| HB | hydrogen bond |
| HP | Helicobacter pylori |
| MD | molecular dynamics |
| QM | quantum mechanical |
| SASA | solvent-accessible surface area (SASA) |
| SB | salt bridge |
| SGCMC | semi-grand canonical Monte Carlo |
| RG | radius of gyration |
| RMSD | root-mean-square deviation |
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