Hii,

I am working on 3D-pharmacophore generation in Discovery studio 2.0. I am trying to develope a pharmacophore model through Hypogen.I want to incorporate a feature in the feature dictionary describing the C-Cl (carbon-chloro) bond. According to me, in DS2.0 the halogens are described as aliphatic and more precisely exocyclic aliphatic in the dictionary as provided below.

QUERY Halide

{

  AND Halide.root

  {

    ATTRIBUTES:

      PROP ( SOURCE "BIOCAD_FRAGMENT" ) ;

      ROOT ;

    TOPOLOGY:

      ATOM X1

ELEMENTS ( HALOGEN )

ALIPHATIC ;

I want to develop a feature using the C-Cl fragment while making the Cl atom as centroid for the mapping atom. My first query is (1) Is there any problem regarding that? I am bit confused as i donot have a clear view about how the C-Cl bond is described in the feature dictionary in DS2.0. 

(2) If i develop a feature using the C-Cl fragment than should it be incorporated in the hydrophobic feature or I can use the feature separately without any incorporation.?

Thanks in advance.