3D Molecular Conformer Generation

3D Molecular Conformer Generation constructs a set of three-dimensional conformers from a SMILES string and reports an energy value for ranking each conformer within the set.

When to use it

This calculation is appropriate when a downstream workflow requires three-dimensional coordinates and only a SMILES representation is available, including the preparation of docking inputs and structural inspection. Multiple conformers are appropriate for sampling the accessible geometries of flexible molecules. A single conformer is appropriate when only one initial structure is required.

Inputs

Input	Required	What it is
`smiles`	yes	SMILES string of the molecule.
`num_conformers`	yes, default `5`	Number of conformers to generate. Range `1` to `100`. Runtime increases proportionally with the requested number.

How to run it

Jobs can be submitted through Azulene Studio, the Python SDK, or the CLI. The Get started page contains installation, authentication, and submission instructions.

In Azulene Studio

Select 3D Molecular Conformer Generation from the tools list. Enter the SMILES string and number of conformers in the Inputs and Parameters step, then select Review and Submit.

From the Python SDK

from azulene import jobs

result = jobs.submit(
    job_type="generate_conformers",
    input_data={
        "smiles": "CCO",
        "num_conformers": 5,
    },
)

From the CLI

Supply the inputs as a JSON string.

azulene jobs submit --job-type generate_conformers \
  --input-data '{"smiles": "CCO", "num_conformers": 5}'

Reading the result

The result contains four fields:

conformers contains the generated structures, with one block for each conformer.
format identifies the coordinate format used for the structure blocks, for example xyz.
energies contains the energy of each conformer in the corresponding structure order.
num_generated reports the number of conformers produced. This value can be lower than num_conformers when the requested count cannot be generated for a constrained molecule.

Studio orders the conformers by ascending energy and displays the individual energies in a bar chart. The generated conformer count is displayed as a summary value.

Notes

The reported energies support comparisons only among conformers of the same molecule. Comparisons between molecules are invalid, and the values are not free energies. Conformer populations cannot be inferred from these values. Larger conformer sets are appropriate for flexible molecules with extensive torsional degrees of freedom.