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Table 8 Classification of the different types of protein-ligand atom contacts in three categories: less probable (0), probable (1) and very probable (2)

From: Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms

Ligand atom types

Protein atom types

 

ACC

NEG

DON

POS

HDX

ALP

ARM

C_l

0

0

0

0

0

0

1

C_r

0

0

0

0

0

1

1

N_+

1

2

0

0

0

0

0

N_d

2

2

0

0

1

0

0

N_a

0

0

1

0

0

0

0

N_r

2

0

0

0

0

0

1

O_a

0

0

1

1

0

0

0

O_-

0

0

1

2

2

0

0

O_h

0

2

1

0

0

0

0