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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
26.4 kcal/mol
Protein clashes
0
Internal clashes
13
Native overlap
contact recall 0.62, Jaccard 0.40
Reason: 13 internal clashes
13 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.831 kcal/mol/HA)
✓ Good fit quality (FQ -7.85)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ High strain energy (26.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-23.276
kcal/mol
LE
-0.831
kcal/mol/HA
Fit Quality
-7.85
FQ (Leeson)
HAC
28
heavy atoms
MW
390
Da
LogP
3.81
cLogP
Final rank
1.8307
rank score
Inter norm
-0.855
normalised
Contacts
15
H-bonds 2
Interaction summary
HBD 1
HY 9
PI 2
CLASH 0
Interaction summary
HBD 1
HY 9
PI 2
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 1.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| 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 | 8 | Native recall | 0.62 |
| Jaccard | 0.40 | 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
-23.276kcal/mol
Ligand efficiency (LE)
-0.8313kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.848
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
389.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.81
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
108.16kcal/mol
Minimised FF energy
81.76kcal/mol
SASA & burial
✓ computed
SASA (unbound)
659.2Ų
Total solvent-accessible surface area of free ligand
BSA total
510.1Ų
Buried surface area upon binding
BSA apolar
433.8Ų
Hydrophobic contacts buried
BSA polar
76.3Ų
Polar contacts buried
Fraction buried
77.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3034.5Ų
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
1544.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)