aRMSDs are calculated for the atoms of the ligand protein since the receptor proteins are always fixed during the simulations. bSequence number denotes which sequence is the predicted conformation belonging to the BD sampling. Each conformation has unique sequence number as a label. Total number denotes how many compact complexes were obtained. From this column one can see where the final predicted complex(es) come from and how many compact complexes can be obtained from one million BD runs. These data are collected to demonstrate the necessary and sufficient condition for one million BD runs. cThe conformation presented here is the 9th conformation by energy ranking. The top 8 conformations are regarded as one cluster RMSD around 30 Å from the crystal structure (see Section 4). dThree million BD runs were conducted for this complex. Usually one million is enough for most complexes; however, due to the positive electrostatics 1.61 kcal mol−1 for this complex, the sampled near-native conformation appeared at around 1.4 million runs.