Metal ion detection is of a paramount importance for health monitoring. The host should properly accommodate the desired ion and be selective with respect to other potential guests, which makes devising ion sensors a demanding task. Recently (Phys. Chem. Chem. Phys. 2023, 25, 32656), we suggested a procedure for a computational design of crown ethers that can capture magnesium ions. In the present contribution we apply the same approach to search for Mg2+ trap with thiophene units, in accord with proposed hosts for Na+ and K+ ions (Adv. Funct. Mater., 2016, 26, 514). Additionally, we present a procedure based on the combination of Density Functional Theory based Molecular Dynamics and the Interacting Quantum Fragments methodology for determination of host‐guest interaction and binding energies in a model with a large number of explicit solvent molecules. The presented strategy could be applied for identification of the right host for an arbitrary guest.