cis peptide bonds in proteins are often rate-limiting steps in protein folding or conformational change and are frequently stabilized by metal ions. In the collagen-binding domain of Clostridium histolyticum collagenase, the binding of calcium ions triggers the formation of a cis peptide bond. We present free energy simulations of the formation of this cis peptide bond using a combined quantum mechanics/molecular mechanics approach together with adaptive umbrella sampling. From these simulations, we have determined that the calcium ions not only stabilize the cis peptide bond thermodynamically but also catalyze its formation; the free energy barrier to the formation of the cis peptide bond decreases from 21.4 kcal/mol in the absence of calcium ions to 10.3 kcal/mol in their presence. Two principal factors contribute to this reduction in the energy barrier. The calcium ions electrostatically stabilize the lone pair on the nitrogen atom that forms during the isomerization. In addition, their attraction to acidic amino acid side chains and formation of a hydrogen bond network constrain the peptide backbone in a way that makes it easier for the nitrogen to pyramidalize. Factors that explain the observed cooperativity of calcium binding are discussed.