By analogy with other nucleases active sites, the scissile phosphate was thus moved to a bridging position between the two ions, so that it replaces the bridging water molecule resolved in the X-ray structure of the isolated enzyme. This small rearrangement implies minimal distorsion of the overall structure (Figure ), which remains compatible with the cryo-EM structure of the complex-of limited resolution in this area and obtained with a mutated active site. It increased the stability of the active site in simulations performed with the standard Amber99ff_OL15 force field (Figure ). However, the two ions still moved apart, thus breaking apart the active site structure, in all four 500ns-replicas. Such active sites with two divalent ions very close in space are notoriously difficult to describe with standard force fields, due to the large electrostatic repulsion between the two ions, which is overestimated in the absence of electronic polarization and charge transfer. We then explored how different computational strategies could stabilize the active site structure. First, we tested a recently-proposed Mg 2+ force field 66 that includes pair-specific Lennard-Jones interactions with RNA phosphate backbone oxygen atoms, specifically tuned to properly capture Mg 2+ -phosphate binding free energy. This modification did not increase the stability of the active site, which fell apart in all 4 replicas within 150 ns.