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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
32.0 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.69, Jaccard 0.45
Reason: 6 internal clashes
6 protein-contact clashes
6 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.484 kcal/mol/HA)
✓ Good fit quality (FQ -4.80)
✓ Good H-bonds (5 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Very high strain energy (32.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-15.978
kcal/mol
LE
-0.484
kcal/mol/HA
Fit Quality
-4.80
FQ (Leeson)
HAC
33
heavy atoms
MW
474
Da
LogP
3.42
cLogP
Interaction summary
HB 5
HY 24
PI 1
CLASH 6
Interaction summary
HB 5
HY 24
PI 1
CLASH 6
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 4.207 | Score | -15.978 |
|---|---|---|---|
| Inter norm | -0.711 | Intra norm | 0.227 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 5 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; high strain Δ 32.0 | ||
| Residues |
ALA209
ALA77
ALA90
ARG74
GLU82
LEU73
LYS211
LYS89
MET70
PHE83
PRO212
PRO213
SER76
TRP81
TYR210
VAL88
| ||
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 | 9 | Native recall | 0.69 |
| Jaccard | 0.45 | 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
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-15.978kcal/mol
Ligand efficiency (LE)
-0.4842kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.804
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
474.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.42
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.97kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
101.15kcal/mol
Minimised FF energy
69.19kcal/mol
SASA & burial
✓ computed
SASA (unbound)
767.1Ų
Total solvent-accessible surface area of free ligand
BSA total
560.8Ų
Buried surface area upon binding
BSA apolar
460.8Ų
Hydrophobic contacts buried
BSA polar
100.0Ų
Polar contacts buried
Fraction buried
73.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3077.9Ų
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
4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1566.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)