[en] Highlights: • Structure and asicity of agmatine species. • The most basic species is bication II-H3 bearing positive charge on butylamino and the C = N groups of agmatine. • The protonation of neutral agmatine II is a much more feasible process than the protonation of the corresponding.monocation II-H3. • The same order of basicity was observed also in water solution. • The complexes modelling of agmatine – protein interaction were also investigated. The paper reports the results of a theoretical study of the conformational behavior and basicity of biogenic amine agmatine. The complexes modelling of agmatine – protein interaction are also under scrutiny of our investigation using the Becke3LYP and B97D levels of the density functional theory. The relative stabilities (Gibbs energies) of individual complexes are by both DFT methods described equally. Hydration has a dramatic effect on the hydrogen bonded complexes studied. The pairing acidic carboxylate group with different agmatine species resulted in charged hydrogen bond complexes containing negatively charged acetate species acting as proton acceptors.