In all the studied systems addition of the surrounding protein in an ONIOM model clearly improves the calculated active-site geometries. This is clearly illustrated in Figure 2-13, which shows the root-mean-square deviation between calculated and experimental structures for four of the studied enzymes. [Pg.47]

Table 4-2 reports the electrostatic and non-electrostatic components of AGsoi in water for the series of compounds included in the study computed from MST calculations. The deviation between experimental and calculated free energies of hydration is in general small, as noted in a mean signed errors (mse) close to zero and a root-mean square deviation around 0.9 kcal/mol, which compares with the statistical parameters obtained in the parametrization of the MST model [15]. [Pg.108]

Table 2. Scale factors for ab initio model vibrational frequencies adapted from (Scott and Radom 1996). Please note that these scale factors are determined by comparing model and measured frequencies on a set gas-phase molecules dominated by molecules containing low atomic-number elements (H-Cl). These scale factors may not be appropriate for dissolved species and molecules containing heavier elements, and it is always a good idea to directly compare calculated and measured frequencies for each molecule studied. The root-mean-squared (rms) deviation of scaled model frequencies relative to measured frequencies is also shown, giving an indication of how reliable each scale factor is. |

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