data_3UQ
#
_chem_comp.id 3UQ
_chem_comp.name "[(1,2,3,4,5-eta)-cyclopentadienyl][(1,2,3,4,4a,8a-eta)-naphthalene]ruthenium(1+)"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H13 Ru"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2014-11-05
_chem_comp.pdbx_modified_date 2015-06-26
_chem_comp.pdbx_ambiguous_flag Y
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 294.334
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 3UQ
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag Y
_chem_comp.pdbx_model_coordinates_db_code 2MW6
_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
3UQ RU RU RU 1 0 N N N N N N 7.967 2.989 2.658 ? ? ? RU 3UQ 1
3UQ CC1 CC1 C 0 1 Y N N N N N 7.247 2.427 4.665 ? ? ? CC1 3UQ 2
3UQ CC2 CC2 C 0 1 Y N N N N N 8.155 3.525 4.783 ? ? ? CC2 3UQ 3
3UQ CC3 CC3 C 0 1 Y N N N N N 7.601 4.638 4.070 ? ? ? CC3 3UQ 4
3UQ CC4 CC4 C 0 1 Y N N N N N 6.134 2.862 3.880 ? ? ? CC4 3UQ 5
3UQ CC5 CC5 C 0 1 Y N N N N N 6.350 4.227 3.513 ? ? ? CC5 3UQ 6
3UQ CA1 CA1 C 0 1 Y Y N N N N ? ? ? ? ? ? CA1 3UQ 7
3UQ CA2 CA2 C 0 1 Y Y N N N N ? ? ? ? ? ? CA2 3UQ 8
3UQ CA3 CA3 C 0 1 Y Y N N N N ? ? ? ? ? ? CA3 3UQ 9
3UQ CA4 CA4 C 0 1 Y Y N N N N ? ? ? ? ? ? CA4 3UQ 10
3UQ CA5 CA5 C 0 1 Y Y N N N N ? ? ? ? ? ? CA5 3UQ 11
3UQ CA6 CA6 C 0 1 Y Y N N N N ? ? ? ? ? ? CA6 3UQ 12
3UQ CA7 CA7 C 0 1 Y Y N N N N ? ? ? ? ? ? CA7 3UQ 13
3UQ CA8 CA8 C 0 1 Y Y N N N N ? ? ? ? ? ? CA8 3UQ 14
3UQ CA9 CA9 C 0 1 Y Y N N N N ? ? ? ? ? ? CA9 3UQ 15
3UQ CA0 CA0 C 0 1 Y Y N N N N ? ? ? ? ? ? CA0 3UQ 16
3UQ HC1 HC1 H 0 1 N N N N N N 7.482 1.380 4.908 ? ? ? HC1 3UQ 17
3UQ HC2 HC2 H 0 1 N N N N N N 9.194 3.454 5.136 ? ? ? HC2 3UQ 18
3UQ HC3 HC3 H 0 1 N N N N N N 8.151 5.549 3.792 ? ? ? HC3 3UQ 19
3UQ HC4 HC4 H 0 1 N N N N N N 5.385 2.197 3.425 ? ? ? HC4 3UQ 20
3UQ HC5 HC5 H 0 1 N N N N N N 5.794 4.770 2.735 ? ? ? HC5 3UQ 21
3UQ HA1 HA1 H 0 1 N Y N N N N ? ? ? ? ? ? HA1 3UQ 22
3UQ HA2 HA2 H 0 1 N Y N N N N ? ? ? ? ? ? HA2 3UQ 23
3UQ HA3 HA3 H 0 1 N Y N N N N ? ? ? ? ? ? HA3 3UQ 24
3UQ HA4 HA4 H 0 1 N Y N N N N ? ? ? ? ? ? HA4 3UQ 25
3UQ HA7 HA7 H 0 1 N Y N N N N ? ? ? ? ? ? HA7 3UQ 26
3UQ HA8 HA8 H 0 1 N Y N N N N ? ? ? ? ? ? HA8 3UQ 27
3UQ HA9 HA9 H 0 1 N Y N N N N ? ? ? ? ? ? HA9 3UQ 28
3UQ HA0 HA0 H 0 1 N Y N N N N ? ? ? ? ? ? HA0 3UQ 29
#
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
3UQ CC1 CC2 DOUB Y N 1
3UQ CC2 CC3 SING Y N 2
3UQ CC3 CC5 DOUB Y N 3
3UQ CC5 CC4 SING Y N 4
3UQ CC4 CC1 SING Y N 5
3UQ HC3 CC3 SING N N 6
3UQ CC1 HC1 SING N N 7
3UQ CC2 HC2 SING N N 8
3UQ HC4 CC4 SING N N 9
3UQ HC5 CC5 SING N N 10
3UQ CA1 CA2 DOUB Y N 11
3UQ CA2 CA3 SING Y N 12
3UQ CA3 CA4 DOUB Y N 13
3UQ CA4 CA5 SING Y N 14
3UQ CA5 CA6 DOUB Y N 15
3UQ CA6 CA1 SING Y N 16
3UQ CA6 CA7 SING Y N 17
3UQ CA7 CA8 DOUB Y N 18
3UQ CA8 CA9 SING Y N 19
3UQ CA9 CA0 DOUB Y N 20
3UQ CA0 CA5 SING Y N 21
3UQ CA1 HA1 SING N N 22
3UQ CA2 HA2 SING N N 23
3UQ CA3 HA3 SING N N 24
3UQ CA4 HA4 SING N N 25
3UQ CA7 HA7 SING N N 26
3UQ CA8 HA8 SING N N 27
3UQ CA9 HA9 SING N N 28
3UQ CA0 HA0 SING N N 29
3UQ CC1 RU SING N N 30
3UQ CC2 RU SING N N 31
3UQ CC3 RU SING N N 32
3UQ CC4 RU SING N N 33
3UQ CC5 RU SING N N 34
3UQ CA1 RU SING N N 35
3UQ CA2 RU SING N N 36
3UQ CA3 RU SING N N 37
3UQ CA4 RU SING N N 38
3UQ CA5 RU SING N N 39
3UQ CA6 RU SING N N 40
#
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
3UQ SMILES ACDLabs 12.01 "[Ru+]%11674389%10%116c%12c8c9c%10c%11%13c6%12cccc%13"
3UQ InChI InChI 1.03 InChI=1S/C10H8.C5H5.Ru/c1-2-6-10-8-4-3-7-9(10)5-1;1-2-4-5-3-1;/h1-8H;1-5H;/q;;+1
3UQ InChIKey InChI 1.03 OPZOOBQSPMUFBC-UHFFFAOYSA-N
3UQ SMILES_CANONICAL CACTVS 3.385 "[Ru+]|12|3|4|5|6|7|8|9(|C%10=C|1C2C|3=C|4%10)|C%11=C|5c%12|6ccccc|7%12C|8=C|9%11"
3UQ SMILES CACTVS 3.385 "[Ru+]|12|3|4|5|6|7|8|9(|C%10=C|1C2C|3=C|4%10)|C%11=C|5c%12|6ccccc|7%12C|8=C|9%11"
3UQ SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C1=CC23=C4([Ru+]2567892%10([CH]3=[CH]5[CH]6=[CH]74)[CH]3=[CH]8C9[CH]2=[CH]%103)C=C1
3UQ SMILES "OpenEye OEToolkits" 1.7.6 C1=CC23=C4([Ru+]2567892%10([CH]3=[CH]5[CH]6=[CH]74)[CH]3=[CH]8C9[CH]2=[CH]%103)C=C1
#
_pdbx_chem_comp_identifier.comp_id 3UQ
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program ACDLabs
_pdbx_chem_comp_identifier.program_version 12.01
_pdbx_chem_comp_identifier.identifier "[(1,2,3,4,5-eta)-cyclopentadienyl][(1,2,3,4,4a,8a-eta)-naphthalene]ruthenium(1+)"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
3UQ 'Create component' 2014-11-05 RCSB
3UQ 'Other modification' 2014-11-06 RCSB
3UQ 'Other modification' 2015-06-08 RCSB
3UQ 'Initial release' 2015-07-01 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 '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
3UQ RU Ru 0.609 0.178 1
3UQ CC1 C 0.750 -1.650 2
3UQ CC2 C 1.804 -1.180 3
3UQ CC3 C 2.134 -0.157 4
3UQ CC4 C -0.257 -1.161 5
3UQ CC5 C 1.573 0.685 6
3UQ CA1 C 0.415 1.779 7
3UQ CA2 C 1.797 1.407 8
3UQ CA3 C 2.144 0.074 9
3UQ CA4 C 0.902 -0.985 10
3UQ CA5 C -0.662 -0.405 11
3UQ CA6 C -0.665 0.933 12
3UQ CA7 C -2.392 1.533 13
3UQ CA8 C -3.557 0.243 14
3UQ CA9 C -2.776 -0.940 15
3UQ CA0 C -1.819 -0.355 16
#
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
3UQ CC1 CC2 DOUBLE NONE 1
3UQ CC2 CC3 SINGLE NONE 2
3UQ CC3 CC5 DOUBLE NONE 3
3UQ CC5 CC4 SINGLE NONE 4
3UQ CC4 CC1 SINGLE NONE 5
3UQ CA1 CA2 DOUBLE NONE 6
3UQ CA2 CA3 SINGLE NONE 7
3UQ CA3 CA4 DOUBLE NONE 8
3UQ CA4 CA5 SINGLE NONE 9
3UQ CA5 CA6 DOUBLE NONE 10
3UQ CA6 CA1 SINGLE NONE 11
3UQ CA6 CA7 SINGLE NONE 12
3UQ CA7 CA8 DOUBLE NONE 13
3UQ CA8 CA9 SINGLE NONE 14
3UQ CA9 CA0 DOUBLE NONE 15
3UQ CA0 CA5 SINGLE NONE 16
3UQ CC4 RU SINGLE NONE 17
3UQ CC1 RU DATIVE NONE 18
3UQ CC2 RU DATIVE NONE 19
3UQ CC3 RU DATIVE NONE 20
3UQ CC5 RU DATIVE NONE 21
3UQ CA1 RU DATIVE NONE 22
3UQ CA2 RU DATIVE NONE 23
3UQ CA3 RU DATIVE NONE 24
3UQ CA4 RU DATIVE NONE 25
3UQ CA5 RU DATIVE NONE 26
3UQ CA6 RU DATIVE NONE 27
#
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
3UQ MurckoScaffold S1 scaffold 'c1ccc23->[Ru+]456789%10%11(C%12C->4=C->5C->6=C->7%12)<-c(c->8c->92)c->%10c->%113c1' 'InChI=1S/C10H8.C5H.Ru/c1-2-6-10-8-4-3-7-9(10)5-1;1-2-4-5-3-1;/h1-8H;1H;/q;;+1' LWFZNYADJYXPRT-UHFFFAOYSA-N
3UQ napthalene F1 fragment c1ccc2ccccc2c1 InChI=1S/C10H8/c1-2-6-10-8-4-3-7-9(10)5-1/h1-8H UFWIBTONFRDIAS-UHFFFAOYSA-N
3UQ 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
3UQ RU S1 1
3UQ CC1 S1 1
3UQ CC2 S1 1
3UQ CC3 S1 1
3UQ CC4 S1 1
3UQ CC5 S1 1
3UQ CA1 S1 1
3UQ CA2 S1 1
3UQ CA3 S1 1
3UQ CA4 S1 1
3UQ CA5 S1 1
3UQ CA6 S1 1
3UQ CA7 S1 1
3UQ CA8 S1 1
3UQ CA9 S1 1
3UQ CA0 S1 1
3UQ CA2 F1 1
3UQ CA3 F1 1
3UQ CA4 F1 1
3UQ CA5 F1 1
3UQ CA6 F1 1
3UQ CA1 F1 1
3UQ CA7 F1 1
3UQ CA8 F1 1
3UQ CA9 F1 1
3UQ CA0 F1 1
3UQ CA1 F2 1
3UQ CA2 F2 1
3UQ CA3 F2 1
3UQ CA4 F2 1
3UQ CA5 F2 1
3UQ CA6 F2 1
3UQ CA5 F2 2
3UQ CA6 F2 2
3UQ CA7 F2 2
3UQ CA8 F2 2
3UQ CA9 F2 2
3UQ CA0 F2 2
#
_pdbe_chem_comp_rdkit_properties.comp_id 3UQ
_pdbe_chem_comp_rdkit_properties.exactmw 295.006
_pdbe_chem_comp_rdkit_properties.amw 294.339
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 0
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 0
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 29
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 1
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.733
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 93.780
_pdbe_chem_comp_rdkit_properties.tpsa 0
_pdbe_chem_comp_rdkit_properties.CrippenClogP 3.859
_pdbe_chem_comp_rdkit_properties.CrippenMR 63.772
_pdbe_chem_comp_rdkit_properties.chi0v 9.592
_pdbe_chem_comp_rdkit_properties.chi1v 15.504
_pdbe_chem_comp_rdkit_properties.chi2v 71.508
_pdbe_chem_comp_rdkit_properties.chi3v 71.508
_pdbe_chem_comp_rdkit_properties.chi4v 123.617
_pdbe_chem_comp_rdkit_properties.chi0n 20.854
_pdbe_chem_comp_rdkit_properties.chi1n 12.445
_pdbe_chem_comp_rdkit_properties.chi2n 13.282
_pdbe_chem_comp_rdkit_properties.chi3n 13.282
_pdbe_chem_comp_rdkit_properties.chi4n 13.992
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.103
_pdbe_chem_comp_rdkit_properties.kappa1 2.284
_pdbe_chem_comp_rdkit_properties.kappa2 0.312
_pdbe_chem_comp_rdkit_properties.kappa3 0.031
_pdbe_chem_comp_rdkit_properties.Phi 0.045
#
#