In the present work, conformational analysis of lignin models was accomplished by considering four cross-link types (3–5′, β-5′, α-O-4 and β-O-4) and three monomer units [guaiacyl (G), p-hydroxyphenyl (H) and syringyl (S)]. Analysis involving the 3–5′ and β-5′ dimers was conducted following the standard procedure, i.e., rotating the monomers around the single bond. On the other hand, analysis of α-O-4 and β-O-4 dimers followed a distinct protocol with the aid of an interesting chemometric tool called Box-Behnken (BB) design. This methodology was applied with the aim of screening the most relevant dihedral angles. The results show that the conformational space for large systems with several dihedral angles can be mapped satisfactorily through the BB approach, reducing the number of dimensions to be treated at the quantum mechanical level. Furthermore, the quantum mechanics-chemometry-quantum mechanics (QM/BB/QM) method proposed here allows us to determine calculated torsional angles for lignin models in good agreement with crystallographic data for some model compounds.