[phenixbb] Ligand Library

Christian Tüting christian.tueting at biochemtech.uni-halle.de
Thu Jul 22 02:02:27 PDT 2021

Dear Phenix-Team, dear Mailing-List,

I have a question regarding bound ligands during refinement. In our
initial structure, we have multiple spheroidenes bound (pdb ligand id
SPO), but experimental data suggest that it should be speroidenones (pdb
ligand id SPN). The difference between these molecules are located in an
additional oxygen at the head group and a different saturation level of
the carbon chain. I mananged to exchange the molecule using Coot, but
during refinement I got following error:

  Number of atoms with unknown nonbonded energy type symbols: 602
    "HETATM18420  C1  SPN B 600 .*.N    C  "
    "HETATM18421  C10 SPN B 600 .*.N    C  "
    "HETATM18422  C11 SPN B 600 .*.N    C  "
    "HETATM18423  C12 SPN B 600 .*.N    C  "
    "HETATM18424  C13 SPN B 600 .*.N    C  "
    "HETATM18425  C14 SPN B 600 .*.N    C  "
    "HETATM18426  C15 SPN B 600 .*.N    C  "
    "HETATM18427  C16 SPN B 600 .*.N    C  "
    "HETATM18428  C17 SPN B 600 .*.N    C  "
    "HETATM18429  C18 SPN B 600 .*.N    C  "
    ... (remaining 592 not shown)

So, as far as I understand this error, the ligand is not in the
restrained in the ligand library. I followed this tutorial:
https://phenix-online.org/documentation/tutorials/elbow.html to generate
the .cif file for refinement. I was just using the pdb file and the
geometry from there, as it was "coot-refined" and thereby I expected the
correct conformation.

The refinement than run fine, but the ligand after refinement is in a
complete wrong conformation and parts of the carbon chain is outside the
density. I am not sure, if this is due to low resolution at these
regions (which are indeed very low compared to other ligands or proteins
in the map), or if during restraining something went wrong.

Is it possible to add this ligand to the phenix ligand library or do you
have any suggestions, how to improve the restraining using the elbow

Thanks in advance

Christian Tüting

Dr. rer. nat. Christian Tüting

Kastritis Laboratory for Biomolecular Research
Cryo-Electron Microscopy & Computational Structural Biology  
Martin-Luther-Universität Halle-Wittenberg
Biozentrum, Room A.2.19
"Kryo-Elektronenmikroskopie an Membranproteinkomplexen"
Weinbergweg 22, 06120 Halle
tel: +49 345 5524985
web (Lab): https://blogs.urz.uni-halle.de/kastritislab/
web (HALOmem): https://www.halomem.de/en/

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