Different result between theoretical structure and PDB structure.

Hello,

I predicted ligand binding sites of theoritical structure and its PDB structure (3D89) using COACH program.
However, the result was different between both structures.

Sequences are little different, but overlapped sequence is same.
When I calculated MCC score, theoretical str is 0.882 and PDB str is -0.071.
I don't know why the pdb str have worse result than theoretical str.

Is it because the sequence is different?

COACH option is below,
LBS true, benchmark -idcut 1.0

Thank you.