Table 1.

^a Key internuclear distances (Å) involving the metal ions of the QM/MM-optimized geometries of PDE10-AMP complex in comparison with the corresponding distances in the X-ray crystal structure (PDB code: 2OUN).¹⁹

Internuclear distances	PDE10-AMP (O3H) b	PDE10-AMP (O1H,O3H)c	PDE10-AMP (O2H,O3H)d	Expt.
Zn(II)-O (OP-bridging)	2.718	2.526	2.663	2.457
Zn(II)-O (Asp-bridging)	2.088	2.000	2.075	2.050
Zn(II)-O (Asp-Zn)	2.042	2.148	2.133	2.074
Zn(II)-N (His1)	2.022	2.031	2.024	2.096
Zn(II)-N (His2)	2.099	2.044	2.071	2.103
Zn(II)-O (PO4)	2.084	2.319	2.085	2.371
Mg(II)-O (OP-bridging)	2.200	2.219	2.140	2.299
Mg(II)-O (Asp-briding)	2.068	2.064	2.085	2.080
Mg(II)-O (W1)	2.116	2.064	2.085	2.190
Mg(II)-O (W2)	2.079	2.053	2.090	2.121
Mg(II)-O (W3)	2.067	2.061	2.095	2.084
Mg(II)-O (PO4)	2.016	2.124	2.137	2.249
Zn(II)-Mg(II)	4.243	4.129	4.146	4.000
O3'-OP(Mg(II))	3.378	2.963	2.735	2.989
O3'-OP(Zn(II))	3.618	3.277	3.643	3.332
N6-OE1(5GP-GLN726)	2.934	3.003	2.986	3.039
N1-NE2(5GP-GLN726)	2.888	2.884	2.892	2.996
MUE (Å) e	0.14	0.07	0.12

^aThe geometries were fully optimized by performing QM/MM calculations at the B3LYP/6-31G*:Amber level.

^bThe charge on AMP = −1 with O3 protonated in the original file. This proton still resides on O3 atom after the QM/MM geometry optimization.

^cThe charge on AMP = 0 with O1 and O3 protonated in the original file. The proton on O3 atom migrated to Oδ atom of Asp674 after the QM/MM geometry optimization. So O1 was only protonated after the geometry optimization.

^dThe charge on AMP = 0 with O2 and O3 protonated in the original file. The proton on O3 atom migrated to Oδ atom of Asp674, the proton on O2 transferred to O3´, the proton on O3´ transferred to His525 after the QM/MM geometry optimization. Therefore, no phosphate oxygen atoms are protonated, and His525 is protonated after the geometry optimization.

^eThe mean unsigned error between the calculated and experimental distances.