Regarding the conformational analysis wtih 'Clean 3D;

Hi. I have produced the initial 3D geometry of molecules with Marvin sketch as follows.

1. paste SMILES in Marvin sketch

2. perform 'Clean 3D'  (exactly, menu 'structure-clean 3D-clean in 3D')

Here I found from the following link that 'clean 3D' performs some kind of conformer analysis and returns low energy conformer

http://www.chemaxon.com/marvin/help/sci/cleanoptions.html

My question is whether the conformer analysis perfomed by clean 3D is equivalent to the conformer analysis which can be performed with the menu (calculation-conformation-conformers).

If not, could you let me know about the details about this analysis such as the specific method used or reference ?

 

Thank you very much in advance for your help.

 

 

 

 

 

 

 

My question is whether the conformer analysis 

perfomed by clean 3D is equivalent to the conformer analysis which can 

be performed with the menu (calculation-conformation-conformers). 

The same code is executed in both cases. The Clean 3D action uses the default parameters which is equivalent with 1 conformer requested to generate.

A brief introduction (usage and inner workings) can be found at https://docs.google.com/document/pub?id=1dgaNFWpBNqexlTRMmWF48II9qkL9e8ALdyFpoIlJfUY

 

Regards,

Gabor

Thank you very much for your answer.

A follow-up question is whether the conformer generated is the one with the lowest energy as you can see in the screenshot below or just a random conformer without any energetic consideration ?

 

 

A follow-up question is whether the conformer 

generated is the one with the lowest energy as you can see in the 

screenshot below or just a random conformer without any energetic 

consideration ?

We found a bug regarding the handling of "Calculate lowest energy conformer"; this will be fixed soon. Currently when this checkbox is checked the result will be the same as the default coordinate generations result.

Clean3D internally generates multiple conformations for fragments and for the molecule; at the end the resulting conformers are optimized and the ones with the best energies are returned. Coordinate diversity limit also considered.

regards,

Gabor