<p>Most universities have a ChemDraw site lincence, so you may want to check that for drawing a non–3D-embedded molecule. Alternatively there are many other programs. PyMOL is not really a good choice. Also there are online drawing tools everywhere, where you can download a SMILES (see below).</p>
<p>Chemical formula is the wrong way to go, unless you are &quot;enumerating&quot;.
The chemical formula of glucose is <code>C6H12O6</code>. This is the same for all hexoses. What you want is a SMILES. This string gives the connectivity of the atoms. For D-glucose it's <code>OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O</code>, the <code>@</code> symbols are chiral centres.
In Cheminformatics making a list of all possible compound with n-carbons is a big deal, this is called enumeration and you likely don't have to reinvent wheel. Furthermore, there are datasets that are filtered by the Lipinski rule.</p>
<ul>
<li><a href="https://gdb.unibe.ch/downloads/" rel="nofollow noreferrer">GDB datasets</a> (if you don't care if you cannot buy it)</li>
<li><a href="https://zinc.docking.org/" rel="nofollow noreferrer">Zinc-DB</a>  (if you care if you can buy it)</li>
<li><a href="https://enamine.net/library-synthesis/real-compounds/real-database" rel="nofollow noreferrer">Enamine Real</a> (if you care if you can buy it reasonably)</li>
</ul>

CC BY-SA 4.0
2021-01-28T17:26:03.753Z
Thank you for the advice. I should clarify, the chemical formula is not what I am starting with, I do have the 2D structures rendered in ChemDraw with the absolute stereochemistry. My problem is really, how to best sample torsional angles at all rotatable bonds to get a reasonable 3D structure?
Sevy
CC BY-SA 4.0
2021-01-28T17:35:15.650Z
Rendered as in exported as a raster image (JPG) or 2D draw (as opposed to 3D embedded)? If the latter, in ChemDraw, right clicking on the molecules allows one to export as a SMILES string, which is can go into one's notes or whatever. For downstream applications, exporting as a mol file is the best bet.
To generate conformers, open-babel is an excellent option and has some ways to generate good diversity of conformers —including ones with unhappy torsions if one wanted. If the ligand is a natural metabolite (e.g. ATP) the biggest caveat docking is getting the protonation right.
Matteo Ferla
CC BY-SA 4.0
2021-01-28T17:38:24.630Z
I should say that compchemists generally used the Python module RDKit —but that requires knowledge of Python.
Matteo Ferla
CC BY-SA 4.0
2021-01-28T18:23:22.543Z
I have them as a JPG image, that's why I used PyMol to build them and get the stereochemistry correct (it's a bit more intuitive for me to see them in 3D rather than to write the SMILES string by hand). I then exported them as a mol file. I have tried both OpenBabel and RDKit, both seem good, I'm just not sure how extensive the conformational search is
Sevy
CC BY-SA 4.0
2021-01-28T09:59:59.630Z
2021-01-28T09:59:59.630Z
Matteo Ferla
<p>Can anyone recommend a protocol for building the 3D structure of a small molecule <em>de novo</em>, given only a 2D rendering? So far my idea has been to build the molecule using the fragment builder in PyMol, then make conformers using Frog2. But I have no idea how realistic the starting structure is from PyMol and how exhaustively the conformers are sampled in Frog2.</p>
<p>The downstream application of this would be to dock the ligand into a protein binding pocket. If anyone has a more rigorous protocol for making sure all the conformational space is fully sampled, it would be greatly appreciated!</p>

<docking><computational-biochemistry><small-molecules>
Building small molecules de novo
# Building small molecules de novo

(Asked by: username_0 on 2021-01-27)

Can anyone recommend a protocol for building the 3D structure of a small molecule *de novo*, given only a 2D rendering? So far my idea has been to build the molecule using the fragment builder in PyMol, then make conformers using Frog2. But I have no idea how realistic the starting structure is from PyMol and how exhaustively the conformers are sampled in Frog2.

The downstream application of this would be to dock the ligand into a protein binding pocket. If anyone has a more rigorous protocol for making sure all the conformational space is fully sampled, it would be greatly appreciated!

**Tags:** docking, computational-biochemistry, small-molecules

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## 1 answers

### Answer by username_1 on 2021-01-28. Score: 1

Most universities have a ChemDraw site lincence, so you may want to check that for drawing a non–3D-embedded molecule. Alternatively there are many other programs. PyMOL is not really a good choice. Also there are online drawing tools everywhere, where you can download a SMILES (see below).

Chemical formula is the wrong way to go, unless you are "enumerating".
The chemical formula of glucose is `C6H12O6`. This is the same for all hexoses. What you want is a SMILES. This string gives the connectivity of the atoms. For D-glucose it's `OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O`, the `@` symbols are chiral centres.
In Cheminformatics making a list of all possible compound with n-carbons is a big deal, this is called enumeration and you likely don't have to reinvent wheel. Furthermore, there are datasets that are filtered by the Lipinski rule.

* [GDB datasets](https://gdb.unibe.ch/downloads/) (if you don't care if you cannot buy it)
* [Zinc-DB](https://zinc.docking.org/) (if you care if you can buy it)
* [Enamine Real](https://enamine.net/library-synthesis/real-compounds/real-database) (if you care if you can buy it reasonably)

> **Comments:**
> **username_0**: Thank you for the advice. I should clarify, the chemical formula is not what I am starting with, I do have the 2D structures rendered in ChemDraw with the absolute stereochemistry. My problem is really, how to best sample torsional angles at all rotatable bonds to get a reasonable 3D structure?  
> **username_1**: Rendered as in exported as a raster image (JPG) or 2D draw (as opposed to 3D embedded)? If the latter, in ChemDraw, right clicking on the molecules allows one to export as a SMILES string, which is can go into one's notes or whatever. For downstream applications, exporting as a mol file is the best bet. To generate conformers, open-babel is an excellent option and has some ways to generate good diversity of conformers —including ones with unhappy torsions if one wanted. If the ligand is a natural metabolite (e.g. ATP) the biggest caveat docking is getting the protonation right.  
> **username_1**: I should say that compchemists generally used the Python module RDKit —but that requires knowledge of Python.  
> **username_0**: I have them as a JPG image, that's why I used PyMol to build them and get the stereochemistry correct (it's a bit more intuitive for me to see them in 3D rather than to write the SMILES string by hand). I then exported them as a mol file. I have tried both OpenBabel and RDKit, both seem good, I'm just not sure how extensive the conformational search is  

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