TABLE 1.
MM potential energy functions and parameters for [1,3]dioxolane-4,5-dicarboxylic acid bis-methylamide
| Kb (b−b0)2
|
||
|---|---|---|
| Bond length | Kb | b0 |
| C1-C2 | 285.0 | 1.525 |
| C1-O5 C2-O3 | 303.0 | 1.404 |
| C4-O3 C4-O5 | 328.0 | 1.391 |
| C1-H6 C2-H7 | 304.0 | 1.084 |
| C4-H8 C4-H9 | 304.0 | 1.085 |
| C1-C10 C2-C12 | 250.0 | 1.524 |
| Kθ (θ−θ0)2
|
KUB (S−S0)2
|
|||
|---|---|---|---|---|
| Bond angle & Urey-Bradley | Kθ | θ0 | KUB | S0 |
| O3-C4-O5 | 78.0 | 107.04 | 25.00 | 2.240 |
| H8-C4-H9 | 36.5 | 110.20 | 5.40 | 1.780 |
| O5-C4-H8 O5-C4-H9 | 38.5 | 109.89 | 22.53 | 2.040 |
| O5-C1-H6 O3-C2-H7 | 37.3 | 109.74 | 22.53 | 2.043 |
| C1-C2-H7 C2-C1-H6 | 41.5 | 112.63 | 22.53 | 2.180 |
| O5-C1-C2 O3-C2-C1 | 85.0 | 102.69 | ||
| C1-O5-C4 C2-O3-C4 | 85.0 | 107.49 | ||
| C1-C10-N14 C2-C12-N16 | 85.0 | 114.90 | ||
| C1-C10-O11 C2-C12-O13 | 80.0 | 120.23 | ||
| O5-C1-C10 O3-C2-C12 | 32.0 | 113.13 | ||
| C2-C1-C10 C1-C2-C12 | 33.0 | 111.64 | ||
| C10-C1-H6 C12-C2-H7 | 22.0 | 107.95 | ||
| Kχ (1 + cos(n χ−δ))
|
|||
|---|---|---|---|
| Torsional angle | Kχ | n | δ |
| O5-C1-C10-O11 | 1.10 | 2 | 180.0 |
| O3-C2-C12-O13 | 1.10 | 2 | 180.0 |
| O5-C1-C2-O3 | 3.00 | 1 | 180.0 |
| 0.48 | 5 | 0.0 | |
|
ɛij[(Rminij/rij)12−(Rminij/rij)6]
|
qi qj/ɛ1 rij
|
|||
|---|---|---|---|---|
| Nonbonded interaction | ɛi | Rmini/2 | qi | |
| C1 C2 | −0.020 | 2.27 | 0.240 | |
| O3 O5 | −0.160 | 1.77 | −0.512 | |
| C4 | −0.055 | 2.17 | 0.540 | |
| H6 H7 | −0.022 | 1.32 | 0.022 | |
| H8 H9 | −0.022 | 1.32 | −0.020 | |
The parameters involving the dioxolane ring are shown. Atom numbering is defined in Fig. 1. The standard CHARMM22 parameters (MacKerell et al., 1998) are used for the peptide bonds.