Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
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
40.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.69, Jaccard 0.47
Reason: no major geometry red flags detected
1 protein-contact clashes
41% of hydrophobic surface appears solvent-exposed (11/27 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 (-0.533 kcal/mol/HA)
✓ Good fit quality (FQ -5.42)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ Extreme strain energy (40.7 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Many internal clashes (17)
Score
-19.192
kcal/mol
LE
-0.533
kcal/mol/HA
Fit Quality
-5.42
FQ (Leeson)
HAC
36
heavy atoms
MW
497
Da
LogP
5.77
cLogP
Interaction summary
HB 2
HY 24
PI 0
CLASH 1
⚠ Exposure 40%
Interaction summary
HB 2
HY 24
PI 0
CLASH 1
⚠ Exposure 40%
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
Partial hydrophobic solvent exposure
41% of hydrophobic surface appears solvent-exposed (11/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 27
Buried (contacted) 16
Exposed 11
LogP 5.77
H-bonds 2
Exposed fragments:
phenyl (5/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 1.707 | Score | -19.192 |
|---|---|---|---|
| Inter norm | -0.728 | Intra norm | 0.194 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 2 |
| Artifact reason | geometry warning; 17 clashes; 3 protein contact clashes; high strain Δ 40.7 | ||
| Residues |
ALA209
ALA77
ALA90
ARG74
ASN245
LEU73
LYS211
LYS89
MET70
PHE83
PRO187
PRO212
PRO213
TYR210
VAL88
| ||
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 | 0.47 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
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 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 17 | 1.7072284370268758 | -0.727521 | -19.1925 | 2 | 15 | 9 | 0.69 | - | - | no | Current |
| 31 | 1.9145000543311115 | -0.730596 | -26.5346 | 2 | 17 | 0 | 0.00 | - | - | no | Open |
| 29 | 3.020862307535669 | -0.646601 | -19.2049 | 3 | 20 | 0 | 0.00 | - | - | no | Open |
| 18 | 3.099639412616397 | -0.651628 | -20.9225 | 5 | 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
-19.192kcal/mol
Ligand efficiency (LE)
-0.5331kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.419
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
497.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.77
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
40.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
53.48kcal/mol
Minimised FF energy
12.82kcal/mol
SASA & burial
✓ computed
SASA (unbound)
795.7Ų
Total solvent-accessible surface area of free ligand
BSA total
546.9Ų
Buried surface area upon binding
BSA apolar
487.8Ų
Hydrophobic contacts buried
BSA polar
59.1Ų
Polar contacts buried
Fraction buried
68.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
89.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3126.1Ų
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
1566.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)