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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
35.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.77, Jaccard 0.56
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 (-0.624 kcal/mol/HA)
✓ Good fit quality (FQ -5.96)
✓ Good H-bonds (3 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Very high strain energy (35.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-18.108
kcal/mol
LE
-0.624
kcal/mol/HA
Fit Quality
-5.96
FQ (Leeson)
HAC
29
heavy atoms
MW
391
Da
LogP
3.16
cLogP
Interaction summary
HB 3
HY 24
PI 1
CLASH 3
Interaction summary
HB 3
HY 24
PI 1
CLASH 3
| Final rank | 3.675 | Score | -18.108 |
|---|---|---|---|
| Inter norm | -0.806 | Intra norm | 0.181 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 3 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; high strain Δ 35.4 | ||
| Residues |
ALA209
ALA77
ALA90
ARG74
GLY85
LEU73
LYS211
LYS89
MET70
PHE83
PRO212
PRO213
SER76
TYR210
VAL88
| ||
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 | ||
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 | 0.56 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 371 | 0.6766080884637871 | -0.850212 | -23.5297 | 6 | 13 | 0 | 0.00 | - | - | no | Open |
| 456 | 1.3298642730659846 | -0.876871 | -20.7915 | 4 | 15 | 0 | 0.00 | - | - | no | Open |
| 371 | 1.6592905543340895 | -1.1365 | -32.2539 | 5 | 15 | 0 | 0.00 | - | - | no | Open |
| 321 | 2.4630441993751795 | -0.956144 | -26.0216 | 9 | 14 | 0 | 0.00 | - | - | no | Open |
| 382 | 2.4869569999026053 | -0.980507 | -24.896 | 6 | 15 | 0 | 0.00 | - | - | no | Open |
| 317 | 3.15422312242859 | -1.11678 | -29.9725 | 9 | 21 | 0 | 0.00 | - | - | no | Open |
| 390 | 3.359899098482382 | -0.766488 | -19.917 | 11 | 14 | 0 | 0.00 | - | - | no | Open |
| 348 | 3.455414740609191 | -1.03631 | -22.4 | 10 | 15 | 0 | 0.00 | - | - | no | Open |
| 482 | 3.675347513604983 | -0.805846 | -18.1081 | 3 | 15 | 10 | 0.77 | - | - | no | Current |
| 420 | 3.9699373391131556 | -0.795492 | -16.2866 | 6 | 17 | 0 | 0.00 | - | - | no | Open |
| 325 | 4.385363427863706 | -0.85659 | -21.0096 | 11 | 17 | 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
-18.108kcal/mol
Ligand efficiency (LE)
-0.6244kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.961
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
391.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.16
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
99.68kcal/mol
Minimised FF energy
64.32kcal/mol
SASA & burial
✓ computed
SASA (unbound)
661.7Ų
Total solvent-accessible surface area of free ligand
BSA total
509.4Ų
Buried surface area upon binding
BSA apolar
414.6Ų
Hydrophobic contacts buried
BSA polar
94.8Ų
Polar contacts buried
Fraction buried
77.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2993.5Ų
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
1533.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)