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
51.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.92, Jaccard 0.57
Reason: strain 51.1 kcal/mol
strain ΔE 51.1 kcal/mol
3 protein-contact clashes
3 intramolecular clashes
45% of hydrophobic surface appears solvent-exposed (15/33 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.541 kcal/mol/HA)
✓ Good fit quality (FQ -5.87)
✓ Good H-bonds (5 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ Extreme strain energy (51.1 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (5)
✗ Many internal clashes (21)
Score
-25.429
kcal/mol
LE
-0.541
kcal/mol/HA
Fit Quality
-5.87
FQ (Leeson)
HAC
47
heavy atoms
MW
654
Da
LogP
2.43
cLogP
Interaction summary
HB 5
HY 24
PI 1
CLASH 3
⚠ Exposure 45%
Interaction summary
HB 5
HY 24
PI 1
CLASH 3
⚠ Exposure 45%
Partial hydrophobic solvent exposure
45% of hydrophobic surface appears solvent-exposed (15/33 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 33
Buried (contacted) 18
Exposed 15
LogP 2.43
H-bonds 5
Exposed fragments:
phenyl (3/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (3/3 atoms exposed)phenyl (2/5 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 2.582 | Score | -25.429 |
|---|---|---|---|
| Inter norm | -0.541 | Intra norm | -0.001 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 5 |
| Artifact reason | geometry warning; 21 clashes; 5 protein contact clashes; high strain Δ 50.4 | ||
| Residues |
ALA209
ALA77
ALA90
ARG74
GLU82
GLY214
GLY215
GLY246
GLY85
LEU73
LYS211
LYS216
LYS89
MET70
PHE83
PRO212
PRO213
SER76
TRP81
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 | 12 | Native recall | 0.92 |
| Jaccard | 0.57 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 35 | 2.581967912586679 | -0.54051 | -25.4294 | 5 | 20 | 12 | 0.92 | - | - | no | Current |
| 49 | 2.803335358551436 | -0.487333 | -17.8535 | 4 | 18 | 0 | 0.00 | - | - | no | Open |
| 52 | 4.01054204587515 | -0.581367 | -25.7408 | 2 | 20 | 0 | 0.00 | - | - | no | Open |
| 27 | 4.531336674023697 | -0.510317 | -18.8961 | 4 | 15 | 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
-25.429kcal/mol
Ligand efficiency (LE)
-0.5411kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.867
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
47HA
Physicochemical properties
Molecular weight
653.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.43
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
51.10kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
242.39kcal/mol
Minimised FF energy
191.29kcal/mol
SASA & burial
✓ computed
SASA (unbound)
958.4Ų
Total solvent-accessible surface area of free ligand
BSA total
698.5Ų
Buried surface area upon binding
BSA apolar
595.2Ų
Hydrophobic contacts buried
BSA polar
103.2Ų
Polar contacts buried
Fraction buried
72.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3287.8Ų
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
1569.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)