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. Author manuscript; available in PMC: 2014 Jan 16.
Published in final edited form as: J Am Chem Soc. 2012 Dec 31;135(2):717–725. doi: 10.1021/ja3084384

Table 1.

RMSD for the CN frequencies calculated with the indicated QM region compared to the frequencies calculated with the entire active site in the QM region.a

M116C-CN
QM Residues RMSD(EQU)b RMSD(No Ligand)b
Probe Only 4.96 5.64
H2O 3.75 5.18
40/H2O 0.71 0.97
103/H2O 3.41 5.06
40/103/H2O 0.98 0.64
40/57/H2O 0.79 0.94
F86C-CN
QM Residues RMSD(EQU)c RMSD(No Ligand)d
Probe Only 16.14 13.05
84 16.20 13.07
103 2.55 2.15
84/103 0.85 0.56
a

RMSD given for a set of 500 configurations in units of cm−1. All calculations include the probe in the QM region.

b

For the M116C-CN system, the entire active site is defined to include the thiocyanate probe, Tyr16, Tyr32, Asn40, Tyr57, Asp103, the nearest active-site water molecule, and EQU when it is present.

c

For the F86C-CN system with bound EQU, the entire active site is defined to include the thiocyanate probe, Met84, Asp103, and EQU.

d

For the F86C-CN system with no ligand in the active site, the entire active site is defined to include the thiocyanate probe, Met84, Asp103, and 2 water molecules.