Dear Yuvaraj,
That is a lovely derivative, but the chemical species involved in that
derivatisation is not HgI4, nor the anion even (HgI4)2- , but is often the
anion (HgI3)- , with a nice symmetrical planar structure - see for instance
https://pubchem.ncbi.nlm.nih.gov/compound/Triiodomercurate_1
The Molfile and SDF files at
https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:51567
contain coordinates for the Mercury and Iodine atoms that should enable you
to create a dictionary for it. Or perhaps someone else can direct you to a
a ready-made refinement dictionary - I couldn't find one.
With best wishes,
Gerard.
--
On Sat, Jan 22, 2022 at 11:04:27PM +0530, YUVARAJ I wrote:
> Respected Professors,
>
> I have solved a protein structure using anomalous signal using
> mercury(II)potassium Iodide(K2HgI4).
>
> I wanted to submit the structure of the protein with mercury(II) potassium
> iodide to PDB.
>
> I am facing problems while making the ligand (HGI4) . HGI4 is not available
> in the pdb.
>
> Make Ligand in CCP4 is showing error
>
> " The input ligands/molecules contains metal or other heavier atoms
>
> Acedrg currently deals with ligands/molecules with following elements only
>
> C, N, O, S, P, B, F, Cl, Br, I, H"
>
> I tried to make cif file from other softwares, given as input in coot, It
> is also showing errors, dictionary no restraints were found.
>
> For generating cif dictionary, I used prodrg server
>
> It is showing error
>
> "PRODRG> Found unsupported atom HG in Molfile.
>
> ERRDRG> Currently only N, C, O, S, P, Cl, Br, F, I are supported. "
>
>
> If I fix each atom seperately such as Hg and Iodine separately, It is
> having clashes with other atoms during validation,
>
> kindly let me know how I can fix this HGI4 ?
>
> I have attached the screenshots for reference.
>
> --
>
> Regards
> Yuvaraj
>
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