Table 3. The binding energy (ΔG_bind) in kcal mol⁻¹, inhibition constant (K_i), and amino acid residue–ligand interactions for the selected compounds and standard drug amoxicillin targeting DNA gyrase B (GyrB) (PDB ID: 6F86).

Ligand compound	ΔGbind	K i a (µM)	Amino acid residues (interactions)
3	−7.31	4.40	Asn46(Hydrogen bond), Glu50(π–anion), Ile78(π–alkyl), Val43(π–alkyl), Val167(π–alkyl), Thr165(π–sigma), Ala47(π–alkyl), Arg76(van der Waals), Pro79(van der Waals), Gly75(van der Waals), Val120(van der Waals)
5	−6.97	7.81	Glu50(π–anion), Ile78(π–alkyl), Arg76(π–alkyl), Ala47(π–alkyl), Thr165(π–sigma),Val43(Carbon hydrogen bond), Gly75(van der Waals), Asp73(van der Waals), Val167(van der Waals) Asn46(van der Waals), Pro79(van der Waals
8	−6.93	8.30	Thr165(Hydrogen bond, π–sigma), Asp73(Hydrogen bond), Gly77(Hydrogen bond), Glu50(π–anion), Ile78(π–alkyl), Val167(π–alkyl), Ala47(π–alkyl), Val43(π–alkyl), Val71(van der Waals), Asn46(van der Waals), Arg76(van der Waals), Gly75(van der Waals), Gly164(van der Waals)
11	−6.85	9.46	Asp49(Hydrogen bond, amide- π stacking), Asp73(Hydrogen bond), Glu50(π–anion), Ile78(π–alkyl, alkyl), Asn46(amide–π stacking), Gly75(van der Waals), Thr165(van der Waals),Ala47(van der Waals), Arg76(van der Waals), Ile94(van der Waals), Ala53(van der Waals)
13	−7.34	4.17	Asp73(Hydrogen bond), Pro79(Carbon hydrogen bond), Gly77(Carbon hydrogen bond), Glu50(π–anion), Ile78(π–alkyl), Ala47(π–alkyl), Val167(π–alkyl), Thr165(π–sigma), Asn46(π–sigma), Ile94(van der Waals), Arg76(van der Waals), Val43(van der Waals)
Amoxicillin	−5.28	135.77	Asn46(Hydrogen bond), Arg76(Hydrogen bond), Glu50(π–anion), Ile78(π–sigma), Asp73(Hydrogen bond), Gly77(Hydrogen bond), Asp49(van der Waals), Gly75(van der Waals), Gly164(van der Waals), Thr165(van der Waals), Ala47 (van der Waals), Pro79(van der Waals), Ile94(van der Waals), Ala53(van der Waals)

^a K _i = exp(ΔG/RT), where R = 1.985 × 10⁻³ kcal mol⁻¹ K⁻¹ and T = 298.15 K.