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 high
Native strong
SASA done
Strain ΔE
15.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.85, Jaccard 0.58
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.945 kcal/mol/HA)
✓ Good fit quality (FQ -9.46)
✓ Good H-bonds (3 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Moderate strain (15.5 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Many internal clashes (12)
Score
-32.138
kcal/mol
LE
-0.945
kcal/mol/HA
Fit Quality
-9.46
FQ (Leeson)
HAC
34
heavy atoms
MW
473
Da
LogP
5.69
cLogP
Interaction summary
HB 3
HY 22
PI 1
CLASH 1
Interaction summary
HB 3
HY 22
PI 1
CLASH 1
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 | 1.337 | Score | -32.138 |
|---|---|---|---|
| Inter norm | -0.734 | Intra norm | -0.212 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 3 |
| Artifact reason | geometry warning; 12 clashes; 4 protein contact clashes | ||
| Residues |
ALA209
ALA90
ARG74
ASN208
ASN245
ASP71
GLY246
GLY85
LEU73
LYS211
LYS89
MET70
PHE83
PRO212
PRO213
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 | 11 | Native recall | 0.85 |
| Jaccard | 0.58 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 497 | 1.3374870325316341 | -0.733609 | -32.1382 | 3 | 17 | 11 | 0.85 | - | - | no | Current |
| 371 | 2.580957224943118 | -0.821017 | -29.8841 | 7 | 18 | 0 | 0.00 | - | - | no | Open |
| 387 | 2.5947672492208738 | -0.689972 | -28.8765 | 8 | 14 | 0 | 0.00 | - | - | no | Open |
| 471 | 2.866230324382139 | -0.693226 | -32.3179 | 4 | 16 | 0 | 0.00 | - | - | no | Open |
| 375 | 3.2130098613086737 | -0.897815 | -19.9026 | 8 | 19 | 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
-32.138kcal/mol
Ligand efficiency (LE)
-0.9452kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.458
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
472.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.69
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
107.57kcal/mol
Minimised FF energy
92.10kcal/mol
SASA & burial
✓ computed
SASA (unbound)
738.2Ų
Total solvent-accessible surface area of free ligand
BSA total
546.2Ų
Buried surface area upon binding
BSA apolar
450.1Ų
Hydrophobic contacts buried
BSA polar
96.1Ų
Polar contacts buried
Fraction buried
74.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3019.8Ų
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
1599.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)