Table 5. NBO Stabilizing Interactions (from Perturbation Theory Contributions) for Benzylpenicillin Atoms Excluding O₁, O₂, and O₃^a.

protonation state	residue	benzylpenicillin atom	NBO analysis (kcal mol–1)	percentage of total NBO orbital stabilization for the state	AVG MD distanceb (Å)	QM/MM distance (Å)	RMSFb (Å)
I	H2O-2	O4	25.3	15%		1.66
I	H2O-3	S1	8.3	5%		2.43
I	H2O-4	N2	24.1	14%		1.79
II	H2O-5	O4	16.9	10%		1.72
II	H2O-6	N2	5.2	3%		2.27
III	H2O-8	O4	13.4	9%		1.76
IV	Thr301	N2	24.3	13%	6.88	1.74	1.18
IV	Asn161	O4	10.8	6%	4.27	2.88	1.37
IV	H2O-9	O4	13.2	7%		1.71
V	H2O-12	N2	21.8	16%		1.68
V	H2O-13	O4	14.6	10%		2.92
V	H2O-14	O4	12.1	9%		2.34
VI	Asn161	O4	12.6	7%	3.15	2.83	1.54
VI	H2O-15	S1	1.7	1%		2.63
VI	H2O-16	O4	16.4	9%		1.73

^aAll values are in kcal mol^–1 (all interactions LP → σ*).

^bNot reported for H₂O molecules due to fluctuation throughout MD simulation.