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 strong
SASA done
Strain ΔE
16.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.50, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
67% of hydrophobic surface is solvent-exposed (10/15 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 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 (-0.937 kcal/mol/HA)
✓ Good fit quality (FQ -8.13)
✓ Strong H-bond network (6 bonds)
✓ Good burial (58% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Moderate strain (16.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-20.607
kcal/mol
LE
-0.937
kcal/mol/HA
Fit Quality
-8.13
FQ (Leeson)
HAC
22
heavy atoms
MW
304
Da
LogP
2.04
cLogP
Final rank
1.8723
rank score
Inter norm
-0.891
normalised
Contacts
7
H-bonds 8
Interaction summary
HBD 1
HBA 5
HY 3
PI 1
CLASH 2
Interaction summary
HBD 1
HBA 5
HY 3
PI 1
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: strict.
| Name | 9IFH | Contacts | 8 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASN402
GLU467
LEU399
PHE396
PRO398
SER394
SER470
THR397
| ||
| Current overlap | 5 | Native recall | 0.62 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 227 | 1.8722576862877631 | -0.891251 | -20.6066 | 8 | 7 | 5 | 0.62 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.607kcal/mol
Ligand efficiency (LE)
-0.9367kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.132
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
304.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.04
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
25.54kcal/mol
Minimised FF energy
8.71kcal/mol
SASA & burial
✓ computed
SASA (unbound)
572.9Ų
Total solvent-accessible surface area of free ligand
BSA total
334.5Ų
Buried surface area upon binding
BSA apolar
286.3Ų
Hydrophobic contacts buried
BSA polar
48.2Ų
Polar contacts buried
Fraction buried
58.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3054.9Ų
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
1503.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)