We find that binding the CoPc catalyst to the CNT walls changes the geometric and electronic structure. To further investigate this, we employed molecular dynamics (MD) calculations using the Universal Force Field (UFF) . These MD simulations used the polarizable charge equilibration (PQEq) scheme for electrostatics and the RexPoN universal nonbond (UNB) van der Waals interactions (UFF is used solely for valence terms). Using UFF + PQEq + UNB allows us to obtain molecular geometries at the accuracy level of high-quality quantum mechanics while at the cost of classical mechanics.