The purpose of this part is to represent the protein overall motions, including changes upon ligand binding and the inherently flexibility of protein or protein-ligand complex. Consequently, to explore how those motions occur, we classified the pairs with overall RMSD greater than 2.0 Å into four parts: (a) pairs of ligand-free structures, (b) pairs of ligand-free and ligand-bound structures, (c) pairs of structures bound with different ligands, (d) pairs of structures bound with same ligand. For each part, we chose a single pair from a set of the same protein pairs with less missing residues and larger RMSD, i.e., the one with the lest missing residues from top 5 largest RMSD.