Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
24.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.83, Jaccard 0.43, H-bond role recall 0.00
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.576 kcal/mol/HA)
✓ Good fit quality (FQ -5.71)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ High strain energy (24.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-19.005
kcal/mol
LE
-0.576
kcal/mol/HA
Fit Quality
-5.71
FQ (Leeson)
HAC
33
heavy atoms
MW
490
Da
LogP
0.45
cLogP
Final rank
2.9687
rank score
Inter norm
-0.678
normalised
Contacts
21
H-bonds 4
Interaction summary
HBA 2
HY 8
PI 1
CLASH 3
Interaction summary
HBA 2
HY 8
PI 1
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 5S9T | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA365
ARG228
ARG331
GLY229
LEU332
LEU334
MET333
PHE198
PHE230
SER364
THR374
VAL366
| ||
| Current overlap | 10 | Native recall | 0.83 |
| Jaccard | 0.43 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
Protein summary
1033 residues
| Protein target | T17 | Atoms | 15160 |
|---|---|---|---|
| Residues | 1033 | Chains | 2 |
| Residue summary | VAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408 | ||
Receptor context
2 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 2
Excluded HETATM 0
Kept cofactors / ions
A:FAD501
B:FAD501
All stored poses for this docking hit
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.005kcal/mol
Ligand efficiency (LE)
-0.5759kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.714
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
490.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.45
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.42kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
182.60kcal/mol
Minimised FF energy
158.18kcal/mol
SASA & burial
✓ computed
SASA (unbound)
777.9Ų
Total solvent-accessible surface area of free ligand
BSA total
600.8Ų
Buried surface area upon binding
BSA apolar
494.4Ų
Hydrophobic contacts buried
BSA polar
106.4Ų
Polar contacts buried
Fraction buried
77.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6638.3Ų
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
8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
2067.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)