Ligand conformational strain energy (LCSE) is an important parameter in computer-aided drug discovery. LCSE may be calculated through quantum mechanical (QM) computations by comparing free and protein pocket-bound ligand structures. How-ever, there is still a dispute on the plausible LCSE range and the methodology to obtain it. In this work, 8 highly flexible ligand structures with a good variety of patterns were chosen to be optimized step-by-step with energy calculations to analyze the differences in struc-ture and relative energies from protein-bound ligands to free ligand with the minimum local energy. The structures with resolutions between high (0.86 × 10⁻¹⁰) and medium (3.1 × 10⁻¹⁰) are calculated through 3 QM methods, namely the density functional theory (DFT) with the M062X-D3 function as well as Hartree-Fock and GFN1-xTB approaches. QM calculation results show that LCSE was lower than 6.0 kcal/mol. In several cases, the energy differences between bound and unbound ligand structures was mainly due to significant errors in the geometrical parameters of the former, highlighting the need of accurate experimental determination of protein-bound ligand structures prior to LCSE analyses.