The coordination of the horminone molecule with hydrated magnesium and calcium divalent ions was studied by means of the density functional theory. All-electron calculations were performed with the B3LYP/6-31G method. The first layer of the water molecules surrounding the metallic cations was included. It was found that the octahedral [horminone(O-a-O-d)-Mg-(H2O)(4)](2+) Complex is more stable than [Mg(H2O)(6)](2+). That is, horminone is able to displace two water units from the hexahydrated complex. This behavior does not occur for Ca2+. Consistently, [horminone(O-a-O-d)-Mg-(H2O)(4)](2+) has a greater metal-ligand binding energy than (horminone(O-a-O-d)-Ca-(H2O)(4)](2+). The preference of horminone by Mg2+ is enlightened by these results. Moreover, its electronic structure, as shown by huge changes in the atomic populations, is strongly perturbed by Mg2+. Indeed, horminone, bonded to [Mg(H2O)(4)](2+), is able to cross the bacterial membrane cell. Once inside, [horminone(O-a-O-d)-Mg-(H2O)(4)](2+) binds to rRNA phosphate groups yielding [horminone(O-a-O-d)-Mg-(H2O)(PO4H2)(PO4H3)(2)](+). These results give insights into how horminone may inhibit the initial steps of protein synthesis. The stability of the studied systems is accounted for in terms of the calculated structural and electronic properties: Mg-O and Ca-O bond lengths, charge transfers, and binding energies.