I. Washing .

to apply to each molecule a cleaning rules like removing extraneous salts ,metal
or adjusting protonation states, and that to assure structure are suitable for subsequent
modelling steps such as conformation enumeration and protein-ligand docking.

protonation. All formation and states of analogue should be taken accounted in the docking like
enansumer and ionized form .

II. To study the electrostatic interaction and repulsion between ligand and the target site
example dipole dipole intermolecular forces .

EM include the deferent confirmation to reach the local minimum.

III. 3. As it play minimum to not any effect in the binding , deletion depend the role of the
molecule in the interaction with the binding site as a water mediated hydrogen binding .

IV. H bond between the meta Cl and the Alanine, stacking interaction aromatic ring and the
NAP.

V. 5.Extra interaction between the ionized oxygen with NAP and tyrosine was formed
.Deprotonation introduce a new electrostatic binding interaction due to anionic oxygen
which can act in the dipole dipole binding compared to the hydroxyl .
 VI. 6.london dG were used firs in the placement of triangle matcher to extract 30 poses , then
GBV /WSA dG where used in the refinement to get the pest 5 poses .

Docking pose ranking Docking Score RSMD_refine Comment

(S) kcal/mol

Pose #1 -7.04490948 1.89892745

Pose #2 -7.00922108 1.81763971

Pose#4 -6.28235674 1.1592052

VII. Result seams fine slit deferent in the alignment.

Top-ranked ligands Docking Score (S) Ligand fitting Ligand interactions

NCI number kcal/mol (score out of 10) (Tyr157 or NADP)

13 -7.37990236 10 Tyr157

652 -5.69262838 8 Non

482 -6.83680677 8.5 Tyr157

What do you think of the results? Does the protocol seem to be ,Have degree of success more
sample and data is required for better result Protocol is effective in a way it provide us with visual
approach for the But time consuming ,and humane error is high .