data_RMN
#
_chem_comp.id RMN
_chem_comp.name "(R)-MANDELIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H8 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2011-06-04
_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 152.147
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code RMN
_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 1MDL
_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
RMN C1 C1 C 0 1 Y N N N N N 36.715 2.157 17.659 0.136 0.370 0.404 C1 RMN 1
RMN C2 C2 C 0 1 Y N N N N N 38.053 1.974 17.343 -0.939 0.812 1.151 C2 RMN 2
RMN C3 C3 C 0 1 Y N N N N N 38.954 2.995 17.556 -1.073 0.419 2.470 C3 RMN 3
RMN C4 C4 C 0 1 Y N N N N N 38.529 4.209 18.075 -0.131 -0.415 3.041 C4 RMN 4
RMN C5 C5 C 0 1 Y N N N N N 37.202 4.408 18.410 0.944 -0.857 2.294 C5 RMN 5
RMN C6 C6 C 0 1 Y N N N N N 36.302 3.379 18.201 1.075 -0.468 0.974 C6 RMN 6
RMN C7 C7 C 0 1 N N R N N N 35.667 1.034 17.416 0.282 0.799 -1.032 C7 RMN 7
RMN C10 C10 C 0 1 N N N N N N 34.686 0.955 18.579 -0.420 -0.190 -1.925 C10 RMN 8
RMN O8 O8 O 0 1 N N N N N N 36.260 -0.264 17.094 1.668 0.849 -1.376 O8 RMN 9
RMN O11 O11 O 0 1 N N N N N N 34.022 1.948 18.730 0.201 -0.791 -2.769 O11 RMN 10
RMN O12 O12 O 0 1 N N N N N N 34.642 -0.032 19.285 -1.738 -0.405 -1.783 O12 RMN 11
RMN H2 H2 H 0 1 N N N N N N 38.400 1.015 16.922 -1.676 1.464 0.705 H2 RMN 12
RMN H3 H3 H 0 1 N N N N N N 40.018 2.840 17.310 -1.914 0.765 3.053 H3 RMN 13
RMN H4 H4 H 0 1 N N N N N N 39.255 5.026 18.223 -0.235 -0.721 4.072 H4 RMN 14
RMN H5 H5 H 0 1 N N N N N N 36.867 5.369 18.835 1.680 -1.509 2.741 H5 RMN 15
RMN H6 H6 H 0 1 N N N N N N 35.243 3.534 18.469 1.916 -0.813 0.391 H6 RMN 16
RMN H7 H7 H 0 1 N N N N N N 35.097 1.318 16.500 -0.161 1.786 -1.164 H7 RMN 17
RMN HO8 HO8 H 0 1 N N N N N N 35.619 -0.950 16.945 2.021 -0.041 -1.246 HO8 RMN 18
RMN HO2 HO2 H 0 1 N N N N N N 34.030 -0.081 20.010 -2.189 -1.040 -2.356 HO2 RMN 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
RMN C1 C2 DOUB Y N 1
RMN C1 C6 SING Y N 2
RMN C1 C7 SING N N 3
RMN C2 C3 SING Y N 4
RMN C2 H2 SING N N 5
RMN C3 C4 DOUB Y N 6
RMN C3 H3 SING N N 7
RMN C4 C5 SING Y N 8
RMN C4 H4 SING N N 9
RMN C5 C6 DOUB Y N 10
RMN C5 H5 SING N N 11
RMN C6 H6 SING N N 12
RMN C7 C10 SING N N 13
RMN C7 O8 SING N N 14
RMN C7 H7 SING N N 15
RMN C10 O11 DOUB N N 16
RMN C10 O12 SING N N 17
RMN O8 HO8 SING N N 18
RMN O12 HO2 SING 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
RMN SMILES ACDLabs 10.04 O=C(O)C(O)c1ccccc1
RMN SMILES_CANONICAL CACTVS 3.341 O[C@@H](C(O)=O)c1ccccc1
RMN SMILES CACTVS 3.341 O[CH](C(O)=O)c1ccccc1
RMN SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1ccc(cc1)[C@H](C(=O)O)O
RMN SMILES "OpenEye OEToolkits" 1.5.0 c1ccc(cc1)C(C(=O)O)O
RMN InChI InChI 1.03 InChI=1S/C8H8O3/c9-7(8(10)11)6-4-2-1-3-5-6/h1-5,7,9H,(H,10,11)/t7-/m1/s1
RMN InChIKey InChI 1.03 IWYDHOAUDWTVEP-SSDOTTSWSA-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
RMN "SYSTEMATIC NAME" ACDLabs 10.04 "(2R)-hydroxy(phenyl)ethanoic acid"
RMN "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R)-2-hydroxy-2-phenyl-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
RMN 'Create component' 1999-07-08 RCSB
RMN 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id RMN
_pdbe_chem_comp_drugbank_details.drugbank_id DB02280
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name '(R)-Mandelic acid'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 611-71-2
_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
RMN '(−)-(R)-mandelic acid' DrugBank ?
RMN '(−)-mandelic acid' DrugBank ?
RMN '(−)-α-hydroxyphenylacetic acid' DrugBank ?
RMN '(2R)-2-hydroxy-2-phenylacetic acid' DrugBank ?
RMN '(R)-2-Hydroxy-2-phenylacetic acid' DrugBank ?
RMN '(R)-α-hydroxybenzeneacetic acid' DrugBank ?
RMN '(R)-α-hydroxyphenylacetic acid' DrugBank ?
RMN 'D-2-phenylglycolic acid' DrugBank ?
RMN 'D-mandelic acid' DrugBank ?
RMN 'D(−)-mandelic acid' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id RMN
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02280
_pdbe_chem_comp_drugbank_classification.parent 'Benzene and substituted derivatives'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Benzene and substituted derivatives'
_pdbe_chem_comp_drugbank_classification.superclass Benzenoids
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as benzene and substituted derivatives. These are aromatic compounds containing one monocyclic ring system consisting of benzene.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
RMN DB02280 'Benzoylformate decarboxylase' 'Pseudomonas putida' P20906 unknown 1
RMN DB02280 'Mandelate racemase' 'Pseudomonas putida' P11444 unknown 2
#
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
RMN C1 C 4.299 -0.608 1
RMN C2 C 3.000 -1.357 2
RMN C3 C 3.000 -2.857 3
RMN C4 C 4.299 -3.607 4
RMN C5 C 5.598 -2.857 5
RMN C6 C 5.598 -1.357 6
RMN C7 C 4.299 0.892 7
RMN C10 C 5.598 1.643 8
RMN O8 O 3.000 1.643 9
RMN O11 O 5.598 3.143 10
RMN O12 O 6.897 0.892 11
#
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
RMN C1 C2 DOUBLE NONE 1
RMN C1 C6 SINGLE NONE 2
RMN C1 C7 SINGLE NONE 3
RMN C2 C3 SINGLE NONE 4
RMN C3 C4 DOUBLE NONE 5
RMN C4 C5 SINGLE NONE 6
RMN C5 C6 DOUBLE NONE 7
RMN C7 C10 SINGLE NONE 8
RMN C7 O8 SINGLE BEGINWEDGE 9
RMN C10 O11 DOUBLE NONE 10
RMN C10 O12 SINGLE NONE 11
#
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
RMN MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
RMN 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
RMN C1 S1 1
RMN C2 S1 1
RMN C3 S1 1
RMN C4 S1 1
RMN C5 S1 1
RMN C6 S1 1
RMN C1 F1 1
RMN C2 F1 1
RMN C3 F1 1
RMN C4 F1 1
RMN C5 F1 1
RMN C6 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id RMN
_pdbe_chem_comp_rdkit_properties.exactmw 152.047
_pdbe_chem_comp_rdkit_properties.amw 152.149
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 19
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 75.324
_pdbe_chem_comp_rdkit_properties.tpsa 57.530
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.750
_pdbe_chem_comp_rdkit_properties.CrippenMR 38.772
_pdbe_chem_comp_rdkit_properties.chi0v 5.225
_pdbe_chem_comp_rdkit_properties.chi1v 2.612
_pdbe_chem_comp_rdkit_properties.chi2v 0.912
_pdbe_chem_comp_rdkit_properties.chi3v 0.912
_pdbe_chem_comp_rdkit_properties.chi4v 0.466
_pdbe_chem_comp_rdkit_properties.chi0n 13.225
_pdbe_chem_comp_rdkit_properties.chi1n 6.429
_pdbe_chem_comp_rdkit_properties.chi2n 0.912
_pdbe_chem_comp_rdkit_properties.chi3n 0.912
_pdbe_chem_comp_rdkit_properties.chi4n 0.466
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.350
_pdbe_chem_comp_rdkit_properties.kappa1 2.318
_pdbe_chem_comp_rdkit_properties.kappa2 3.163
_pdbe_chem_comp_rdkit_properties.kappa3 1.782
_pdbe_chem_comp_rdkit_properties.Phi 0.667
#
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
RMN UniChem ChEMBL CHEMBL292411
RMN UniChem DrugBank DB02280
RMN UniChem PDBe RMN
RMN UniChem 'KEGG LIGAND' C01983
RMN UniChem ChEBI 17656
RMN UniChem ZINC ZINC000000164392
RMN UniChem eMolecules 483435
RMN UniChem fdasrs PPL7YW1M9W
RMN UniChem HMDB HMDB0062635
RMN UniChem NMRShiftDB 70128283
RMN UniChem ACTor 14447-35-9
RMN UniChem ACTor 14447-36-0
RMN UniChem MetaboLights MTBLC17656
RMN UniChem BRENDA 103798
RMN UniChem BRENDA 137330
RMN UniChem BRENDA 140948
RMN UniChem BRENDA 154472
RMN UniChem BRENDA 163743
RMN UniChem BRENDA 170068
RMN UniChem BRENDA 18072
RMN UniChem BRENDA 204528
RMN UniChem BRENDA 29882
RMN UniChem BRENDA 3457
RMN UniChem BRENDA 69631
RMN UniChem BRENDA 735
RMN UniChem BRENDA 8589
RMN UniChem ChemicalBook CB9411418
RMN UniChem MedChemExpress HY-Y0585
RMN UniChem 'Probes And Drugs' PD020326
RMN UniChem SureChEMBL SCHEMBL165161
RMN UniChem 'PubChem TPHARMA' 15146876
RMN UniChem PubChem 11914
RMN UniChem Mcule MCULE-7674691218
RMN UniChem Nikkaji J43.326H
RMN UniChem BindingDb 16421
RMN UniChem 'EPA CompTox Dashboard' DTXSID4046523
#
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
RMN C1 0.027 -0.050 -0.423 ETKDGv3 1
RMN C2 0.676 0.634 -1.385 ETKDGv3 2
RMN C3 1.949 1.323 -1.086 ETKDGv3 3
RMN C4 2.471 1.264 0.144 ETKDGv3 4
RMN C5 1.777 0.507 1.205 ETKDGv3 5
RMN C6 0.623 -0.117 0.939 ETKDGv3 6
RMN C7 -1.268 -0.776 -0.732 ETKDGv3 7
RMN C10 -2.352 -0.388 0.237 ETKDGv3 8
RMN O8 -1.071 -2.168 -0.745 ETKDGv3 9
RMN O11 -2.985 0.689 0.068 ETKDGv3 10
RMN O12 -2.631 -1.187 1.343 ETKDGv3 11
RMN H2 0.279 0.690 -2.391 ETKDGv3 12
RMN H3 2.457 1.875 -1.865 ETKDGv3 13
RMN H4 3.404 1.767 0.364 ETKDGv3 14
RMN H5 2.206 0.457 2.198 ETKDGv3 15
RMN H6 0.126 -0.671 1.726 ETKDGv3 16
RMN H7 -1.625 -0.489 -1.746 ETKDGv3 17
RMN HO8 -0.715 -2.439 0.141 ETKDGv3 18
RMN HO2 -3.348 -0.922 2.007 ETKDGv3 19
#