data_TNF
#
_chem_comp.id TNF
_chem_comp.name "PICRIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H3 N3 O7"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms 2,4,6-TRINITROPHENOL
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2002-02-27
_chem_comp.pdbx_modified_date 2021-03-13
_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 229.104
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code TNF
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1GVS
_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
TNF C1 C1 C 0 1 Y N N N N N 20.122 9.119 21.290 1.192 0.000 -0.005 C1 TNF 1
TNF C2 C2 C 0 1 Y N N N N N 20.791 10.439 21.266 0.497 1.201 -0.005 C2 TNF 2
TNF C3 C3 C 0 1 Y N N N N N 21.548 10.930 20.176 -0.884 1.198 -0.003 C3 TNF 3
TNF C4 C4 C 0 1 Y N N N N N 21.686 10.125 19.039 -1.574 0.000 0.000 C4 TNF 4
TNF N4 N4 N 1 1 N N N N N N 22.455 10.604 17.869 -3.055 0.000 0.004 N4 TNF 5
TNF N2 N2 N 1 1 N N N N N N 20.667 11.315 22.429 1.235 2.484 -0.007 N2 TNF 6
TNF O1 O1 O 0 1 N N N N N N 19.453 8.684 22.244 2.551 0.000 -0.008 O1 TNF 7
TNF O21 O21 O -1 1 N N N N N N 21.707 11.701 22.992 0.625 3.538 -0.007 O21 TNF 8
TNF O22 O22 O 0 1 N N N N N N 19.559 11.577 22.834 2.453 2.486 -0.009 O22 TNF 9
TNF O41 O41 O -1 1 N N N N N N 22.328 11.769 17.525 -3.664 1.055 0.004 O41 TNF 10
TNF C6 C6 C 0 1 Y N N N N N 20.349 8.374 20.054 0.497 -1.201 -0.008 C6 TNF 11
TNF C5 C5 C 0 1 Y N N N N N 21.099 8.864 18.980 -0.884 -1.198 0.000 C5 TNF 12
TNF O42 O42 O 0 1 N N N N N N 22.870 9.761 17.106 -3.664 -1.055 0.006 O42 TNF 13
TNF N6 N6 N 1 1 N N N N N N 19.776 7.024 19.890 1.235 -2.484 -0.009 N6 TNF 14
TNF O61 O61 O -1 1 N N N N N N 20.276 6.283 19.029 0.625 -3.538 -0.002 O61 TNF 15
TNF O62 O62 O 0 1 N N N N N N 19.078 6.582 20.759 2.453 -2.486 -0.016 O62 TNF 16
TNF H3 H3 H 0 1 N N N N N N 22.020 11.926 20.221 -1.426 2.133 -0.003 H3 TNF 17
TNF H1 H1 H 0 1 N N N N N N 19.024 7.837 22.259 2.833 0.001 0.917 H1 TNF 18
TNF H5 H5 H 0 1 N N N N N N 21.227 8.245 18.076 -1.426 -2.133 0.003 H5 TNF 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
TNF C1 C2 DOUB Y N 1
TNF C1 O1 SING N N 2
TNF C1 C6 SING Y N 3
TNF C2 C3 SING Y N 4
TNF C2 N2 SING N N 5
TNF C3 C4 DOUB Y N 6
TNF C3 H3 SING N N 7
TNF C4 N4 SING N N 8
TNF C4 C5 SING Y N 9
TNF N4 O41 SING N N 10
TNF N4 O42 DOUB N N 11
TNF N2 O21 SING N N 12
TNF N2 O22 DOUB N N 13
TNF O1 H1 SING N N 14
TNF C6 C5 DOUB Y N 15
TNF C6 N6 SING N N 16
TNF C5 H5 SING N N 17
TNF N6 O61 SING N N 18
TNF N6 O62 DOUB N N 19
#
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
TNF SMILES ACDLabs 10.04 O=[N+]([O-])c1cc(cc([N+]([O-])=O)c1O)[N+]([O-])=O
TNF SMILES_CANONICAL CACTVS 3.341 Oc1c(cc(cc1[N+]([O-])=O)[N+]([O-])=O)[N+]([O-])=O
TNF SMILES CACTVS 3.341 Oc1c(cc(cc1[N+]([O-])=O)[N+]([O-])=O)[N+]([O-])=O
TNF SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1c(cc(c(c1[N+](=O)[O-])O)[N+](=O)[O-])[N+](=O)[O-]
TNF SMILES "OpenEye OEToolkits" 1.5.0 c1c(cc(c(c1[N+](=O)[O-])O)[N+](=O)[O-])[N+](=O)[O-]
TNF InChI InChI 1.03 InChI=1S/C6H3N3O7/c10-6-4(8(13)14)1-3(7(11)12)2-5(6)9(15)16/h1-2,10H
TNF InChIKey InChI 1.03 OXNIZHLAWKMVMX-UHFFFAOYSA-N
#
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
TNF "SYSTEMATIC NAME" ACDLabs 10.04 2,4,6-trinitrophenol
TNF "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 2,4,6-trinitrophenol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
TNF 'Create component' 2002-02-27 EBI
TNF 'Modify descriptor' 2011-06-04 RCSB
TNF 'Modify synonyms' 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id TNF
_pdbx_chem_comp_synonyms.name 2,4,6-TRINITROPHENOL
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_details.comp_id TNF
_pdbe_chem_comp_drugbank_details.drugbank_id DB03651
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'Picric acid'
_pdbe_chem_comp_drugbank_details.description 'Used as antiseptic, astringent, and stimulant for epitheliazation.'
_pdbe_chem_comp_drugbank_details.cas_number 88-89-1
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
TNF 2,4,6-TRINITROPHENOL wwPDB ?
TNF 'Picricum acidum' DrugBank ?
TNF Trinitrophenol DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id TNF
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03651
_pdbe_chem_comp_drugbank_classification.parent Nitrophenols
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class Phenols
_pdbe_chem_comp_drugbank_classification.superclass Benzenoids
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as nitrophenols. These are compounds containing a nitrophenol moiety, which consists of a benzene ring bearing both a hydroxyl group and a nitro group on two different ring carbon atoms.'
#
_pdbe_chem_comp_drugbank_targets.comp_id TNF
_pdbe_chem_comp_drugbank_targets.drugbank_id DB03651
_pdbe_chem_comp_drugbank_targets.name 'Pentaerythritol tetranitrate reductase'
_pdbe_chem_comp_drugbank_targets.organism 'Enterobacter cloacae'
_pdbe_chem_comp_drugbank_targets.uniprot_id P71278
_pdbe_chem_comp_drugbank_targets.pharmacologically_active unknown
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
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
TNF C1 C 6.897 1.643 1
TNF C2 C 8.196 0.892 2
TNF C3 C 8.196 -0.608 3
TNF C4 C 6.897 -1.357 4
TNF N4 N 6.897 -2.857 5
TNF N2 N 9.495 1.643 6
TNF O1 O 6.897 3.143 7
TNF O21 O 10.794 0.892 8
TNF O22 O 9.495 3.143 9
TNF O41 O 5.598 -3.607 10
TNF C6 C 5.598 0.892 11
TNF C5 C 5.598 -0.608 12
TNF O42 O 8.196 -3.607 13
TNF N6 N 4.299 1.643 14
TNF O61 O 3.000 0.892 15
TNF O62 O 4.299 3.143 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
TNF C1 C2 DOUBLE NONE 1
TNF C1 O1 SINGLE NONE 2
TNF C1 C6 SINGLE NONE 3
TNF C2 C3 SINGLE NONE 4
TNF C2 N2 SINGLE NONE 5
TNF C3 C4 DOUBLE NONE 6
TNF C4 N4 SINGLE NONE 7
TNF C4 C5 SINGLE NONE 8
TNF N4 O41 SINGLE NONE 9
TNF N4 O42 DOUBLE NONE 10
TNF N2 O21 SINGLE NONE 11
TNF N2 O22 DOUBLE NONE 12
TNF C6 C5 DOUBLE NONE 13
TNF C6 N6 SINGLE NONE 14
TNF N6 O61 SINGLE NONE 15
TNF N6 O62 DOUBLE NONE 16
#
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
TNF MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
TNF 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
TNF C1 S1 1
TNF C2 S1 1
TNF C3 S1 1
TNF C4 S1 1
TNF C6 S1 1
TNF C5 S1 1
TNF C1 F1 1
TNF C2 F1 1
TNF C3 F1 1
TNF C4 F1 1
TNF C5 F1 1
TNF C6 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id TNF
_pdbe_chem_comp_rdkit_properties.exactmw 228.997
_pdbe_chem_comp_rdkit_properties.amw 229.104
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 10
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 19
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 10
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_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 90.486
_pdbe_chem_comp_rdkit_properties.tpsa 149.650
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.487
_pdbe_chem_comp_rdkit_properties.CrippenMR 44.988
_pdbe_chem_comp_rdkit_properties.chi0v 7.199
_pdbe_chem_comp_rdkit_properties.chi1v 3.470
_pdbe_chem_comp_rdkit_properties.chi2v 1.451
_pdbe_chem_comp_rdkit_properties.chi3v 1.451
_pdbe_chem_comp_rdkit_properties.chi4v 0.830
_pdbe_chem_comp_rdkit_properties.chi0n 10.199
_pdbe_chem_comp_rdkit_properties.chi1n 4.879
_pdbe_chem_comp_rdkit_properties.chi2n 1.451
_pdbe_chem_comp_rdkit_properties.chi3n 1.451
_pdbe_chem_comp_rdkit_properties.chi4n 0.830
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.780
_pdbe_chem_comp_rdkit_properties.kappa1 7.504
_pdbe_chem_comp_rdkit_properties.kappa2 3.763
_pdbe_chem_comp_rdkit_properties.kappa3 1.842
_pdbe_chem_comp_rdkit_properties.Phi 1.765
#
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
TNF UniChem ChEMBL CHEMBL108541
TNF UniChem DrugBank DB03651
TNF UniChem PDBe TNF
TNF UniChem ChEBI 46149
TNF UniChem ZINC ZINC000001883067
TNF UniChem atlas TNF
TNF UniChem fdasrs A49OS0F91S
TNF UniChem HMDB HMDB0256536
TNF UniChem NMRShiftDB 10015990
TNF UniChem 'EPA CompTox Dashboard' DTXSID4025909
TNF UniChem DrugCentral 4626
TNF UniChem BRENDA 221524
TNF UniChem ChemicalBook CB1195194
TNF UniChem rxnorm 'PICRIC ACID'
TNF UniChem 'Probes And Drugs' PD006733
TNF UniChem eMolecules 487621
TNF UniChem SureChEMBL SCHEMBL8745
TNF UniChem 'PubChem TPHARMA' 14843796
TNF UniChem PubChem 6954
TNF UniChem Mcule MCULE-8917344355
TNF UniChem ACTor 189195-39-9
TNF UniChem ACTor 88-89-1
TNF UniChem BindingDb 34612
TNF UniChem BRENDA 202770
#
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
TNF C1 -1.085 0.618 -0.071 ETKDGv3 1
TNF C2 -1.014 -0.547 -0.755 ETKDGv3 2
TNF C3 0.259 -1.315 -0.751 ETKDGv3 3
TNF C4 1.332 -0.878 -0.072 ETKDGv3 4
TNF N4 2.565 -1.621 -0.088 ETKDGv3 5
TNF N2 -2.128 -1.038 -1.528 ETKDGv3 6
TNF O1 -2.228 1.413 -0.182 ETKDGv3 7
TNF O21 -3.414 -0.624 -1.267 ETKDGv3 8
TNF O22 -1.951 -1.922 -2.391 ETKDGv3 9
TNF O41 2.676 -2.790 -0.805 ETKDGv3 10
TNF C6 0.079 1.074 0.749 ETKDGv3 11
TNF C5 1.224 0.373 0.715 ETKDGv3 12
TNF O42 3.558 -1.210 0.548 ETKDGv3 13
TNF N6 -0.018 2.226 1.603 ETKDGv3 14
TNF O61 1.094 2.996 1.855 ETKDGv3 15
TNF O62 -1.055 2.431 2.265 ETKDGv3 16
TNF H3 0.315 -2.237 -1.315 ETKDGv3 17
TNF H1 -2.279 2.356 0.180 ETKDGv3 18
TNF H5 2.069 0.695 1.311 ETKDGv3 19
#