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 mixed
SASA done
Strain ΔE
20.0 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.54, Jaccard 0.35
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.953 kcal/mol/HA)
✓ Good fit quality (FQ -8.12)
✓ Good H-bonds (3 bonds)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (87%)
✗ High strain energy (20.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-20.005
kcal/mol
LE
-0.953
kcal/mol/HA
Fit Quality
-8.12
FQ (Leeson)
HAC
21
heavy atoms
MW
278
Da
LogP
3.70
cLogP
Final rank
2.1994
rank score
Inter norm
-1.172
normalised
Contacts
14
H-bonds 4
Interaction summary
HBD 3
HY 9
PI 1
CLASH 3
Interaction summary
HBD 3
HY 9
PI 1
CLASH 3
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 | 9IFF | Contacts | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA209
ARG74
ASN208
GLY214
GLY215
GLY85
LEU73
LYS211
MET70
PHE83
PRO212
PRO213
VAL88
| ||
| Current overlap | 7 | Native recall | 0.54 |
| Jaccard | 0.35 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
Protein summary
489 residues
| Protein target | T15 | Atoms | 7420 |
|---|---|---|---|
| Residues | 489 | 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:204 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 418 | 0.03247301991387262 | -1.58204 | -32.313 | 7 | 17 | 0 | 0.00 | - | - | no | Open |
| 492 | 0.44576200602707305 | -1.23635 | -26.0025 | 3 | 14 | 0 | 0.00 | - | - | no | Open |
| 454 | 1.1165945291874089 | -1.16858 | -21.1829 | 9 | 15 | 0 | 0.00 | - | - | no | Open |
| 526 | 2.199368054563858 | -1.17195 | -20.0049 | 4 | 14 | 7 | 0.54 | - | - | no | Current |
| 497 | 2.63911690871143 | -1.2373 | -24.1456 | 5 | 16 | 0 | 0.00 | - | - | no | Open |
| 469 | 3.5897017914932636 | -1.30138 | -25.547 | 6 | 9 | 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
-20.005kcal/mol
Ligand efficiency (LE)
-0.9526kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.125
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
278.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.70
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
104.09kcal/mol
Minimised FF energy
84.04kcal/mol
SASA & burial
✓ computed
SASA (unbound)
526.4Ų
Total solvent-accessible surface area of free ligand
BSA total
432.1Ų
Buried surface area upon binding
BSA apolar
376.1Ų
Hydrophobic contacts buried
BSA polar
56.0Ų
Polar contacts buried
Fraction buried
82.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
87.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2953.6Ų
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
4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1501.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)