Table 1 Atom types defined in this work and their correspondence with MOL2 types

C_l

Aliphatic carbon – sp3 hybridized

C.1, C.2, C.3

C_r

Aromatic carbon – sp2 hybridized, included in aromatic rings and in guanidine or carboxyl groups

C.ar, C.cat, C.2

N_+

Positive nitrogen – sp 2 or sp 3 hybridized, protonated, forming a group with a positive charge (e.g. guanidine group)

N.4, N.pl3

N_d

Nitrogen donor of a hydrogen bond – sp 2 hybridized, protonated (e.g. amine group)

N.2, N.ar, N.am

N_a

Nitrogen acceptor of hydrogen bond – not all valences covered by heavy atoms, not protonated

N.2, N.ar, N.3, N.1

N_r

Aromatic nitrogen – sp 2 hybridized, with all its valences covered by heavy atoms

N.ar, N.pl3

N_h

"Hydroxyl" nitrogen in histidines – sp 2 hybridized, undefined protonation

N.2

O_a

Oxygen acceptor of hydrogen bond – not protonated

O.2, O.3

O_-

Negative oxygen – negatively charged (e.g. nitro group, carboxyl group)

O.co2

O_h

Hydroxyl oxygen – protonated (OH group)

O.2, O.3