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Table 1 Average validation scores for ligands in PDB and PDB_REDO

From: The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites

Validation score a PDB average b PDB_REDO average b
RSR c 0.120 0.104
RSCC c 0.90 0.92
Heat of formation (kJ/mol) d −1011 −1067
Hydrogen bonding energy (kJ/mol) d −57.7 −58.8
Hydrophobic contact strength d,e 16.20 16.43
π-π interaction strength d,e 1.26 1.28
Cation-π interaction strength d,e 1.17 1.19
Number of atomic clashes d 9.1 7.9
  1. a A smaller value is better for RSR, heat of formation (strained ligand conformations give higher values), hydrogen bonding energy and number of atomic clashes. A larger value is better for RSCC, hydrophobic contact strength, π-π interaction strength and cation-π interaction strength.
  2. b Average over 16,904 ligands (13,703 for heat of formation) in 5,932 structure models.
  3. c Calculated using EDSTATS [27].
  4. d Calculated using YASARA [32] using the atomic coordinates as is.
  5. e The average reported is the average sum of all interactions for a single ligand.