Actually my synthesized macrocyclic ligand has three different isomer. Now when I want to draw these in pdb format then no option is found to mention axial or equatorial group. If I don’t mention which one is axial or equatorial then in case of optimization in gausian software all the structures will treated as one structure and give same value for all of them. So it will impossible to differentiate the structures. How can I solve this problem?

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