Interaction analysis of HIV-1 antibody 2G12 and Man9GlcNAc2 ligand: Theoretical calculations by fragment molecular orbital and MD methods

- We assess glycan moieties' role in the interaction dynamically and energetically.
- Man D1 is the crucial glycan moiety in the ligand recognition.
- The notable functions of Man 4 and Man 4′ are pointed out.
- The significance of the branched structure is theoretically indicated.