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. 2004 Apr;13(4):946–957. doi: 10.1110/ps.03129704

Table 5.

Calculated change in binding free energy and its components, using MM/PB potential (kcal/mole), on substitution of C4 functional group for H via direct perturbation (DP) and via relaxed perturbation using DDD and GB solvent models

Perturbation Inline graphic Inline graphic Inline graphic Inline graphic
N-DANA → H-DANA (DP) 125.8 −0.5 −85.2 40.1
N-DANA → H-DANA (GB) 129.4 −1.9 −87.1 40.4
N-DANA → H-DANA (DDD) 133.1 −10.5 −91.9 30.7
DANA → H-DANA (GB) −6.0 1.7 2.2 −2.1
DANA → H-DANA (DDD) −4.5 −0.2 3.2 −1.5
GANA → H-DANA (GB) 126.8 7.3 −86.6 47.5
GANA → H-DANA (DDD) 132.2 −0.1 −94.8 37.3
NMe3-DANA → H-DANA (GB) 103.0 4.1 −65.5 41.6
NMe3-DANA → H-DANA (DDD) 96.4 1.8 −64.3 33.9