CCL: Software for 2D to 3D conversion that removes molecules that have (at least) one chiral center with unknown stereochemistry

[Gerard Pujadas <gerard.pujadas]_[gmail.com>]

 Dear CCL list members,

we have an sdf file where the
 ligands are in 2D and we would like to convert it onto
 3D structures. Moreover, during that process we would like to remove
 all the ligands that have unknown chirality of at least one chiral
 center (in other words, we want to build one stereochemistry
 unambiguous 3D database). Reading the description of the SDF format at http://www.symyx.com/downloads/public/ctfile/ctfile.pdf"
 target="_blank">http://www.symyx.com/downloads/public/ctfile/ctfile.pdf
 we though that we could made a simply PERL script that looks for all
 the molecules that have at least one bond with the label "  4" at
 the
 10-12 column of the bond block. Unfortunately this seems to be no
 possible because the sdf file that we want to use as input (obtained
 > from Reaxys) does not include this "  4" label (or not always
 include
 it) to indicate unknown chirality. For instance, the next molecule has two
 chiral centers with
 unknown chirality but nothing in the sdf annotation is telling this:

Reaxys_1162

HDR
  7  7  0  0  0  0  0  0  0  0999 V2000
    0.9496    0.9496    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7604    1.5381    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.2585    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.2595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5682    0.9496    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2594    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.5208    1.2595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
M  REG 1162
M  END

We use LigPrep
 (Schrödinger) for 2D to 3D conversion of ligand sdf files but, at present,
 it cannot remove molecules that have (at least) one chiral center with unknown
 stereochemistry during such conversion.
 
Thus, I wonder if there is any program (either in graphical or command-line
 mode) that can do that (at this point it is important to remember that the
 existence of a chiral center has to be searched by the software at the moment of
 building the 3D structure because the SDF file does not mention the existence of
 chiral centers with unknown chirality).
 
If you need more information about this question or something is not clear
 for you, please do not hesitate to write me

With many thanks in
 advances

Yours sincerely

Gerard

 

-- 
Gerard Pujadas
http://bioquimica.urv.cat/eng/fitxa.jsp?id=22
Nutrigenomics
 Research Group
Biochemistry and Biotechnology Department
 Universitat Rovira i Virgili
Tarragona, Catalonia