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
44.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.69, Jaccard 0.50
Reason: strain 44.2 kcal/mol
strain ΔE 44.2 kcal/mol
2 protein-contact clashes
35% of hydrophobic surface appears solvent-exposed (7/20 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 (-0.801 kcal/mol/HA)
✓ Good fit quality (FQ -7.73)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (67% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Extreme strain energy (44.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-24.040
kcal/mol
LE
-0.801
kcal/mol/HA
Fit Quality
-7.73
FQ (Leeson)
HAC
30
heavy atoms
MW
461
Da
LogP
4.40
cLogP
Interaction summary
HB 6
HY 10
PI 0
CLASH 2
⚠ Exposure 35%
Interaction summary
HB 6
HY 10
PI 0
CLASH 2
⚠ Exposure 35%
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
35% of hydrophobic surface appears solvent-exposed (7/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20
Buried (contacted) 13
Exposed 7
LogP 4.4
H-bonds 6
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 4.401 | Score | -24.040 |
|---|---|---|---|
| Inter norm | -0.832 | Intra norm | 0.030 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 6 |
| Artifact reason | geometry warning; 10 clashes; 3 protein clashes; high strain Δ 44.1 | ||
| Residues |
ALA209
ALA90
ARG74
ASN245
ASP71
GLY214
GLY215
LYS211
LYS216
LYS89
MET70
PRO212
PRO213
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 | 0.50 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 491 | 0.6568242934034779 | -0.855812 | -26.9155 | 1 | 19 | 0 | 0.00 | - | - | no | Open |
| 461 | 1.4757152030497325 | -0.727168 | -18.8759 | 4 | 13 | 0 | 0.00 | - | - | no | Open |
| 419 | 2.301587904267888 | -0.810249 | -24.2859 | 5 | 12 | 0 | 0.00 | - | - | no | Open |
| 482 | 2.4509505637358693 | -0.954137 | -28.3986 | 5 | 15 | 0 | 0.00 | - | - | no | Open |
| 397 | 2.6910133316567784 | -1.10832 | -33.2889 | 9 | 20 | 0 | 0.00 | - | - | no | Open |
| 433 | 3.1237119935793745 | -1.03561 | -30.7711 | 8 | 19 | 0 | 0.00 | - | - | no | Open |
| 403 | 3.806388656164234 | -0.820277 | -23.8419 | 13 | 15 | 0 | 0.00 | - | - | no | Open |
| 434 | 3.821146497143834 | -0.80197 | -21.889 | 8 | 11 | 0 | 0.00 | - | - | no | Open |
| 396 | 3.989000081121798 | -0.947387 | -21.9904 | 7 | 10 | 0 | 0.00 | - | - | no | Open |
| 519 | 4.4009244236670835 | -0.83158 | -24.0403 | 6 | 14 | 9 | 0.69 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.040kcal/mol
Ligand efficiency (LE)
-0.8013kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.730
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
461.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.40
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
44.21kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
71.74kcal/mol
Minimised FF energy
27.53kcal/mol
SASA & burial
✓ computed
SASA (unbound)
708.4Ų
Total solvent-accessible surface area of free ligand
BSA total
476.7Ų
Buried surface area upon binding
BSA apolar
341.7Ų
Hydrophobic contacts buried
BSA polar
134.9Ų
Polar contacts buried
Fraction buried
67.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2952.6Ų
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
1606.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)