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
7.6 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.69, Jaccard 0.53
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.
✓ Low conformational strain (7.6 kcal/mol)
✓ Excellent LE (-0.938 kcal/mol/HA)
✓ Good fit quality (FQ -8.28)
✓ Good H-bonds (5 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (97%)
✗ Geometry warnings
✗ Protein-contact clashes (7)
✗ Internal clashes (6)
Score
-21.570
kcal/mol
LE
-0.938
kcal/mol/HA
Fit Quality
-8.28
FQ (Leeson)
HAC
23
heavy atoms
MW
345
Da
LogP
4.33
cLogP
Interaction summary
HB 5
HY 24
PI 0
CLASH 4
Interaction summary
HB 5
HY 24
PI 0
CLASH 4
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 | 0.825 | Score | -21.570 |
|---|---|---|---|
| Inter norm | -1.050 | Intra norm | 0.112 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 5 |
| Artifact reason | geometry warning; 6 clashes; 7 protein contact clashes | ||
| Residues |
ALA209
ALA90
ARG74
ASN208
LEU73
LYS211
LYS89
MET70
PRO212
PRO213
TYR210
TYR69
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 673 | -0.2870957527735501 | -1.47119 | -32.8162 | 5 | 13 | 0 | 0.00 | - | - | no | Open |
| 662 | 0.692809738121724 | -1.43211 | -31.3557 | 4 | 15 | 0 | 0.00 | - | - | no | Open |
| 666 | 0.8249783486502428 | -1.05017 | -21.57 | 5 | 13 | 9 | 0.69 | - | - | no | Current |
| 658 | 1.2691902380682223 | -1.11054 | -25.1576 | 3 | 16 | 0 | 0.00 | - | - | no | Open |
| 664 | 2.3219346743576095 | -0.948762 | -20.4673 | 6 | 14 | 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
-21.570kcal/mol
Ligand efficiency (LE)
-0.9378kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.277
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
345.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.33
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
7.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
61.40kcal/mol
Minimised FF energy
53.78kcal/mol
SASA & burial
✓ computed
SASA (unbound)
560.5Ų
Total solvent-accessible surface area of free ligand
BSA total
449.2Ų
Buried surface area upon binding
BSA apolar
437.1Ų
Hydrophobic contacts buried
BSA polar
12.1Ų
Polar contacts buried
Fraction buried
80.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
97.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3004.8Ų
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
1546.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)