Protein-Ligand PCA/covariance analysis

Question

[Bioinformatician_in_trouble]

Hi there,

This is my first time doing a PCA/Covariance analysis of a 20ns Protein-Ligand simulation using gmx covar and gmx anaeig commands from Gromacs. From all the selections that the commands gave, I have chosen backbone. The resulting plots are attached. Plot 1 is eigenvectors vrs eigenvalues and plot2 is 2d scatter plot. Yellow is my reference and blue and green are my hit molecules. Can someone please help me analyze this? TIA

1. https://ibb.co/8KQBgTQ

2. https://ibb.co/JdxJ0jQ