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 medium
Native strong
SASA done
Strain ΔE
38.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.64, 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
Yes
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.653 kcal/mol/HA)
✓ Good fit quality (FQ -6.36)
✓ Good H-bonds (3 bonds)
✓ Good burial (56% SASA buried)
✓ Lipophilic contacts well-matched (88%)
✗ Very high strain energy (38.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-20.239
kcal/mol
LE
-0.653
kcal/mol/HA
Fit Quality
-6.36
FQ (Leeson)
HAC
31
heavy atoms
MW
407
Da
LogP
5.25
cLogP
Final rank
2.7945
rank score
Inter norm
-0.610
normalised
Contacts
10
H-bonds 5
Interaction summary
HBA 3
HY 4
PI 1
CLASH 2
Interaction summary
HBA 3
HY 4
PI 1
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.
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: permissive.
| 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 | 0.64 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 618 | 2.7809451592393097 | -0.756201 | -23.113 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 625 | 2.7945369204124924 | -0.609663 | -20.239 | 5 | 10 | 7 | 0.88 | 0.00 | - | no | Current |
| 629 | 2.9601670035022902 | -0.694595 | -21.1592 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 610 | 3.9280906801648916 | -0.927958 | -27.8575 | 10 | 15 | 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
-20.239kcal/mol
Ligand efficiency (LE)
-0.6529kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.360
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
407.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.25
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
125.08kcal/mol
Minimised FF energy
86.47kcal/mol
SASA & burial
✓ computed
SASA (unbound)
708.6Ų
Total solvent-accessible surface area of free ligand
BSA total
396.5Ų
Buried surface area upon binding
BSA apolar
347.1Ų
Hydrophobic contacts buried
BSA polar
49.5Ų
Polar contacts buried
Fraction buried
56.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
87.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3160.9Ų
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
1518.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)