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
46.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.85, Jaccard 0.52
Reason: strain 46.5 kcal/mol
strain ΔE 46.5 kcal/mol
3 protein-contact clashes
3 intramolecular clashes
74% of hydrophobic surface is solvent-exposed (34/46 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 (-0.535 kcal/mol/HA)
✓ Good fit quality (FQ -5.98)
✓ Good burial (64% SASA buried)
✓ Lipophilic contacts well-matched (95%)
✗ Extreme strain energy (46.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (31)
Score
-28.912
kcal/mol
LE
-0.535
kcal/mol/HA
Fit Quality
-5.98
FQ (Leeson)
HAC
54
heavy atoms
MW
727
Da
LogP
7.59
cLogP
Final rank
5.7010
rank score
Inter norm
-0.479
normalised
Contacts
19
H-bonds 3
Interaction summary
HBD 2
HY 10
PI 0
CLASH 3
Interaction summary
HBD 2
HY 10
PI 0
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
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 | 0.52 | 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 | Open |
| 75 | 5.700971264321272 | -0.478973 | -28.9123 | 3 | 19 | 11 | 0.85 | - | - | no | Current |
| 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
-28.912kcal/mol
Ligand efficiency (LE)
-0.5354kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.976
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
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
46.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
223.76kcal/mol
Minimised FF energy
177.29kcal/mol
SASA & burial
✓ computed
SASA (unbound)
1083.1Ų
Total solvent-accessible surface area of free ligand
BSA total
689.1Ų
Buried surface area upon binding
BSA apolar
655.1Ų
Hydrophobic contacts buried
BSA polar
34.0Ų
Polar contacts buried
Fraction buried
63.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
95.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3474.9Ų
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
1544.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)