data_F5T
#
_chem_comp.id F5T
_chem_comp.name "cis-bis(mi2-acetato-O, O')-(mi2-trifluoroacetato-O, O')-diaquo-dirhodium (II)"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H11 F3 O8 Rh2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 2
_chem_comp.pdbx_initial_date 2022-01-19
_chem_comp.pdbx_modified_date 2022-08-22
_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 473.953
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code F5T
_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 7QPW
_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
F5T RH1 RH1 RH 1 0 N N N N N N 12.361 4.558 20.073 12.361 4.558 20.073 RH1 F5T 1
F5T RH2 RH2 RH 1 0 N N N N N N 10.999 6.290 20.977 10.999 6.290 20.977 RH2 F5T 2
F5T O1 O1 O 0 1 N N N N N N 13.737 5.095 21.570 13.737 5.095 21.570 O1 F5T 3
F5T O2 O2 O 0 1 N N N N N N 12.483 6.660 22.397 12.483 6.660 22.397 O2 F5T 4
F5T O3 O3 O 0 1 N N N N N N 10.999 4.030 18.600 10.999 4.030 18.600 O3 F5T 5
F5T O4 O4 O 0 1 N N N N N N 9.625 5.839 19.485 9.625 5.839 19.485 O4 F5T 6
F5T O0 O5 O 0 1 N N N N N N 11.486 3.188 21.386 11.486 3.188 21.386 O0 F5T 7
F5T O9 O6 O 0 1 N N N N N N 10.204 4.817 22.232 10.204 4.817 22.232 O9 F5T 8
F5T O7 O7 O 0 1 N N N N N N 13.108 6.052 18.842 13.108 6.052 18.842 O7 F5T 9
F5T O8 O8 O 0 1 N N N N N N 11.920 7.663 19.694 11.920 7.663 19.694 O8 F5T 10
F5T C1 C1 C 0 1 N N N N N N 13.517 5.981 22.358 13.517 5.981 22.358 C1 F5T 11
F5T C2 C2 C 0 1 N N N N N N 14.708 6.320 23.288 14.708 6.320 23.288 C2 F5T 12
F5T C3 C3 C 0 1 N N N N N N 12.761 7.246 18.900 12.761 7.246 18.900 C3 F5T 13
F5T C4 C4 C 0 1 N N N N N N 13.640 7.760 17.737 13.640 7.760 17.737 C4 F5T 14
F5T C5 C5 C 0 1 N N N N N N 10.559 3.652 22.068 10.559 3.652 22.068 C5 F5T 15
F5T C6 C6 C 0 1 N N N N N N 9.495 2.840 22.880 9.495 2.840 22.880 C6 F5T 16
F5T F1 F1 F 0 1 N N N N N N 10.002 1.588 22.873 10.002 1.588 22.873 F1 F5T 17
F5T F2 F2 F 0 1 N N N N N N 9.189 3.181 24.163 9.189 3.181 24.163 F2 F5T 18
F5T F3 F3 F 0 1 N N N N N N 8.341 2.862 22.173 8.341 2.862 22.173 F3 F5T 19
F5T H1 H1 H 0 1 N N N N N N 10.467 3.304 18.905 10.467 3.304 18.905 H1 F5T 20
F5T H2 H2 H 0 1 N N N N N N 9.017 5.181 19.802 9.017 5.181 19.802 H2 F5T 21
F5T H3 H3 H 0 1 N N N N N N 13.114 5.269 23.093 13.114 5.269 23.093 H3 F5T 22
F5T H4 H4 H 0 1 N N N N N N 14.421 7.134 23.970 14.421 7.134 23.970 H4 F5T 23
F5T H5 H5 H 0 1 N N N N N N 14.981 5.430 23.874 14.981 5.430 23.874 H5 F5T 24
F5T H6 H6 H 0 1 N N N N N N 15.569 6.637 22.681 15.569 6.637 22.681 H6 F5T 25
F5T H7 H7 H 0 1 N N N N N N 13.566 7.460 19.618 13.566 7.460 19.618 H7 F5T 26
F5T H8 H8 H 0 1 N N N N N N 13.483 8.841 17.608 13.483 8.841 17.608 H8 F5T 27
F5T H9 H9 H 0 1 N N N N N N 14.699 7.568 17.965 14.699 7.568 17.965 H9 F5T 28
F5T H10 H10 H 0 1 N N N N N N 13.364 7.236 16.810 13.364 7.236 16.810 H10 F5T 29
F5T H11 H11 H 0 1 N N N N N N 11.212 3.707 22.951 11.212 3.707 22.951 H11 F5T 30
#
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
F5T C4 C3 SING N N 1
F5T O3 RH1 SING N N 2
F5T O7 C3 SING N N 3
F5T O7 RH1 SING N N 4
F5T C3 O8 SING N N 5
F5T O4 RH2 SING N N 6
F5T O8 RH2 SING N N 7
F5T RH1 RH2 SING N N 8
F5T RH1 O0 SING N N 9
F5T RH1 O1 SING N N 10
F5T RH2 O9 SING N N 11
F5T RH2 O2 SING N N 12
F5T O0 C5 SING N N 13
F5T O1 C1 SING N N 14
F5T C5 O9 SING N N 15
F5T C5 C6 SING N N 16
F5T F3 C6 SING N N 17
F5T C1 O2 SING N N 18
F5T C1 C2 SING N N 19
F5T F1 C6 SING N N 20
F5T C6 F2 SING N N 21
F5T O3 H1 SING N N 22
F5T O4 H2 SING N N 23
F5T C1 H3 SING N N 24
F5T C2 H4 SING N N 25
F5T C2 H5 SING N N 26
F5T C2 H6 SING N N 27
F5T C3 H7 SING N N 28
F5T C4 H8 SING N N 29
F5T C4 H9 SING N N 30
F5T C4 H10 SING N N 31
F5T C5 H11 SING N N 32
#
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
F5T InChI InChI 1.06 InChI=1S/C2HF3O2.2C2H4O2.2H2O.2Rh/c3-2(4,5)1(6)7;2*1-2(3)4;;;;/h1H;2*2H,1H3;2*1H2;;/q3*-2;;;2*+5/p-2
F5T InChIKey InChI 1.06 AAVQFBAKNWVTEL-UHFFFAOYSA-L
F5T SMILES_CANONICAL CACTVS 3.385 C[C@@H]1O[Rh+]2(O)O[C@@H](C)O[Rh+](O)(O1)O[C@H](O2)C(F)(F)F
F5T SMILES CACTVS 3.385 C[CH]1O[Rh+]2(O)O[CH](C)O[Rh+](O)(O1)O[CH](O2)C(F)(F)F
F5T SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CC1O[Rh+]23(OC(O[Rh+]2(O1)(OC(O3)C(F)(F)F)O)C)O
F5T SMILES "OpenEye OEToolkits" 2.0.7 CC1O[Rh+]23(OC(O[Rh+]2(O1)(OC(O3)C(F)(F)F)O)C)O
#
_pdbx_chem_comp_identifier.comp_id F5T
_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
3,7-dimethyl-1,5-bis(oxidanyl)-10-(trifluoromethyl)-2,4,6,8,9,11-hexaoxa-1$l^{5},5$l^{5}-dirhodatricyclo[3.3.3.0^{1,5}]undecane
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
F5T 'Create component' 2022-01-19 PDBE
F5T 'Modify synonyms' 2022-02-16 PDBE
F5T 'Modify charge' 2022-02-16 PDBE
F5T 'Modify synonyms' 2022-02-17 PDBE
F5T 'Initial release' 2022-03-02 RCSB
F5T 'Modify descriptor' 2022-08-22 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
F5T RH1 Rh 1.393 -0.099 1
F5T RH2 Rh -0.415 -2.076 2
F5T O1 O 0.739 1.300 3
F5T O2 O -1.837 -0.870 4
F5T O3 O 0.446 -0.356 5
F5T O4 O -0.314 0.233 6
F5T O0 O 2.335 -1.859 7
F5T O9 O 1.105 -3.240 8
F5T O7 O 1.113 -1.355 9
F5T O8 O 0.401 -2.282 10
F5T C1 C -1.246 1.054 11
F5T C2 C -2.643 1.682 12
F5T C3 C 0.572 -1.458 13
F5T C4 C -0.966 -0.486 14
F5T C5 C 1.594 -2.192 15
F5T C6 C 0.083 2.285 16
F5T F1 F -0.962 3.571 17
F5T F2 F -1.944 2.505 18
F5T F3 F 0.546 3.643 19
#
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
F5T C3 C4 SINGLE BEGINDASH 1
F5T O3 RH1 SINGLE NONE 2
F5T O7 C3 SINGLE NONE 3
F5T O7 RH1 SINGLE NONE 4
F5T C3 O8 SINGLE NONE 5
F5T O4 RH2 SINGLE NONE 6
F5T O8 RH2 SINGLE NONE 7
F5T RH1 RH2 SINGLE NONE 8
F5T RH1 O0 SINGLE NONE 9
F5T RH1 O1 SINGLE NONE 10
F5T RH2 O9 SINGLE NONE 11
F5T RH2 O2 SINGLE NONE 12
F5T O0 C5 SINGLE NONE 13
F5T O1 C1 SINGLE NONE 14
F5T C5 O9 SINGLE NONE 15
F5T C5 C6 SINGLE BEGINWEDGE 16
F5T F3 C6 SINGLE NONE 17
F5T C1 O2 SINGLE NONE 18
F5T C1 C2 SINGLE BEGINDASH 19
F5T F1 C6 SINGLE NONE 20
F5T C6 F2 SINGLE NONE 21
#
_pdbe_chem_comp_substructure.comp_id F5T
_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[O][Rh+]23[O]C[O][Rh+]2([O]1)[O]C[O]3'
_pdbe_chem_comp_substructure.substructure_inchis 'InChI=1S/3CH2O2.2Rh/c3*2-1-3;;/h3*1H2;;/q3*-2;2*+4'
_pdbe_chem_comp_substructure.substructure_inchikeys ZDDDJHQHTWCDNI-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
F5T RH1 S1 1
F5T RH2 S1 1
F5T O1 S1 1
F5T O2 S1 1
F5T O0 S1 1
F5T O9 S1 1
F5T O7 S1 1
F5T O8 S1 1
F5T C1 S1 1
F5T C3 S1 1
F5T C5 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id F5T
_pdbe_chem_comp_rdkit_properties.exactmw 473.851
_pdbe_chem_comp_rdkit_properties.amw 473.952
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_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 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 30
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 13
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 3
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 3
_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 121.962
_pdbe_chem_comp_rdkit_properties.tpsa 95.840
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.306
_pdbe_chem_comp_rdkit_properties.CrippenMR 39.715
_pdbe_chem_comp_rdkit_properties.chi0v 11.344
_pdbe_chem_comp_rdkit_properties.chi1v 12.871
_pdbe_chem_comp_rdkit_properties.chi2v 20.516
_pdbe_chem_comp_rdkit_properties.chi3v 20.516
_pdbe_chem_comp_rdkit_properties.chi4v 16.712
_pdbe_chem_comp_rdkit_properties.chi0n 19.067
_pdbe_chem_comp_rdkit_properties.chi1n 9.058
_pdbe_chem_comp_rdkit_properties.chi2n 1.535
_pdbe_chem_comp_rdkit_properties.chi3n 1.535
_pdbe_chem_comp_rdkit_properties.chi4n 0.988
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.717
_pdbe_chem_comp_rdkit_properties.kappa1 6.453
_pdbe_chem_comp_rdkit_properties.kappa2 3.376
_pdbe_chem_comp_rdkit_properties.kappa3 1.517
_pdbe_chem_comp_rdkit_properties.Phi 1.147
#
#
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
F5T RH1 -0.173 0.795 -3.042 ETKDGv3 1
F5T RH2 0.522 2.633 0.592 ETKDGv3 2
F5T O1 0.285 2.009 -0.628 ETKDGv3 3
F5T O2 0.577 1.653 1.601 ETKDGv3 4
F5T O3 -0.357 -1.614 -2.384 ETKDGv3 5
F5T O4 -0.007 -3.003 1.373 ETKDGv3 6
F5T O0 1.415 -0.300 -1.258 ETKDGv3 7
F5T O9 1.349 -1.059 0.887 ETKDGv3 8
F5T O7 -1.386 0.070 -0.851 ETKDGv3 9
F5T O8 -1.004 -0.666 1.269 ETKDGv3 10
F5T C1 0.522 2.624 0.601 ETKDGv3 11
F5T C2 -0.593 3.613 0.905 ETKDGv3 12
F5T C3 -1.986 -0.256 0.365 ETKDGv3 13
F5T C4 -2.996 -1.375 0.159 ETKDGv3 14
F5T C5 2.189 -0.724 -0.176 ETKDGv3 15
F5T C6 3.030 -1.932 -0.577 ETKDGv3 16
F5T F1 2.210 -2.973 -0.974 ETKDGv3 17
F5T F2 3.868 -1.591 -1.624 ETKDGv3 18
F5T F3 3.798 -2.344 0.497 ETKDGv3 19
F5T H1 -0.495 -2.538 -2.056 ETKDGv3 20
F5T H2 -0.256 -3.555 0.590 ETKDGv3 21
F5T H3 1.494 3.158 0.559 ETKDGv3 22
F5T H4 -0.404 4.108 1.881 ETKDGv3 23
F5T H5 -1.571 3.088 0.949 ETKDGv3 24
F5T H6 -0.635 4.390 0.112 ETKDGv3 25
F5T H7 -2.500 0.641 0.769 ETKDGv3 26
F5T H8 -3.782 -1.047 -0.554 ETKDGv3 27
F5T H9 -3.477 -1.634 1.126 ETKDGv3 28
F5T H10 -2.493 -2.278 -0.248 ETKDGv3 29
F5T H11 2.855 0.106 0.139 ETKDGv3 30
#