Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Receptor not available — ligand geometry only, interactions disabled.
Viewer legend
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
52.2 kcal/mol
Protein clashes
0
Internal clashes
9
Native overlap
contact recall 0.79, Jaccard 0.71, H-bond role recall 0.43
Reason: 9 internal clashes, strain 52.2 kcal/mol
strain ΔE 52.2 kcal/mol
9 intramolecular clashes
100% of hydrophobic surface is solvent-exposed (15/15 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.388 kcal/mol/HA)
✓ Good fit quality (FQ -12.05)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Extreme strain energy (52.2 kcal/mol)
✗ No H-bonds detected
✗ Geometry warnings
✗ Internal clashes (9)
Score
-30.535
kcal/mol
LE
-1.388
kcal/mol/HA
Fit Quality
-12.05
FQ (Leeson)
HAC
22
heavy atoms
MW
300
Da
LogP
0.85
cLogP
Interaction summary
HB 0
HY 0
PI 0
CLASH 0
⚠ Exposure 100%
Interaction summary
HB 0
HY 0
PI 0
CLASH 0
⚠ Exposure 100%
Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (15/15 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 15
Buried (contacted) 0
Exposed 15
LogP 0.85
H-bonds 0
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 2.747 | Score | -30.535 |
|---|---|---|---|
| Inter norm | -1.277 | Intra norm | -0.111 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 6 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes; high strain Δ 52.2 | ||
| Residues |
ALA111
ALA67
ARG154
ARG277
ASN112
GLU274
GLY236
GLY237
GLY276
HIS197
LYS69
PHE238
PRO113
PRO275
SER200
TYR278
TYR389
| ||
Protein summary
411 residues
| Protein target | T13 | Atoms | 6340 |
|---|---|---|---|
| Residues | 411 | Chains | 1 |
| Residue summary | VAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1F3T | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA111
ALA67
ARG154
ARG277
ASP332
ASP88
CYS70
GLU274
GLY236
GLY237
GLY276
HIS197
LYS69
PHE238
PRO275
SER200
TYR278
TYR331
TYR389
| ||
| Current overlap | 15 | Native recall | 0.79 |
| Jaccard | 0.71 | RMSD | - |
| HB strict | 4 | Strict recall | 0.44 |
| HB same residue+role | 3 | HB role recall | 0.43 |
| HB same residue | 4 | HB residue recall | 0.57 |
HB · H-bonds
No hb · h-bonds detected for this pose.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
No hy · hydrophobic contacts detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 25 | -0.3769812657365905 | -1.49243 | -35.3418 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 28 | 1.9063884205772796 | -1.11862 | -20.8248 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 11 | 1.9354423717711704 | -1.15859 | -27.306 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 9 | 2.746681848096203 | -1.27654 | -30.535 | 6 | 17 | 15 | 0.79 | 0.43 | - | no | Current |
| 29 | 3.1934369242828557 | -1.0322 | -23.0522 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 21 | 3.2373255068012856 | -1.29213 | -25.3679 | 11 | 17 | 0 | 0.00 | 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
-30.535kcal/mol
Ligand efficiency (LE)
-1.3880kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.050
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
300.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.85
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
52.17kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
175.53kcal/mol
Minimised FF energy
123.36kcal/mol
SASA & burial
✓ computed
SASA (unbound)
505.3Ų
Total solvent-accessible surface area of free ligand
BSA total
403.9Ų
Buried surface area upon binding
BSA apolar
309.4Ų
Hydrophobic contacts buried
BSA polar
94.5Ų
Polar contacts buried
Fraction buried
79.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2485.2Ų
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
3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1367.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)