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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
49.1 kcal/mol
Protein clashes
0
Internal clashes
9
Native overlap
contact recall 0.93, Jaccard 0.87, H-bond role recall 0.56
Reason: 9 internal clashes, strain 49.1 kcal/mol
strain ΔE 49.1 kcal/mol
9 intramolecular clashes
60% of hydrophobic surface is solvent-exposed (9/15 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 (-1.097 kcal/mol/HA)
✓ Good fit quality (FQ -9.68)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (66% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Extreme strain energy (49.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-25.222
kcal/mol
LE
-1.097
kcal/mol/HA
Fit Quality
-9.68
FQ (Leeson)
HAC
23
heavy atoms
MW
333
Da
LogP
2.02
cLogP
Interaction summary
HB 10
HY 5
PI 2
CLASH 0
⚠ Exposure 60%
Interaction summary
HB 10
HY 5
PI 2
CLASH 0
⚠ Exposure 60%
Solvent-exposed hydrophobic surface — desolvation penalty likely
60% of hydrophobic surface is solvent-exposed (9/15 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) 6
Exposed 9
LogP 2.02
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 1.930 | Score | -25.222 |
|---|---|---|---|
| Inter norm | -1.092 | Intra norm | -0.004 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 10 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash; high strain Δ 49.1 | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
ASP10
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
PRO12
SER71
TYR46
| ||
Protein summary
305 residues
| Protein target | T21 | Atoms | 4646 |
|---|---|---|---|
| Residues | 305 | Chains | 2 |
| Residue summary | ARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3K7O | Contacts | 14 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG137
ARG141
ASN103
HIS102
HIS138
ASP10
CYS69
GLY70
GLY74
HIS11
ILE73
PRO12
SER71
TYR46
| ||
| Current overlap | 13 | Native recall | 0.93 |
| Jaccard | 0.87 | RMSD | - |
| HB strict | 5 | Strict recall | 0.42 |
| HB same residue+role | 5 | HB role recall | 0.56 |
| HB same residue | 6 | HB residue recall | 0.75 |
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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2 | 1.929549775469642 | -1.09235 | -25.2218 | 10 | 14 | 13 | 0.93 | 0.56 | - | no | Current |
| 1 | 2.878511730692373 | -1.25533 | -26.3754 | 14 | 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
-25.222kcal/mol
Ligand efficiency (LE)
-1.0966kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.678
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
332.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.02
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
49.08kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
122.41kcal/mol
Minimised FF energy
73.33kcal/mol
SASA & burial
✓ computed
SASA (unbound)
580.3Ų
Total solvent-accessible surface area of free ligand
BSA total
385.6Ų
Buried surface area upon binding
BSA apolar
268.8Ų
Hydrophobic contacts buried
BSA polar
116.9Ų
Polar contacts buried
Fraction buried
66.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2124.7Ų
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
2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
816.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)