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 strong
SASA done
Strain ΔE
23.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.50, 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. 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.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.478 kcal/mol/HA)
✓ Good fit quality (FQ -4.74)
✓ Good H-bonds (5 bonds)
✓ Good burial (53% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ High strain energy (23.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-15.778
kcal/mol
LE
-0.478
kcal/mol/HA
Fit Quality
-4.74
FQ (Leeson)
HAC
33
heavy atoms
MW
454
Da
LogP
4.80
cLogP
Final rank
3.7865
rank score
Inter norm
-0.568
normalised
Contacts
13
H-bonds 6
Interaction summary
HBD 1
HBA 4
HY 4
PI 2
CLASH 2
Interaction summary
HBD 1
HBA 4
HY 4
PI 2
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 | 9IFH | Contacts | 8 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASN402
GLU467
LEU399
PHE396
PRO398
SER394
SER470
THR397
| ||
| Current overlap | 7 | Native recall | 0.88 |
| Jaccard | 0.50 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 257 | 1.4920287375308006 | -0.944617 | -23.8107 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 251 | 2.6766618478585213 | -0.788192 | -19.5632 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 384 | 2.841947707759492 | -0.722835 | -22.3314 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 227 | 3.5547341151590794 | -0.929113 | -28.3877 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 309 | 3.786488279726842 | -0.56847 | -15.7779 | 6 | 13 | 7 | 0.88 | 0.00 | - | no | Current |
| 212 | 4.583895943610404 | -0.862298 | -25.2616 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 189 | 5.2780681559421225 | -0.881399 | -25.4739 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 226 | 5.73927763117588 | -0.991721 | -27.141 | 12 | 26 | 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
-15.778kcal/mol
Ligand efficiency (LE)
-0.4781kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.744
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
453.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.80
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
63.02kcal/mol
Minimised FF energy
39.55kcal/mol
SASA & burial
✓ computed
SASA (unbound)
780.7Ų
Total solvent-accessible surface area of free ligand
BSA total
416.2Ų
Buried surface area upon binding
BSA apolar
321.8Ų
Hydrophobic contacts buried
BSA polar
94.4Ų
Polar contacts buried
Fraction buried
53.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3220.7Ų
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
1500.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)