Why not consider atoms in protein instead of amino acid?

[dxyzx0]

Thank you for your brilliant work in the paper.

But You consider each atom in the compound and each amino acid in the protein, I wonder whether can I consider the atoms in the protein instead of amino acid?

Since we want to know the interactions between compound and proteins, why we don't consider both the atoms within these 2 structures?

I know that the protein may be very long and the amino acid sequence is already lone enough. However, Can we cut off the protein into much smaller sequence, which contains the interaction pocket? Is there an automatic way to accomplish this task?

Thank you very much!!!