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 0.92, Jaccard 0.75
Reason: no major geometry red flags detected
2 protein-contact clashes
35% of hydrophobic surface appears solvent-exposed (7/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.915 kcal/mol/HA)
✓ Good fit quality (FQ -8.83)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Very high strain energy (38.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-27.457
kcal/mol
LE
-0.915
kcal/mol/HA
Fit Quality
-8.83
FQ (Leeson)
HAC
30
heavy atoms
MW
411
Da
LogP
0.92
cLogP
Interaction summary
HB 12
HY 19
PI 0
CLASH 2
⚠ Exposure 35%
Interaction summary
HB 12
HY 19
PI 0
CLASH 2
⚠ Exposure 35%
Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (7/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20
Buried (contacted) 13
Exposed 7
LogP 0.92
H-bonds 12
Exposed fragments:
phenyl (2/5 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 3.056 | Score | -27.457 |
|---|---|---|---|
| Inter norm | -0.997 | Intra norm | 0.082 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 12 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash; high strain Δ 38.7 | ||
| Residues |
ALA209
ALA90
ARG74
ASN208
ASN245
GLY214
GLY215
GLY246
LEU73
LYS211
MET70
PHE83
PRO212
PRO213
VAL88
| ||
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 | ||
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 | 12 | Native recall | 0.92 |
| Jaccard | 0.75 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 86 | 1.3201264683957115 | -0.864526 | -23.4481 | 7 | 19 | 0 | 0.00 | - | - | no | Open |
| 125 | 2.369476885666318 | -0.973188 | -27.5063 | 6 | 20 | 0 | 0.00 | - | - | no | Open |
| 99 | 3.0564802030326783 | -0.996931 | -27.457 | 12 | 15 | 12 | 0.92 | - | - | no | Current |
| 84 | 4.842302807097063 | -0.847311 | -24.0171 | 12 | 16 | 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
-27.457kcal/mol
Ligand efficiency (LE)
-0.9152kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.829
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
411.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.92
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.71kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
174.54kcal/mol
Minimised FF energy
135.83kcal/mol
SASA & burial
✓ computed
SASA (unbound)
658.6Ų
Total solvent-accessible surface area of free ligand
BSA total
476.2Ų
Buried surface area upon binding
BSA apolar
367.1Ų
Hydrophobic contacts buried
BSA polar
109.1Ų
Polar contacts buried
Fraction buried
72.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3009.3Ų
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
1533.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)