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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
46.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.62, Jaccard 0.47
Reason: strain 46.6 kcal/mol
strain ΔE 46.6 kcal/mol
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.803 kcal/mol/HA)
✓ Good fit quality (FQ -7.82)
✓ Strong H-bond network (10 bonds)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Extreme strain energy (46.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-24.890
kcal/mol
LE
-0.803
kcal/mol/HA
Fit Quality
-7.82
FQ (Leeson)
HAC
31
heavy atoms
MW
434
Da
LogP
-0.43
cLogP
Interaction summary
HB 10
HY 13
PI 0
CLASH 3
Interaction summary
HB 10
HY 13
PI 0
CLASH 3
| Final rank | 5.810 | Score | -24.890 |
|---|---|---|---|
| Inter norm | -0.801 | Intra norm | -0.002 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 10 |
| Artifact reason | geometry warning; 15 clashes; 3 protein clashes; high strain Δ 46.6 | ||
| Residues |
ALA244
ARG74
ASN245
ASP71
GLY214
GLY215
LEU73
LYS211
MET70
PRO212
PRO213
TYR408
| ||
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 | 8 | Native recall | 0.62 |
| Jaccard | 0.47 | 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
No pi · π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 84 | 1.9283747913911469 | -0.937103 | -29.9449 | 8 | 20 | 0 | 0.00 | - | - | no | Open |
| 85 | 1.9638541658565332 | -1.04432 | -33.1247 | 10 | 16 | 0 | 0.00 | - | - | no | Open |
| 82 | 2.7477651806865784 | -0.704502 | -22.1569 | 6 | 9 | 0 | 0.00 | - | - | no | Open |
| 61 | 2.9989557037730235 | -1.02195 | -30.4885 | 6 | 17 | 0 | 0.00 | - | - | no | Open |
| 95 | 3.5606381975773203 | -0.992076 | -29.9451 | 7 | 18 | 0 | 0.00 | - | - | no | Open |
| 87 | 3.609197073864286 | -0.990527 | -28.2491 | 8 | 18 | 0 | 0.00 | - | - | no | Open |
| 50 | 4.410605974812835 | -0.739197 | -19.1231 | 6 | 15 | 0 | 0.00 | - | - | no | Open |
| 56 | 5.214374327704846 | -0.914804 | -22.8988 | 10 | 19 | 0 | 0.00 | - | - | no | Open |
| 46 | 5.301391019846421 | -1.08605 | -29.5892 | 16 | 18 | 0 | 0.00 | - | - | no | Open |
| 67 | 5.810432988084876 | -0.801214 | -24.8901 | 10 | 12 | 8 | 0.62 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.890kcal/mol
Ligand efficiency (LE)
-0.8029kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.822
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
434.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.43
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
46.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
188.52kcal/mol
Minimised FF energy
141.91kcal/mol
SASA & burial
✓ computed
SASA (unbound)
669.2Ų
Total solvent-accessible surface area of free ligand
BSA total
413.2Ų
Buried surface area upon binding
BSA apolar
288.2Ų
Hydrophobic contacts buried
BSA polar
125.0Ų
Polar contacts buried
Fraction buried
61.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2957.3Ų
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
1542.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)