AF3 cannot predict correct ligand isomer even using userCDD

Hi,

I'm trying to predict a protein-ligand complex, but AF provides the wrong isomeric form of the ligand. To avoid that, I generated the ligand with openbabel (which gives the correct isomer), then I generated a one-line cif file for the userCCD option in the JSON input. No success!

I feel that AF3 is not considering my input, or I'm not using the correct flags. Here's the command :

> docker run     --volume ${input_dir}:${input_dir}\\
               --volume ${output_dir}:${output_dir}\\
               --volume /mnt/bio-8t-disk1/alphafold/:/mnt/bio-8t-disk1/alphafold/ \\
               --volume /mnt/bio-8t-disk1/alphafold/public_databases:/mnt/bio-8t-disk1/alphafold/public_databases \\
               --gpus all alphafold3 \\
  python3 run_alphafold.py --model_dir=/mnt/bio-8t-disk1/alphafold --db_dir=/mnt/bio-8t-disk1/alphafold/public_databases \\
               --json_path=${input_dir} --output_dir=${output_dir} --input_dir=${input_dir} \\
               --pdb_database_path='/mnt/bio-8t-disk1/alphafold/public_databases/mmcif_files' \\
               --norun_data_pipeline --buckets 512 --num_diffusion_samples `10

I've tested all versions (1, 2, 3, and 4) in the JSON file with no success. I obtain the correct isomer in 1 out of 10 conformers. Checking every prediction is not feasible when performing virtual screening... I installed AF3 in the past week. It means that I'm using the newest version.

Is there a command or flag to force AF to always generate the correct isomer from userCCD?

Best,