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 high
Native strong
SASA done
Strain ΔE
14.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.50, Jaccard 0.30, H-bond role recall 1.00
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.648 kcal/mol/HA)
✓ Good fit quality (FQ -6.43)
✓ Good H-bonds (3 bonds)
✓ Deep burial (66% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Moderate strain (14.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (20)
Score
-21.396
kcal/mol
LE
-0.648
kcal/mol/HA
Fit Quality
-6.43
FQ (Leeson)
HAC
33
heavy atoms
MW
439
Da
LogP
5.92
cLogP
Final rank
3.3214
rank score
Inter norm
-0.732
normalised
Contacts
14
H-bonds 5
Interaction summary
HBA 3
HY 5
PI 1
CLASH 1
Interaction summary
HBA 3
HY 5
PI 1
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
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 | 6 | Native recall | 0.50 |
| Jaccard | 0.30 | RMSD | - |
| HB strict | 1 | Strict recall | 1.00 |
| HB same residue+role | 1 | HB role recall | 1.00 |
| HB same residue | 1 | HB residue recall | 1.00 |
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
-21.396kcal/mol
Ligand efficiency (LE)
-0.6484kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.433
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
438.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.92
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.20kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
86.89kcal/mol
Minimised FF energy
72.70kcal/mol
SASA & burial
✓ computed
SASA (unbound)
745.8Ų
Total solvent-accessible surface area of free ligand
BSA total
495.8Ų
Buried surface area upon binding
BSA apolar
394.3Ų
Hydrophobic contacts buried
BSA polar
101.5Ų
Polar contacts buried
Fraction buried
66.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6623.3Ų
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
2080.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)