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
20.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.88, Jaccard 0.54, H-bond role recall 1.00
Reason: no major geometry red flags detected
1 protein-contact clashes
42% of hydrophobic surface appears solvent-exposed (11/26 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.620 kcal/mol/HA)
✓ Good fit quality (FQ -6.04)
✓ Good burial (63% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ High strain energy (20.7 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (19)
Score
-19.222
kcal/mol
LE
-0.620
kcal/mol/HA
Fit Quality
-6.04
FQ (Leeson)
HAC
31
heavy atoms
MW
409
Da
LogP
4.57
cLogP
Final rank
1.8151
rank score
Inter norm
-0.620
normalised
Contacts
12
H-bonds 6
Interaction summary
HBD 1
HBA 1
HY 4
PI 1
CLASH 1
Interaction summary
HBD 1
HBA 1
HY 4
PI 1
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
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 | 0.54 | RMSD | - |
| HB strict | 2 | Strict recall | 1.00 |
| HB same residue+role | 1 | HB role recall | 1.00 |
| HB same residue | 1 | HB residue recall | 1.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 560 | 1.5524363376816304 | -0.743418 | -20.5292 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 529 | 1.815148662072829 | -0.62049 | -19.2224 | 6 | 12 | 7 | 0.88 | 1.00 | - | no | Current |
| 516 | 1.8766063905365975 | -0.821197 | -24.9157 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 550 | 2.5648728586241805 | -0.720981 | -21.2854 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 517 | 3.30870723637248 | -0.718914 | -23.5334 | 4 | 10 | 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
-19.222kcal/mol
Ligand efficiency (LE)
-0.6201kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.041
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
409.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.57
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
139.81kcal/mol
Minimised FF energy
119.12kcal/mol
SASA & burial
✓ computed
SASA (unbound)
678.2Ų
Total solvent-accessible surface area of free ligand
BSA total
429.8Ų
Buried surface area upon binding
BSA apolar
381.6Ų
Hydrophobic contacts buried
BSA polar
48.1Ų
Polar contacts buried
Fraction buried
63.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3196.6Ų
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
1495.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)