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

From: COCONUT online: Collection of Open Natural Products database

Natural product feature Field name in MongoDB—uniqueNaturalProduct collection Displayed on the website
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