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
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
41.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.69, Jaccard 0.50
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
54% of hydrophobic surface appears solvent-exposed (13/24 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 (-0.713 kcal/mol/HA)
✓ Good fit quality (FQ -7.07)
✓ Strong H-bond network (8 bonds)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Extreme strain energy (41.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-23.513
kcal/mol
LE
-0.713
kcal/mol/HA
Fit Quality
-7.07
FQ (Leeson)
HAC
33
heavy atoms
MW
471
Da
LogP
-0.41
cLogP
Interaction summary
HB 8
HY 6
PI 0
CLASH 3
⚠ Exposure 54%
Interaction summary
HB 8
HY 6
PI 0
CLASH 3
⚠ Exposure 54%
Partial hydrophobic solvent exposure
54% of hydrophobic surface appears solvent-exposed (13/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 24
Buried (contacted) 11
Exposed 13
LogP -0.41
H-bonds 8
Exposed fragments:
phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 3.991 | Score | -23.513 |
|---|---|---|---|
| Inter norm | -0.782 | Intra norm | 0.070 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 8 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; high strain Δ 41.9 | ||
| Residues |
ALA244
ARG74
ASN208
ASN245
ASP71
GLY214
GLY215
GLY246
LEU73
LYS211
LYS216
MET70
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 | 9 | Native recall | 0.69 |
| Jaccard | 0.50 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 94 | 0.8968455091820249 | -1.00617 | -31.9861 | 3 | 16 | 0 | 0.00 | - | - | no | Open |
| 113 | 1.2787634175823281 | -0.946846 | -30.1424 | 6 | 16 | 0 | 0.00 | - | - | no | Open |
| 87 | 2.5833270075649684 | -0.72041 | -23.1843 | 6 | 14 | 0 | 0.00 | - | - | no | Open |
| 91 | 3.9910595760413226 | -0.782021 | -23.5128 | 8 | 14 | 9 | 0.69 | - | - | no | Current |
| 122 | 4.087349949128517 | -0.776292 | -23.4709 | 4 | 11 | 0 | 0.00 | - | - | no | Open |
| 70 | 4.520502492898979 | -0.836386 | -22.2364 | 11 | 18 | 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
-23.513kcal/mol
Ligand efficiency (LE)
-0.7125kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.069
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
470.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.41
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
41.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
296.88kcal/mol
Minimised FF energy
254.98kcal/mol
SASA & burial
✓ computed
SASA (unbound)
732.4Ų
Total solvent-accessible surface area of free ligand
BSA total
455.7Ų
Buried surface area upon binding
BSA apolar
352.6Ų
Hydrophobic contacts buried
BSA polar
103.1Ų
Polar contacts buried
Fraction buried
62.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3034.7Ų
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
1557.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)