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xcTDO is a tetramer protein, in which the active site is formed from the dimer. The shortest distances between the active site in chain A and residues in chain C: Glu224,11.8 Å; Val227, 12.9 Å; Thr231, 12.8 Å; Phe276, 11.9 Å; Arg279, 9.3 Å; Thr280, 11.3 Å; and Val282, 11.4 Å. To estimate the error of excluding these residues in chain C, we superimposed the X-ray crystal tetramer structure and the ONIOM-optimized reactant. We then took coordinates of these residues in chain C, added hydrogen atoms, and represented them as the point charges. Additional B3LYP calculations show negligible error of these electrostatic interactions (data in parentheses in column 12 of Table S3; maximum error of 0.2 kcal/mol). ONIOM-calculated free energies are put in Table S3. More reliable QM/MM free energy calculations will be performed and reported in due course
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xcTDO is a tetramer protein, in which the active site is formed from the dimer. The shortest distances between the active site in chain A and residues in chain C: Glu224,11.8 Å; Val227, 12.9 Å; Thr231, 12.8 Å; Phe276, 11.9 Å; Arg279, 9.3 Å; Thr280, 11.3 Å; and Val282, 11.4 Å. To estimate the error of excluding these residues in chain C, we superimposed the X-ray crystal tetramer structure and the ONIOM-optimized reactant. We then took coordinates of these residues in chain C, added hydrogen atoms, and represented them as the point charges. Additional B3LYP calculations show negligible error of these electrostatic interactions (data in parentheses in column 12 of Table S3; maximum error of 0.2 kcal/mol). ONIOM-calculated free energies are put in Table S3. More reliable QM/MM free energy calculations will be performed and reported in due course.
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