Dear Abdulfatal,

(1) First,  you should search the literature for the chemical structures of these  compounds.

(2) You should know the receptor or the enzyme's active site that these compounds are bound to.

(3) You should find the global minimum structures for those compounds using UUF followed by semi-empirical method such as AM1 and PM3.

(4) Then you run a docking of these compounds with their corresponding receptor or enzyme. There are many docking programs; such as Amber, Charm and etc.

These docking calculations give you a picture on the energy binding of the compound and the receptor. strong binding is characterized will low energy and vice versa. 

Hoping this will be helpful,

Rafik

1. First you should select the receptor of specific disease and download it (its from protein data bank) as the format of .pdb file

2. Then you download your ligands(its your plant compounds) from pubchemcompound , you will get it as the form of .sdf

3. you need to convert the .sdf into .pdb (the most favorable software is OpenBabel or can convert by online tools).

4. Then have to upload the ligand & receptor.

5. Then simply can dock the online software of moleculardockingserver or hex 8.0 

http://www.dockingserver.com/web

6.  you will get result as docking score as well as images

All the Best

Thank you all for your good suggestion and solution to my problem