# Ligand Formatting

**URL:** <https://ask.bioexcel.eu/t/ligand-formatting/5275>\
**Category:** HADDOCK\
**Created:** [October 1, 2024, 9:50am UTC](https://ask.bioexcel.eu/t/ligand-formatting/5275 "2024-10-01T09:50:08Z")\
**Posts on this page:** 1\
**Showing post:** 2

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**Author:** ![VGPReys](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/vgpreys/32/960_2.png) [@VGPReys](https://ask.bioexcel.eu/u/VGPReys)\
**Post date:** [October 2, 2024, 7:46am UTC](https://ask.bioexcel.eu/t/ligand-formatting/5275/2 "2024-10-02T07:46:34Z")

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- To know if your file is properly formatted, you can refer to this online resource : [https://cupnet.net/pdb-format/](https://cupnet.net/pdb-format/).
- Also, make sure the file extension is the appropriate one: `.pdb`.
- I just tried an example using [OpenBabel online version 3.1.1](https://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html), with a Chlorine atom, (SMILES to PDB, 3D coordinates, add hydrogen) and it was functional.

See one not-functional and functional example (from SMILES `ClCCCCOc1ccccc1`):

- File with wrong file extension:  
[obabel\_with\_chlorine.pdb.txt](https://ask.bioexcel.eu/uploads/short-url/jzHiPz2aw6xxW2jg3nf8OuX4rDz.txt) (3.8 KB)
- File with `.pdb` file extension:  
[obabel\_with\_chlorine.pdb](https://ask.bioexcel.eu/uploads/short-url/AmfbhMmiwgZdDsu2GExjpa9WknR.pdb) (4.3 KB)

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