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
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
23.5 kcal/mol
Protein clashes
0
Internal clashes
14
Native overlap
contact recall 0.54, Jaccard 0.47
Reason: 14 internal clashes
14 intramolecular clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Daphnia EC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Algae IC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Bioaccum.
B — Bioaccumulative (BCF>2000)
Persistent
Yes
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.708 kcal/mol/HA)
✓ Good fit quality (FQ -6.76)
✓ Good burial (61% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ High strain energy (23.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-20.540
kcal/mol
LE
-0.708
kcal/mol/HA
Fit Quality
-6.76
FQ (Leeson)
HAC
29
heavy atoms
MW
417
Da
LogP
6.21
cLogP
Final rank
1.0358
rank score
Inter norm
-0.712
normalised
Contacts
9
H-bonds 2
Interaction summary
HBD 1
HY 5
PI 3
CLASH 0
Interaction summary
HBD 1
HY 5
PI 3
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
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 | 6RB5 | Contacts | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASP116
GLU18
GLY112
ILE106
LEU17
MET113
SER109
THR117
THR335
TRP21
TYR110
VAL53
VAL58
| ||
| Current overlap | 7 | Native recall | 0.54 |
| Jaccard | 0.47 | 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 | T18 | Atoms | 7550 |
|---|---|---|---|
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 619 | 1.0357649891295575 | -0.712271 | -20.5399 | 2 | 9 | 7 | 0.54 | - | - | no | Current |
| 598 | 1.1609293363911366 | -0.916148 | -28.6471 | 4 | 14 | 0 | 0.00 | - | - | no | Open |
| 613 | 1.3510130234537063 | -1.24287 | -36.6547 | 2 | 22 | 0 | 0.00 | - | - | no | Open |
| 604 | 3.739881015500972 | -0.895706 | -25.0102 | 4 | 11 | 0 | 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
-20.540kcal/mol
Ligand efficiency (LE)
-0.7083kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.761
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
416.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.21
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.53kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
101.94kcal/mol
Minimised FF energy
78.41kcal/mol
SASA & burial
✓ computed
SASA (unbound)
658.6Ų
Total solvent-accessible surface area of free ligand
BSA total
399.5Ų
Buried surface area upon binding
BSA apolar
330.0Ų
Hydrophobic contacts buried
BSA polar
69.5Ų
Polar contacts buried
Fraction buried
60.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3125.0Ų
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
1495.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)