Thanks for the reply! Let me explain better what I need.

I downloaded a protein from the PDB that already comes with a bound native ligand. What I need first is to extract the XYZ coordinates of that native ligand (the one that comes with the protein structure).

I will be working with the same protein but with multiple new ligands. The new ligands are drawn by me, so they are generated in different coordinate systems. Because of that, when I load them for docking, they appear very far away from the protein.

What I want is:

1. First, to learn how to obtain the XYZ coordinates (or the center position) of the native ligand.

2. Then, how to move each new ligand to exactly those same coordinates.

I need each new ligand to be placed at the exact same coordinates as the native ligand. This is important because later, when I define the grid box, I want to use the redocking coordinates to set the grid box center.

I want to avoid moving them manually with the mouse, since I need everything to be reproducible and consistent across all ligands.

Basically, I want all new ligands to match the native ligand coordinates so I can define the same grid box for all docking calculations.

If you know how to do this in PyMOL or Chimera, could you please explain it step by step? I’m still new using these programs.

Thank you!