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

Table 1 Average validation scores for ligands in PDB and PDB_REDO

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

^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.
^b Average over 16,904 ligands (13,703 for heat of formation) in 5,932 structure models.
^c Calculated using EDSTATS [27].
^d Calculated using YASARA [32] using the atomic coordinates as is.
^e The average reported is the average sum of all interactions for a single ligand.

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