--------------------------------------------------------- BIOVIA, San Diego 2007 LibDock version: 2.3 Build date: Oct 14 2018 D. Diller & K. Merz (2001). "High Throughput Docking for Library Design and Library Prioritization." Proteins: Struct., Funct., and Genet. 43:113-124. --------------------------------------------------------- Checked out license feature: DS_LibDock [for msi] (1 copy) Start time: Sat Sep 24 10:42:14 2022 Reading: LibDock.inp parameter file Setting FE_STERIC_SOFTNESS = 0.50 Setting FE_HBOND_SOFTNESS = 1.50 Setting FE_HBOND_RMIN = 3.00 Setting FE_HBOND_EPSILON = 2.00 Setting FE_STERIC_RMIN = 4.05 Setting FE_STERIC_EPSILON = 0.40 Setting FE_METAL_ACC_RMIN = 2.20 Setting FE_METAL_ACC_EPSILON = 6.00 Setting APOLAR_POLAR_WT = 1.00 Setting APOLAR_POLAR_PENALTY = 0.00 Setting STERIC_OUTER_CUTOFF = 6.00 Setting STERIC_INNER_CUTOFF = 5.00 Setting HBOND_OUTER_CUTOFF = 4.00 Setting HBOND_INNER_CUTOFF = 3.00 Turning Electrostatic Repulsion off Setting ELEC_REP_SOFTNESS = 7.90 Setting ELEC_REP_STRENGTH = 285.50 Setting VDW_PENALTY_FACTOR = 10.00 Setting VDW_PENALTY_FRACTION = 1.50 Using the High Quality Parameters for the Surface Area Using the High Quality Parameters Host Name = AbdusemiAbduweli Verbose = 0 SASA_WEIGHT = 0.20 Grids for scoring = Max Hits to Save = 100 Max Hits to Optimize = 100 Num BFGS Steps = 50 Max Hits per Conformations = 30 Max Number of Starting Conformations = 1000 Maximum fraction of steric clashes = 0.10 Final Cluster Radius = 0.50 Final Score Cutoff = 0.50 Apolar SASA Cutoff = 15.00 Polar SASA Cutoff = 5.00 tSQ = 0.50 tSQ_HB = 1.50 HBondRmin = 3.00 HBondRminSQ = 9.00 HBondEpsilon = 2.00 StericRmin = 4.05 StericRminSQ = 16.40 StericEpsilon = 0.40 MetalAccRmin = 2.20 MetalAccRminSQ = 4.84 MetalAccEpsilon = 6.00 ApolarPolarWt = 1.00 ApolarPolarPenalty = 0.00 global_outer_cutoff = 6.00 global_inner_cutoff = 5.00 global_outer_hb_cutoff = 4.00 global_inner_hb_cutoff = 3.00 HBondRepOn = 0 tSQ_HB_REP = 7.90 HBondRep = 285.50 Intermediate Cluster Radius = 1.00 Set Score Label: LibDockScore #################################################################### ####################### PARAMETER VALUES ########################### #################################################################### # HS_FILE Hotspots-3GEN.pdb # DB_FILE sd_file.lst # TOLERANCE 0.25 # PROTEIN_PDB 3GEN.pdb # PROTEIN_FORMAT 1 # XLO -26.74 # XHI -7.27 # YLO -3.02 # YHI 16.46 # ZLO -24.83 # ZHI -5.35 # FAILED_FILE LibDock_out-fail.sd # APPEND_SPOT_INFO 1 # APPEND_RMSD_INFO 0 #################################################################### ##################### END OF PARAMETER VALUES ###################### #################################################################### Reading Hotspot file: Hotspots-3GEN.pdb Number of Polar Hotspots: 100 Number of APolar Hotspots: 100 Use Default Energy Parameters #################################################### # Van der Waals parameters SP3_SP3_HT 2.00 SP3_SP2_HT 15.00 SP2_SP2_HT 1.00 DOUBLE_BOND_HT 24.00 ATTRACTIVE 6 REPULSIVE 12 H 1.00 0.05 C 1.91 0.10 O 1.66 0.20 N 1.85 0.20 S 2.00 0.20 P 2.10 0.20 I 2.03 0.20 F 1.75 0.20 CL 1.76 0.20 BR 1.87 0.20 B 2.01 0.09 D 0.65 0.02 A 0.00 0.00 R 0.00 0.00 #################################################### There are 4350 atoms in that file There are 1150 protein atoms Protein Preparation time: 0.44 [s] ================== 1) File: molecule-1.sd Name: 3GEN_ligand conformers: 52 Number of hits: 100 CPU time: 3.19 [s] ================== Ligands processed: 1 100 Poses were saved in sd file format to: LibDock_out.sd CPU time: 3.73[s] End time: Sat Sep 24 10:42:17 2022 Released LibDock License