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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
36.8 kcal/mol
Protein clashes
0
Internal clashes
5
Native overlap
contact recall 0.62, Jaccard 0.36, H-bond role recall 0.00
Reason: no major geometry red flags detected
5 intramolecular clashes
61% of hydrophobic surface is solvent-exposed (17/28 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.498 kcal/mol/HA)
✓ Good fit quality (FQ -5.06)
✓ Good H-bonds (4 bonds)
✓ Good burial (52% SASA buried)
✓ Lipophilic contacts well-matched (98%)
✗ Very high strain energy (36.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-17.927
kcal/mol
LE
-0.498
kcal/mol/HA
Fit Quality
-5.06
FQ (Leeson)
HAC
36
heavy atoms
MW
505
Da
LogP
-1.64
cLogP
Final rank
1.6838
rank score
Inter norm
-0.537
normalised
Contacts
11
H-bonds 4
Interaction summary
HBD 3
HBA 1
HY 3
PI 0
CLASH 0
Interaction summary
HBD 3
HBA 1
HY 3
PI 0
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 9IFH | Contacts | 8 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASN402
GLU467
LEU399
PHE396
PRO398
SER394
SER470
THR397
| ||
| Current overlap | 5 | Native recall | 0.62 |
| Jaccard | 0.36 | 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
492 residues
| Protein target | T20 | Atoms | 7539 |
|---|---|---|---|
| Residues | 492 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:221 | ||
Receptor context
1 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 1
Excluded HETATM 0
Kept cofactors / ions
A: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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 462 | -0.2924236749244264 | -0.897491 | -30.3221 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 529 | 0.2266800236437038 | -0.763306 | -24.8595 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 535 | 0.510708423527471 | -0.726438 | -24.7716 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 506 | 0.6125424365817946 | -0.750888 | -22.9192 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 496 | 1.6838300499446746 | -0.537129 | -17.9266 | 4 | 11 | 5 | 0.62 | 0.00 | - | no | Current |
| 524 | 1.9630116217514917 | -0.66271 | -20.2398 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 521 | 2.0654308346565085 | -0.584516 | -20.0515 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 552 | 2.3810170928493584 | -0.702076 | -24.8734 | 6 | 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
-17.927kcal/mol
Ligand efficiency (LE)
-0.4980kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.061
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
504.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-1.64
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
36.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
140.71kcal/mol
Minimised FF energy
103.95kcal/mol
SASA & burial
✓ computed
SASA (unbound)
814.5Ų
Total solvent-accessible surface area of free ligand
BSA total
421.9Ų
Buried surface area upon binding
BSA apolar
414.4Ų
Hydrophobic contacts buried
BSA polar
7.5Ų
Polar contacts buried
Fraction buried
51.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
98.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3406.8Ų
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
4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1463.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)