For example, we determined a pose for a ligand as a docking result, then toward the drug design and developed a conformer.
Your question is not clear but as much i can understand you are talking about the predicted docked pose, its binding insilico and its binding with protein inside a cell. Docking software predict a ligand binding mode and their binding energy but it is not 100% accurate. Docking protocols are just presumptive and usually not close to real situation. Flexibility in a ligand is the major reason for its changing 3d confirmation. Protein flexibility also accounts for ligand binding. Fair enough chances are there that you predict a ligand with a certain binding confirmation insilico and when you explore it under real situation you find it different.
Now this difference hugeness depends upon your insilico experiment conditions that you applied and considered while experimenting. Current docking softwares and algoritmhs are capable enough to produce almost identical results with only constraints of right mix of parameters and conditions.
If i can remember, the bound -active- conformation of a drug lies within 0.5 kcal/mol from a near local minima. If you have multiple free rotating single bonds it means that a huge number of potential conformations are accessible under the physiological conditions. I agree with Dr.Rajnikant that -if you perform in silico docking- don't leave the software to stray away otherwise it will give you crazy solutions and you should apply some constraints based on your knowledge of the active bound conformations from similar studies or experiments -if any-.
The predictied conformation is just one of possibly many potential conformations for a small molecule. In the body, the conformation can certainly change based on the enviroment: pH of the tissue/plasma/cytosol, other binding partners, etc. Anything in the environment that can stabilize or favor another conformation can change your small molecule.
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