Molecular quantum similarity is evaluated for enantiomers in the case of molecules showing conformational flexibility, using our earlier proposed Boltzmann weighted similarity index. The conformers of the enantiomers of the amino acids alanine, asparagine, cysteine, leucine, serine, and valine were examined. Next to studying global indices, the evaluation of local similarity is carried out using our earlier proposed local similarity index based on the Hirshfeld partitioning, to further illustrate Mezey's holographic electron density theorem in chiral systems and to quantify dissimilarity of enantiomers.