data_RHD
#
_chem_comp.id RHD
_chem_comp.name "RHODIUM HEXAMINE ION"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAI
_chem_comp.formula "H18 N6 Rh"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 3
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2023-09-23
_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 205.089
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code RHD
_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 Y
_chem_comp.pdbx_model_coordinates_db_code 165D
_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
RHD RH RH RH 3 0 N N N N N N -6.700 12.013 36.949 -0.016 -0.002 -0.008 RH RHD 1
RHD N1 N1 N 0 1 N N N N N N -5.506 13.363 35.871 -1.305 -0.531 -1.299 N1 RHD 2
RHD N2 N2 N 0 1 N N N N N N -5.920 10.430 35.816 1.273 0.527 1.283 N2 RHD 3
RHD N3 N3 N 0 1 N N N N N N -7.886 10.655 38.019 1.347 -0.858 -1.018 N3 RHD 4
RHD N4 N4 N 0 1 N N N N N N -7.467 13.605 38.082 -1.379 0.855 1.002 N4 RHD 5
RHD N5 N5 N 0 1 N N N N N N -5.158 11.767 38.356 0.285 1.610 -0.969 N5 RHD 6
RHD N6 N6 N 0 1 N N N N N N -8.237 12.239 35.542 -0.317 -1.613 0.953 N6 RHD 7
RHD HN11 HN11 H 0 0 N N N N N N -5.665 14.291 36.207 ? ? ? HN11 RHD 8
RHD HN12 HN12 H 0 0 N N N N N N -4.542 13.125 35.992 -0.911 -1.314 -1.798 HN12 RHD 9
RHD HN13 HN13 H 0 0 N N N N N N -5.742 13.315 34.900 -2.100 -0.883 -0.788 HN13 RHD 10
RHD HN21 HN21 H 0 0 N N N N N N -6.331 9.570 36.118 ? ? ? HN21 RHD 11
RHD HN22 HN22 H 0 0 N N N N N N -6.129 10.578 34.849 1.852 -0.280 1.463 HN22 RHD 12
RHD HN23 HN23 H 0 0 N N N N N N -4.929 10.388 35.940 1.864 1.214 0.839 HN23 RHD 13
RHD HN31 HN31 H 0 0 N N N N N N -8.500 11.156 38.628 ? ? ? HN31 RHD 14
RHD HN32 HN32 H 0 0 N N N N N N -8.425 10.107 37.379 2.127 -0.219 -1.053 HN32 RHD 15
RHD HN33 HN33 H 0 0 N N N N N N -7.298 10.053 38.560 1.649 -1.656 -0.479 HN33 RHD 16
RHD HN41 HN41 H 0 0 N N N N N N -8.126 13.254 38.747 ? ? ? HN41 RHD 17
RHD HN42 HN42 H 0 0 N N N N N N -6.719 14.062 38.563 -0.920 1.533 1.591 HN42 RHD 18
RHD HN43 HN43 H 0 0 N N N N N N -7.921 14.257 37.475 -1.942 1.375 0.346 HN43 RHD 19
RHD HN51 HN51 H 0 0 N N N N N N -5.450 11.122 39.062 ? ? ? HN51 RHD 20
RHD HN52 HN52 H 0 0 N N N N N N -4.343 11.413 37.898 0.305 2.354 -0.288 HN52 RHD 21
RHD HN53 HN53 H 0 0 N N N N N N -4.947 12.649 38.777 1.214 1.547 -1.356 HN53 RHD 22
RHD HN61 HN61 H 0 0 N N N N N N -9.016 11.669 35.804 ? ? ? HN61 RHD 23
RHD HN62 HN62 H 0 0 N N N N N N -8.521 13.197 35.510 0.591 -1.977 1.200 HN62 RHD 24
RHD HN63 HN63 H 0 0 N N N N N N -7.907 11.959 34.640 -0.772 -1.356 1.816 HN63 RHD 25
#
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
RHD RH N1 SING N N 1
RHD RH N2 SING N N 2
RHD RH N3 SING N N 3
RHD RH N4 SING N N 4
RHD RH N5 SING N N 5
RHD RH N6 SING N N 6
RHD N1 HN11 SING N N 7
RHD N1 HN12 SING N N 8
RHD N1 HN13 SING N N 9
RHD N2 HN21 SING N N 10
RHD N2 HN22 SING N N 11
RHD N2 HN23 SING N N 12
RHD N3 HN31 SING N N 13
RHD N3 HN32 SING N N 14
RHD N3 HN33 SING N N 15
RHD N4 HN41 SING N N 16
RHD N4 HN42 SING N N 17
RHD N4 HN43 SING N N 18
RHD N5 HN51 SING N N 19
RHD N5 HN52 SING N N 20
RHD N5 HN53 SING N N 21
RHD N6 HN61 SING N N 22
RHD N6 HN62 SING N N 23
RHD N6 HN63 SING N N 24
#
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
RHD InChI InChI 1.06 InChI=1S/6H3N.Rh/h6*1H3;/q;;;;;;+3
RHD InChIKey InChI 1.06 JGYYKTIOJIEIKU-UHFFFAOYSA-N
RHD SMILES_CANONICAL CACTVS 3.385 N.N.N.N.N.N.[Rh+3]
RHD SMILES CACTVS 3.385 N.N.N.N.N.N.[Rh+3]
RHD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[NH3][Rh+3]([NH3])([NH3])([NH3])([NH3])[NH3]"
RHD SMILES "OpenEye OEToolkits" 2.0.7 "[NH3][Rh+3]([NH3])([NH3])([NH3])([NH3])[NH3]"
#
_pdbx_chem_comp_identifier.comp_id RHD
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier hexakis($l^{4}-azanyl)rhodium(3+)
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
RHD 'Create component' 1999-07-08 RCSB
RHD 'Modify descriptor' 2023-09-23 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
RHD RH Rh 5.173 0.000 1
RHD N1 N 6.472 0.750 2
RHD N2 N 3.874 -0.750 3
RHD N3 N 3.874 0.750 4
RHD N4 N 5.173 -1.500 5
RHD N5 N 5.173 1.500 6
RHD N6 N 6.583 -0.513 7
#
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
RHD RH N1 SINGLE NONE 1
RHD RH N2 SINGLE NONE 2
RHD RH N3 SINGLE NONE 3
RHD RH N4 SINGLE NONE 4
RHD RH N5 SINGLE NONE 5
RHD RH N6 SINGLE NONE 6
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id RHD
_pdbe_chem_comp_rdkit_properties.exactmw 205.063
_pdbe_chem_comp_rdkit_properties.amw 205.092
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 18
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 6
_pdbe_chem_comp_rdkit_properties.NumHBA 0
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 7
_pdbe_chem_comp_rdkit_properties.NumAtoms 25
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_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 67.732
_pdbe_chem_comp_rdkit_properties.tpsa 165.840
_pdbe_chem_comp_rdkit_properties.CrippenClogP -7.847
_pdbe_chem_comp_rdkit_properties.CrippenMR 17.329
_pdbe_chem_comp_rdkit_properties.chi0v 4.655
_pdbe_chem_comp_rdkit_properties.chi1v 5.292
_pdbe_chem_comp_rdkit_properties.chi2v 0
_pdbe_chem_comp_rdkit_properties.chi3v 0
_pdbe_chem_comp_rdkit_properties.chi4v 0
_pdbe_chem_comp_rdkit_properties.chi0n 21.017
_pdbe_chem_comp_rdkit_properties.chi1n 8.944
_pdbe_chem_comp_rdkit_properties.chi2n 0
_pdbe_chem_comp_rdkit_properties.chi3n 0
_pdbe_chem_comp_rdkit_properties.chi4n 0
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.383
_pdbe_chem_comp_rdkit_properties.kappa1 0.506
_pdbe_chem_comp_rdkit_properties.kappa2 0.782
_pdbe_chem_comp_rdkit_properties.kappa3 834.482
_pdbe_chem_comp_rdkit_properties.Phi 0.057
#
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
RHD UniChem PDBe RHD
RHD UniChem ChEBI 33891
RHD UniChem PubChem 50936006
RHD UniChem PubChem 6857561
#
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
RHD RH 0.030 0.008 -0.052 ETKDGv3 1
RHD N1 1.612 1.108 1.180 ETKDGv3 2
RHD N2 -1.269 1.300 1.388 ETKDGv3 3
RHD N3 -1.217 -0.981 -1.664 ETKDGv3 4
RHD N4 1.502 -1.509 -0.824 ETKDGv3 5
RHD N5 -0.689 -1.926 1.020 ETKDGv3 6
RHD N6 0.054 2.007 -1.087 ETKDGv3 7
RHD HN11 1.652 1.989 1.739 ETKDGv3 8
RHD HN12 2.479 1.082 0.599 ETKDGv3 9
RHD HN13 1.683 0.318 1.859 ETKDGv3 10
RHD HN21 -1.250 0.844 2.328 ETKDGv3 11
RHD HN22 -1.375 2.325 1.556 ETKDGv3 12
RHD HN23 -2.144 0.981 0.917 ETKDGv3 13
RHD HN31 -0.880 -0.571 -2.563 ETKDGv3 14
RHD HN32 -1.537 -1.952 -1.879 ETKDGv3 15
RHD HN33 -2.066 -0.440 -1.387 ETKDGv3 16
RHD HN41 1.442 -2.388 -1.386 ETKDGv3 17
RHD HN42 2.198 -1.685 -0.066 ETKDGv3 18
RHD HN43 1.915 -0.781 -1.449 ETKDGv3 19
RHD HN51 -0.571 -2.948 0.838 ETKDGv3 20
RHD HN52 -0.118 -1.704 1.866 ETKDGv3 21
RHD HN53 -1.689 -1.784 1.287 ETKDGv3 22
RHD HN61 0.723 1.625 -1.793 ETKDGv3 23
RHD HN62 0.381 2.971 -0.855 ETKDGv3 24
RHD HN63 -0.866 2.111 -1.571 ETKDGv3 25
#