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The 2D structure (SD format) of a steroid with bond directions is converted by LigPrep to the full 3-dimensional structure shown above, using default settings. All chiral centers demonstrate the correct chiralities consistent with the initial bond directions. In addition, the NH3+ counter ion is removed and the carboxylate group is properly ionized.

LigPrep: Versatile generation of accurate 3D molecular models

LigPrep goes far beyond simple 2D to 3D structure conversions by including tautomeric, stereochemical, and ionization variations, as well as energy minimization and flexible filters to generate fully customized ligand libraries that are optimized for further computational analyses.

The Advantages of Accurate 3D Ligand Libraries

Computational methods have become an indispensable part of lead identification efforts. Nearly all methods require accurate 3D molecular models as a starting point. However, many corporate and purchasable compound databases contain only 2D molecular structures. Efficient and accurate 2D to 3D conversion is therefore a key precursor to computational analyses.

Beyond simple one-to-one structural conversion, it is equally important to generate scientifically sound molecular models that enumerate the different structural and chemical possibilities a ligand could sample, as these variations could lead to dramatically different results in subsequent computations. A versatile conversion program that can be configured to generate ligand libraries with the desired structural and chemical features can significantly streamline the entire in silico drug discovery process.