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 strong
SASA done
Strain ΔE
15.9 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.77, Jaccard 0.56
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.929 kcal/mol/HA)
✓ Good fit quality (FQ -8.77)
✓ Good H-bonds (5 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Moderate strain (15.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-26.006
kcal/mol
LE
-0.929
kcal/mol/HA
Fit Quality
-8.77
FQ (Leeson)
HAC
28
heavy atoms
MW
401
Da
LogP
1.49
cLogP
Final rank
5.1358
rank score
Inter norm
-0.859
normalised
Contacts
15
H-bonds 5
Interaction summary
HBA 5
HY 8
PI 1
CLASH 5
Interaction summary
HBA 5
HY 8
PI 1
CLASH 5
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
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 | 10 | Native recall | 0.77 |
| Jaccard | 0.56 | 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
-26.006kcal/mol
Ligand efficiency (LE)
-0.9288kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.768
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
401.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.49
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
86.62kcal/mol
Minimised FF energy
70.71kcal/mol
SASA & burial
✓ computed
SASA (unbound)
639.0Ų
Total solvent-accessible surface area of free ligand
BSA total
492.0Ų
Buried surface area upon binding
BSA apolar
355.9Ų
Hydrophobic contacts buried
BSA polar
136.2Ų
Polar contacts buried
Fraction buried
77.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2944.1Ų
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
1533.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)