FAIRMol

Z56960380

Pose ID 4001 Compound 2466 Pose 615

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T06
T. brucei DHFR T. brucei
Ligand Z56960380
PDB8RHT↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
21.6 kcal/mol
Protein clashes
4
Internal clashes
5
Native overlap
contact recall 0.48, Jaccard 0.38, H-bond role recall 0.00
Burial
89%
Hydrophobic fit
82%
Reason: no major geometry red flags detected
4 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.710 kcal/mol/HA) ✓ Good fit quality (FQ -6.54) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ High strain energy (21.6 kcal/mol) ✗ No H-bonds detected ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Internal clashes (6)
Score
-18.454
kcal/mol
LE
-0.710
kcal/mol/HA
Fit Quality
-6.54
FQ (Leeson)
HAC
26
heavy atoms
MW
426
Da
LogP
4.91
cLogP
Strain ΔE
21.6 kcal/mol
SASA buried
89%
Lipo contact
82% BSA apolar/total
SASA unbound
634 Ų
Apolar buried
461 Ų

Interaction summary

HB 0 HY 24 PI 5 CLASH 5

HB · H-bonds
No hb · h-bonds detected for this pose.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank0.914Score-18.454
Inter norm-0.969Intra norm0.212
Top1000noExcludedno
Contacts15H-bonds0
Artifact reasongeometry warning; 6 clashes; 7 protein contact clashes; 1 cofactor-context clash; moderate strain Δ 21.6
Residues
ALA34 ARG100 ARG59 ASP54 GLN56 GLU50 ILE47 LEU97 MET55 NDP301 PHE58 PHE94 PRO52 PRO91 VAL33

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name8RHTContacts21
PoseOpen native poseHB0
IFP residues
ALA34 ASP54 HIS182 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE233 PHE58 PHE94 PRO91 SER89 THR184 THR86 TRP49 TYR166 TYR57 VAL32 VAL33
Current overlap10Native recall0.48
Jaccard0.38RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

223 residues
Protein targetT06Atoms3452
Residues223Chains1
Residue summaryARG:408; VAL:352; LYS:308; LEU:304; PRO:238; ILE:209; GLU:195; THR:182; SER:176; ALA:160; PHE:140; ASN:126; GLY:126; ASP:108; GLN:85; NDP:74

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:NDP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
634 0.7610902009089585 -0.911569 -24.2437 6 15 0 0.00 0.00 - no Open
615 0.9140960673762193 -0.968828 -18.4541 0 15 10 0.48 0.00 - no Current
619 2.980557400356469 -0.918108 -25.7627 5 11 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -18.454kcal/mol
Ligand efficiency (LE) -0.7098kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.539
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 426.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.91
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 21.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 161.80kcal/mol
Minimised FF energy 140.22kcal/mol

SASA & burial

✓ computed
SASA (unbound) 633.7Ų
Total solvent-accessible surface area of free ligand
BSA total 563.3Ų
Buried surface area upon binding
BSA apolar 460.6Ų
Hydrophobic contacts buried
BSA polar 102.7Ų
Polar contacts buried
Fraction buried 88.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1730.4Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 1808.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 598.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)