MOE Description

Two different procedures and two steps were used.

• STEP 1
  

  1. Systematic sampling. Bond angle increments were derived from a the atom types and the hybridization states of the neighboring atoms. Resulting conformations were minimized to a gradient of 0.005 using the MMFF94x forcefield with distance dependent electrostatics as implemented in MOE2009.0609. The single lowest energy conformer is supposed to represent the global energy minimum. This procedure was used for all molecules from the Blind set and for all molecules with up to 6 rotatable bonds from other sets.
  2. Stochastic conformational search. More flexible molecules were sampled using the stochastic conformational search in 750 independent iterations each. Resulting conformations were minimized to a gradient of 0.005 using the MMFF94x forcefield with distance dependent electrostatics as implemented in MOE2009.0609. The single lowest energy conformer is supposed to represent a conformer close to the global energy minimum.

• STEP 2
  

  The optimized with molecular mechanic molecules were further optimized using AM1 method of Mopac 7.1.