data_VQ6
#
_chem_comp.id VQ6
_chem_comp.name "(2R)-(cyclopropylamino)(2,6-difluorophenyl)acetic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H11 F2 N O2"
_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 227.207
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VQ6
_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 7FKR
_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
VQ6 C7 C1 C 0 1 N N N N N N 53.373 20.313 19.206 -0.742 -1.412 -0.919 C7 VQ6 1
VQ6 C8 C2 C 0 1 N N N N N N 54.794 18.978 21.852 -2.703 0.206 0.908 C8 VQ6 2
VQ6 C9 C3 C 0 1 N N N N N N 55.180 18.254 23.106 -4.013 0.609 0.230 C9 VQ6 3
VQ6 O1 O1 O 0 1 N N N N N N 53.907 19.328 18.746 0.025 -2.496 -1.115 O1 VQ6 4
VQ6 C1 C4 C 0 1 Y N N N N N 49.285 20.442 20.694 2.484 1.573 -0.816 C1 VQ6 5
VQ6 C5 C5 C 0 1 Y N N N N N 50.009 22.058 22.217 3.197 0.068 0.906 C5 VQ6 6
VQ6 C6 C6 C 0 1 N N R N N N 53.047 20.406 20.854 -0.482 -0.507 0.258 C6 VQ6 7
VQ6 C4 C7 C 0 1 Y N N N N N 51.287 21.707 22.010 1.912 -0.442 0.992 C4 VQ6 8
VQ6 C3 C8 C 0 1 Y N N N N N 51.645 20.724 21.124 0.916 0.048 0.166 C3 VQ6 9
VQ6 C2 C9 C 0 1 Y N N N N N 50.576 20.083 20.488 1.201 1.060 -0.735 C2 VQ6 10
VQ6 F1 F1 F 0 1 N N N N N N 50.758 19.059 19.709 0.227 1.547 -1.534 F1 VQ6 11
VQ6 F F2 F 0 1 N N N N N N 52.156 22.292 22.721 1.635 -1.427 1.875 F VQ6 12
VQ6 C C10 C 0 1 Y N N N N N 49.019 21.429 21.550 3.481 1.075 0.002 C VQ6 13
VQ6 O O2 O 0 1 N N N N N N 52.990 21.368 18.646 -1.638 -1.159 -1.689 O VQ6 14
VQ6 N N1 N 0 1 N N N N N N 53.392 19.049 21.447 -1.449 0.598 0.250 N VQ6 15
VQ6 C10 C11 C 0 1 N N N N N N 55.198 19.734 23.066 -3.564 1.319 1.508 C10 VQ6 16
VQ6 H1 H1 H 0 1 N N N N N N 55.534 18.947 21.039 -2.680 -0.750 1.432 H1 VQ6 17
VQ6 H2 H2 H 0 1 N N N N N N 54.415 17.729 23.696 -3.946 1.164 -0.705 H2 VQ6 18
VQ6 H3 H3 H 0 1 N N N N N N 56.125 17.693 23.149 -4.853 -0.083 0.307 H3 VQ6 19
VQ6 H4 H4 H 0 1 N N N N N N 54.024 19.439 17.810 -0.180 -3.046 -1.883 H4 VQ6 20
VQ6 H5 H5 H 0 1 N N N N N N 48.485 19.937 20.173 2.708 2.360 -1.521 H5 VQ6 21
VQ6 H6 H6 H 0 1 N N N N N N 49.772 22.845 22.918 3.976 -0.320 1.545 H6 VQ6 22
VQ6 H7 H7 H 0 1 N N N N N N 53.706 21.176 21.283 -0.587 -1.075 1.183 H7 VQ6 23
VQ6 H8 H8 H 0 1 N N N N N N 47.995 21.730 21.712 4.483 1.473 -0.064 H8 VQ6 24
VQ6 H9 H9 H 0 1 N N N N N N 52.815 18.889 22.248 -1.059 1.424 0.678 H9 VQ6 25
VQ6 H11 H11 H 0 1 N N N N N N 56.158 20.271 23.083 -4.107 1.096 2.426 H11 VQ6 26
VQ6 H12 H12 H 0 1 N N N N N N 54.447 20.307 23.630 -3.201 2.343 1.413 H12 VQ6 27
#
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
VQ6 O C7 DOUB N N 1
VQ6 O1 C7 SING N N 2
VQ6 C7 C6 SING N N 3
VQ6 F1 C2 SING N N 4
VQ6 C2 C1 DOUB Y N 5
VQ6 C2 C3 SING Y N 6
VQ6 C1 C SING Y N 7
VQ6 C6 C3 SING N N 8
VQ6 C6 N SING N N 9
VQ6 C3 C4 DOUB Y N 10
VQ6 N C8 SING N N 11
VQ6 C C5 DOUB Y N 12
VQ6 C8 C10 SING N N 13
VQ6 C8 C9 SING N N 14
VQ6 C4 C5 SING Y N 15
VQ6 C4 F SING N N 16
VQ6 C10 C9 SING N N 17
VQ6 C8 H1 SING N N 18
VQ6 C9 H2 SING N N 19
VQ6 C9 H3 SING N N 20
VQ6 O1 H4 SING N N 21
VQ6 C1 H5 SING N N 22
VQ6 C5 H6 SING N N 23
VQ6 C6 H7 SING N N 24
VQ6 C H8 SING N N 25
VQ6 N H9 SING N N 26
VQ6 C10 H11 SING N N 27
VQ6 C10 H12 SING N N 28
#
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
VQ6 SMILES ACDLabs 12.01 OC(=O)C(NC1CC1)c1c(F)cccc1F
VQ6 InChI InChI 1.06 InChI=1S/C11H11F2NO2/c12-7-2-1-3-8(13)9(7)10(11(15)16)14-6-4-5-6/h1-3,6,10,14H,4-5H2,(H,15,16)/t10-/m1/s1
VQ6 InChIKey InChI 1.06 LLCVJLSDVSYPMV-SNVBAGLBSA-N
VQ6 SMILES_CANONICAL CACTVS 3.385 OC(=O)[C@H](NC1CC1)c2c(F)cccc2F
VQ6 SMILES CACTVS 3.385 OC(=O)[CH](NC1CC1)c2c(F)cccc2F
VQ6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1cc(c(c(c1)F)[C@H](C(=O)O)NC2CC2)F
VQ6 SMILES "OpenEye OEToolkits" 2.0.7 c1cc(c(c(c1)F)C(C(=O)O)NC2CC2)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
VQ6 "SYSTEMATIC NAME" ACDLabs 12.01 "(2R)-(cyclopropylamino)(2,6-difluorophenyl)acetic acid"
VQ6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{R})-2-[2,6-bis(fluoranyl)phenyl]-2-(cyclopropylamino)ethanoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VQ6 'Create component' 2022-09-02 RCSB
VQ6 '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
VQ6 C7 C 4.299 1.226 1
VQ6 C8 C 6.897 2.725 2
VQ6 C9 C 6.147 4.024 3
VQ6 O1 O 3.000 0.475 4
VQ6 C1 C 6.897 -3.275 5
VQ6 C5 C 4.299 -3.275 6
VQ6 C6 C 5.598 0.475 7
VQ6 C4 C 4.299 -1.774 8
VQ6 C3 C 5.598 -1.024 9
VQ6 C2 C 6.897 -1.774 10
VQ6 F1 F 8.196 -1.024 11
VQ6 F F 3.000 -1.024 12
VQ6 C C 5.598 -4.024 13
VQ6 O O 4.299 2.725 14
VQ6 N N 6.897 1.226 15
VQ6 C10 C 7.647 4.024 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
VQ6 O C7 DOUBLE NONE 1
VQ6 O1 C7 SINGLE NONE 2
VQ6 C7 C6 SINGLE NONE 3
VQ6 F1 C2 SINGLE NONE 4
VQ6 C2 C1 DOUBLE NONE 5
VQ6 C2 C3 SINGLE NONE 6
VQ6 C1 C SINGLE NONE 7
VQ6 C6 C3 SINGLE NONE 8
VQ6 C6 N SINGLE BEGINDASH 9
VQ6 C3 C4 DOUBLE NONE 10
VQ6 N C8 SINGLE NONE 11
VQ6 C C5 DOUBLE NONE 12
VQ6 C8 C10 SINGLE NONE 13
VQ6 C8 C9 SINGLE NONE 14
VQ6 C4 C5 SINGLE NONE 15
VQ6 C4 F SINGLE NONE 16
VQ6 C10 C9 SINGLE NONE 17
#
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
VQ6 MurckoScaffold S1 scaffold c1ccc(CNC2CC2)cc1 InChI=1S/C10H13N/c1-2-4-9(5-3-1)8-11-10-6-7-10/h1-5,10-11H,6-8H2 USBAUXJPPHVCTF-UHFFFAOYSA-N
VQ6 cyclopropane F1 fragment C1CC1 InChI=1S/C3H6/c1-2-3-1/h1-3H2 LVZWSLJZHVFIQJ-UHFFFAOYSA-N
VQ6 peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
VQ6 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
VQ6 C8 S1 1
VQ6 C9 S1 1
VQ6 C1 S1 1
VQ6 C5 S1 1
VQ6 C6 S1 1
VQ6 C4 S1 1
VQ6 C3 S1 1
VQ6 C2 S1 1
VQ6 C S1 1
VQ6 N S1 1
VQ6 C10 S1 1
VQ6 C8 F1 1
VQ6 C10 F1 1
VQ6 C9 F1 1
VQ6 O F2 1
VQ6 C7 F2 1
VQ6 C6 F2 1
VQ6 N F2 1
VQ6 C1 F3 1
VQ6 C2 F3 1
VQ6 C3 F3 1
VQ6 C4 F3 1
VQ6 C5 F3 1
VQ6 C F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id VQ6
_pdbe_chem_comp_rdkit_properties.exactmw 227.076
_pdbe_chem_comp_rdkit_properties.amw 227.210
_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 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 27
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.364
_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 1
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 106.686
_pdbe_chem_comp_rdkit_properties.tpsa 49.330
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.788
_pdbe_chem_comp_rdkit_properties.CrippenMR 52.627
_pdbe_chem_comp_rdkit_properties.chi0v 7.520
_pdbe_chem_comp_rdkit_properties.chi1v 3.983
_pdbe_chem_comp_rdkit_properties.chi2v 1.674
_pdbe_chem_comp_rdkit_properties.chi3v 1.674
_pdbe_chem_comp_rdkit_properties.chi4v 0.970
_pdbe_chem_comp_rdkit_properties.chi0n 18.520
_pdbe_chem_comp_rdkit_properties.chi1n 9.339
_pdbe_chem_comp_rdkit_properties.chi2n 1.674
_pdbe_chem_comp_rdkit_properties.chi3n 1.674
_pdbe_chem_comp_rdkit_properties.chi4n 0.970
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.490
_pdbe_chem_comp_rdkit_properties.kappa1 3.768
_pdbe_chem_comp_rdkit_properties.kappa2 4.173
_pdbe_chem_comp_rdkit_properties.kappa3 2.190
_pdbe_chem_comp_rdkit_properties.Phi 0.983
#
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
VQ6 UniChem PDBe VQ6
VQ6 UniChem ZINC ZINC000037183603
VQ6 UniChem PubChem 93280638
#
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
VQ6 C7 0.309 -2.497 0.539 ETKDGv3 1
VQ6 C8 1.868 0.139 0.292 ETKDGv3 2
VQ6 C9 3.010 1.062 -0.107 ETKDGv3 3
VQ6 O1 1.573 -2.890 0.971 ETKDGv3 4
VQ6 C1 -2.707 0.998 -1.248 ETKDGv3 5
VQ6 C5 -2.343 1.033 1.158 ETKDGv3 6
VQ6 C6 0.159 -1.430 -0.519 ETKDGv3 7
VQ6 C4 -1.266 0.038 0.976 ETKDGv3 8
VQ6 C3 -0.976 -0.440 -0.259 ETKDGv3 9
VQ6 C2 -1.738 0.092 -1.425 ETKDGv3 10
VQ6 F1 -1.450 -0.329 -2.683 ETKDGv3 11
VQ6 F -0.575 -0.363 2.073 ETKDGv3 12
VQ6 C -3.027 1.487 0.105 ETKDGv3 13
VQ6 O -0.711 -3.089 0.984 ETKDGv3 14
VQ6 N 1.437 -0.750 -0.803 ETKDGv3 15
VQ6 C10 1.610 1.626 0.085 ETKDGv3 16
VQ6 H1 1.951 -0.266 1.323 ETKDGv3 17
VQ6 H2 3.710 1.316 0.717 ETKDGv3 18
VQ6 H3 3.333 1.012 -1.169 ETKDGv3 19
VQ6 H4 1.682 -3.622 1.663 ETKDGv3 20
VQ6 H5 -3.256 1.381 -2.099 ETKDGv3 21
VQ6 H6 -2.574 1.399 2.151 ETKDGv3 22
VQ6 H7 -0.109 -2.003 -1.434 ETKDGv3 23
VQ6 H8 -3.813 2.219 0.241 ETKDGv3 24
VQ6 H9 1.335 -0.224 -1.704 ETKDGv3 25
VQ6 H11 1.092 1.905 -0.857 ETKDGv3 26
VQ6 H12 1.472 2.195 1.028 ETKDGv3 27
#