[phenixbb] Fitting ligand using coot

Hi all, I tried to fit the ligand using the coot -> calculate-> other modeling tools-> Find ligands. I have imported cif to coot and also opened the pdb file of my ligand. However, coot do not identify the ligand and asks to adjust r.m.s.d. I can see the density for my ligand. Could anyone suggest me what could be the problem or if I am missing anything here. Best regards. Bishwa