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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
43.5 kcal/mol
Protein clashes
2
Internal clashes
14
Native overlap
contact recall 0.92, Jaccard 0.63
Reason: 14 internal clashes, strain 43.5 kcal/mol
strain ΔE 43.5 kcal/mol
2 protein-contact clashes
14 intramolecular clashes
35% of hydrophobic surface appears solvent-exposed (11/31 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.795 kcal/mol/HA)
✓ Good fit quality (FQ -8.01)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (95%)
✗ Extreme strain energy (43.5 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (14)
Score
-27.810
kcal/mol
LE
-0.795
kcal/mol/HA
Fit Quality
-8.01
FQ (Leeson)
HAC
35
heavy atoms
MW
473
Da
LogP
3.76
cLogP
Interaction summary
HB 2
HY 24
PI 1
CLASH 0
⚠ Exposure 35%
Interaction summary
HB 2
HY 24
PI 1
CLASH 0
⚠ Exposure 35%
Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (11/31 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 31
Buried (contacted) 20
Exposed 11
LogP 3.76
H-bonds 2
Exposed fragments:
phenyl (4/5 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 1.341 | Score | -27.810 |
|---|---|---|---|
| Inter norm | -0.733 | Intra norm | -0.061 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 2 |
| Artifact reason | geometry warning; 14 clashes; 2 protein contact clashes; high strain Δ 43.5 | ||
| Residues |
ALA209
ALA67
ALA90
ARG74
ASN208
GLY214
GLY215
GLY66
GLY85
LEU73
LYS211
LYS89
MET70
PRO212
PRO213
TYR210
TYR69
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 | 0.63 | 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
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.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 259 | 1.3411997614173343 | -0.733456 | -27.8096 | 2 | 18 | 12 | 0.92 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.810kcal/mol
Ligand efficiency (LE)
-0.7946kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.014
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
472.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.76
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
43.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
109.33kcal/mol
Minimised FF energy
65.79kcal/mol
SASA & burial
✓ computed
SASA (unbound)
799.7Ų
Total solvent-accessible surface area of free ligand
BSA total
597.4Ų
Buried surface area upon binding
BSA apolar
567.2Ų
Hydrophobic contacts buried
BSA polar
30.2Ų
Polar contacts buried
Fraction buried
74.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
94.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3264.0Ų
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
1508.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)