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
28.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.58, Jaccard 0.32, H-bond role recall 0.00
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
40% of hydrophobic surface appears solvent-exposed (4/10 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.250 kcal/mol/HA)
✓ Good fit quality (FQ -10.46)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (80% SASA buried)
✗ High strain energy (28.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-25.010
kcal/mol
LE
-1.250
kcal/mol/HA
Fit Quality
-10.46
FQ (Leeson)
HAC
20
heavy atoms
MW
313
Da
LogP
0.81
cLogP
Final rank
3.1266
rank score
Inter norm
-1.224
normalised
Contacts
17
H-bonds 11
Interaction summary
HBD 4
HBA 3
HY 2
PI 0
CLASH 3
Interaction summary
HBD 4
HBA 3
HY 2
PI 0
CLASH 3
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 | 7 | Native recall | 0.58 |
| Jaccard | 0.32 | 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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 336 | 0.4844925064188378 | -1.39656 | -27.4507 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 349 | 1.1863918513579474 | -1.5105 | -29.9063 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 337 | 1.381328489051882 | -1.29645 | -28.1728 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 278 | 1.3816063438262176 | -1.23041 | -24.2745 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 402 | 1.6036568051311582 | -1.42934 | -28.6624 | 13 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 231 | 2.233432618713564 | -1.2498 | -24.5852 | 15 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 257 | 2.3622034295832517 | -1.46745 | -28.4593 | 9 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 297 | 2.3754379684594595 | -1.21827 | -20.0212 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 322 | 2.806279579150012 | -1.14305 | -24.5776 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 321 | 3.1266169303527573 | -1.22396 | -25.01 | 11 | 17 | 7 | 0.58 | 0.00 | - | no | Current |
| 327 | 3.316554828658691 | -0.968003 | -19.9316 | 3 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 374 | 3.55323396923254 | -1.61668 | -32.5631 | 12 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.010kcal/mol
Ligand efficiency (LE)
-1.2505kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.464
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
20HA
Physicochemical properties
Molecular weight
313.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.81
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-57.06kcal/mol
Minimised FF energy
-85.37kcal/mol
SASA & burial
✓ computed
SASA (unbound)
470.7Ų
Total solvent-accessible surface area of free ligand
BSA total
377.2Ų
Buried surface area upon binding
BSA apolar
201.8Ų
Hydrophobic contacts buried
BSA polar
175.4Ų
Polar contacts buried
Fraction buried
80.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
53.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6251.9Ų
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
2079.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)