3D structures generation

Hello Chemaxon developers,

I used reactor module to generate virtual collection of compounds in both SD file format and mol2 file format. My molecules have 4 stereo centers which need to be retained in the reaction, which I specified when generating the library. 

I was using Schrodinger package to generate 3D structures from 2D structures.This process messing up my stereochemical information. 

Is there any way of fixing this problem. Does chemaxon have any module which I can use to generate 3D strucutues from 2D strucutures ? 

Any help in this regard is greatly appreciated.,

Attached is mol2 file of library generated. Please consider this file as propriatory. 

Dr. Spandan Chennamadhavuni
CMLD Research Associate
Center for Chemical Methodology and Library Development (CMLD-BU)
590 Commonwealth Avenue, 
Boston, MA 02215
Phone: 617-358-0934 (office)
http://cmld.bu.edu/center/personnel/staff.html

Dear Schennam !

In MarvinSketch there is a 3D cleaning functionality that is used to generate 3D coordinates for molecules

represented in 1D or 2D. You can reach that feature through Structure > Clean 3D.

You can also study the stereo center labels after cleaning through View > Stereo.

If you have any further questions about this feature, please feel free to ask.

Daniel

Dear Daniel,

Thanks a lot for the reply. It appears that 3D clean-up in chemskech only support up to 100 molecules. Its keeping the stereochemistry intact, but doing it for thousands of compounds can be tidious. 

I generated the library with thousands of compounds using reactor with specific stereochemistry.

How do I save the 3D structures of all these compounds into single file ?. I have to do docking of these molecules.\

Thanks for your help.

Regards,

Dr. Spandan Chennamadhavuni

Dear Spandan !

Yes, there is a limitation that you can handle at most 100 molecules on the canvas at once.

To extend this, I think you should use the Marvin API to automatize the process : that would allow

to "clean3d" thousands of molecules one-after-one. The question is whether you are familiar enough with

Java to use the toolkits of the API.

When you have multiple structures on the canvas, Marvin automatically offers to save them in one single file or not.

Using the API would also allow to append all 3D source into one single file. 

 

Daniel

Dear Daniel,

 

Thanks a lot for the info. I am not familier with java API. I am currently trying to use ligprep of schrodinger and CORINA of molecular network. If I am not successful in using them, I will learn and use marvin API for automating the process. Ideally I would like to use chemaxon modules itself to do this job.

 

Regards,

Dr. Spandan Chennamadhavuni

Dear Shennan !

Let me give you another hint : there is a command line version of Marvin, MolConverter, which can be used

through your command line . It has many options, among which the -3 is the one that invokes 3D coordinate

generation.

I highly recommend you the

http://www.chemaxon.com/marvin/help/applications/molconvert.html

user documentation page to study all  available options of MolConverter. You can also specifiy the outputting of

the tool with an option (single ot multiple file saving ). With that you don't have to write Java code. 

Daniel

 

 

 

Hello Daniel,

 

Thanks for the clue. This worked fine.  I entered "molconvert -3 mol2 *.sdf -o *.mol2" (* = input file name and output file name). BINGO...It worked. It converted all my 2D structures 3000 of them into 3D structures and retained the stereochemical information. It gave only one conformation. I am assuming its the lowest energy one ?

I also tried to incorporate clean 3D in standerdizer ...but it gave distorted 3D structures ? Is any difference?

Thanks for all your help. Now I use all chemaxon modules in my work flow...awesome..

Dear Schennan !

If you want a full list of possible options for 3D cleaning, please use  -H3D option with molconverter.

Also take a look at http://www.chemaxon.com/marvin/help/sci/cleanoptions.html#3d for the same. 

Well, if you want any detailed information on Standardizer, please post your question in the Standardizer support

forum here.

Daniel

 

Hello Daniel,

I used Reactor to generate 365000 compound library. When I tried to generate 3D using command line prompt, using molconverter, it crashed after 70,000 compounds. Is there any time limit or limit in the size of SD file or no. of compounds that could be used for generating 3D structures. 

Thanks for your help..

Regards,

Dr. Spandan

Dear Schennam !

There is a time limit for cleaning : that is 2 minutes for normal cleaning process by default.

But you can set that : use the timelimit option and set it to the desired value, e.g. [timelimit]{600} (in seconds)

By theory there is no limit on the number of the compounds, but in your case an OutOfMemory error could occur as

the library is big. I think you should print more verbose messages during cleaning. You can do this by increasing

the verbosity level of molconverter with the option verbose. The default value 1 is the minimal, increase it to get

more error messages. That will hopefully show what went wrong. 

 

Daniel