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Table 3 Overall effects of the choice of the force field and energy window upon the average RMSD and ST values between the computationally generated conformations and the experimental conformations for the 25,972 3-D reference structures

From: PubChem3D: Conformer generation

  

Torsion Search Force Fielda

Energy window (kcal/mol)

Fragment Force Fielda

Full

NoEstat

Trunc

  

RMSD

ST

RMSD

ST

RMSD

ST

5

Full

0.69

0.89

0.48

0.93

0.47

0.93

 

NoEstat

0.69

0.89

0.48

0.93

0.47

0.93

 

Trunc

0.71

0.89

0.48

0.93

0.46

0.93

10

Full

0.52

0.92

0.42

0.94

0.42

0.94

 

NoEstat

0.52

0.92

0.42

0.94

0.42

0.94

 

Trunc

0.52

0.92

0.41

0.94

0.42

0.94

15

Full

0.46

0.93

0.40

0.94

0.40

0.95

 

NoEstat

0.46

0.93

0.40

0.94

0.40

0.95

 

Trunc

0.46

0.93

0.40

0.94

0.40

0.95

  1. aFull = the 94s variant of the Merck molecular force field (MMFF94s); NoEstat = MMFF94s without coulombic interaction terms; Trunc = MMFF94s without coulombic and van der Waals interaction terms.