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Explicit water molecules prevent non-native N2(G)…O4′(G+1) H-bonds in the QMopt AA structure. Left - the X-ray water position (red ball, only oxygen is visible), which is essentially identical in all observed instances. Center - example of the water position after the QM optimization; note that the water molecule has somewhat relocated. Right - the non-native H-bond in absence of the explicit water molecule.
