Just delete counterion and align organic part.

@ Timur I Madzhidov

thanks for the answer. but i have a doubt...

many persons suggest that- if we are taking a salt of the compound, then the in-vitro activity (IC50) is due to the combined salt & organic part but not only due to organic part of the molecule. so i am bit confused. if u can provide any article which can testify ur suggestion, it would be much beneficial to me.

@ Rajesh Patil

I havn't referred yet any QSAR model built with inorganic salts for any biological activity in terms of IC50 value. In my opinion the biological activity is not because of the salt form or ion or fragment but is because of lowest energy conformer occupying the favorable site of receptor. Receptors can recognize only size, shape etc. where as to reach this site the molecule should pass through number of membranes (here your salt and free forms come in picture). So while using some databases like zinc etc. salt forms should be converted to organic form and build the QSAR. Most of the computational woks like energy minimization, geometry optimization with QM or MM will fail if you use salt form. We can not compute some descriptors like logP and related descriptors with salt form. So even if the IC50 is measured with salt form you have to go with organic part. I am not sure any experimental reports justifying this would be available as these things are obvious in medicinal chemistry. 

GOOD QUESTION. MY OPINION IS A BIT DIFFERENT. ITS NOT REPORTED ANYWHRE THAT WE CAN'S USE SALT FORM FOR QSAR. SALTS ARE USUALLY PREPARED TO ENHANCE SOLUBILITY OF THE COMPOUNDS.  YES INORGANIC METAL COMPLEXES ARE DIFFERENT. IF  ACTIVITY RESIDES IN SALT FORM THEN IT WON'T BE ADVISABLE TO SEPARATE INORGANIC AND ORGANIC COMPONENTS. U MUST TAKE THE STRUCTURE AS IT IS. SECOND QUE. WHAT SHALL BE CRITERIA FOR SELECTION OF COMPDS FOR QSAR. 

HERE THE ANS IS- 1.YOU SHALL HAVE MANY COMPDS. AS MANY AS POSSIBLE. MINIMUM 20 PLUS. 

2. THERE SHALL BE A GREAT DEAL OF VARIATION IN CHEMICAL COMPOSITION OF ALL DERIVATIVES. AND IN TURN VARIATION IN BIOLOGICAL ACTIVITY.

3. ACTIVITY SHALL BE CLEARLY DEFINABLE. IC50, ED50, MIC, ETC. CTIVITY IN TERMS OF % IS NOT PREFERABLE.

4. SYNTHESIS AND ACTIVITY SHALL PREFERABLY BE CARRIED OUT IN SAME LAB, SAME GROUP OF RESEARCHERS ETC.

ALL THE VERY BEST...

RMSD (root-mean-square deviation) parameters used to evaluate the conformational changes of the component fragments in the final compounds and to identify the potential leads are the main criteria for the 3D-QSAR model development.

You should consider the pH of biological tests and include in your dataset the ionization state that most probably is responsible for activity. Also consider possible counterparts in binding sites.