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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native mixed
SASA done
Strain ΔE
18.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.33, Jaccard 0.18, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Daphnia EC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.966 kcal/mol/HA)
✓ Good fit quality (FQ -8.78)
✓ Good H-bonds (5 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Moderate strain (18.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-24.138
kcal/mol
LE
-0.966
kcal/mol/HA
Fit Quality
-8.78
FQ (Leeson)
HAC
25
heavy atoms
MW
354
Da
LogP
3.73
cLogP
Final rank
2.1388
rank score
Inter norm
-0.970
normalised
Contacts
14
H-bonds 7
Interaction summary
HBD 1
HBA 4
HY 7
PI 1
CLASH 2
Interaction summary
HBD 1
HBA 4
HY 7
PI 1
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
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 | 4 | Native recall | 0.33 |
| Jaccard | 0.18 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 574 | 1.1312051985470015 | -0.939435 | -19.2616 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 576 | 1.7780358649461194 | -1.28763 | -30.539 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 602 | 2.0507560126483133 | -1.01307 | -21.9618 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 600 | 2.1388450417912015 | -0.969677 | -24.1377 | 7 | 14 | 4 | 0.33 | 0.00 | - | no | Current |
| 571 | 3.941488146223378 | -1.11702 | -30.045 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 573 | 4.1861124646984695 | -1.10317 | -24.9592 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 591 | 4.274920705282722 | -0.942757 | -23.3028 | 7 | 11 | 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
-24.138kcal/mol
Ligand efficiency (LE)
-0.9655kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.777
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
354.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.73
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
71.46kcal/mol
Minimised FF energy
53.40kcal/mol
SASA & burial
✓ computed
SASA (unbound)
594.2Ų
Total solvent-accessible surface area of free ligand
BSA total
474.2Ų
Buried surface area upon binding
BSA apolar
346.3Ų
Hydrophobic contacts buried
BSA polar
127.8Ų
Polar contacts buried
Fraction buried
79.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6426.1Ų
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
2084.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)