Mass convert many 2D molecules to 3D?

User b85e2e3247

13-05-2011 16:22:32

If my goal is to take 100 to 1000 small molecules and convert them to 3D then 'clean' in 3D (to achieve lowest energy conformation), is JChem my best option? I am new to Jchem and do not yet understand all of its capabilities, but I assume that after actually generating these molecules in Marvin I should utilize JChem to do these subsequent steps?


Any advice helps,

Thank you

ChemAxon fa971619eb

13-05-2011 17:09:55

JChem provides several ways to do this, and the best one really depends on what you are wanting to do with the generated 3D structures. You ask the question in the Instant JChem forum - does that mean you want to use them in Instant JChem, or do you just want to generate a file (SD file?) containing 3D structures.

Also, do you want true lowest energy conformer, or just a 3D strucutre that looks reasonable for display.


User b85e2e3247

13-05-2011 17:23:01


Thanks for the response, I really appreciate it.

I posted this in the instant JChen forum because I am a new user and assumed this would be the simplest way to complete the task, but I do have a full version and academic license so really any method is an option.

I do need the lowest energy conformer because my next step is to load the 3D library into a docking software to see how well they bind to proteins, so I need to 1) take my 2D library to 3D 2) make sure these 3D molecules are in their lowest energy conformation after being 'cleaned', then 3) save this 3D library as a .sdf or .mol file for later uploading into the docking program.

What are the methods to go 2D to to 3D with a large library?

Thank you very much for the help and quick response!

ChemAxon fa971619eb

13-05-2011 17:44:25

Then I think your best approach is probably to use the molconvert command-line program:

This should allow you to convert a file with 2D into one with 3D structures.

In your case Instant JChem is probably not the best route, as although you can generate 3D structures using a chemical terms expression, it will be more difficult to generate a file containing those 3D structures.


User b85e2e3247

13-05-2011 17:49:36

Where does the user actual input  a comand line program? Also, what would be a better method if not through instant JChem?

Thanks again for the responses,


User dc29f3beec

13-05-2011 22:09:25

Does this go in a Terminal window?

ChemAxon fa971619eb

14-05-2011 06:34:31

Basically you need to install the JChem package: />and then run the molconvert program from a terminal.

I've asked someone with more experience here to provide more instructions, and maybe suggest otther alternatives.