Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

RHD : Summary

Code

RHD

One-letter code

X

Molecule name

RHODIUM HEXAMINE ION

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 hexakis($l^{4}-azanyl)rhodium(3+)

Formula

H18 N6 Rh

Formal charge

3

Molecular weight

205.089 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 N.N.N.N.N.N.[Rh+3]
SMILES OpenEye OEToolkits 2.0.7 [NH3][Rh+3]([NH3])([NH3])([NH3])([NH3])[NH3]
Canonical SMILES CACTVS 3.385 N.N.N.N.N.N.[Rh+3]
Canonical SMILES OpenEye OEToolkits 2.0.7 [NH3][Rh+3]([NH3])([NH3])([NH3])([NH3])[NH3]

IUPAC InChI

InChI=1S/6H3N.Rh/h6*1H3;/q;;;;;;+3

IUPAC InChI key

JGYYKTIOJIEIKU-UHFFFAOYSA-N
RHD

wwPDB Information

Atom count

25 (7 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAI

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2023-09-23

Status

Released

Obsoleted

Not Assigned



RHD : Atoms of Molecule

Total Number of Atoms: 25
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 RH RH RH N N N 3 -0.016 -0.002 -0.008
2 N1 N N1 N N N 0 -1.305 -0.531 -1.299
3 N2 N N2 N N N 0 1.273 0.527 1.283
4 N3 N N3 N N N 0 1.347 -0.858 -1.018
5 N4 N N4 N N N 0 -1.379 0.855 1.002
6 N5 N N5 N N N 0 0.285 1.61 -0.969
7 N6 N N6 N N N 0 -0.317 -1.613 0.953
8 HN11 H HN11 N N N 0
9 HN12 H HN12 N N N 0 -0.911 -1.314 -1.798
10 HN13 H HN13 N N N 0 -2.1 -0.883 -0.788
11 HN21 H HN21 N N N 0
12 HN22 H HN22 N N N 0 1.852 -0.28 1.463
13 HN23 H HN23 N N N 0 1.864 1.214 0.839
14 HN31 H HN31 N N N 0
15 HN32 H HN32 N N N 0 2.127 -0.219 -1.053
16 HN33 H HN33 N N N 0 1.649 -1.656 -0.479
17 HN41 H HN41 N N N 0
18 HN42 H HN42 N N N 0 -0.92 1.533 1.591
19 HN43 H HN43 N N N 0 -1.942 1.375 0.346
20 HN51 H HN51 N N N 0
21 HN52 H HN52 N N N 0 0.305 2.354 -0.288
22 HN53 H HN53 N N N 0 1.214 1.547 -1.356
23 HN61 H HN61 N N N 0
24 HN62 H HN62 N N N 0 0.591 -1.977 1.2
25 HN63 H HN63 N N N 0 -0.772 -1.356 1.816



RHD : Chemical Bonds

Total Number of Bonds: 24
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 RH N1 RH N sing 1.9 N N
2 RH N2 RH N sing 1.9 N N
3 RH N3 RH N sing 1.9 N N
4 RH N4 RH N sing 1.9 N N
5 RH N5 RH N sing 1.9 N N
6 RH N6 RH N sing 1.9 N N
7 N1 HN11 N H sing N N
8 N1 HN12 N H sing 1.01 N N
9 N1 HN13 N H sing 1.01 N N
10 N2 HN21 N H sing N N
11 N2 HN22 N H sing 1.01 N N
12 N2 HN23 N H sing 1.01 N N
13 N3 HN31 N H sing N N
14 N3 HN32 N H sing 1.01 N N
15 N3 HN33 N H sing 1.01 N N
16 N4 HN41 N H sing N N
17 N4 HN42 N H sing 1.01 N N
18 N4 HN43 N H sing 1.01 N N
19 N5 HN51 N H sing N N
20 N5 HN52 N H sing 1.01 N N
21 N5 HN53 N H sing 1.01 N N
22 N6 HN61 N H sing N N
23 N6 HN62 N H sing 1.01 N N
24 N6 HN63 N H sing 1.01 N N



RHD : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
RHD 165d Open in New Window Bound ligand 4 1
RHD 1id9 Open in New Window Bound ligand 2 1
RHD 1idw Open in New Window Bound ligand 2 1
RHD 1iha Open in New Window Bound ligand 2 1