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
32.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.77, Jaccard 0.48
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.715 kcal/mol/HA)
✓ Good fit quality (FQ -7.10)
✓ Good H-bonds (3 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (87%)
✗ Very high strain energy (32.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-23.605
kcal/mol
LE
-0.715
kcal/mol/HA
Fit Quality
-7.10
FQ (Leeson)
HAC
33
heavy atoms
MW
471
Da
LogP
1.54
cLogP
Interaction summary
HB 3
HY 24
PI 1
CLASH 3
Interaction summary
HB 3
HY 24
PI 1
CLASH 3
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
| Final rank | 3.242 | Score | -23.605 |
|---|---|---|---|
| Inter norm | -0.764 | Intra norm | 0.049 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 3 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes; high strain Δ 32.5 | ||
| Residues |
ALA209
ALA77
ALA90
ARG74
GLU82
GLY85
LEU73
LYS211
LYS89
MET70
PHE83
PRO187
PRO212
PRO213
SER76
TRP81
TYR210
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 | 10 | Native recall | 0.77 |
| Jaccard | 0.48 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 135 | 1.1656826978506472 | -0.985977 | -28.9249 | 8 | 15 | 0 | 0.00 | - | - | no | Open |
| 82 | 2.9250018274398606 | -0.857986 | -25.9459 | 13 | 18 | 0 | 0.00 | - | - | no | Open |
| 110 | 3.241795225483599 | -0.76395 | -23.605 | 3 | 18 | 10 | 0.77 | - | - | no | Current |
| 139 | 3.4303026026578687 | -0.658142 | -18.0844 | 5 | 12 | 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
-23.605kcal/mol
Ligand efficiency (LE)
-0.7153kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.097
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
470.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.54
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.52kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
54.49kcal/mol
Minimised FF energy
21.96kcal/mol
SASA & burial
✓ computed
SASA (unbound)
804.9Ų
Total solvent-accessible surface area of free ligand
BSA total
612.6Ų
Buried surface area upon binding
BSA apolar
531.4Ų
Hydrophobic contacts buried
BSA polar
81.2Ų
Polar contacts buried
Fraction buried
76.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
86.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3182.6Ų
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
1512.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)