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
23.8 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.69, Jaccard 0.53
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.626 kcal/mol/HA)
✓ Good fit quality (FQ -6.04)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (66% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ High strain energy (23.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-18.777
kcal/mol
LE
-0.626
kcal/mol/HA
Fit Quality
-6.04
FQ (Leeson)
HAC
30
heavy atoms
MW
409
Da
LogP
3.80
cLogP
Interaction summary
HB 7
HY 15
PI 0
CLASH 5
Interaction summary
HB 7
HY 15
PI 0
CLASH 5
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 3.170 | Score | -18.777 |
|---|---|---|---|
| Inter norm | -0.783 | Intra norm | 0.157 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 7 |
| Artifact reason | geometry warning; 13 clashes; 1 protein clash; moderate strain Δ 23.8 | ||
| Residues |
ALA90
ARG74
ASN245
ASP71
GLY214
GLY215
LEU73
LYS211
LYS89
MET70
PRO212
PRO213
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 | 9 | Native recall | 0.69 |
| Jaccard | 0.53 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 337 | 1.894088803071696 | -0.894578 | -20.0103 | 6 | 19 | 0 | 0.00 | - | - | no | Open |
| 238 | 2.796868091957932 | -1.03812 | -28.1541 | 16 | 17 | 0 | 0.00 | - | - | no | Open |
| 390 | 3.170255678907523 | -0.782884 | -18.7773 | 7 | 13 | 9 | 0.69 | - | - | no | Current |
| 263 | 3.4365558718772338 | -0.856627 | -17.9044 | 6 | 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
-18.777kcal/mol
Ligand efficiency (LE)
-0.6259kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.038
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
409.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.80
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
33.48kcal/mol
Minimised FF energy
9.65kcal/mol
SASA & burial
✓ computed
SASA (unbound)
687.2Ų
Total solvent-accessible surface area of free ligand
BSA total
456.2Ų
Buried surface area upon binding
BSA apolar
382.0Ų
Hydrophobic contacts buried
BSA polar
74.2Ų
Polar contacts buried
Fraction buried
66.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3009.4Ų
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
1547.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)