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 |