Table S1: Physicochemical descriptors used
Descriptor
Num_Rings
Num_AromaticRings
Num_AliphaticRings
Num_RingAssemblies
Num_Chains
Num_ChainAssemblies
Num_BridgeBonds
Index
1
2
3
4
5
6
7
Num_TerminalRotomers
8
Heavy_Atom_Bonds
Hydrogen_Atom_Bonds
SingleBonds_Frac
DoubleBonds_Frac
TripleBonds_Frac
BridgeBonds_Frac
RingBonds_Frac
Aliphatic_Ringbonds_Frac
AromaticBonds_Frac
StereoBonds_Frac
9
10
11
12
13
14
15
16
17
18
RotatableBonds_Frac
19
Num_PositiveAtoms
Num_NegativeAtoms
20
21
Num_H_Acceptors
22
Num_H_Donors
Num_Halogens
Num_SP3_Carbons
Num_SP2_Carbons
Num_SP_Carbons
SP3_Carbon_Fraction
SP2_Carbons_Fraction
SP_Carbon_Fraction
Carbon_fraction
Hydrogen_fraction
Nitrogen_fraction
Oxygen_fraction
Heteroatom_fraction
Sulphur_fraction
Phosphorus_fraction
Halogen_fraction
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
Description
Number of rings in the molecule
Number of aromatic rings
Number of non-aromatic rings (2 - 1)
Number of fragments after removing non-ring bonds
Unbranched chains needed to cover all the non-ring bonds in the molecule
Number of fragments after removing Rings
Bonds in bridgehead systems (any rings that share more than one bond in common)
A non-terminal sp3 atom connected to three terminal atoms of the same type, or a non-terminal sp2
atom connected to two terminal atoms of the same type
Bonds between heavy atoms
Bond to hydrogen atoms
Fraction of total bonds that are single
Fraction of total bonds that are double
Fraction of total bonds that are triple
Fraction of total bonds that is a bridgebond
Fraction of total bonds in ring systems
Fraction of total bonds in a non aromatic ring
Fraction of total bonds in an aromatic ring
Fraction of total bonds that are marked CisBondStereo, TransBondStereo, or UnknownBondStereo
Fraction of total bonds that are single bonds between heavy atoms that are both not in a ring and not
terminal (special case amide C-N bonds are not rotatable)
Number of Atoms with a positive charge.
Number of Atoms with a negative charge.
Heteroatoms (O, N, S, or P) with one or more lone pairs, excluding atoms with positive formal
charges, amide and pyrrole-type N, and aromatic O and S atoms in heterocyclic rings
Heteroatoms (O, N, S, or P) with one or more attached H atoms
Sum of F, CL, I and Br
Number of SP3 hybridized carbon atoms
Number of SP2 hybridized carbon atoms
Number of SP hybridized carbon atoms
Fraction of total carbons that is SP3 hybridized
Fraction of total carbons that is SP2 hybridized
Fraction of total carbons that is SP hybridized
Fraction of atoms that is C
Fraction of atoms that is H
Fraction of atoms that is N
Fraction of atoms that is O
Fraction of atoms that is O,N,S, or P
Fraction of atoms that is S
Fraction of atoms that is P
Fraction of atoms that is F, Cl, I, or Br
1
OtherAtom_fraction
StereoAtom_Fraction
PositiveAtom_Fraction
NegativeAtom_Fraction
H_Acceptors_Fraction
H_Donors_fraction
Molecular_Weight
LogP
LogD
Solubility
FormalCharge
Molecular_Volume
Molecular_SurfaceArea
Molecular_PolarSurfaceArea
Molecular_PolarSurfaceArea_Fraction
Molecular_SASA
Molecular_PolarSASA_Fraction
Lipinski_Pass
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
Rigidity_Index
57
drugLikeness
Small_Molecule
Biological
Peptide
Organic_Non_Peptidic
Inorganic
Cmp_Acid
Cmp_Base
Cmp_Neutral
Cmp_Zwitterion
Cmp_Species_Undefined
58
59
60
61
62
63
64
65
66
67
68
Fraction of atoms that is not one of the above
Fraction of atoms marked EvenAtomStereo, OddAtomStereo, or UnknownAtomStereo
Fraction of atoms with a positive charge
Fraction of atoms with a negative charge
Fraction of atoms that is hydrogen bond acceptor
Fraction of atoms that is hdyrogen bond donor
Molecular weight (calc Molsoft ICM [76])
Average value of ACD LogP, Accelrys AlogP and Molsoft ICM logP [76,77,79]
Average value of ACD LogD, Accelrys LogD at pH 7.4 [77,79]
Average value of Accelrys solubility and molsoft solubility [76,77]
Formal charge of the molecule at pH 7.4 (ionized in Molsoft ICM [76])
Molecular volume (calculated in Molsoft ICM [76])
Molecular Surface Area (2D Method)
Polar surface area (Molsoft ICM [76])
Fraction of total surface area that is polar
Solvent Accessible Surface Area
Fraction of SASA that is polar
N_Count + o_Count <= 10, MW <= 500, H_donors <= 5, AlogP <=5
(AromaticBonds_Frac + (1-RotatableBonds_Frac) + Aliphatic_Ringbonds_Frac + (1SingleBonds_Frac) + DoubleBonds_Frac + TripleBonds_Frac + BridgeBonds_Frac) / 7
Druglikenes (calculated in Molsoft ICM [76])
Binary flag for molecule class as calculated in ChEMBL
Binary flag for molecule class as calculated in ChEMBL
Binary flag for molecule class as calculated in ChEMBL
Binary flag for molecule class as calculated in ChEMBL
Binary flag for molecule class as calculated in ChEMBL
Binary flag for ACD Molecular species
Binary flag for ACD Molecular species
Binary flag for ACD Molecular species
Binary flag for ACD Molecular species
ACD Molecular species unknown / cannot be calculated
2