Table 2 Molecular features present in COCONUT and in their disponibility in the web interface

COCONUT identifier

coconut_id

x

List of SMILES with stereochemistry and their provenance

absolute_smiles

x

AlogP (Ghose-Crippen LogKow)

alogp

x

AlogP2

alogp2

x

AMR—molar refractivity

amralogp

Annotation level of the NP (from 1 to 5)

annotationLevel

x

BCUT decriptor (Eigenvalue based)

bcutDescriptor

Bond number in the NP

bond_count

x

BPol descriptor

bpol

x

CAS number

cas

x

List of literature DOIs mentioning the NP

citationDOI

x

Boolean—if the molecule contains linear sugars

contains_linear_sugars

Boolean—if the molecule contains circular sugars

contains_ring_sugars

Boolean—if the molecule contains sugar moieties

contains_sugar

deepSMILES

deep_smiles

x

Eccentric Connectivity Index Descriptor

eccentricConnectivityIndexDescriptor

x

List of tl Functional Groups

ertlFuntionalFragments

List of Ertl Functional Groups in pseudo SMILES

ertlFunctionalFragmentsPseudoSmiles

FMF descriptor

fmfDescriptor

x

List of data sources containing the NP

found_in_databases

Fragment complexity descriptor

fragmentComplexityDescriptor

x

List of circular fragments (molecular signatures) of the deglycosylated NP

fragments

List of circular fragments (molecular signatures) of the whole NP

fragmentsWithSugar

Fractional CSP3 Descriptor (non-flatness of a molecule)

fsp3

x

List of continents and regions where the organism producing the NP is found

geoLocation

Gravitational index descriptor (heavy atoms only)

gravitationalIndexHeavyAtoms

Hydrogen bond acceptor count

hBondAcceptorCount

Hydrogen bond donor count

hBondDonorCount

Number of heavy atoms in the NP

heavy_atom_number

x

Hybridization Ratio Descriptor (fraction of sp3 carbons to sp2 carbons)

hybridizationRatioDescriptor

InChI (without stereochemistry)

inchi

x

InChI key

inchikey

x

IUPAC name

iupac_name

x

First kappa shape index

kappaShapeIndex1

Second kappa shape index

kappaShapeIndex2

Third kappa shape index

kappaShapeIndex3

Number of failures in the Lipinski rule of 5

lipinskiRuleOf5Failures

x

LogP descriptor (Mannhold version)

manholdlogp

Maximal number of rings in the NP

max_number_of_rings

x

Minimal number of rings in the NP

min_number_of_rings

x

Molecular formula

molecular_formula

x

Molecular weight

molecular_weight

x

Murcko Framework

murcko_framework

x

Official name (when available)

name

x

NP-likeness score

npl_score

x

NP-likeness score computed on the glycosylated molecule

npl_sugar_score

Total number of carbons

number_of_carbons

x

Total number of nitrogens

number_of_nitrogens

Total number of oxygens

number_of_oxygens

Number of sporo atoms

numberSpiroAtoms

Petitjean Number Descriptor

petitjeanNumber

x

Petitjean geometrical shape index

petitjeanShapeGeom

Petitjean geometrical shape index

petitjeanShapeTopo

PubChem fingerprint in MongoDB BinData format

pubchemBits

PubChem fingerprint as list of booleans

pubchemFingerprint

SMILES with all hydrogen explicit

smiles

x

Number of heavy atoms of the deglycosylated moiety

sugar_free_heavy_atom_number

SILES of the deglycosylated moiety

sugar_free_smiles

Total atom number of the deglycosylated moiety

sugar_free_total_atom_number

List of synonym names of the NP

synonyms

x

List of NCBI taxonomy identifiers of organisms producing the NP

taxid

List of organisms producing the NP in text form

textTaxa

Topological polar surface area descriptor

topoPSA

Total atom count in the NP (incuding hydrogens)

total_atom_number

Fractional polar surface area descriptor

tpsaEfficiency

Unique SMILES (CDK)

unique_smiles

x

Volume descriptor

vabcDescriptor

Vertex adjacency information

vertexAdjMagnitude

Wiener Path Number

wienerPathNumber

x

Wiener Polarity Number

wienerPolarityNumber

XLogP descriptor

xlogp

x

Cross-references to toher chemical ressources

xrefs

x

Zagreb Index

zagrebIndex

x

Chemical superclass of the NP computed with ClassyFire

chemicalSuperClass

x

Chemical class of the NP computed with ClassyFire

chemicalClass

x

Chemical subclass of the NP computed with ClassyFire

chemicalSubClass

x

Direct parent in the chemical ontology of the NP computed with ClassyFire

directParentClassification

x