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Table 1 The list of atom and bond types used in labeling interfacial graphs

From: FragVLib a free database mining software for generating "Fragment-based Virtual Library" using pocket similarity search of ligand-receptor complexes

Atom Description
C.3 Carbon sp3
C.2 Carbon sp2
C.1 Carbon sp
C.ar Carbon aromatic
C.cat Carbocation
N.3 Nitrogen sp3
N.2 Nitrogen sp2
N.1 Nitrogen sp
N.ar Nitrogen aromatic
N.am Nitrogen amide
N.pl3 Nitrogen trigonal planar
N.4 Nitrogen sp3 positively charged
O.3 Oxygen sp3
O.2 Oxygen sp2
O.co2 Oxygen in carboxylates and phosphates
S.3 Sulfur sp3
S.2 Sulfur sp2
S.O Sulfoxide Sulfur
S.O2 Sulfone Sulfur
P.3 Phosphorous sp3
F Fluorine
Cl Chlorine
Br Bromine
I Iodine
Li Lithium
Na Sodium
Mg Magnesium
Al Aluminum
Si Silicon
K Potassium
Ca Calcium
Cr.th Chromium (tetrahedral)
Cr.oh Chromium (octahedral)
Mn Manganese
Fe Iron
Co.oh Cobalt (octahedral)
Cu Copper
Se Selenium
Mo Molybdenum
Sn Tin
Zn Zinc
Bond Description
1 Single bond
2 Double bond
3 Triple bond
am Amide
ar Aromatic
nc Not connected
  1. An option for labeling each atom type with the number of hydrogen atoms is available. This way, an sp3 Oxygen with one hydrogen atom is distinguished from an sp3 Oxygen with no hydrogen atoms; this is useful for hydrogen-bonding interactions.