User`s guide

Advanced Structures

ACD/ChemSketch User’s Guide 26

5. Click the right mouse button to quickly switch to the Select/Move tool and drag the NH2

group to the OH group as shown:

6. Click on the Clean Structure button to obtain the following structure:

Try to draw any other cyclic peptide, for instance Gramicidine S:

5.3 3D Optimization

This section explains how to create structures that have “realistic” angles and bond lengths.

There is no need to explain how difficult it is to draw such molecules proportionally. The 3D-

Optimization and 3D Rotation options will help you to quickly cope with this task. These options

make it possible to create complex structures in ACD/ChemSketch with ease.

The 3D optimization algorithm is a proprietary version of molecular mechanics with the force field

initially based on CHARMM parameterization

. The modifications involve some simplification and

were intended to increase the stability and speed of computation. Note that 3D-optimizer is NOT

a full-scale molecular mechanics engine. Its design aims to reliably reproduce reasonable

conformations from (possibly very unreasonable) 2D drawings, rather than to precisely optimize

3D structures.

If 3D-optimizer produces the conformation different from what you have expected, do not be

surprised. It is the very essence of conformational analysis that molecules typically have many

conformations. The optimizer finds only one, and it may not be one you expect. For example, you

probably expect a cyclohexane fragment to be a chair, but the optimizer may generate twist-boat,

which is also one of its suitable conformations (indeed, in many structures this fragment exists in

B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M.

Karplus. CHARMM: A program for macromolecular energy, minimization, and dynamics

calculations. J. Comput. Chem. 4 187-217 (1983).