Table 5. Results of the quantum refinements of the Cu_D site of pMMO with three different sizes of the QM system (no water, water or bigger) and different values of the w_x weight factor (keeping w_c = 1 and w_QM = 7.5).

The table shows the Cu–ligand distances (in Å) for OD1 of Asn227C (Asn), NE2 of His231C (H1) and His245C (H2), and O of HOH406C (W1) and HOH415C (W2). In addition, the strain energy [ΔE_QM1 in (kJ mol⁻¹), relative to the QM system optimized under vacuum with the H_L atoms fixed], the average difference in the three or five Cu–ligand distances shown between the quantum-refined structure and the structure used to calculate ΔE_QM1 (Δd_av), and the average RSCC score for the four, six or ten residues in the QM system are given. Note that the three latter estimates depend on the size of the QM system (therefore different values are given for the deposited structure).

	Distance to Cu (Å)
w x	Asn	H1	H2	W1	W2	ΔEQM1	Δdav	RSCCav
No water
Deposited	2.21	2.00	1.50			300	0.16	0.89
0	2.09	1.91	1.92			21	0.10	0.86
0.01	2.09	1.91	1.92			21	0.10	0.86
0.03	2.08	1.92	1.92			20	0.11	0.86
0.1	2.09	1.91	1.92			19	0.10	0.86
0.3	2.08	1.91	1.92			20	0.10	0.86
1	2.09	1.90	1.91			21	0.10	0.86
3	2.09	1.91	1.92			21	0.10	0.86
3.6 (auto)	2.10	1.91	1.91			20	0.11	0.86
10	2.10	1.91	1.92			19	0.14	0.85
30	2.02	1.92	1.94			38	0.33	0.84
100	2.53	1.95	1.92			100	0.90	0.83
300	3.33	2.08	1.99			257	1.04	0.80
1000	3.31	2.52	2.07			1812	0.63	0.77
Water
Deposited	2.21	2.00	1.50	3.81	3.30	383	0.39	0.83
0	2.11	1.93	1.97	2.92	2.52	39	0.34	0.80
0.01	2.11	1.93	1.97	2.92	2.52	39	0.34	0.80
0.03	2.11	1.93	1.97	2.92	2.52	39	0.34	0.80
0.1	2.12	1.93	1.97	2.91	2.53	38	0.35	0.80
0.3	2.12	1.93	1.97	2.90	2.53	38	0.35	0.80
1	2.13	1.94	1.97	2.88	2.54	37	0.35	0.80
3	2.13	1.94	1.98	2.87	2.63	35	0.37	0.80
4.9 (auto)	2.12	1.93	1.97	2.86	2.66	30	0.38	0.80
10	2.11	1.94	1.96	2.72	2.81	34	0.44	0.77
30	2.36	2.01	1.95	2.12	3.26	43	0.61	0.69
100	3.45	2.08	1.98	2.04	4.10	148	0.98	0.71
300	3.29	2.15	2.12	2.36	4.49	341	1.00	0.71
1000	3.59	2.49	2.13	3.56	4.79	2046	0.95	0.64
Bigger
Deposited	2.21	2.00	1.50	3.81	3.30	499	0.36	0.84
0	2.25	1.96	2.02	3.29	2.15	99	0.11	0.81
0.01	2.25	1.93	2.04	3.30	2.06	93	0.12	0.81
0.03	2.25	1.95	2.02	3.29	2.14	99	0.11	0.81
0.1	2.25	1.95	2.02	3.29	2.14	98	0.11	0.81
0.3	2.25	1.95	2.04	3.28	2.11	96	0.12	0.81
1	2.25	1.94	2.04	3.28	2.09	95	0.12	0.81
3	2.26	1.93	2.05	3.28	2.06	94	0.13	0.81
5.2 (auto)	2.28	1.92	2.06	3.29	2.03	93	0.14	0.81
10	2.29	1.94	2.06	3.53	2.02	85	0.10	0.81
30	2.44	1.94	2.11	3.72	1.97	105	0.11	0.79
100	2.92	1.0	2.61	3.47	1.88	219	0.38	0.75
300	3.18	1.90	3.21	3.32	1.83	691	0.59	0.70
1000	3.62	2.50	2.11	4.11	2.40	4485	0.54	0.67