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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
50.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.58, Jaccard 0.27, H-bond role recall 1.00
Reason: strain 50.2 kcal/mol
strain ΔE 50.2 kcal/mol
1 protein-contact clashes
39% of hydrophobic surface appears solvent-exposed (9/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
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 High
Ames Clear
DILI Low
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.565 kcal/mol/HA)
✓ Good fit quality (FQ -5.65)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Extreme strain energy (50.2 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (7)
✗ Many internal clashes (15)
Score
-19.193
kcal/mol
LE
-0.565
kcal/mol/HA
Fit Quality
-5.65
FQ (Leeson)
HAC
34
heavy atoms
MW
461
Da
LogP
3.08
cLogP
Final rank
2.2105
rank score
Inter norm
-0.669
normalised
Contacts
21
H-bonds 12
Interaction summary
HBD 2
HBA 4
HY 6
PI 3
CLASH 1
Interaction summary
HBD 2
HBA 4
HY 6
PI 3
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.
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 | 7 | Native recall | 0.58 |
| Jaccard | 0.27 | 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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 427 | 1.3468576735481605 | -0.808417 | -18.675 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 372 | 1.6823460811845725 | -0.78016 | -19.7888 | 7 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 411 | 2.2104857339584942 | -0.669199 | -19.1927 | 12 | 21 | 7 | 0.58 | 1.00 | - | no | Current |
| 444 | 2.4534108204004426 | -0.764614 | -17.3765 | 9 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 378 | 3.765478119320939 | -0.643558 | -19.7646 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 337 | 5.369926118840396 | -0.895866 | -25.0991 | 15 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 313 | 5.56934551442081 | -0.761521 | -17.001 | 13 | 17 | 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
-19.193kcal/mol
Ligand efficiency (LE)
-0.5645kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.648
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
461.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.08
Lipinski: ≤ 5
Rotatable bonds
12
Conformational strain (MMFF94s)
Strain energy (ΔE)
50.21kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
131.23kcal/mol
Minimised FF energy
81.02kcal/mol
SASA & burial
✓ computed
SASA (unbound)
783.1Ų
Total solvent-accessible surface area of free ligand
BSA total
666.8Ų
Buried surface area upon binding
BSA apolar
520.3Ų
Hydrophobic contacts buried
BSA polar
146.5Ų
Polar contacts buried
Fraction buried
85.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6597.4Ų
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
2088.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)