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It is challenging to parameterize the force field for calcium ions (Ca2+) incalcium-binding proteins because of their unique coordination chemistry thatinvolves the surrounding atoms required for stability. In this work, weobserved wide variation in Ca2+ binding loop conformations of the Ca2+-bindingprotein calmodulin (CaM), which adopts the most populated ternary structuresdetermined from the MD simulations, followed by ab initio quantum mechanical(QM) calculations on all twelve amino acids in the loop that coordinate Ca2+ inaqueous solution. Ca2+ charges were derived by fitting to the electrostaticpotential (ESP) in the context of a classical or polarizable force field (PFF).We discovered that the atomic radius of Ca2+ in conventional force fields istoo large for the QM calculation to capture the variation in the coordinationgeometry of Ca2+ in its ionic form, leading to unphysical charges.Specifically, we found that the fitted atomic charges of Ca2+ in the context ofPFF depend on the coordinating geometry of electronegative atoms from the aminoacids in the loop. Although nearby water molecules do not influence the atomiccharge of Ca2+, they are crucial for compensating for the coordination of Ca2+due to the conformational flexibility in the EF-hand loop. Our method advancesthe development of force fields for metal ions and protein binding sites indynamic environments.

Determining the atomic charge of calcium ion requires the information of its coordination geometry in an EF-hand motif