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Chemical validity and consistency
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| File loads |
The input molecule can be loaded into a molecule object by RDKit |
| Sanitisation |
The input molecule passes RDKit's chemical sanitisation checks |
| Molecular formula |
The molecular formula of the input molecule is the same as that of the true molecule |
| Bonds |
The bonds in the input molecule are the same as in the true molecule |
| Tetrahedral chirality |
The specified tetrahedral chirality in the input molecule is the same as in the true molecule |
| Double bond stereochemistry |
The specified double bond stereochemistry in the input molecule is the same as in the true molecule |
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Intramolecular validity
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| Bond lengths |
The bond lengths in the input molecule are within 0.75 of the lower and 1.25 of the upper bounds determined by distance geometry |
| Bond angles |
The angles in the input molecule are within 0.75 of the lower and 1.25 of the upper bounds determined by distance geometry |
| Planar aromatic rings |
All atoms in aromatic rings with 5 or 6 members are within 0.25 Å of the closest shared plane |
| Planar double bonds |
The two carbons of aliphatic carbon–carbon double bonds and their four neighbours are within 0.25 Å of the closest shared plane |
| Internal steric clash |
The interatomic distance between pairs of non-covalently bound atoms is above 0.7 of the lower bound determined by distance geometry |
| Energy ratio |
The calculated energy of the input molecule is no more than 100 times the average energy of an ensemble of 50 conformations generated for the input molecule. The energy is calculated using the UFF32 in RDKit and the conformations are generated with ETKDGv3 followed by force field relaxation using the UFF with up to 200 iterations |
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Intermolecular validity
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| Minimum protein–ligand distance |
The distance between protein–ligand atom pairs is larger than 0.75 times the sum of the pairs van der Waals radii |
| Minimum distance to organic cofactors |
The distance between ligand and organic cofactor atoms is larger than 0.75 times the sum of the pairs van der Waals radii |
| Minimum distance to inorganic cofactors |
The distance between ligand and inorganic cofactor atoms is larger than 0.75 times the sum of the pairs covalent radii |
| Volume overlap with protein |
The share of ligand volume that intersects with the protein is less than 7.5%. The volumes are defined by the van der Waals radii around the heavy atoms scaled by 0.8 |
| Volume overlap with organic cofactors |
The share of ligand volume that intersects with organic cofactors is less than 7.5%. The volumes are defined by the van der Waals radii around the heavy atoms scaled by 0.8 |
| Volume overlap with inorganic cofactors |
The share of ligand volume that intersects with inorganic cofactors is less than 7.5%. The volumes are defined by the van der Waals radii around the heavy atoms scaled by 0.5 |
