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Promethium Tutorials

Calculate Conformers from SMILES: Nemorexant Example Using Default Settings

 

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Step 1

After logging into your Promethium account, on top navigation bar, click on "Workflows" -> "Conformer Search".

 

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Step 2

On the Conformer page:

  • Add a name for the job: e.g. "Nemorexant with default settings"

  • Add the following SMILES string to the SMILES input field: CC1=C(C=CC2=C1N=C(N2)C3(CCCN3C(=O)C4=C(C=CC(=C4)OC)N5N=CC=N5)C)Cl

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Step 3

On bottom right, click "Review" and subsequently "Submit"

Promethium Tutorial 3 picture

What happens now?

By default, there are 4 customizable filtering stages. Initial conformers are generated from stochastic sampling of the torsion angles.

  • Stage 1: The initial conformers are optimized with a molecular mechanics force field.
  • Stage 2: The lowest energy conformers are re-optimized using the ANI neural network potential.
  • Stage 3: The lowest energy conformers are re-optimized at the B3LYP-D3/def2-SVP level of theory.
  • Stage 4 (optional): The energy of each conformer is recalculated at the  ωB97M-V/def2-TZVP level of theory. 
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