data_OD0
#
_chem_comp.id OD0
_chem_comp.name "(1~{S},2~{R},3~{S},6~{S})-6-fluoranylcyclohex-4-ene-1,2,3-triol"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H9 F O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-09-05
_chem_comp.pdbx_modified_date 2024-03-08
_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 148.132
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code OD0
_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 8AX3
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
OD0 O1 O1 O 0 1 N N N N N N 22.402 -2.152 32.797 -2.749 -0.656 -0.247 O1 OD0 1
OD0 C1 C1 C 0 1 N N S N N N 21.487 -1.571 31.854 -1.469 -0.496 0.369 C1 OD0 2
OD0 C2 C2 C 0 1 N N N N N N 20.052 -1.885 32.145 -0.654 -1.737 0.152 C2 OD0 3
OD0 C3 C3 C 0 1 N N N N N N 19.077 -1.054 31.805 0.600 -1.735 -0.169 C3 OD0 4
OD0 C4 C4 C 0 1 N N S N N N 19.305 0.305 31.200 1.411 -0.491 -0.380 C4 OD0 5
OD0 F1 F1 F 0 1 N N N N N N 18.439 0.484 30.119 2.663 -0.645 0.226 F1 OD0 6
OD0 C5 C5 C 0 1 N N S N N N 20.738 0.494 30.727 0.698 0.715 0.237 C5 OD0 7
OD0 O2 O2 O 0 1 N N N N N N 21.027 1.876 30.506 1.341 1.920 -0.183 O2 OD0 8
OD0 C6 C6 C 0 1 N N R N N N 21.679 -0.058 31.774 -0.759 0.714 -0.242 C6 OD0 9
OD0 O3 O3 O 0 1 N N N N N N 23.035 0.268 31.471 -1.405 1.916 0.182 O3 OD0 10
OD0 H1 H1 H 0 1 N N N N N N 22.267 -3.092 32.832 -3.262 -1.399 0.098 H1 OD0 11
OD0 H2 H2 H 0 1 N N N N N N 21.717 -1.978 30.858 -1.601 -0.333 1.439 H2 OD0 12
OD0 H3 H3 H 0 1 N N N N N N 19.806 -2.811 32.644 -1.145 -2.692 0.272 H3 OD0 13
OD0 H4 H4 H 0 1 N N N N N N 18.058 -1.371 31.972 1.092 -2.688 -0.292 H4 OD0 14
OD0 H5 H5 H 0 1 N N N N N N 19.098 1.063 31.970 1.545 -0.324 -1.448 H5 OD0 15
OD0 H6 H6 H 0 1 N N N N N N 20.877 -0.071 29.794 0.726 0.640 1.324 H6 OD0 16
OD0 H7 H7 H 0 1 N N N N N N 21.926 1.969 30.212 2.272 1.979 0.074 H7 OD0 17
OD0 H8 H8 H 0 1 N N N N N N 21.406 0.375 32.748 -0.787 0.644 -1.330 H8 OD0 18
OD0 H9 H9 H 0 1 N N N N N N 23.605 -0.089 32.142 -2.331 1.981 -0.088 H9 OD0 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
OD0 F1 C4 SING N N 1
OD0 O2 C5 SING N N 2
OD0 C5 C4 SING N N 3
OD0 C5 C6 SING N N 4
OD0 C4 C3 SING N N 5
OD0 O3 C6 SING N N 6
OD0 C6 C1 SING N N 7
OD0 C3 C2 DOUB N N 8
OD0 C1 C2 SING N N 9
OD0 C1 O1 SING N N 10
OD0 O1 H1 SING N N 11
OD0 C1 H2 SING N N 12
OD0 C2 H3 SING N N 13
OD0 C3 H4 SING N N 14
OD0 C4 H5 SING N N 15
OD0 C5 H6 SING N N 16
OD0 O2 H7 SING N N 17
OD0 C6 H8 SING N N 18
OD0 O3 H9 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
OD0 InChI InChI 1.06 "InChI=1S/C6H9FO3/c7-3-1-2-4(8)6(10)5(3)9/h1-6,8-10H/t3-,4-,5+,6+/m0/s1"
OD0 InChIKey InChI 1.06 DGGHLTXNAWHUTK-UNTFVMJOSA-N
OD0 SMILES_CANONICAL CACTVS 3.385 "O[C@H]1C=C[C@H](F)[C@@H](O)[C@@H]1O"
OD0 SMILES CACTVS 3.385 "O[CH]1C=C[CH](F)[CH](O)[CH]1O"
OD0 SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C1=C[C@@H]([C@H]([C@@H]([C@H]1O)O)O)F"
OD0 SMILES "OpenEye OEToolkits" 3.1.0.0 "C1=CC(C(C(C1O)O)O)F"
#
_pdbx_chem_comp_identifier.comp_id OD0
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 3.1.0.0
_pdbx_chem_comp_identifier.identifier "(1~{S},2~{R},3~{S},6~{S})-6-fluoranylcyclohex-4-ene-1,2,3-triol"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
OD0 'Create component' 2022-09-05 PDBE
OD0 'Initial release' 2024-03-13 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
OD0 O1 O 3.805 -2.482 1
OD0 C1 C 5.104 -1.732 2
OD0 C2 C 6.404 -2.482 3
OD0 C3 C 7.702 -1.732 4
OD0 C4 C 7.702 -0.233 5
OD0 F1 F 9.002 0.517 6
OD0 C5 C 6.404 0.517 7
OD0 O2 O 6.404 2.018 8
OD0 C6 C 5.104 -0.233 9
OD0 O3 O 3.805 0.517 10
#
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
OD0 C4 F1 SINGLE BEGINWEDGE 1
OD0 C5 O2 SINGLE BEGINDASH 2
OD0 C5 C4 SINGLE NONE 3
OD0 C5 C6 SINGLE NONE 4
OD0 C4 C3 SINGLE NONE 5
OD0 C6 O3 SINGLE BEGINWEDGE 6
OD0 C6 C1 SINGLE NONE 7
OD0 C3 C2 DOUBLE NONE 8
OD0 C1 C2 SINGLE NONE 9
OD0 C1 O1 SINGLE BEGINDASH 10
#
_pdbe_chem_comp_substructure.comp_id OD0
_pdbe_chem_comp_substructure.substructure_name MurckoScaffold
_pdbe_chem_comp_substructure.id S1
_pdbe_chem_comp_substructure.substructure_type scaffold
_pdbe_chem_comp_substructure.substructure_smiles C1=CCCCC1
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C6H10/c1-2-4-6-5-3-1/h1-2H,3-6H2
_pdbe_chem_comp_substructure.substructure_inchikeys HGCIXCUEYOPUTN-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
OD0 C1 S1 1
OD0 C2 S1 1
OD0 C3 S1 1
OD0 C4 S1 1
OD0 C5 S1 1
OD0 C6 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id OD0
_pdbe_chem_comp_rdkit_properties.exactmw 148.054
_pdbe_chem_comp_rdkit_properties.amw 148.133
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 19
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.667
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_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 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 70.322
_pdbe_chem_comp_rdkit_properties.tpsa 60.690
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.023
_pdbe_chem_comp_rdkit_properties.CrippenMR 32.056
_pdbe_chem_comp_rdkit_properties.chi0v 4.603
_pdbe_chem_comp_rdkit_properties.chi1v 2.301
_pdbe_chem_comp_rdkit_properties.chi2v 0.898
_pdbe_chem_comp_rdkit_properties.chi3v 0.898
_pdbe_chem_comp_rdkit_properties.chi4v 0.428
_pdbe_chem_comp_rdkit_properties.chi0n 13.603
_pdbe_chem_comp_rdkit_properties.chi1n 6.526
_pdbe_chem_comp_rdkit_properties.chi2n 0.898
_pdbe_chem_comp_rdkit_properties.chi3n 0.898
_pdbe_chem_comp_rdkit_properties.chi4n 0.428
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.450
_pdbe_chem_comp_rdkit_properties.kappa1 2.029
_pdbe_chem_comp_rdkit_properties.kappa2 2.654
_pdbe_chem_comp_rdkit_properties.kappa3 1.183
_pdbe_chem_comp_rdkit_properties.Phi 0.539
#
#
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
OD0 O1 -2.425 0.916 0.220 ETKDGv3 1
OD0 C1 -1.268 0.429 -0.407 ETKDGv3 2
OD0 C2 -0.311 1.573 -0.668 ETKDGv3 3
OD0 C3 1.024 1.445 -0.572 ETKDGv3 4
OD0 C4 1.689 0.221 0.008 ETKDGv3 5
OD0 F1 2.854 -0.038 -0.693 ETKDGv3 6
OD0 C5 0.777 -1.019 -0.038 ETKDGv3 7
OD0 O2 1.336 -2.074 0.703 ETKDGv3 8
OD0 C6 -0.633 -0.662 0.480 ETKDGv3 9
OD0 O3 -1.456 -1.801 0.530 ETKDGv3 10
OD0 H1 -2.966 1.365 -0.481 ETKDGv3 11
OD0 H2 -1.533 -0.020 -1.392 ETKDGv3 12
OD0 H3 -0.714 2.501 -1.063 ETKDGv3 13
OD0 H4 1.647 2.301 -0.815 ETKDGv3 14
OD0 H5 1.959 0.449 1.062 ETKDGv3 15
OD0 H6 0.694 -1.353 -1.097 ETKDGv3 16
OD0 H7 1.373 -1.789 1.654 ETKDGv3 17
OD0 H8 -0.540 -0.264 1.516 ETKDGv3 18
OD0 H9 -1.506 -2.179 -0.387 ETKDGv3 19
#