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 mixed
SASA done
Strain ΔE
24.9 kcal/mol
Protein clashes
7
Internal clashes
11
Native overlap
contact recall 0.54, Jaccard 0.37
Reason: 11 internal clashes
7 protein-contact clashes
11 intramolecular clashes
100% of hydrophobic surface is solvent-exposed (23/23 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 (-0.673 kcal/mol/HA)
✓ Good fit quality (FQ -6.49)
✓ Good burial (59% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ High strain energy (24.9 kcal/mol)
✗ No H-bonds detected
✗ Geometry warnings
✗ Protein-contact clashes (7)
✗ Many internal clashes (11)
Score
-20.189
kcal/mol
LE
-0.673
kcal/mol/HA
Fit Quality
-6.49
FQ (Leeson)
HAC
30
heavy atoms
MW
409
Da
LogP
3.80
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 (23/23 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 23
Buried (contacted) 0
Exposed 23
LogP 3.8
H-bonds 0
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (2/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
| Final rank | 1.596 | Score | -20.189 |
|---|---|---|---|
| Inter norm | -0.733 | Intra norm | 0.060 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 6 |
| Artifact reason | geometry warning; 11 clashes; 7 protein contact clashes; moderate strain Δ 20.3 | ||
| Residues |
CYS52
GLU18
GLY13
GLY15
GLY49
ILE339
LEU17
MET113
SER14
THR335
TRP21
TYR110
VAL53
| ||
Protein summary
493 residues
| Protein target | T18 | Atoms | 7550 |
|---|---|---|---|
| Residues | 493 | 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:276; MET:221 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| Name | 6RB5 | Contacts | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASP116
GLU18
GLY112
ILE106
LEU17
MET113
SER109
THR117
THR335
TRP21
TYR110
VAL53
VAL58
| ||
| Current overlap | 7 | Native recall | 0.54 |
| Jaccard | 0.37 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 326 | 0.8463483689542309 | -0.870388 | -21.6678 | 2 | 18 | 0 | 0.00 | - | - | no | Open |
| 232 | 1.304524843400454 | -0.906194 | -22.3766 | 10 | 20 | 0 | 0.00 | - | - | no | Open |
| 285 | 1.5960647736233116 | -0.733449 | -20.1889 | 6 | 13 | 7 | 0.54 | - | - | no | Current |
| 269 | 1.6024263538927392 | -1.38981 | -38.5187 | 6 | 19 | 0 | 0.00 | - | - | no | Open |
| 262 | 2.1697761990306184 | -0.904519 | -24.0477 | 6 | 20 | 0 | 0.00 | - | - | no | Open |
| 262 | 2.996589456804839 | -1.22398 | -31.5346 | 8 | 18 | 0 | 0.00 | - | - | no | Open |
| 309 | 3.4096127523200597 | -0.7676 | -21.1377 | 6 | 15 | 0 | 0.00 | - | - | no | Open |
| 389 | 4.281442896893412 | -0.794253 | -18.3294 | 8 | 14 | 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
-20.189kcal/mol
Ligand efficiency (LE)
-0.6730kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.492
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
409.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.80
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
52.90kcal/mol
Minimised FF energy
28.01kcal/mol
SASA & burial
✓ computed
SASA (unbound)
664.4Ų
Total solvent-accessible surface area of free ligand
BSA total
394.8Ų
Buried surface area upon binding
BSA apolar
314.9Ų
Hydrophobic contacts buried
BSA polar
79.8Ų
Polar contacts buried
Fraction buried
59.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3173.2Ų
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
4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1450.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)