Table 1. Complex II Featuring Interactions of Ammonium Ions with One Phosphate (interaction mode P) or Two (interaction mode P2) at Different Levels of Hydration, Undergoing QM/MM Simulations^a.

	NWat	HN (NAmm···OWat)	HN (PDNA···OWat)	interaction mode	interacting nucleotides
IIa	82	2.5	2.0	P	G3-p-A4
IIb	55	2.5	1.5	P	G3-p-A4
IIc	50	2.0	2.0	P	G3-p-A4
IId	79	3.5	4.0	P	G1-p-C2
IIe	64	4.0	0.5	P	G1-p-C2
IIf	67	2.0	2.0/2.0	P2	G3-p-A4-p-A5
IIg	44	1.5	2.0/1.5	P2	G3-p-A4-p-A5
IIh	32	1.0	1.0/2.5	P2	G3-p-A4-p-A5
IIi	49	1.5	2.0/5.0	P2	G1-p-C2-p-G3
IIj	32	1.5	0.5/2.5	P2	G1-p-C2-p-G3

^aN_Wat is the total number of water molecules in the starting systems. The HN values are calculated from the last 1.25 ps of the QM/MM equilibration phase for the ammonium and phosphate moieties involved in the studied proton transfer. The interaction modes are depicted in Figure 4.