Table 2. Changes in Lennard-Jones parameters made to bring computed HFEs in line with experiment.
These changes, as described in the main text, were implemented to bring the HFEs of amino acid side chain analogs, as computed by thermodynamic integration, into agreement with experimental data or values inferred from experiment. Only σ, not ε, parameters were altered.
| Atom Type | Instances | Original σ, Å | New σ, Å |
|---|---|---|---|
|
| |||
| OH | Hydroxyl oxygens | 3.0664 | 2.9578 |
| O | Amide oxygens | 2.9600 | 3.2072 |
| N9 | Primary amide nitrogens | 3.2500 | 3.4924 |
| SH | Thiol sulfur | 3.5636 | 3.3498 |
| O2 | Carboxylate oxygen | 2.9600 | 3.3150 |
| N3 | Terminal and Lys amino nitrogen | 3.2500 | 3.0061 |