Asignation of HACC to pharmacophore model Align-it

[Helena den Haan]

Dear all,

I am trying to build a pharmacophore model for TAE-684 using Align-it pymol pluggin. 

I expexted to find an HACC feature in N5 just as in N3, but I do not have it. If I look in the PDB poseveiw attached 2D diagram it is shown an hydrogen bond between N5 and an H from VAL468, but according to the pharmacophore model from Align-it this bond could not happen (see imagen).

I read in the description of the tool this: " A nitrogen has no localized lone pair electrons if the nitrogen obeys one of the following patterns:

                                                                     - N is part of an aromatic ring and has three bonds attached to it (e.g. pyrrole)

                                                                     - ... "

According to this nor N5 neither N3 should be HACC, am I right? But to me this does not make sence...

Could anyone help me?

Many thanks,

Helena