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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
31.4 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.92, Jaccard 0.63
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.652 kcal/mol/HA)
✓ Good fit quality (FQ -6.58)
✓ Good H-bonds (3 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Very high strain energy (31.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-22.829
kcal/mol
LE
-0.652
kcal/mol/HA
Fit Quality
-6.58
FQ (Leeson)
HAC
35
heavy atoms
MW
492
Da
LogP
1.91
cLogP
Final rank
3.1993
rank score
Inter norm
-0.705
normalised
Contacts
18
H-bonds 5
Interaction summary
HBD 1
HBA 2
HY 6
PI 1
CLASH 4
Interaction summary
HBD 1
HBA 2
HY 6
PI 1
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
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 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 115 | 1.4028695381437135 | -0.944725 | -26.3156 | 4 | 14 | 0 | 0.00 | - | - | no | Open |
| 90 | 2.704813851204706 | -0.711295 | -24.1711 | 2 | 18 | 0 | 0.00 | - | - | no | Open |
| 94 | 3.1993237758746558 | -0.704553 | -22.829 | 5 | 18 | 12 | 0.92 | - | - | no | Current |
| 102 | 3.3611055003370893 | -0.695238 | -25.8017 | 3 | 21 | 0 | 0.00 | - | - | no | Open |
| 91 | 3.661011180748689 | -0.60391 | -21.9617 | 7 | 16 | 0 | 0.00 | - | - | no | Open |
| 83 | 4.058036207553674 | -0.835089 | -25.7585 | 6 | 15 | 0 | 0.00 | - | - | no | Open |
| 78 | 4.0591009172098715 | -0.773424 | -25.6746 | 6 | 16 | 0 | 0.00 | - | - | no | Open |
| 45 | 4.428821280584197 | -0.795132 | -19.8429 | 10 | 15 | 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
-22.829kcal/mol
Ligand efficiency (LE)
-0.6523kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.579
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
491.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.91
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.43kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
66.97kcal/mol
Minimised FF energy
35.54kcal/mol
SASA & burial
✓ computed
SASA (unbound)
817.6Ų
Total solvent-accessible surface area of free ligand
BSA total
589.4Ų
Buried surface area upon binding
BSA apolar
444.0Ų
Hydrophobic contacts buried
BSA polar
145.5Ų
Polar contacts buried
Fraction buried
72.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3106.2Ų
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
1538.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)