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Deformations of the three most common cyclodextrins (α, β, and γ) were induced to form inclusion compounds with sertraline and abacavir. The deformations were obtained from classical molecular dynamics (CMD) using as starting point X‐ray structures. The molecular dynamics were performed in two ways, over the cyclodextrins with and without the presence of a guest. Two characteristic rings within these cyclodextrins were used to measure the distortions observed along with the molecular dynamics. A docking approach was used to build inclusion compounds over the structures obtained from CMD without the presence of sertraline or abacavir. Thus, we compared structures of inclusion compounds obtained from deformations induced by the presence of a guest or with intrinsic deformations exhibited by each cyclodextrin. After this step, each structure was optimized by the PBE0‐D3/6‐31G(d,p) method, and the electron density delivered by this method was used to perform the quantum theory of atoms in molecules approach to analyze intermolecular contacts between sertraline, or abacavir, and three cyclodextrins. From this procedure, we found that inclusion compounds obtained from X‐ray structures present the highest energies over the potential energy surface. Thus, for getting low‐lying energy structures of inclusion compounds, deformations on cyclodextrins are necessary. [ABSTRACT FROM AUTHOR]