data_VI5
#
_chem_comp.id VI5
_chem_comp.name N-(3-fluorophenyl)-N~2~-methylglycinamide
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H11 F N2 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-08-29
_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 182.195
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VI5
_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 7FOB
_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
VI5 N1 N1 N 0 1 N N N N N N -3.292 13.646 -33.793 -0.537 -1.102 0.363 N1 VI5 1
VI5 C7 C1 C 0 1 Y N N N N N -0.100 13.087 -35.558 2.580 0.834 0.096 C7 VI5 2
VI5 C8 C2 C 0 1 Y N N N N N -1.138 13.789 -34.939 1.243 0.527 0.281 C8 VI5 3
VI5 C1 C3 C 0 1 N N N N N N -4.781 15.400 -32.980 -2.938 -0.513 0.290 C1 VI5 4
VI5 C5 C4 C 0 1 Y N N N N N -1.215 11.015 -35.253 3.061 -1.483 -0.297 C5 VI5 5
VI5 C6 C5 C 0 1 Y N N N N N -0.127 11.714 -35.718 3.487 -0.172 -0.193 C6 VI5 6
VI5 C4 C6 C 0 1 Y N N N N N -2.263 11.665 -34.637 1.728 -1.794 -0.113 C4 VI5 7
VI5 C3 C7 C 0 1 Y N N N N N -2.211 13.040 -34.483 0.814 -0.789 0.176 C3 VI5 8
VI5 C2 C8 C 0 1 N N N N N N -3.556 14.972 -33.829 -1.490 -0.227 -0.015 C2 VI5 9
VI5 F F1 F 0 1 N N N N N N 0.943 13.743 -36.015 2.999 2.114 0.192 F VI5 10
VI5 O O1 O 0 1 N N N N N N -2.931 15.814 -34.454 -1.182 0.789 -0.600 O VI5 11
VI5 N N2 N 0 1 N N N N N N -5.577 16.475 -33.716 -3.771 0.584 -0.221 N VI5 12
VI5 C C9 C 0 1 N N N N N N -4.809 17.778 -33.772 -5.193 0.339 0.058 C VI5 13
VI5 H1 H1 H 0 1 N N N N N N -3.893 13.060 -33.249 -0.787 -1.950 0.761 H1 VI5 14
VI5 H2 H2 H 0 1 N N N N N N -1.105 14.862 -34.822 0.535 1.311 0.507 H2 VI5 15
VI5 H3 H3 H 0 1 N N N N N N -5.425 14.526 -32.804 -3.233 -1.447 -0.189 H3 VI5 16
VI5 H4 H4 H 0 1 N N N N N N -4.434 15.800 -32.016 -3.072 -0.599 1.368 H4 VI5 17
VI5 H5 H5 H 0 1 N N N N N N -1.249 9.942 -35.372 3.771 -2.265 -0.523 H5 VI5 18
VI5 H6 H6 H 0 1 N N N N N N 0.692 11.200 -36.200 4.530 0.069 -0.337 H6 VI5 19
VI5 H7 H7 H 0 1 N N N N N N -3.116 11.108 -34.278 1.396 -2.818 -0.196 H7 VI5 20
VI5 H8 H8 H 0 1 N N N N N N -6.442 16.626 -33.238 -3.616 0.726 -1.208 H8 VI5 21
VI5 H10 H10 H 0 1 N N N N N N -5.405 18.533 -34.306 -5.503 -0.589 -0.422 H10 VI5 22
VI5 H11 H11 H 0 1 N N N N N N -4.606 18.128 -32.749 -5.343 0.259 1.135 H11 VI5 23
VI5 H12 H12 H 0 1 N N N N N N -3.857 17.620 -34.301 -5.787 1.166 -0.331 H12 VI5 24
#
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
VI5 F C7 SING N N 1
VI5 C6 C7 DOUB Y N 2
VI5 C6 C5 SING Y N 3
VI5 C7 C8 SING Y N 4
VI5 C5 C4 DOUB Y N 5
VI5 C8 C3 DOUB Y N 6
VI5 C4 C3 SING Y N 7
VI5 C3 N1 SING N N 8
VI5 O C2 DOUB N N 9
VI5 C2 N1 SING N N 10
VI5 C2 C1 SING N N 11
VI5 C N SING N N 12
VI5 N C1 SING N N 13
VI5 N1 H1 SING N N 14
VI5 C8 H2 SING N N 15
VI5 C1 H3 SING N N 16
VI5 C1 H4 SING N N 17
VI5 C5 H5 SING N N 18
VI5 C6 H6 SING N N 19
VI5 C4 H7 SING N N 20
VI5 N H8 SING N N 21
VI5 C H10 SING N N 22
VI5 C H11 SING N N 23
VI5 C H12 SING N N 24
#
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
VI5 SMILES ACDLabs 12.01 O=C(Nc1cccc(F)c1)CNC
VI5 InChI InChI 1.06 InChI=1S/C9H11FN2O/c1-11-6-9(13)12-8-4-2-3-7(10)5-8/h2-5,11H,6H2,1H3,(H,12,13)
VI5 InChIKey InChI 1.06 RQKDJHXAPOJIDX-UHFFFAOYSA-N
VI5 SMILES_CANONICAL CACTVS 3.385 CNCC(=O)Nc1cccc(F)c1
VI5 SMILES CACTVS 3.385 CNCC(=O)Nc1cccc(F)c1
VI5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CNCC(=O)Nc1cccc(c1)F
VI5 SMILES "OpenEye OEToolkits" 2.0.7 CNCC(=O)Nc1cccc(c1)F
#
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
VI5 "SYSTEMATIC NAME" ACDLabs 12.01 N-(3-fluorophenyl)-N~2~-methylglycinamide
VI5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 ~{N}-(3-fluorophenyl)-2-(methylamino)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
VI5 'Create component' 2022-08-29 RCSB
VI5 '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
VI5 N1 N 5.598 0.000 1
VI5 C7 C 4.299 -3.750 2
VI5 C8 C 4.299 -2.250 3
VI5 C1 C 6.897 2.250 4
VI5 C5 C 6.897 -3.750 5
VI5 C6 C 5.598 -4.500 6
VI5 C4 C 6.897 -2.250 7
VI5 C3 C 5.598 -1.500 8
VI5 C2 C 6.897 0.750 9
VI5 F F 3.000 -4.500 10
VI5 O O 8.196 0.000 11
VI5 N N 8.196 3.000 12
VI5 C C 8.196 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
VI5 F C7 SINGLE NONE 1
VI5 C6 C7 DOUBLE NONE 2
VI5 C6 C5 SINGLE NONE 3
VI5 C7 C8 SINGLE NONE 4
VI5 C5 C4 DOUBLE NONE 5
VI5 C8 C3 DOUBLE NONE 6
VI5 C4 C3 SINGLE NONE 7
VI5 C3 N1 SINGLE NONE 8
VI5 O C2 DOUBLE NONE 9
VI5 C2 N1 SINGLE NONE 10
VI5 C2 C1 SINGLE NONE 11
VI5 C N SINGLE NONE 12
VI5 N C1 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
VI5 MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
VI5 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
VI5 peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
VI5 phenyl F3 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
VI5 C7 S1 1
VI5 C8 S1 1
VI5 C5 S1 1
VI5 C6 S1 1
VI5 C4 S1 1
VI5 C3 S1 1
VI5 N1 F1 1
VI5 C2 F1 1
VI5 O F1 1
VI5 C1 F1 1
VI5 O F2 1
VI5 C2 F2 1
VI5 C1 F2 1
VI5 N F2 1
VI5 C7 F3 1
VI5 C6 F3 1
VI5 C5 F3 1
VI5 C4 F3 1
VI5 C3 F3 1
VI5 C8 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id VI5
_pdbe_chem_comp_rdkit_properties.exactmw 182.086
_pdbe_chem_comp_rdkit_properties.amw 182.198
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.222
_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 91.524
_pdbe_chem_comp_rdkit_properties.tpsa 41.130
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.603
_pdbe_chem_comp_rdkit_properties.CrippenMR 48.132
_pdbe_chem_comp_rdkit_properties.chi0v 6.181
_pdbe_chem_comp_rdkit_properties.chi1v 3.038
_pdbe_chem_comp_rdkit_properties.chi2v 0.946
_pdbe_chem_comp_rdkit_properties.chi3v 0.946
_pdbe_chem_comp_rdkit_properties.chi4v 0.542
_pdbe_chem_comp_rdkit_properties.chi0n 17.181
_pdbe_chem_comp_rdkit_properties.chi1n 8.432
_pdbe_chem_comp_rdkit_properties.chi2n 0.946
_pdbe_chem_comp_rdkit_properties.chi3n 0.946
_pdbe_chem_comp_rdkit_properties.chi4n 0.542
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.420
_pdbe_chem_comp_rdkit_properties.kappa1 2.542
_pdbe_chem_comp_rdkit_properties.kappa2 4.568
_pdbe_chem_comp_rdkit_properties.kappa3 3.209
_pdbe_chem_comp_rdkit_properties.Phi 0.893
#
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
VI5 UniChem PDBe VI5
VI5 UniChem ZINC ZINC000003298516
VI5 UniChem SureChEMBL SCHEMBL7141741
VI5 UniChem PubChem 2414098
#
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
VI5 N1 0.110 0.336 -0.495 ETKDGv3 1
VI5 C7 -3.436 -0.959 -0.155 ETKDGv3 2
VI5 C8 -2.029 -0.821 -0.587 ETKDGv3 3
VI5 C1 2.357 -0.443 -1.400 ETKDGv3 4
VI5 C5 -3.117 0.987 1.280 ETKDGv3 5
VI5 C6 -3.953 -0.101 0.733 ETKDGv3 6
VI5 C4 -1.841 1.111 0.894 ETKDGv3 7
VI5 C3 -1.253 0.154 -0.074 ETKDGv3 8
VI5 C2 1.007 -0.739 -0.818 ETKDGv3 9
VI5 F -4.205 -1.952 -0.666 ETKDGv3 10
VI5 O 0.700 -1.934 -0.556 ETKDGv3 11
VI5 N 3.407 -0.616 -0.388 ETKDGv3 12
VI5 C 3.462 0.531 0.523 ETKDGv3 13
VI5 H1 0.500 1.304 -0.465 ETKDGv3 14
VI5 H2 -1.650 -1.498 -1.341 ETKDGv3 15
VI5 H3 2.383 0.579 -1.841 ETKDGv3 16
VI5 H4 2.536 -1.157 -2.234 ETKDGv3 17
VI5 H5 -3.541 1.685 1.991 ETKDGv3 18
VI5 H6 -4.983 -0.198 1.050 ETKDGv3 19
VI5 H7 -1.235 1.912 1.298 ETKDGv3 20
VI5 H8 4.325 -0.657 -0.888 ETKDGv3 21
VI5 H10 3.648 1.475 -0.034 ETKDGv3 22
VI5 H11 2.517 0.616 1.101 ETKDGv3 23
VI5 H12 4.290 0.384 1.248 ETKDGv3 24
#