data_R2U
#
_chem_comp.id R2U
_chem_comp.name "Ru2-(OH)6 cluster"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "H6 O6 Ru2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-11-22
_chem_comp.pdbx_modified_date 2023-06-23
_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 304.184
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code R2U
_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 8BPU
_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
R2U O3 O1 O 0 1 N N N N N N -39.860 -8.005 -21.722 -1.830 0.851 1.509 O3 R2U 1
R2U O4 O2 O 0 1 N N N N N N -39.771 -9.769 -20.311 1.830 -0.856 1.506 O4 R2U 2
R2U O5 O3 O 0 1 N N N N N N -41.954 -7.213 -19.863 -1.810 -1.749 0.002 O5 R2U 3
R2U O6 O4 O 0 1 N N N N N N -41.486 -8.684 -18.177 1.810 1.749 0.008 O6 R2U 4
R2U O7 O5 O 0 1 N N N N N N -39.977 -5.831 -18.318 -1.830 0.856 -1.496 O7 R2U 5
R2U O8 O6 O 0 1 N N N N N N -39.235 -7.425 -17.061 1.830 -0.851 -1.498 O8 R2U 6
R2U RU1 RU1 RU 0 0 N N N N N N -39.965 -6.923 -20.019 -1.210 -0.009 0.005 RU1 R2U 7
R2U RU2 RU2 RU 0 0 N N N N N N -39.521 -8.663 -18.637 1.210 0.009 0.005 RU2 R2U 8
R2U H1 H1 H 0 1 N N N N N N -38.961 -8.027 -22.029 -1.552 1.775 1.576 H1 R2U 9
R2U H2 H2 H 0 1 N N N N N N -39.646 -10.688 -20.106 1.551 -1.780 1.571 H2 R2U 10
R2U H3 H3 H 0 1 N N N N N N -42.279 -6.774 -19.086 -1.521 -2.263 -0.764 H3 R2U 11
R2U H4 H4 H 0 1 N N N N N N -41.629 -8.196 -17.375 1.521 2.266 -0.756 H4 R2U 12
R2U H5 H5 H 0 1 N N N N N N -40.870 -5.739 -18.006 -2.794 0.887 -1.562 H5 R2U 13
R2U H6 H6 H 0 1 N N N N N N -39.375 -7.904 -16.252 2.794 -0.882 -1.565 H6 R2U 14
#
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
R2U O3 RU1 SING N N 1
R2U O4 RU2 SING N N 2
R2U RU1 O5 SING N N 3
R2U RU1 RU2 SING N N 4
R2U RU1 O7 SING N N 5
R2U RU2 O6 SING N N 6
R2U RU2 O8 SING N N 7
R2U O3 H1 SING N N 8
R2U O4 H2 SING N N 9
R2U O5 H3 SING N N 10
R2U O6 H4 SING N N 11
R2U O7 H5 SING N N 12
R2U O8 H6 SING N N 13
#
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
R2U InChI InChI 1.06 InChI=1S/6H2O.2Ru/h6*1H2;;/q;;;;;;2*+3/p-6
R2U InChIKey InChI 1.06 AOQXTNLYRQGSLC-UHFFFAOYSA-H
R2U SMILES_CANONICAL CACTVS 3.385 O[Ru](O)(O)[Ru](O)(O)O
R2U SMILES CACTVS 3.385 O[Ru](O)(O)[Ru](O)(O)O
R2U SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 O[Ru](O)(O)[Ru](O)(O)O
R2U SMILES "OpenEye OEToolkits" 3.1.0.0 O[Ru](O)(O)[Ru](O)(O)O
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
R2U 'Create component' 2022-11-22 PDBE
R2U 'Initial release' 2023-06-28 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
R2U O3 O -0.108 -1.673 1
R2U O4 O 0.108 1.673 2
R2U O5 O 1.392 -1.680 3
R2U O6 O -1.392 1.680 4
R2U O7 O 1.950 0.366 5
R2U O8 O -1.950 -0.366 6
R2U RU1 Ru 0.648 -0.378 7
R2U RU2 Ru -0.648 0.378 8
#
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
R2U O3 RU1 SINGLE NONE 1
R2U O4 RU2 SINGLE NONE 2
R2U RU1 O5 SINGLE NONE 3
R2U RU1 RU2 SINGLE NONE 4
R2U RU1 O7 SINGLE NONE 5
R2U RU2 O6 SINGLE NONE 6
R2U RU2 O8 SINGLE NONE 7
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id R2U
_pdbe_chem_comp_rdkit_properties.exactmw 305.825
_pdbe_chem_comp_rdkit_properties.amw 304.182
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 6
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 8
_pdbe_chem_comp_rdkit_properties.NumAtoms 14
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 59.455
_pdbe_chem_comp_rdkit_properties.tpsa 121.380
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.347
_pdbe_chem_comp_rdkit_properties.CrippenMR 13.313
_pdbe_chem_comp_rdkit_properties.chi0v 6.633
_pdbe_chem_comp_rdkit_properties.chi1v 9.498
_pdbe_chem_comp_rdkit_properties.chi2v 6.563
_pdbe_chem_comp_rdkit_properties.chi3v 6.563
_pdbe_chem_comp_rdkit_properties.chi4v 0
_pdbe_chem_comp_rdkit_properties.chi0n 9.157
_pdbe_chem_comp_rdkit_properties.chi1n 3.441
_pdbe_chem_comp_rdkit_properties.chi2n 0.188
_pdbe_chem_comp_rdkit_properties.chi3n 0.188
_pdbe_chem_comp_rdkit_properties.chi4n 0
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 1.007
_pdbe_chem_comp_rdkit_properties.kappa1 2.943
_pdbe_chem_comp_rdkit_properties.kappa2 2.324
_pdbe_chem_comp_rdkit_properties.kappa3 2.525
_pdbe_chem_comp_rdkit_properties.Phi 0.855
#
_pdbe_chem_comp_external_mappings.comp_id R2U
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id R2U
#
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
R2U O3 -0.390 1.550 -1.170 ETKDGv3 1
R2U O4 2.463 -0.214 -0.130 ETKDGv3 2
R2U O5 -1.036 -0.589 -1.823 ETKDGv3 3
R2U O6 -0.624 -2.477 1.101 ETKDGv3 4
R2U O7 -2.104 0.509 0.017 ETKDGv3 5
R2U O8 1.324 0.959 1.840 ETKDGv3 6
R2U RU1 -0.447 0.746 -0.449 ETKDGv3 7
R2U RU2 1.012 0.081 0.501 ETKDGv3 8
R2U H1 0.460 2.007 -0.947 ETKDGv3 9
R2U H2 1.865 -0.613 -0.810 ETKDGv3 10
R2U H3 -0.581 -1.467 -1.871 ETKDGv3 11
R2U H4 -0.058 -1.679 0.949 ETKDGv3 12
R2U H5 -2.218 0.222 0.958 ETKDGv3 13
R2U H6 0.334 0.966 1.834 ETKDGv3 14
#