data_6M4
#
_chem_comp.id 6M4
_chem_comp.name 1,1-dihydroxy-1,3-dihydro-2,1-benzoxaborol-1-ium
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C7 H8 B O3'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge -1
_chem_comp.pdbx_initial_date 2016-05-04
_chem_comp.pdbx_modified_date 2024-09-27
_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 150.948
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 6M4
_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 5JQ0
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
_chem_comp.pdbx_pcm Y
#
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
6M4 C5 C1 C 0 1 Y N N N N N -5.941 4.017 14.293 1.977 -1.162 -0.006 C5 6M4 1
6M4 C4 C2 C 0 1 Y N N N N N -6.696 4.601 15.292 2.862 -0.097 0.005 C4 6M4 2
6M4 C3 C3 C 0 1 Y N N N N N -6.852 3.982 16.535 2.385 1.200 0.016 C3 6M4 3
6M4 C2 C4 C 0 1 Y N N N N N -6.246 2.758 16.787 1.021 1.437 0.015 C2 6M4 4
6M4 C1 C5 C 0 1 Y N N N N N -5.478 2.154 15.785 0.142 0.377 0.003 C1 6M4 5
6M4 C6 C6 C 0 1 Y N N N N N -5.334 2.787 14.550 0.621 -0.925 -0.006 C6 6M4 6
6M4 C7 C7 C 0 1 N N N N N N -4.480 2.000 13.605 -0.593 -1.824 -0.013 C7 6M4 7
6M4 O1 O1 O 0 1 N N N N N N -4.355 0.755 14.305 -1.702 -1.009 -0.428 O1 6M4 8
6M4 B1 B1 B -1 1 N N N N N N -4.641 0.764 15.751 -1.413 0.270 -0.005 B1 6M4 9
6M4 O3 O2 O 0 1 N N N N N N -5.289 -0.446 16.147 -1.942 1.183 -0.875 O3 6M4 10
6M4 O2 O3 O 0 1 N N N N N N -3.444 0.879 16.526 -1.906 0.472 1.253 O2 6M4 11
6M4 H1 H1 H 0 1 N N N N N N -5.823 4.501 13.335 2.350 -2.176 -0.019 H1 6M4 12
6M4 H2 H2 H 0 1 N N N N N N -7.174 5.552 15.109 3.926 -0.281 0.006 H2 6M4 13
6M4 H3 H3 H 0 1 N N N N N N -7.446 4.457 17.302 3.077 2.029 0.025 H3 6M4 14
6M4 H4 H4 H 0 1 N N N N N N -6.366 2.277 17.747 0.647 2.451 0.024 H4 6M4 15
6M4 H5 H5 H 0 1 N N N N N N -3.500 2.477 13.456 -0.447 -2.644 -0.717 H5 6M4 16
6M4 H6 H6 H 0 1 N N N N N N -4.975 1.866 12.632 -0.772 -2.218 0.988 H6 6M4 17
6M4 H7 H7 H 0 1 N N N N N N -5.465 -0.421 17.080 -2.906 1.144 -0.948 H7 6M4 18
6M4 H8 H8 H 0 1 N N N N N N -3.664 0.882 17.450 -2.868 0.387 1.318 H8 6M4 19
#
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
6M4 C7 O1 SING N N 1
6M4 C7 C6 SING N N 2
6M4 C5 C6 DOUB Y N 3
6M4 C5 C4 SING Y N 4
6M4 O1 B1 SING N N 5
6M4 C6 C1 SING Y N 6
6M4 C4 C3 DOUB Y N 7
6M4 B1 C1 SING N N 8
6M4 B1 O3 SING N N 9
6M4 B1 O2 SING N N 10
6M4 C1 C2 DOUB Y N 11
6M4 C3 C2 SING Y N 12
6M4 C5 H1 SING N N 13
6M4 C4 H2 SING N N 14
6M4 C3 H3 SING N N 15
6M4 C2 H4 SING N N 16
6M4 C7 H5 SING N N 17
6M4 C7 H6 SING N N 18
6M4 O3 H7 SING N N 19
6M4 O2 H8 SING N N 20
#
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
6M4 SMILES ACDLabs 12.01 'c1c2c(ccc1)[B+](OC2)(O)O'
6M4 InChI InChI 1.03 'InChI=1S/C7H8BO3/c9-8(10)7-4-2-1-3-6(7)5-11-8/h1-4,9-10H,5H2/q-1'
6M4 InChIKey InChI 1.03 LFYLOXDIRWAWMG-UHFFFAOYSA-N
6M4 SMILES_CANONICAL CACTVS 3.385 'O[B-]1(O)OCc2ccccc12'
6M4 SMILES CACTVS 3.385 'O[B-]1(O)OCc2ccccc12'
6M4 SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.7 '[B-]1(c2ccccc2CO1)(O)O'
6M4 SMILES 'OpenEye OEToolkits' 2.0.7 '[B-]1(c2ccccc2CO1)(O)O'
#
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
6M4 'SYSTEMATIC NAME' ACDLabs 12.01 1,1-dihydroxy-1,3-dihydro-2,1-benzoxaborol-1-ium
6M4 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 2.0.7 '7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-triene'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
6M4 'Create component' 2016-05-04 PDBE
6M4 'Initial release' 2016-10-19 RCSB
6M4 'Other modification' 2019-10-18 PDBE
6M4 'Modify PCM' 2024-09-27 PDBE
#
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_pdbx_chem_comp_pcm.comp_id_linking_atom
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
1 6M4 HIS None 'Covalent chemical modification' 'Amino-acid side chain' 'Any position' B1 ND1 ? ?
2 6M4 HIS None 'Covalent chemical modification' 'Amino-acid side chain' 'Any position' B1 NE2 ? ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 '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
6M4 C5 C -1.383 -1.912 1
6M4 C4 C -2.682 -1.161 2
6M4 C3 C -2.680 0.339 3
6M4 C2 C -1.381 1.088 4
6M4 C1 C -0.082 0.337 5
6M4 C6 C -0.084 -1.163 6
6M4 C7 C 1.343 -1.628 7
6M4 O1 O 2.225 -0.415 8
6M4 B1 B 1.345 0.799 9
6M4 O3 O 2.644 1.548 10
6M4 O2 O 0.735 2.170 11
#
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
6M4 C7 O1 SINGLE NONE 1
6M4 C7 C6 SINGLE NONE 2
6M4 C5 C6 DOUBLE NONE 3
6M4 C5 C4 SINGLE NONE 4
6M4 O1 B1 SINGLE NONE 5
6M4 C6 C1 SINGLE NONE 6
6M4 C4 C3 DOUBLE NONE 7
6M4 B1 C1 SINGLE NONE 8
6M4 B1 O3 SINGLE NONE 9
6M4 B1 O2 SINGLE NONE 10
6M4 C1 C2 DOUBLE NONE 11
6M4 C3 C2 SINGLE NONE 12
#
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
6M4 MurckoScaffold S1 scaffold '[BH2-]1OCc2ccccc21' InChI=1S/C7H8BO/c1-2-4-7-6(3-1)5-9-8-7/h1-4H,5,8H2/q-1 FJSLOUSHIUKAKT-UHFFFAOYSA-N
6M4 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
6M4 C5 S1 1
6M4 C4 S1 1
6M4 C3 S1 1
6M4 C2 S1 1
6M4 C1 S1 1
6M4 C6 S1 1
6M4 C7 S1 1
6M4 O1 S1 1
6M4 B1 S1 1
6M4 C5 F1 1
6M4 C6 F1 1
6M4 C1 F1 1
6M4 C2 F1 1
6M4 C3 F1 1
6M4 C4 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 6M4
_pdbe_chem_comp_rdkit_properties.exactmw 151.057
_pdbe_chem_comp_rdkit_properties.amw 150.950
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 19
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.143
_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 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_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 75.669
_pdbe_chem_comp_rdkit_properties.tpsa 49.690
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.707
_pdbe_chem_comp_rdkit_properties.CrippenMR 40.791
_pdbe_chem_comp_rdkit_properties.chi0v 5.302
_pdbe_chem_comp_rdkit_properties.chi1v 2.950
_pdbe_chem_comp_rdkit_properties.chi2v 1.386
_pdbe_chem_comp_rdkit_properties.chi3v 1.386
_pdbe_chem_comp_rdkit_properties.chi4v 0.863
_pdbe_chem_comp_rdkit_properties.chi0n 13.302
_pdbe_chem_comp_rdkit_properties.chi1n 6.766
_pdbe_chem_comp_rdkit_properties.chi2n 1.386
_pdbe_chem_comp_rdkit_properties.chi3n 1.386
_pdbe_chem_comp_rdkit_properties.chi4n 0.863
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.835
_pdbe_chem_comp_rdkit_properties.kappa1 2.325
_pdbe_chem_comp_rdkit_properties.kappa2 2.074
_pdbe_chem_comp_rdkit_properties.kappa3 0.958
_pdbe_chem_comp_rdkit_properties.Phi 0.438
#
_pdbe_chem_comp_external_mappings.comp_id 6M4
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 122177116
#
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
6M4 C5 1.461 -1.300 -0.436 ETKDGv3 1
6M4 C4 2.503 -0.350 0.035 ETKDGv3 2
6M4 C3 2.148 0.859 0.513 ETKDGv3 3
6M4 C2 0.714 1.244 0.570 ETKDGv3 4
6M4 C1 -0.191 0.360 0.136 ETKDGv3 5
6M4 C6 0.179 -0.919 -0.370 ETKDGv3 6
6M4 C7 -1.022 -1.684 -0.776 ETKDGv3 7
6M4 O1 -2.173 -0.887 -0.526 ETKDGv3 8
6M4 B1 -1.741 0.428 0.053 ETKDGv3 9
6M4 O3 -2.337 0.587 1.397 ETKDGv3 10
6M4 O2 -2.175 1.521 -0.845 ETKDGv3 11
6M4 H1 1.734 -2.273 -0.822 ETKDGv3 12
6M4 H2 3.547 -0.633 -0.007 ETKDGv3 13
6M4 H3 2.905 1.552 0.857 ETKDGv3 14
6M4 H4 0.416 2.212 0.952 ETKDGv3 15
6M4 H5 -0.968 -1.928 -1.858 ETKDGv3 16
6M4 H6 -1.088 -2.624 -0.188 ETKDGv3 17
6M4 H7 -2.034 1.464 1.745 ETKDGv3 18
6M4 H8 -1.877 2.370 -0.429 ETKDGv3 19
#