Table 2. Test of different strain energies and reference structures.

The results are based on the quantum refinement with different w_x weight factors (w_c = 1 and w_QM = 7.5 for all) for the Mn site in the B subunit of MnSOD shown also in Table 1 ▸. E₁, E₂ and E₃ are the QM energies (in kJ mol⁻¹) of the QM region in the quantum-refined structure, the QM/MM-optimized structure (i.e. with w_x = 0, but started from the quantum-refined structures with different w_x) and in the isolated QM region optimized by QM, keeping the H_L atoms fixed at the starting quantum-refined structure. ΔE₁ = E₁ − E₂ and ΔE₃ = E₁ − E₃, both calculated for each row. ΔE₂ = E₁ − E₂ also, but using only the lowest value for E₂ (i.e. that obtained for w_x = 0). Δd₂ and Δd₃ are the average deviations of seven key distances (those included in Table 1 ▸) of the two sets of reference structures from those obtained with w_x = 0. The actual distances are shown in Table S2 and the corresponding distances for the quantum-refined structures are shown in Table 1 ▸.

w x	E1 (kJ mol−1)	E2 (kJ mol−1)	E3 (kJ mol−1)	ΔE1 (kJ mol−1)	ΔE2 (kJ mol−1)	ΔE3 (kJ mol−1)	Δd2 (Å)	Δd3 (Å)
0	7912123	−7912123	−7912160	0	0	37	0.000	0.000
0.01	−7912120	−7912121	−7912160	1	3	40	0.018	0.013
0.03	−7912119	−7912122	−7912160	4	4	41	0.014	0.015
0.1	−7912119	−7912122	−7912160	4	4	41	0.014	0.015
0.3	−7912122	−7912122	−7912160	1	1	38	0.015	0.015
1	−7912120	−7912122	−7912160	2	3	40	0.014	0.014
3	−7912097	−7912120	−7912158	22	25	60	0.012	0.012
10	−7911999	−7912116	−7912156	117	124	157	0.010	0.001
30	−7911678	−7912120	−7912155	442	445	477	0.009	0.004
100	−7910497	−7912111	−7912156	1615	1626	1660	0.011	0.007