Semiempirical methods can be applied to calculations of much larger systems than classical ab initio or DFT methods, reaching accuracy sometimes comparable with more advanced levels of theory. These methods are important tools that can be used in research projects focused in structure‐based drug design (SBDD). Thus, a notion of the precision of each method in describing key‐interactions with target receptors is necessary. With this goal in mind, we applied several semiempirical methods (AM1, PM3, PM6, PM6‐D3, PM6‐D3H4, PM6‐DH2, PM6‐DH+, and PM7) for evaluation of the key‐interactions of some zinc‐dependent histone deacetylase (HDAC) inhibitors revealed by crystallographic structures, for which the AM1 and PM7 Hamiltonians generally failed to geometrically describe the bidentate coordination of the pan‐HDAC inhibitors with the Zn(II) ion. In addition, we also applied the same evaluations to Nexturastat A, a histone deacetylase 6 (HDAC6) selective inhibitor, in complex with the HDAC6, to find out how each semiempirical method represent the monodentate coordination profile with the Zn(II) ion when there is a competition with a hydrogen bond in the system. Our results showed a significant difference in the profile of each method and highlighted PM6‐DH2 as the best method for the description of the key‐interactions of Nexturastat A in HDAC6. Our data reinforce the necessity to always compare several semiempirical methods before performing SBDD studies with them.