data_VYZ
#
_chem_comp.id VYZ
_chem_comp.name N-(4-nitrophenyl)acetamide
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H8 N2 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-09-02
_chem_comp.pdbx_modified_date 2022-10-28
_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 180.161
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VYZ
_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 7FNV
_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
VYZ N1 N1 N 0 1 N N N N N N 10.914 0.997 -12.800 3.177 -0.187 0.071 N1 VYZ 1
VYZ C7 C1 C 0 1 Y N N N N N 9.977 -0.051 -9.329 -0.496 -0.784 -0.384 C7 VYZ 2
VYZ O1 O1 O 0 1 N N N N N N 10.916 -0.063 -13.354 3.933 0.743 0.291 O1 VYZ 3
VYZ C1 C2 C 0 1 N N N N N N 9.230 0.312 -6.498 -3.251 -0.198 0.108 C1 VYZ 4
VYZ C5 C3 C 0 1 Y N N N N N 10.576 1.051 -11.366 1.720 0.052 -0.035 C5 VYZ 5
VYZ C6 C4 C 0 1 Y N N N N N 10.277 -0.114 -10.682 0.864 -1.004 -0.284 C6 VYZ 6
VYZ C4 C5 C 0 1 Y N N N N N 10.576 2.283 -10.737 1.219 1.332 0.115 C4 VYZ 7
VYZ C3 C6 C 0 1 Y N N N N N 10.282 2.349 -9.401 -0.140 1.558 0.022 C3 VYZ 8
VYZ C2 C7 C 0 1 Y N N N N N 9.983 1.185 -8.683 -1.003 0.500 -0.234 C2 VYZ 9
VYZ O2 O2 O 0 1 N N N N N N 11.175 2.021 -13.363 3.621 -1.313 -0.067 O2 VYZ 10
VYZ N N2 N 0 1 N N N N N N 9.707 1.324 -7.321 -2.379 0.727 -0.339 N VYZ 11
VYZ O O3 O 0 1 N N N N N N 9.012 -0.805 -6.918 -2.846 -1.262 0.525 O VYZ 12
VYZ C C8 C 0 1 N N N N N N 9.013 0.719 -5.063 -4.731 0.090 0.091 C VYZ 13
VYZ H1 H1 H 0 1 N N N N N N 9.741 -0.951 -8.781 -1.164 -1.609 -0.583 H1 VYZ 14
VYZ H2 H2 H 0 1 N N N N N N 10.277 -1.064 -11.197 1.259 -2.003 -0.401 H2 VYZ 15
VYZ H3 H3 H 0 1 N N N N N N 10.805 3.181 -11.292 1.890 2.155 0.310 H3 VYZ 16
VYZ H4 H4 H 0 1 N N N N N N 10.281 3.305 -8.898 -0.531 2.558 0.140 H4 VYZ 17
VYZ H5 H5 H 0 1 N N N N N N 9.865 2.220 -6.907 -2.706 1.551 -0.735 H5 VYZ 18
VYZ H6 H6 H 0 1 N N N N N N 8.638 -0.142 -4.490 -4.902 1.087 -0.315 H6 VYZ 19
VYZ H7 H7 H 0 1 N N N N N N 9.965 1.060 -4.631 -5.237 -0.647 -0.532 H7 VYZ 20
VYZ H8 H8 H 0 1 N N N N N N 8.278 1.536 -5.021 -5.123 0.039 1.106 H8 VYZ 21
#
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
VYZ O2 N1 DOUB N N 1
VYZ O1 N1 DOUB N N 2
VYZ N1 C5 SING N N 3
VYZ C5 C4 DOUB Y N 4
VYZ C5 C6 SING Y N 5
VYZ C4 C3 SING Y N 6
VYZ C6 C7 DOUB Y N 7
VYZ C3 C2 DOUB Y N 8
VYZ C7 C2 SING Y N 9
VYZ C2 N SING N N 10
VYZ N C1 SING N N 11
VYZ O C1 DOUB N N 12
VYZ C1 C SING N N 13
VYZ C7 H1 SING N N 14
VYZ C6 H2 SING N N 15
VYZ C4 H3 SING N N 16
VYZ C3 H4 SING N N 17
VYZ N H5 SING N N 18
VYZ C H6 SING N N 19
VYZ C H7 SING N N 20
VYZ C H8 SING N N 21
#
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
VYZ SMILES ACDLabs 12.01 O=C(C)Nc1ccc(cc1)N(=O)=O
VYZ InChI InChI 1.06 InChI=1S/C8H8N2O3/c1-6(11)9-7-2-4-8(5-3-7)10(12)13/h2-5H,1H3,(H,9,11)
VYZ InChIKey InChI 1.06 NQRLPDFELNCFHW-UHFFFAOYSA-N
VYZ SMILES_CANONICAL CACTVS 3.385 CC(=O)Nc1ccc(cc1)[N](=O)=O
VYZ SMILES CACTVS 3.385 CC(=O)Nc1ccc(cc1)[N](=O)=O
VYZ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CC(=O)Nc1ccc(cc1)N(=O)=O
VYZ SMILES "OpenEye OEToolkits" 2.0.7 CC(=O)Nc1ccc(cc1)N(=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
VYZ "SYSTEMATIC NAME" ACDLabs 12.01 N-(4-nitrophenyl)acetamide
VYZ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 ~{N}-(4-nitrophenyl)ethanamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VYZ 'Create component' 2022-09-02 RCSB
VYZ 'Initial release' 2022-11-02 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
VYZ N1 N 4.299 -3.750 1
VYZ C7 C 3.000 0.000 2
VYZ O1 O 5.598 -4.500 3
VYZ C1 C 5.598 3.000 4
VYZ C5 C 4.299 -2.250 5
VYZ C6 C 3.000 -1.500 6
VYZ C4 C 5.598 -1.500 7
VYZ C3 C 5.598 0.000 8
VYZ C2 C 4.299 0.750 9
VYZ O2 O 3.000 -4.500 10
VYZ N N 4.299 2.250 11
VYZ O O 6.897 2.250 12
VYZ C C 5.598 4.500 13
#
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
VYZ O2 N1 SINGLE NONE 1
VYZ O1 N1 DOUBLE NONE 2
VYZ N1 C5 SINGLE NONE 3
VYZ C5 C4 DOUBLE NONE 4
VYZ C5 C6 SINGLE NONE 5
VYZ C4 C3 SINGLE NONE 6
VYZ C6 C7 DOUBLE NONE 7
VYZ C3 C2 DOUBLE NONE 8
VYZ C7 C2 SINGLE NONE 9
VYZ C2 N SINGLE NONE 10
VYZ N C1 SINGLE NONE 11
VYZ O C1 DOUBLE NONE 12
VYZ C1 C SINGLE NONE 13
#
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
VYZ MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
VYZ amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
VYZ phenyl F2 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
VYZ C7 S1 1
VYZ C5 S1 1
VYZ C6 S1 1
VYZ C4 S1 1
VYZ C3 S1 1
VYZ C2 S1 1
VYZ N F1 1
VYZ C1 F1 1
VYZ O F1 1
VYZ C F1 1
VYZ C7 F2 1
VYZ C6 F2 1
VYZ C5 F2 1
VYZ C4 F2 1
VYZ C3 F2 1
VYZ C2 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id VYZ
_pdbe_chem_comp_rdkit_properties.exactmw 180.053
_pdbe_chem_comp_rdkit_properties.amw 180.163
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 21
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.125
_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 85.823
_pdbe_chem_comp_rdkit_properties.tpsa 72.240
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.792
_pdbe_chem_comp_rdkit_properties.CrippenMR 45.752
_pdbe_chem_comp_rdkit_properties.chi0v 6.119
_pdbe_chem_comp_rdkit_properties.chi1v 2.990
_pdbe_chem_comp_rdkit_properties.chi2v 0.995
_pdbe_chem_comp_rdkit_properties.chi3v 0.995
_pdbe_chem_comp_rdkit_properties.chi4v 0.548
_pdbe_chem_comp_rdkit_properties.chi0n 14.119
_pdbe_chem_comp_rdkit_properties.chi1n 6.937
_pdbe_chem_comp_rdkit_properties.chi2n 0.995
_pdbe_chem_comp_rdkit_properties.chi3n 0.995
_pdbe_chem_comp_rdkit_properties.chi4n 0.548
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.910
_pdbe_chem_comp_rdkit_properties.kappa1 3.098
_pdbe_chem_comp_rdkit_properties.kappa2 3.661
_pdbe_chem_comp_rdkit_properties.kappa3 2.551
_pdbe_chem_comp_rdkit_properties.Phi 0.873
#
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
VYZ UniChem ChEMBL CHEMBL131469
VYZ UniChem PDBe VYZ
VYZ UniChem ZINC ZINC000016321384
VYZ UniChem fdasrs PH3B066365
VYZ UniChem 'PubChem TPHARMA' 14794103
VYZ UniChem PubChem 7691
VYZ UniChem ACTor 104-04-1
VYZ UniChem ACTor 68239-25-8
VYZ UniChem BRENDA 133571
VYZ UniChem BRENDA 4851
VYZ UniChem BRENDA 50853
VYZ UniChem BRENDA 9896
VYZ UniChem ChemicalBook CB1191136
VYZ UniChem 'EPA CompTox Dashboard' DTXSID5059290
VYZ UniChem eMolecules 27678428
VYZ UniChem eMolecules 477225
VYZ UniChem SureChEMBL SCHEMBL642700
VYZ UniChem Mcule MCULE-4712987402
#
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
VYZ N1 4.052 -0.166 0.335 ETKDGv3 1
VYZ C7 0.409 -1.041 0.079 ETKDGv3 2
VYZ O1 4.548 -1.306 0.448 ETKDGv3 3
VYZ C1 -2.591 -0.370 0.416 ETKDGv3 4
VYZ C5 2.628 -0.002 0.203 ETKDGv3 5
VYZ C6 1.734 -1.189 0.193 ETKDGv3 6
VYZ C4 2.085 1.222 0.079 ETKDGv3 7
VYZ C3 0.622 1.384 -0.053 ETKDGv3 8
VYZ C2 -0.190 0.314 -0.030 ETKDGv3 9
VYZ O2 4.890 0.926 0.340 ETKDGv3 10
VYZ N -1.609 0.496 -0.173 ETKDGv3 11
VYZ O -2.267 -1.194 1.314 ETKDGv3 12
VYZ C -4.029 -0.228 0.038 ETKDGv3 13
VYZ H1 -0.217 -1.923 0.037 ETKDGv3 14
VYZ H2 2.150 -2.186 0.264 ETKDGv3 15
VYZ H3 2.704 2.109 0.076 ETKDGv3 16
VYZ H4 0.212 2.381 -0.152 ETKDGv3 17
VYZ H5 -1.953 1.345 -0.678 ETKDGv3 18
VYZ H6 -4.116 -0.027 -1.050 ETKDGv3 19
VYZ H7 -4.584 -1.161 0.273 ETKDGv3 20
VYZ H8 -4.478 0.615 0.603 ETKDGv3 21
#