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
30.9 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.92, Jaccard 0.58, H-bond role recall 0.00
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.606 kcal/mol/HA)
✓ Good fit quality (FQ -6.11)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (92%)
✗ Very high strain energy (30.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-21.198
kcal/mol
LE
-0.606
kcal/mol/HA
Fit Quality
-6.11
FQ (Leeson)
HAC
35
heavy atoms
MW
538
Da
LogP
1.68
cLogP
Final rank
2.9242
rank score
Inter norm
-0.675
normalised
Contacts
18
H-bonds 2
Interaction summary
HBD 2
HY 8
PI 2
CLASH 5
Interaction summary
HBD 2
HY 8
PI 2
CLASH 5
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 | 11 | Native recall | 0.92 |
| Jaccard | 0.58 | 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
-21.198kcal/mol
Ligand efficiency (LE)
-0.6056kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.109
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
538.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.68
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.88kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
305.93kcal/mol
Minimised FF energy
275.05kcal/mol
SASA & burial
✓ computed
SASA (unbound)
790.0Ų
Total solvent-accessible surface area of free ligand
BSA total
600.5Ų
Buried surface area upon binding
BSA apolar
551.6Ų
Hydrophobic contacts buried
BSA polar
48.9Ų
Polar contacts buried
Fraction buried
76.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
91.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6670.6Ų
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
2128.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)