Table 3.

Bonding characterization of similar pharmacophore hits for compound 2 from ZINC database against HER2

S no	Ligand name	Structure	RMSD (Å)	Bonding interaction	Bond length	Bond type	Dock score (S)	Binding energy (kcal/mol) (MM-GB/VI)	Binding affinity (pKi)
1	ZINC67903192		0.538	Met801 O--------H	2.20	H-don	−32.2	−40.13	11.21
				Asp863 OD------H	1.26	H-don
				Lys736 NZ-------O	2.59	H-acc
				Leu726 CD------O	3.01	H-acc
2	ZINC59763389		0.792	Ser728 O---------H	3.79	H-don	−28.4	−34.24	10.33
				Met801 O--------H	2.19	H-don
				Tyr803 O--------H	1.80	H-don
				Asp863 OD-----H	2.02	H-don
				Met801 N-------O	2.92	H-acc
				Lys736 N2------O	2.50	H-acc
3	ZINC85816423		0.601	Ser728 O---------H	1.66	H-don	−27.2	−26.23	9.62
				Asp808 OD-----H	1.75	H-don
				Arg849 NE-------O	2.78	H-acc
				Arg849 NH------O	3.09	H-acc

Abbreviation: RMSD, root mean square deviation.