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
72.7 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.85, Jaccard 0.50
Reason: strain 72.7 kcal/mol
strain ΔE 72.7 kcal/mol
4 protein-contact clashes
4 intramolecular clashes
59% of hydrophobic surface appears solvent-exposed (27/46 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 (-0.481 kcal/mol/HA)
✓ Good fit quality (FQ -5.36)
✓ Good burial (64% SASA buried)
✓ Lipophilic contacts well-matched (96%)
✗ Extreme strain energy (72.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (29)
Score
-25.951
kcal/mol
LE
-0.481
kcal/mol/HA
Fit Quality
-5.36
FQ (Leeson)
HAC
54
heavy atoms
MW
727
Da
LogP
7.59
cLogP
Interaction summary
HB 2
HY 24
PI 0
CLASH 4
⚠ Exposure 58%
Interaction summary
HB 2
HY 24
PI 0
CLASH 4
⚠ Exposure 58%
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
59% of hydrophobic surface appears solvent-exposed (27/46 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 46
Buried (contacted) 19
Exposed 27
LogP 7.59
H-bonds 2
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 5.679 | Score | -25.951 |
|---|---|---|---|
| Inter norm | -0.492 | Intra norm | -0.002 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 2 |
| Artifact reason | geometry warning; 29 clashes; 2 protein clashes; high strain Δ 72.5 | ||
| Residues |
ALA209
ALA67
ALA90
ARG74
ASN245
ASP84
GLY214
GLY215
GLY66
GLY85
LEU73
LYS211
LYS89
MET70
PRO212
PRO213
SER86
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 | 11 | Native recall | 0.85 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 55 | 3.3497979919415495 | -0.464673 | -26.1912 | 3 | 17 | 0 | 0.00 | - | - | no | Open |
| 53 | 3.3758863606086744 | -0.464402 | -25.8528 | 4 | 17 | 0 | 0.00 | - | - | no | Open |
| 54 | 3.577924600809405 | -0.451894 | -28.7976 | 3 | 17 | 0 | 0.00 | - | - | no | Open |
| 87 | 4.13827499297359 | -0.389581 | -24.1811 | 5 | 12 | 0 | 0.00 | - | - | no | Open |
| 56 | 4.18770120335156 | -0.462654 | -28.0377 | 3 | 17 | 0 | 0.00 | - | - | no | Open |
| 52 | 4.322987441457952 | -0.456955 | -29.3071 | 3 | 16 | 0 | 0.00 | - | - | no | Open |
| 74 | 4.64585637414439 | -0.460571 | -29.366 | 4 | 20 | 11 | 0.85 | - | - | no | Open |
| 89 | 5.0128806381886335 | -0.357608 | -20.2348 | 8 | 11 | 0 | 0.00 | - | - | no | Open |
| 72 | 5.3307022059735445 | -0.507201 | -27.1817 | 4 | 21 | 13 | 1.00 | - | - | no | Open |
| 91 | 5.437408225175003 | -0.441797 | -29.9598 | 7 | 15 | 0 | 0.00 | - | - | no | Open |
| 92 | 5.444837849737617 | -0.444097 | -28.2973 | 7 | 17 | 0 | 0.00 | - | - | no | Open |
| 73 | 5.678919712128663 | -0.491703 | -25.9507 | 2 | 20 | 11 | 0.85 | - | - | no | Current |
| 75 | 5.700971264321272 | -0.478973 | -28.9123 | 3 | 19 | 11 | 0.85 | - | - | no | Open |
| 76 | 5.778532105396608 | -0.481828 | -25.7334 | 2 | 19 | 12 | 0.92 | - | - | no | Open |
| 88 | 5.871724657289681 | -0.39485 | -22.2877 | 5 | 10 | 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
-25.951kcal/mol
Ligand efficiency (LE)
-0.4806kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.364
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
54HA
Physicochemical properties
Molecular weight
726.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
7.59
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
72.72kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
243.85kcal/mol
Minimised FF energy
171.13kcal/mol
SASA & burial
✓ computed
SASA (unbound)
1077.3Ų
Total solvent-accessible surface area of free ligand
BSA total
687.0Ų
Buried surface area upon binding
BSA apolar
658.1Ų
Hydrophobic contacts buried
BSA polar
28.9Ų
Polar contacts buried
Fraction buried
63.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
95.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3467.2Ų
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
1546.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)