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 mixed
SASA done
Strain ΔE
28.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.50, Jaccard 0.38
Reason: no major geometry red flags detected
2 protein-contact clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Daphnia EC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Low
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.796 kcal/mol/HA)
✓ Good fit quality (FQ -7.52)
✓ Good H-bonds (4 bonds)
✓ Good burial (61% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ High strain energy (28.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-22.292
kcal/mol
LE
-0.796
kcal/mol/HA
Fit Quality
-7.52
FQ (Leeson)
HAC
28
heavy atoms
MW
415
Da
LogP
3.30
cLogP
Final rank
3.5944
rank score
Inter norm
-0.832
normalised
Contacts
10
H-bonds 5
Interaction summary
HBD 1
HBA 3
HY 5
PI 0
CLASH 2
Interaction summary
HBD 1
HBA 3
HY 5
PI 0
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
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 | 6RB5 | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA90
ARG74
GLY85
LEU73
LYS89
MET70
PHE83
PRO212
PRO213
SER86
SER87
VAL88
| ||
| Current overlap | 6 | Native recall | 0.50 |
| Jaccard | 0.38 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
Protein summary
493 residues
| Protein target | T16 | Atoms | 7551 |
|---|---|---|---|
| Residues | 493 | 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:276; 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 389 | 1.0100870340828332 | -0.922035 | -31.2434 | 3 | 12 | 0 | 0.00 | - | - | no | Open |
| 443 | 1.3557831225986772 | -0.846877 | -22.5883 | 4 | 15 | 0 | 0.00 | - | - | no | Open |
| 400 | 1.631019400497935 | -0.919535 | -26.0195 | 7 | 18 | 0 | 0.00 | - | - | no | Open |
| 370 | 1.6682791093365517 | -0.818645 | -26.6835 | 2 | 18 | 0 | 0.00 | - | - | no | Open |
| 473 | 3.594387911761717 | -0.831817 | -22.2922 | 5 | 10 | 6 | 0.50 | - | - | no | Current |
| 371 | 3.6478569150137328 | -0.991393 | -26.9697 | 8 | 16 | 0 | 0.00 | - | - | no | Open |
| 381 | 3.7225659766329655 | -1.10643 | -28.7845 | 11 | 22 | 0 | 0.00 | - | - | no | Open |
| 375 | 4.595955954185859 | -0.990361 | -24.2501 | 9 | 21 | 1 | 0.08 | - | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.292kcal/mol
Ligand efficiency (LE)
-0.7962kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.516
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
414.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.30
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
42.88kcal/mol
Minimised FF energy
14.82kcal/mol
SASA & burial
✓ computed
SASA (unbound)
646.4Ų
Total solvent-accessible surface area of free ligand
BSA total
394.2Ų
Buried surface area upon binding
BSA apolar
285.6Ų
Hydrophobic contacts buried
BSA polar
108.6Ų
Polar contacts buried
Fraction buried
61.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3017.3Ų
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
4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1552.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)