data_RQD
#
_chem_comp.id RQD
_chem_comp.name "methyl 4-fluoro-L-phenylalaninate"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H12 F N O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-02-20
_chem_comp.pdbx_modified_date 2020-05-29
_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 197.206
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code RQD
_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 5R1X
_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
RQD C4 C1 C 0 1 Y N N N N N 26.546 1.933 60.487 0.880 0.140 -0.489 C4 RQD 1
RQD C5 C2 C 0 1 Y N N N N N 25.307 2.367 60.934 1.633 -1.008 -0.650 C5 RQD 2
RQD C6 C3 C 0 1 Y N N N N N 24.270 1.484 61.122 2.984 -0.996 -0.362 C6 RQD 3
RQD C7 C4 C 0 1 Y N N N N N 24.476 0.169 60.801 3.585 0.168 0.089 C7 RQD 4
RQD C8 C5 C 0 1 Y N N N N N 25.653 -0.295 60.300 2.830 1.317 0.250 C8 RQD 5
RQD C9 C6 C 0 1 Y N N N N N 26.699 0.596 60.171 1.479 1.302 -0.039 C9 RQD 6
RQD F F1 F 0 1 N N N N N N 23.503 -0.716 61.056 4.905 0.181 0.371 F RQD 7
RQD C3 C7 C 0 1 N N N N N N 27.725 2.872 60.411 -0.592 0.127 -0.810 C3 RQD 8
RQD C2 C8 C 0 1 N N S N N N 28.068 3.342 58.998 -1.383 -0.260 0.441 C2 RQD 9
RQD N N1 N 0 1 N N N N N N 29.439 3.874 58.842 -1.056 -1.641 0.820 N RQD 10
RQD C1 C9 C 0 1 N N N N N N 27.044 4.428 58.751 -2.859 -0.155 0.155 C1 RQD 11
RQD O1 O1 O 0 1 N N N N N N 25.936 4.195 58.367 -3.498 -1.148 -0.100 O1 RQD 12
RQD O O2 O 0 1 N N N N N N 27.508 5.628 59.013 -3.464 1.043 0.184 O RQD 13
RQD C C10 C 0 1 N N N N N N 26.952 6.702 58.221 -4.888 1.070 -0.102 C RQD 14
RQD H9 H1 H 0 1 N N N N N N 25.154 3.416 61.138 1.164 -1.916 -1.001 H9 RQD 15
RQD H10 H2 H 0 1 N N N N N N 23.320 1.818 61.512 3.572 -1.893 -0.487 H10 RQD 16
RQD H11 H3 H 0 1 N N N N N N 25.765 -1.330 60.012 3.297 2.225 0.601 H11 RQD 17
RQD H12 H4 H 0 1 N N N N N N 27.656 0.242 59.816 0.890 2.199 0.086 H12 RQD 18
RQD H7 H5 H 0 1 N N N N N N 28.604 2.355 60.824 -0.900 1.118 -1.143 H7 RQD 19
RQD H8 H6 H 0 1 N N N N N N 27.499 3.758 61.023 -0.785 -0.598 -1.601 H8 RQD 20
RQD H H7 H 0 1 N N N N N N 27.904 2.516 58.291 -1.123 0.412 1.258 H RQD 21
RQD H1 H8 H 0 1 N N N N N N 30.101 3.144 59.009 -1.288 -2.285 0.078 H1 RQD 22
RQD H2 H9 H 0 1 N N N N N N 29.557 4.225 57.913 -0.084 -1.724 1.079 H2 RQD 23
RQD H5 H11 H 0 1 N N N N N N 27.409 7.656 58.523 -5.065 0.676 -1.103 H5 RQD 24
RQD H4 H12 H 0 1 N N N N N N 27.158 6.517 57.156 -5.416 0.457 0.628 H4 RQD 25
RQD H6 H13 H 0 1 N N N N N N 25.865 6.750 58.381 -5.251 2.096 -0.045 H6 RQD 26
#
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
RQD C O SING N N 1
RQD O1 C1 DOUB N N 2
RQD C1 C2 SING N N 3
RQD C1 O SING N N 4
RQD N C2 SING N N 5
RQD C2 C3 SING N N 6
RQD C9 C8 DOUB Y N 7
RQD C9 C4 SING Y N 8
RQD C8 C7 SING Y N 9
RQD C3 C4 SING N N 10
RQD C4 C5 DOUB Y N 11
RQD C7 F SING N N 12
RQD C7 C6 DOUB Y N 13
RQD C5 C6 SING Y N 14
RQD C5 H9 SING N N 15
RQD C6 H10 SING N N 16
RQD C8 H11 SING N N 17
RQD C9 H12 SING N N 18
RQD C3 H7 SING N N 19
RQD C3 H8 SING N N 20
RQD C2 H SING N N 21
RQD N H1 SING N N 22
RQD N H2 SING N N 23
RQD C H5 SING N N 24
RQD C H4 SING N N 25
RQD C H6 SING N N 26
#
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
RQD SMILES ACDLabs 12.01 c1(ccc(F)cc1)CC(N)C(OC)=O
RQD InChI InChI 1.03 InChI=1S/C10H12FNO2/c1-14-10(13)9(12)6-7-2-4-8(11)5-3-7/h2-5,9H,6,12H2,1H3/t9-/m0/s1
RQD InChIKey InChI 1.03 NCSHKOSBEYDZFY-VIFPVBQESA-N
RQD SMILES_CANONICAL CACTVS 3.385 COC(=O)[C@@H](N)Cc1ccc(F)cc1
RQD SMILES CACTVS 3.385 COC(=O)[CH](N)Cc1ccc(F)cc1
RQD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 COC(=O)[C@H](Cc1ccc(cc1)F)N
RQD SMILES "OpenEye OEToolkits" 2.0.6 COC(=O)C(Cc1ccc(cc1)F)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
RQD "SYSTEMATIC NAME" ACDLabs 12.01 "methyl 4-fluoro-L-phenylalaninate"
RQD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "methyl (2~{S})-2-azanyl-3-(4-fluorophenyl)propanoate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
RQD 'Create component' 2020-02-20 RCSB
RQD 'Initial release' 2020-06-03 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
RQD C4 C 4.299 -0.750 1
RQD C5 C 3.000 -1.500 2
RQD C6 C 3.000 -3.000 3
RQD C7 C 4.299 -3.750 4
RQD C8 C 5.598 -3.000 5
RQD C9 C 5.598 -1.500 6
RQD F F 4.299 -5.250 7
RQD C3 C 4.299 0.750 8
RQD C2 C 5.598 1.500 9
RQD N N 6.897 0.750 10
RQD C1 C 5.598 3.000 11
RQD O1 O 4.299 3.750 12
RQD O O 6.897 3.750 13
RQD C C 6.897 5.250 14
#
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
RQD C O SINGLE NONE 1
RQD O1 C1 DOUBLE NONE 2
RQD C1 C2 SINGLE NONE 3
RQD C1 O SINGLE NONE 4
RQD C2 N SINGLE BEGINWEDGE 5
RQD C2 C3 SINGLE NONE 6
RQD C9 C8 SINGLE NONE 7
RQD C9 C4 DOUBLE NONE 8
RQD C8 C7 DOUBLE NONE 9
RQD C3 C4 SINGLE NONE 10
RQD C4 C5 SINGLE NONE 11
RQD C7 F SINGLE NONE 12
RQD C7 C6 SINGLE NONE 13
RQD C5 C6 DOUBLE NONE 14
#
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
RQD MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
RQD peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
RQD 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
RQD C4 S1 1
RQD C5 S1 1
RQD C6 S1 1
RQD C7 S1 1
RQD C8 S1 1
RQD C9 S1 1
RQD O1 F1 1
RQD C1 F1 1
RQD C2 F1 1
RQD N F1 1
RQD C4 F2 1
RQD C9 F2 1
RQD C8 F2 1
RQD C7 F2 1
RQD C6 F2 1
RQD C5 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id RQD
_pdbe_chem_comp_rdkit_properties.exactmw 197.085
_pdbe_chem_comp_rdkit_properties.amw 197.209
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 26
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.300
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 98.647
_pdbe_chem_comp_rdkit_properties.tpsa 52.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.814
_pdbe_chem_comp_rdkit_properties.CrippenMR 49.829
_pdbe_chem_comp_rdkit_properties.chi0v 6.642
_pdbe_chem_comp_rdkit_properties.chi1v 3.275
_pdbe_chem_comp_rdkit_properties.chi2v 1.124
_pdbe_chem_comp_rdkit_properties.chi3v 1.124
_pdbe_chem_comp_rdkit_properties.chi4v 0.578
_pdbe_chem_comp_rdkit_properties.chi0n 18.642
_pdbe_chem_comp_rdkit_properties.chi1n 9.169
_pdbe_chem_comp_rdkit_properties.chi2n 1.124
_pdbe_chem_comp_rdkit_properties.chi3n 1.124
_pdbe_chem_comp_rdkit_properties.chi4n 0.578
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.420
_pdbe_chem_comp_rdkit_properties.kappa1 2.792
_pdbe_chem_comp_rdkit_properties.kappa2 4.715
_pdbe_chem_comp_rdkit_properties.kappa3 2.813
_pdbe_chem_comp_rdkit_properties.Phi 0.940
#
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
RQD UniChem PDBe RQD
RQD UniChem ZINC ZINC000031969754
RQD UniChem SureChEMBL SCHEMBL2833
RQD UniChem PubChem 7018988
RQD UniChem Nikkaji J807.432A
#
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
RQD C4 -1.361 -0.276 0.387 ETKDGv3 1
RQD C5 -1.922 1.095 0.304 ETKDGv3 2
RQD C6 -3.195 1.283 -0.066 ETKDGv3 3
RQD C7 -4.049 0.123 -0.394 ETKDGv3 4
RQD C8 -3.549 -1.117 -0.325 ETKDGv3 5
RQD C9 -2.143 -1.328 0.079 ETKDGv3 6
RQD F -5.338 0.317 -0.767 ETKDGv3 7
RQD C3 0.082 -0.471 0.777 ETKDGv3 8
RQD C2 1.037 -0.181 -0.397 ETKDGv3 9
RQD N 0.891 -1.192 -1.447 ETKDGv3 10
RQD C1 2.454 -0.165 0.103 ETKDGv3 11
RQD O1 3.022 -1.246 0.424 ETKDGv3 12
RQD O 3.121 1.056 0.237 ETKDGv3 13
RQD C 4.456 1.151 0.720 ETKDGv3 14
RQD H9 -1.300 1.950 0.540 ETKDGv3 15
RQD H10 -3.600 2.285 -0.126 ETKDGv3 16
RQD H11 -4.171 -1.969 -0.567 ETKDGv3 17
RQD H12 -1.753 -2.338 0.117 ETKDGv3 18
RQD H7 0.310 0.220 1.619 ETKDGv3 19
RQD H8 0.251 -1.505 1.154 ETKDGv3 20
RQD H 0.804 0.823 -0.819 ETKDGv3 21
RQD H1 1.580 -0.981 -2.206 ETKDGv3 22
RQD H2 -0.050 -1.081 -1.887 ETKDGv3 23
RQD H5 5.142 0.587 0.053 ETKDGv3 24
RQD H4 4.763 2.216 0.735 ETKDGv3 25
RQD H6 4.517 0.744 1.752 ETKDGv3 26
#