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
38.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.85, Jaccard 0.65
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.644 kcal/mol/HA)
✓ Good fit quality (FQ -6.44)
✓ Good H-bonds (5 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Very high strain energy (38.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-21.887
kcal/mol
LE
-0.644
kcal/mol/HA
Fit Quality
-6.44
FQ (Leeson)
HAC
34
heavy atoms
MW
461
Da
LogP
3.08
cLogP
Final rank
4.9371
rank score
Inter norm
-0.777
normalised
Contacts
15
H-bonds 8
Interaction summary
HBD 3
HBA 2
HY 7
PI 1
CLASH 2
Interaction summary
HBD 3
HBA 2
HY 7
PI 1
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.
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 | 11 | Native recall | 0.85 |
| Jaccard | 0.65 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 379 | 1.7515119447063427 | -0.628624 | -16.1568 | 7 | 18 | 0 | 0.00 | - | - | no | Open |
| 428 | 2.1508479025996894 | -0.801565 | -19.3286 | 5 | 18 | 0 | 0.00 | - | - | no | Open |
| 368 | 3.090122770978229 | -0.741059 | -15.222 | 13 | 13 | 0 | 0.00 | - | - | no | Open |
| 448 | 3.187813687353957 | -0.756461 | -24.6559 | 5 | 15 | 0 | 0.00 | - | - | no | Open |
| 373 | 3.331493017527665 | -0.760459 | -20.8381 | 6 | 17 | 0 | 0.00 | - | - | no | Open |
| 338 | 4.6424814593420125 | -0.949318 | -28.0247 | 14 | 23 | 0 | 0.00 | - | - | no | Open |
| 473 | 4.937071202872829 | -0.776684 | -21.8871 | 8 | 15 | 11 | 0.85 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.887kcal/mol
Ligand efficiency (LE)
-0.6437kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.441
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
461.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.08
Lipinski: ≤ 5
Rotatable bonds
12
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
120.00kcal/mol
Minimised FF energy
81.31kcal/mol
SASA & burial
✓ computed
SASA (unbound)
793.5Ų
Total solvent-accessible surface area of free ligand
BSA total
561.9Ų
Buried surface area upon binding
BSA apolar
444.4Ų
Hydrophobic contacts buried
BSA polar
117.5Ų
Polar contacts buried
Fraction buried
70.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3111.4Ų
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
1544.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)