[3dem] Seeking guidance regarding fitting a small molecule ligand to a protein , using a cryoEM map

[Daniel Asarnow]

Hi Sagnik,
Are there two copies of the molecule/does it have two reactive moieties? Or
is it a case where you see both in superposition in the map but each copy
only has one covalent bond formed?

If the latter you may find this paper interesting.
https://urldefense.com/v3/__https://www.science.org/doi/full/10.1126/science.aaw2922__;!!Mih3wA!AUKi-ePUFiX1RrX4C-k_sJPBHl4TYyC514STt0q4uFxdhfwiRR0mSVZUbjQswntgAloxvVW38lJ0lH_wyJk$ 

To supplement Dom's reply, you can also use those elbow parameters with
ISOLDE in ChimeraX and use the ISOLDE > Model building > Make bond action
to create a new bond. Though you may need to generate parameters for a
combined residue along the lines of e.g. P1L (palmitocysteine) to continue
the simulation.

Best,
-da

On Wed, Oct 15, 2025 at 8:20 AM Sagnik Sen via 3dem <3dem at ncmir.ucsd.edu>
wrote:

> Dear all,
>
> We have a sample where a small molecule ligand is bound to a homodimer
> protein. It forms covalent bonds with the Sulfur of a Cysteine on both the
> chains. We currently have a cryoEM map of 2.5 Å and we can clearly see
> the ligand density on both the chains, after fitting the protein model to
> the map.
>
> We are also able to roughly fit the ligand using Coot but seek inputs with
> respect to forming the bond. Placement of the ligand in the density near to
> the Cysteine and doing real space refinement does not make the bond.
>
> We do have a PDB and restraints file for the ligand, made using Phenix
> eLBOW. Do we need to edit the PDB files for both the protein and the ligand
> to make the link? IF so, what is a good way to do that?
>
> Or is there a way to fit this using Phenix?
>
> Thanks and best regards,
> Sagnik
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