data_B5J
#
_chem_comp.id B5J
_chem_comp.name methyltriphenylphosphonium
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C19 H18 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2021-11-12
_chem_comp.pdbx_modified_date 2022-02-25
_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 277.320
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code B5J
_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 7SSU
_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
B5J C10 C1 C 0 1 Y N N N N N -9.806 28.852 23.787 1.520 -2.113 -0.154 C10 B5J 1
B5J C13 C2 C 0 1 Y N N N N N -8.964 30.736 21.958 -0.624 -3.856 -0.269 C13 B5J 2
B5J C15 C3 C 0 1 Y N N N N N -11.716 26.217 22.198 1.338 1.073 0.143 C15 B5J 3
B5J C17 C4 C 0 1 Y N N N N N -13.524 24.637 21.895 2.196 2.501 -1.577 C17 B5J 4
B5J C20 C5 C 0 1 Y N N N N N -12.625 27.116 22.750 2.504 1.243 0.866 C20 B5J 5
B5J C01 C6 C 0 1 N N N N N N -8.983 25.649 23.304 0.047 0.056 2.617 C01 B5J 6
B5J C03 C7 C 0 1 Y N N N N N -9.225 26.143 20.355 -1.590 0.629 0.206 C03 B5J 7
B5J C04 C8 C 0 1 Y N N N N N -7.864 26.255 20.087 -2.059 0.252 -1.038 C04 B5J 8
B5J C05 C9 C 0 1 Y N N N N N -7.350 25.876 18.853 -3.281 0.717 -1.487 C05 B5J 9
B5J C06 C10 C 0 1 Y N N N N N -8.186 25.367 17.869 -4.033 1.561 -0.691 C06 B5J 10
B5J C07 C11 C 0 1 Y N N N N N -9.542 25.243 18.131 -3.564 1.938 0.553 C07 B5J 11
B5J C08 C12 C 0 1 Y N N N N N -10.056 25.623 19.365 -2.345 1.468 1.004 C08 B5J 12
B5J C09 C13 C 0 1 Y N N N N N -9.595 28.457 22.470 0.259 -1.685 0.220 C09 B5J 13
B5J C11 C14 C 0 1 Y N N N N N -9.605 30.166 24.190 1.707 -3.411 -0.590 C11 B5J 14
B5J C12 C15 C 0 1 Y N N N N N -9.181 31.116 23.274 0.635 -4.282 -0.648 C12 B5J 15
B5J C14 C16 C 0 1 Y N N N N N -9.164 29.416 21.552 -0.813 -2.555 0.157 C14 B5J 16
B5J C16 C17 C 0 1 Y N N N N N -12.180 24.973 21.780 1.184 1.702 -1.078 C16 B5J 17
B5J C18 C18 C 0 1 Y N N N N N -14.425 25.541 22.442 3.362 2.671 -0.854 C18 B5J 18
B5J C19 C19 C 0 1 Y N N N N N -13.972 26.782 22.868 3.516 2.042 0.367 C19 B5J 19
B5J P02 P1 P 1 1 N N N N N N -9.897 26.652 22.032 0.014 0.018 0.794 P02 B5J 20
B5J H1 H1 H 0 1 N N N N N N -10.133 28.121 24.512 2.357 -1.433 -0.108 H1 B5J 21
B5J H2 H2 H 0 1 N N N N N N -8.636 31.471 21.238 -1.461 -4.536 -0.314 H2 B5J 22
B5J H3 H3 H 0 1 N N N N N N -13.868 23.670 21.558 2.075 2.992 -2.531 H3 B5J 23
B5J H4 H4 H 0 1 N N N N N N -12.282 28.082 23.090 2.625 0.752 1.820 H4 B5J 24
B5J H5 H5 H 0 1 N N N N N N -9.344 25.913 24.309 -0.749 -0.577 3.008 H5 B5J 25
B5J H6 H6 H 0 1 N N N N N N -9.158 24.578 23.122 1.010 -0.311 2.970 H6 B5J 26
B5J H7 H7 H 0 1 N N N N N N -7.906 25.862 23.234 -0.101 1.079 2.961 H7 B5J 27
B5J H8 H8 H 0 1 N N N N N N -7.200 26.641 20.846 -1.471 -0.407 -1.660 H8 B5J 28
B5J H9 H9 H 0 1 N N N N N N -6.293 25.978 18.658 -3.647 0.423 -2.459 H9 B5J 29
B5J H10 H10 H 0 1 N N N N N N -7.785 25.071 16.911 -4.986 1.929 -1.044 H10 B5J 30
B5J H11 H11 H 0 1 N N N N N N -10.202 24.849 17.372 -4.152 2.597 1.175 H11 B5J 31
B5J H12 H12 H 0 1 N N N N N N -11.113 25.514 19.559 -1.979 1.762 1.976 H12 B5J 32
B5J H13 H13 H 0 1 N N N N N N -9.779 30.448 25.218 2.690 -3.745 -0.887 H13 B5J 33
B5J H14 H14 H 0 1 N N N N N N -9.022 32.139 23.581 0.783 -5.299 -0.982 H14 B5J 34
B5J H15 H15 H 0 1 N N N N N N -8.985 29.136 20.525 -1.797 -2.221 0.454 H15 B5J 35
B5J H16 H16 H 0 1 N N N N N N -11.486 24.259 21.361 0.273 1.569 -1.643 H16 B5J 36
B5J H17 H17 H 0 1 N N N N N N -15.469 25.281 22.535 4.153 3.294 -1.244 H17 B5J 37
B5J H18 H18 H 0 1 N N N N N N -14.667 27.491 23.293 4.427 2.175 0.932 H18 B5J 38
#
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
B5J C06 C07 DOUB Y N 1
B5J C06 C05 SING Y N 2
B5J C07 C08 SING Y N 3
B5J C05 C04 DOUB Y N 4
B5J C08 C03 DOUB Y N 5
B5J C04 C03 SING Y N 6
B5J C03 P02 SING N N 7
B5J C14 C13 DOUB Y N 8
B5J C14 C09 SING Y N 9
B5J C16 C17 DOUB Y N 10
B5J C16 C15 SING Y N 11
B5J C17 C18 SING Y N 12
B5J C13 C12 SING Y N 13
B5J P02 C15 SING N N 14
B5J P02 C09 SING N N 15
B5J P02 C01 SING N N 16
B5J C15 C20 DOUB Y N 17
B5J C18 C19 DOUB Y N 18
B5J C09 C10 DOUB Y N 19
B5J C20 C19 SING Y N 20
B5J C12 C11 DOUB Y N 21
B5J C10 C11 SING Y N 22
B5J C10 H1 SING N N 23
B5J C13 H2 SING N N 24
B5J C17 H3 SING N N 25
B5J C20 H4 SING N N 26
B5J C01 H5 SING N N 27
B5J C01 H6 SING N N 28
B5J C01 H7 SING N N 29
B5J C04 H8 SING N N 30
B5J C05 H9 SING N N 31
B5J C06 H10 SING N N 32
B5J C07 H11 SING N N 33
B5J C08 H12 SING N N 34
B5J C11 H13 SING N N 35
B5J C12 H14 SING N N 36
B5J C14 H15 SING N N 37
B5J C16 H16 SING N N 38
B5J C18 H17 SING N N 39
B5J C19 H18 SING N N 40
#
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
B5J SMILES ACDLabs 12.01 C[P+](c1ccccc1)(c1ccccc1)c1ccccc1
B5J InChI InChI 1.03 InChI=1S/C19H18P/c1-20(17-11-5-2-6-12-17,18-13-7-3-8-14-18)19-15-9-4-10-16-19/h2-16H,1H3/q+1
B5J InChIKey InChI 1.03 AZFQCTBZOPUVOW-UHFFFAOYSA-N
B5J SMILES_CANONICAL CACTVS 3.385 C[P+](c1ccccc1)(c2ccccc2)c3ccccc3
B5J SMILES CACTVS 3.385 C[P+](c1ccccc1)(c2ccccc2)c3ccccc3
B5J SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C[P+](c1ccccc1)(c2ccccc2)c3ccccc3
B5J SMILES "OpenEye OEToolkits" 2.0.7 C[P+](c1ccccc1)(c2ccccc2)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
B5J "SYSTEMATIC NAME" ACDLabs 12.01 methyl(triphenyl)phosphanium
B5J "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 methyl(triphenyl)phosphanium
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
B5J 'Create component' 2021-11-12 RCSB
B5J 'Other modification' 2021-11-23 RCSB
B5J 'Initial release' 2022-03-02 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
B5J C10 C 6.750 1.299 1
B5J C13 C 8.250 -1.299 2
B5J C15 C 4.500 1.500 3
B5J C17 C 5.799 3.750 4
B5J C20 C 3.201 2.250 5
B5J C01 C 3.000 0.000 6
B5J C03 C 4.500 -1.500 7
B5J C04 C 5.799 -2.250 8
B5J C05 C 5.799 -3.750 9
B5J C06 C 4.500 -4.500 10
B5J C07 C 3.201 -3.750 11
B5J C08 C 3.201 -2.250 12
B5J C09 C 6.000 0.000 13
B5J C11 C 8.250 1.299 14
B5J C12 C 9.000 0.000 15
B5J C14 C 6.750 -1.299 16
B5J C16 C 5.799 2.250 17
B5J C18 C 4.500 4.500 18
B5J C19 C 3.201 3.750 19
B5J P02 P 4.500 0.000 20
#
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
B5J C06 C07 DOUBLE NONE 1
B5J C06 C05 SINGLE NONE 2
B5J C07 C08 SINGLE NONE 3
B5J C05 C04 DOUBLE NONE 4
B5J C08 C03 DOUBLE NONE 5
B5J C04 C03 SINGLE NONE 6
B5J C03 P02 SINGLE NONE 7
B5J C14 C13 DOUBLE NONE 8
B5J C14 C09 SINGLE NONE 9
B5J C16 C17 DOUBLE NONE 10
B5J C16 C15 SINGLE NONE 11
B5J C17 C18 SINGLE NONE 12
B5J C13 C12 SINGLE NONE 13
B5J P02 C15 SINGLE NONE 14
B5J P02 C09 SINGLE NONE 15
B5J P02 C01 SINGLE NONE 16
B5J C15 C20 DOUBLE NONE 17
B5J C18 C19 DOUBLE NONE 18
B5J C09 C10 DOUBLE NONE 19
B5J C20 C19 SINGLE NONE 20
B5J C12 C11 DOUBLE NONE 21
B5J C10 C11 SINGLE NONE 22
#
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
B5J MurckoScaffold S1 scaffold 'c1ccc([PH+](c2ccccc2)c2ccccc2)cc1' InChI=1S/C18H15P/c1-4-10-16(11-5-1)19(17-12-6-2-7-13-17)18-14-8-3-9-15-18/h1-15H/p+1 RIOQSEWOXXDEQQ-UHFFFAOYSA-O
B5J 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
B5J C10 S1 1
B5J C13 S1 1
B5J C15 S1 1
B5J C17 S1 1
B5J C20 S1 1
B5J C03 S1 1
B5J C04 S1 1
B5J C05 S1 1
B5J C06 S1 1
B5J C07 S1 1
B5J C08 S1 1
B5J C09 S1 1
B5J C11 S1 1
B5J C12 S1 1
B5J C14 S1 1
B5J C16 S1 1
B5J C18 S1 1
B5J C19 S1 1
B5J P02 S1 1
B5J C10 F1 1
B5J C09 F1 1
B5J C14 F1 1
B5J C13 F1 1
B5J C12 F1 1
B5J C11 F1 1
B5J C15 F1 2
B5J C16 F1 2
B5J C17 F1 2
B5J C18 F1 2
B5J C19 F1 2
B5J C20 F1 2
B5J C03 F1 3
B5J C08 F1 3
B5J C07 F1 3
B5J C06 F1 3
B5J C05 F1 3
B5J C04 F1 3
#
_pdbe_chem_comp_rdkit_properties.comp_id B5J
_pdbe_chem_comp_rdkit_properties.exactmw 277.114
_pdbe_chem_comp_rdkit_properties.amw 277.327
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 0
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 0
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 38
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 1
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.053
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 3
_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 146.285
_pdbe_chem_comp_rdkit_properties.tpsa 0
_pdbe_chem_comp_rdkit_properties.CrippenClogP 3.610
_pdbe_chem_comp_rdkit_properties.CrippenMR 91.072
_pdbe_chem_comp_rdkit_properties.chi0v 10.842
_pdbe_chem_comp_rdkit_properties.chi1v 7.183
_pdbe_chem_comp_rdkit_properties.chi2v 5.150
_pdbe_chem_comp_rdkit_properties.chi3v 5.150
_pdbe_chem_comp_rdkit_properties.chi4v 3.581
_pdbe_chem_comp_rdkit_properties.chi0n 27.947
_pdbe_chem_comp_rdkit_properties.chi1n 14.394
_pdbe_chem_comp_rdkit_properties.chi2n 2.467
_pdbe_chem_comp_rdkit_properties.chi3n 2.467
_pdbe_chem_comp_rdkit_properties.chi4n 1.569
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.910
_pdbe_chem_comp_rdkit_properties.kappa1 3.642
_pdbe_chem_comp_rdkit_properties.kappa2 5.607
_pdbe_chem_comp_rdkit_properties.kappa3 2.280
_pdbe_chem_comp_rdkit_properties.Phi 1.021
#
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
B5J UniChem ChEMBL CHEMBL1179021
B5J UniChem PDBe B5J
B5J UniChem ZINC ZINC000042784648
B5J UniChem fdasrs 05G6U0TXS3
B5J UniChem 'PubChem TPHARMA' 16733611
B5J UniChem ACTor 15912-74-0
B5J UniChem Nikkaji J2.227.717K
B5J UniChem BindingDb 50422429
B5J UniChem 'EPA CompTox Dashboard' DTXSID20166591
B5J UniChem Nikkaji J231.696J
B5J UniChem eMolecules 10468986
B5J UniChem PubChem 74506
B5J UniChem Mcule MCULE-8922506077
#
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
B5J C10 2.718 0.241 -0.680 ETKDGv3 1
B5J C13 2.886 1.451 1.858 ETKDGv3 2
B5J C15 -0.314 -1.554 -0.717 ETKDGv3 3
B5J C17 0.178 -3.730 0.291 ETKDGv3 4
B5J C20 -1.269 -2.096 -1.490 ETKDGv3 5
B5J C01 -0.009 0.782 -2.487 ETKDGv3 6
B5J C03 -1.311 1.088 0.140 ETKDGv3 7
B5J C04 -1.549 2.528 -0.121 ETKDGv3 8
B5J C05 -2.480 3.194 0.575 ETKDGv3 9
B5J C06 -3.268 2.498 1.611 ETKDGv3 10
B5J C07 -3.046 1.202 1.863 ETKDGv3 11
B5J C08 -2.015 0.466 1.102 ETKDGv3 12
B5J C09 1.594 0.587 -0.032 ETKDGv3 13
B5J C11 4.039 0.508 -0.073 ETKDGv3 14
B5J C12 4.119 1.084 1.132 ETKDGv3 15
B5J C14 1.688 1.214 1.309 ETKDGv3 16
B5J C16 0.433 -2.417 0.231 ETKDGv3 17
B5J C18 -0.856 -4.323 -0.581 ETKDGv3 18
B5J C19 -1.544 -3.547 -1.426 ETKDGv3 19
B5J P02 -0.013 0.220 -0.755 ETKDGv3 20
B5J H1 2.674 -0.244 -1.647 ETKDGv3 21
B5J H2 2.954 1.909 2.836 ETKDGv3 22
B5J H3 0.724 -4.359 0.982 ETKDGv3 23
B5J H4 -1.852 -1.482 -2.164 ETKDGv3 24
B5J H5 -1.040 0.741 -2.896 ETKDGv3 25
B5J H6 0.651 0.126 -3.090 ETKDGv3 26
B5J H7 0.365 1.824 -2.541 ETKDGv3 27
B5J H8 -0.968 3.050 -0.869 ETKDGv3 28
B5J H9 -2.652 4.245 0.383 ETKDGv3 29
B5J H10 -4.021 3.039 2.169 ETKDGv3 30
B5J H11 -3.618 0.691 2.627 ETKDGv3 31
B5J H12 -1.836 -0.574 1.339 ETKDGv3 32
B5J H13 4.941 0.234 -0.605 ETKDGv3 33
B5J H14 5.085 1.279 1.579 ETKDGv3 34
B5J H15 0.793 1.481 1.855 ETKDGv3 35
B5J H16 1.185 -1.992 0.884 ETKDGv3 36
B5J H17 -1.058 -5.385 -0.532 ETKDGv3 37
B5J H18 -2.307 -3.978 -2.062 ETKDGv3 38
#