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
44.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.92, Jaccard 0.63
Reason: strain 44.4 kcal/mol
strain ΔE 44.4 kcal/mol
1 protein-contact clashes
38% of hydrophobic surface appears solvent-exposed (12/32 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 (-0.719 kcal/mol/HA)
✓ Good fit quality (FQ -7.36)
✓ Good H-bonds (3 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (95%)
✗ Extreme strain energy (44.4 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Many internal clashes (15)
Score
-26.600
kcal/mol
LE
-0.719
kcal/mol/HA
Fit Quality
-7.36
FQ (Leeson)
HAC
37
heavy atoms
MW
502
Da
LogP
2.91
cLogP
Interaction summary
HB 3
HY 24
PI 1
CLASH 1
⚠ Exposure 37%
Interaction summary
HB 3
HY 24
PI 1
CLASH 1
⚠ Exposure 37%
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
Partial hydrophobic solvent exposure
38% of hydrophobic surface appears solvent-exposed (12/32 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 32
Buried (contacted) 20
Exposed 12
LogP 2.91
H-bonds 3
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 1.577 | Score | -26.600 |
|---|---|---|---|
| Inter norm | -0.701 | Intra norm | -0.018 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 3 |
| Artifact reason | geometry warning; 15 clashes; 3 protein contact clashes; high strain Δ 44.4 | ||
| Residues |
ALA209
ALA67
ALA90
ARG74
ASN208
GLY214
GLY215
GLY66
GLY85
LEU73
LYS211
LYS89
MET70
PRO212
PRO213
TYR210
TYR69
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 | 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 | - |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 235 | 1.5767116465898587 | -0.700507 | -26.6 | 3 | 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
-26.600kcal/mol
Ligand efficiency (LE)
-0.7189kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.360
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
501.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.91
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
44.36kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
191.43kcal/mol
Minimised FF energy
147.07kcal/mol
SASA & burial
✓ computed
SASA (unbound)
831.0Ų
Total solvent-accessible surface area of free ligand
BSA total
603.9Ų
Buried surface area upon binding
BSA apolar
573.0Ų
Hydrophobic contacts buried
BSA polar
30.9Ų
Polar contacts buried
Fraction buried
72.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
94.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3287.3Ų
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
1511.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)