Figure 1.

Representative QM/MM partitioning of a metal-containing biological system, showing the catalytic site of the spliceosome (total atoms 370,000 atoms). Proteins are shown with white surface and green new cartoons, distinct RNA strands are shown in blue, orange, cyan and green ribbons. The cycle on the right reports a close view of the QM region (highlighted with a transparent surface), composed by the Mg²⁺ ions (yellow), and the remaining RNA nucleobases and phosphate shown in licorice and ball and sticks and colored by atom name. The remaining part of the system, including RNA strands (shown as blue and orange ribbons), water molecules (shown as red sticks), protein and counter ions (not shown) are treated at the classical (MM) level. Adapted from Ref [94] with permission of Copyright © 2020, American Chemical Society.