The number of hydrogen bonds between the protein and the RNA and within RNA are shown in Table and Figure shows kernel density estimate plots. The hydrogen bond numbers for the crystal structures were calculated with both "strong" (donor-acceptor distance <3.0Å and angle >135°) and "weak" hydrogen bond definition (accordingly, <3.5Å and >120°), because the hydrogen bonding in the crystal structures was generally not agreeing with the stricter criteria. One possible reason for the low number of the hydrogen bonds in the initial structures might be relatively low resolution: 2.89 Å for RIG-I (X-ray) and 3.54 Å Cas12J (cryoEM) complexes. The discrepancy between the number of "strong" hydrogen bonds in the starting structure and the average from the simulations is especially clear in the case of Cas12J complex, which is the only cryoEM structure among studied here complexes with the lowest resolution. Ago2 complex is X-ray structure with 1.8 Å resolution, here the underestimated number of hydrogen bonds could be caused by the water mediating the hydrogen bonding, which could not be accessed by the calculation method we applied.