Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
74.8 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.42, Jaccard 0.22, H-bond role recall 0.00
Reason: strain 74.8 kcal/mol
strain ΔE 74.8 kcal/mol
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.937 kcal/mol/HA)
✓ Good fit quality (FQ -8.52)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (80% SASA buried)
✗ Extreme strain energy (74.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-23.436
kcal/mol
LE
-0.937
kcal/mol/HA
Fit Quality
-8.52
FQ (Leeson)
HAC
25
heavy atoms
MW
386
Da
LogP
1.70
cLogP
Final rank
5.3047
rank score
Inter norm
-0.928
normalised
Contacts
16
H-bonds 13
Interaction summary
HBD 3
HBA 4
HY 3
PI 0
CLASH 4
Interaction summary
HBD 3
HBA 4
HY 3
PI 0
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
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 | 5 | Native recall | 0.42 |
| Jaccard | 0.22 | 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
-23.436kcal/mol
Ligand efficiency (LE)
-0.9374kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.522
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
386.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.70
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
74.79kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-23.64kcal/mol
Minimised FF energy
-98.43kcal/mol
SASA & burial
✓ computed
SASA (unbound)
542.2Ų
Total solvent-accessible surface area of free ligand
BSA total
433.1Ų
Buried surface area upon binding
BSA apolar
243.3Ų
Hydrophobic contacts buried
BSA polar
189.8Ų
Polar contacts buried
Fraction buried
79.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
56.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6339.8Ų
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
2072.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)