Ligand-bound models for Summary

Interpreting 'Ligand confidence'

4 - High Confidence: The expected ligand was easily interpretable from clear density, and subsequent refinement was well-behaved. This ligand can be trusted.
3 - Clear density, unexpected ligand: Density very clearly showed a well-defined ligand, but that ligand was unexpected in that crystal/dataset. The observed ligand was modelled anyway, because its presence could be explained in some way.
2 - Correct ligand, weak density: Though density was weak, it was possible to model the expected ligand, possibly including other circumstantial evidence (e.g. similar ligand in another model).
1 - Low Confidence: The ligand model is to be treated with scepticism, because the evidence (density, identity, pose) were not convincing.

Interpreting 'Model status':

6 - Deposited: The model has been deposited in the PDB.
5 - Deposition ready: The model is fully error-free, in every residue, and is ready for deposition.
4 - CompChem ready: The model is complete and correct in the region of the bound ligand. There may be remaining small errors elsewhere in the structure, but they are far away and unlikely to be relevant to any computational analysis or compound design.

Interpreting 'Ligand validation' spider plots:

Quality (RSCC) reflects the fit of the atoms to the experimental density, and should typically be greater than 0.7.
Accuracy (RSZD) measures the amount of difference density that is found around these atoms, and should be below 3.
B-factor ratio measures the consistency of the model with surrounding protein, and is calculated from the B factors of respectively the changed atoms and all side-chain atoms within 4Å. Large values (>3) reflect poor evidence for the model, and intermediate values (1.5+) indicate errors in refinement or modelling; for weakly-binding ligands, systematically large ratios may be justifiable.
RMSD compares the positions of all atoms built into event density, with their positions after final refinement, and should be below 1Å.
Precision (RSZO/OCC) measures how clear the density is after refinement. (This is not a quality indicator, but is related to strength of binding but not in a straightforward way.)

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Model Name	Compound SMILES	Compound Structure	Site Name	Ligand Confidence	Model Status	Ligand Validation	Event Map 3D	Comment	PDB Identifier	Resol	Spacegroup	Cell	PDB	MTZ	Event Map
Model Name	Compound SMILES	Compound Structure	Site Name	Ligand Confidence	Model Status	Ligand Validation	Event Map 3D	Comment	PDB Identifier	Resol	Spacegroup	Cell	PDB	MTZ	Event Map
BAZ2BA-x434_event1	c1cc2c(cc1N)cn[nH]2		None	4 - High Confidence	5 - Deposition ready			None	5PB7	1.65	C 2 2 21	81 96 57 90 90 90	Save	Save	Save
BAZ2BA-x481_event1	CC(c1ccc(cc1)O)=O		None	4 - High Confidence	5 - Deposition ready			None	5PB8	1.65	C 2 2 21	81 97 58 90 90 90	Save	Save	Save
BAZ2BA-x492_event1	CC(c1cccc(c1)O)=O		None	4 - High Confidence	5 - Deposition ready			None	5PB9	1.78	C 2 2 21	81 96 57 90 90 90	Save	Save	Save
BAZ2BA-x509_event1	c1cc(C(O)=O)nc(c1)O		None	4 - High Confidence	5 - Deposition ready			None	5PBA	1.92	C 2 2 21	80 97 58 90 90 90	Save	Save	Save
BAZ2BA-x529_event1	c1ccc2c(c1)c(ccn2)O		None	4 - High Confidence	5 - Deposition ready			None	5PBB	1.78	C 2 2 21	82 96 57 90 90 90	Save	Save	Save
BAZ2BA-x538_event1	c1c(nc[nH]1)[Br]		None	3 - Clear density, unexpected ligand	5 - Deposition ready			None	5PBC	1.77	C 2 2 21	82 96 57 90 90 90	Save	Save	Save
BAZ2BA-x559_event1	CC(Nc1ccc(cc1)C(O)=O)=O		None	4 - High Confidence	5 - Deposition ready			None	5PBD	1.78	C 2 2 21	82 96 58 90 90 90	Save	Save	Save
BAZ2BA-x575_event1	CC(Nc1ccc(cc1)O)=O		None	4 - High Confidence	5 - Deposition ready			None	5PBE	1.83	C 2 2 21	83 97 58 90 90 90	Save	Save	Save
BAZ2BA-x583_event1	C1Cc2ccc(cc2NC1=O)O		None	4 - High Confidence	5 - Deposition ready			None	5PBF	1.80	C 2 2 21	81 96 57 90 90 90	Save	Save	Save