O
LKZ SMILES CACTVS 3.385 CC(=O)CC(=O)CC(=O)CC(=O)CC(=O)CC=O
LKZ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CC(=O)CC(=O)CC(=O)CC(=O)CC(=O)CC=O
LKZ SMILES "OpenEye OEToolkits" 2.0.7 CC(=O)CC(=O)CC(=O)CC(=O)CC(=O)CC=O
#
_pdbx_chem_comp_identifier.comp_id LKZ
_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 3,5,7,9,11-pentakis(oxidanylidene)dodecanal
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
LKZ 'Create component' 2019-08-22 PDBE
LKZ 'Initial release' 2020-05-27 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
LKZ C4 C 5.598 1.125 1
LKZ C5 C 6.897 0.375 2
LKZ C6 C 8.196 1.125 3
LKZ C7 C 9.495 0.375 4
LKZ C8 C 10.794 1.125 5
LKZ C10 C 15.990 1.125 6
LKZ C22 C 4.299 0.375 7
LKZ C11 C 17.290 0.375 8
LKZ O19 O 18.588 1.125 9
LKZ C3 C 14.691 0.375 10
LKZ O23 O 14.691 -1.125 11
LKZ C2 C 13.392 1.125 12
LKZ C9 C 12.093 0.375 13
LKZ O20 O 12.093 -1.125 14
LKZ O21 O 9.495 -1.125 15
LKZ O22 O 6.897 -1.125 16
LKZ O24 O 3.000 1.125 17
LKZ C23 C 4.299 -1.125 18
#
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
LKZ O22 C5 DOUBLE NONE 1
LKZ C8 C7 SINGLE NONE 2
LKZ C8 C9 SINGLE NONE 3
LKZ C6 C7 SINGLE NONE 4
LKZ C6 C5 SINGLE NONE 5
LKZ O20 C9 DOUBLE NONE 6
LKZ C7 O21 DOUBLE NONE 7
LKZ C5 C4 SINGLE NONE 8
LKZ C9 C2 SINGLE NONE 9
LKZ C23 C22 SINGLE NONE 10
LKZ O24 C22 DOUBLE NONE 11
LKZ O23 C3 DOUBLE NONE 12
LKZ C22 C4 SINGLE NONE 13
LKZ C2 C3 SINGLE NONE 14
LKZ C3 C10 SINGLE NONE 15
LKZ C10 C11 SINGLE NONE 16
LKZ C11 O19 DOUBLE NONE 17
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id LKZ
_pdbe_chem_comp_rdkit_properties.exactmw 254.079
_pdbe_chem_comp_rdkit_properties.amw 254.238
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 11
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 32
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 123.392
_pdbe_chem_comp_rdkit_properties.tpsa 102.420
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.001
_pdbe_chem_comp_rdkit_properties.CrippenMR 59.858
_pdbe_chem_comp_rdkit_properties.chi0v 8.449
_pdbe_chem_comp_rdkit_properties.chi1v 3.975
_pdbe_chem_comp_rdkit_properties.chi2v 1.073
_pdbe_chem_comp_rdkit_properties.chi3v 1.073
_pdbe_chem_comp_rdkit_properties.chi4v 0.584
_pdbe_chem_comp_rdkit_properties.chi0n 22.449
_pdbe_chem_comp_rdkit_properties.chi1n 10.975
_pdbe_chem_comp_rdkit_properties.chi2n 1.073
_pdbe_chem_comp_rdkit_properties.chi3n 1.073
_pdbe_chem_comp_rdkit_properties.chi4n 0.584
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.980
_pdbe_chem_comp_rdkit_properties.kappa1 4.291
_pdbe_chem_comp_rdkit_properties.kappa2 8.161
_pdbe_chem_comp_rdkit_properties.kappa3 8.204
_pdbe_chem_comp_rdkit_properties.Phi 1.946
#
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
LKZ UniChem PDBe LKZ
LKZ UniChem PubChem 146672932
#
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
LKZ C4 3.147 -1.286 1.187 ETKDGv3 1
LKZ C5 2.528 -0.854 -0.114 ETKDGv3 2
LKZ C6 1.525 0.265 -0.164 ETKDGv3 3
LKZ C7 0.155 -0.278 -0.463 ETKDGv3 4
LKZ C8 -0.504 -0.035 -1.793 ETKDGv3 5
LKZ C10 -3.855 0.378 0.628 ETKDGv3 6
LKZ C22 4.588 -0.861 1.243 ETKDGv3 7
LKZ C11 -5.326 0.310 0.898 ETKDGv3 8
LKZ O19 -5.866 -0.761 1.124 ETKDGv3 9
LKZ C3 -3.528 -0.263 -0.694 ETKDGv3 10
LKZ O23 -3.615 -1.476 -0.815 ETKDGv3 11
LKZ C2 -3.049 0.566 -1.853 ETKDGv3 12
LKZ C9 -1.615 0.969 -1.652 ETKDGv3 13
LKZ O20 -1.349 2.124 -1.353 ETKDGv3 14
LKZ O21 -0.433 -0.925 0.391 ETKDGv3 15
LKZ O22 2.848 -1.422 -1.148 ETKDGv3 16
LKZ O24 5.468 -1.675 1.010 ETKDGv3 17
LKZ C23 4.960 0.560 1.543 ETKDGv3 18
LKZ H1 3.068 -2.391 1.281 ETKDGv3 19
LKZ H2 2.602 -0.845 2.049 ETKDGv3 20
LKZ H3 1.839 0.995 -0.940 ETKDGv3 21
LKZ H4 1.492 0.811 0.802 ETKDGv3 22
LKZ H5 0.231 0.344 -2.534 ETKDGv3 23
LKZ H6 -0.896 -1.000 -2.183 ETKDGv3 24
LKZ H7 -3.297 -0.133 1.442 ETKDGv3 25
LKZ H8 -3.543 1.444 0.620 ETKDGv3 26
LKZ H9 -5.918 1.220 0.904 ETKDGv3 27
LKZ H10 -3.141 -0.009 -2.800 ETKDGv3 28
LKZ H11 -3.692 1.468 -1.950 ETKDGv3 29
LKZ H12 5.527 0.984 0.688 ETKDGv3 30
LKZ H13 5.593 0.595 2.454 ETKDGv3 31
LKZ H14 4.055 1.181 1.713 ETKDGv3 32
#