Hydrogen added to ligand against intent?

[nyubachi]

Hello,

Thank you very much for your time and your always thoughtful answers.

I have a question about "Protein_ligand.ipynb".

The original ligand file is hydrogenated at pH 7.5.
Also, in this notebook, Add_ligand_hydrogens: No.
As you can see in the image, there is no hydrogen atom bonded to the carboxyl group. I doubt that Charge = 0 is shown.

And when the simulation is finished, a PDB file of the protein-ligand complex is created, though,
In the PDB file of the protein-ligand complex, a hydrogen atom is added to the carboxyl group of the ligand.
The image shows only the ligand extracted.

My intention is not to have the hydrogen atom automatically added,
Is this inevitable?
Or was the hydrogen atom added by accident at some stage?

I may be asking strange questions due to my ignorance.
In that case, I apologize.

Thank you in advance,

nyubachi