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
Promising
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
16.5 kcal/mol
Protein clashes
0
Internal clashes
7
Native overlap
contact recall 0.46, Jaccard 0.32
Reason: 7 internal clashes
7 intramolecular clashes
45% of hydrophobic surface appears solvent-exposed (5/11 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.125 kcal/mol/HA)
✓ Good fit quality (FQ -9.02)
✓ Good H-bonds (5 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Moderate strain (16.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-20.256
kcal/mol
LE
-1.125
kcal/mol/HA
Fit Quality
-9.02
FQ (Leeson)
HAC
18
heavy atoms
MW
265
Da
LogP
1.99
cLogP
Final rank
2.5272
rank score
Inter norm
-1.364
normalised
Contacts
12
H-bonds 5
Interaction summary
HBD 3
HBA 2
HY 6
PI 1
CLASH 0
Interaction summary
HBD 3
HBA 2
HY 6
PI 1
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
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: 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 | 6 | Native recall | 0.46 |
| Jaccard | 0.32 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 432 | 1.50916021506044 | -1.60024 | -25.7335 | 8 | 20 | 0 | 0.00 | - | - | no | Open |
| 405 | 1.7998442543703592 | -2.02521 | -38.4745 | 9 | 11 | 0 | 0.00 | - | - | no | Open |
| 527 | 2.5271626374165113 | -1.36405 | -20.2563 | 5 | 12 | 6 | 0.46 | - | - | no | Current |
| 431 | 3.2058566580264554 | -1.55184 | -28.9653 | 12 | 17 | 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
-20.256kcal/mol
Ligand efficiency (LE)
-1.1254kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.019
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
18HA
Physicochemical properties
Molecular weight
264.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.99
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.52kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
94.87kcal/mol
Minimised FF energy
78.35kcal/mol
SASA & burial
✓ computed
SASA (unbound)
473.2Ų
Total solvent-accessible surface area of free ligand
BSA total
381.7Ų
Buried surface area upon binding
BSA apolar
275.6Ų
Hydrophobic contacts buried
BSA polar
106.1Ų
Polar contacts buried
Fraction buried
80.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2825.6Ų
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
1527.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)