Immobilized metal ion affinity chromatography (IMAC) has become a widespread analytical and preparative separation method for therapeutic proteins, peptides nucleic acids, hormones, and enzymes. N‐Methacryloyl‐l‐histidine Methyl Ester (MAH) monomer is recently used as a synthesized affinity ligand in IMAC. It is capable of chelating with many transition metal ions such as Zn2+, Ni2+, and Cu2+ ions through its histidine residue. In this way, proteins can bind selectively to these immobilized metal ions through MAH as a ligand in affinity chromatography. In this study, we applied the computational docking method on the interactions that occur between the MAH monomer and its complexes with Zn2+ ions as ligands and protein molecules as targets. MAH monomer was drawn and created using the Avogadro software as an optimization tool. Human insulin (Ins) molecule and horse heart cytochrome C (Cyt C) were selected as target proteins to interact with MAH monomer as affinity ligand. Automated docking software AutoDock v4.2 was used for docking of MAH monomer to Ins and Cyt C, respectively. The affinity ligand complexes with Zn2+ ions bound to one, two, and three moles of MAH were studied and compared separately. The lowest binding energies of Ins and Cyt C proteins in 1:1 mol ratio of MAH‐Zn2+ were found as (−4.14) and (−4.92) kcal/mol, respectively.