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 0.77, 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 (-0.721 kcal/mol/HA)
✓ Good fit quality (FQ -7.09)
✓ Good H-bonds (4 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ High strain energy (23.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-23.061
kcal/mol
LE
-0.721
kcal/mol/HA
Fit Quality
-7.09
FQ (Leeson)
HAC
32
heavy atoms
MW
483
Da
LogP
4.98
cLogP
Interaction summary
HB 4
HY 24
PI 1
CLASH 5
Interaction summary
HB 4
HY 24
PI 1
CLASH 5
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 | 3.421 | Score | -23.061 |
|---|---|---|---|
| Inter norm | -0.760 | Intra norm | 0.040 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 4 |
| Artifact reason | geometry warning; 14 clashes; 1 protein clash; moderate strain Δ 23.8 | ||
| Residues |
ALA209
ALA67
ALA90
ASN208
GLY214
GLY215
GLY66
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 | 10 | Native recall | 0.77 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 91 | 1.51326537791791 | -0.999212 | -33.5504 | 11 | 10 | 0 | 0.00 | - | - | no | Open |
| 101 | 2.4397926028027057 | -0.746353 | -24.047 | 2 | 13 | 0 | 0.00 | - | - | no | Open |
| 82 | 3.4205284963813716 | -0.760303 | -23.0608 | 4 | 16 | 10 | 0.77 | - | - | no | Current |
| 61 | 4.8097081665091315 | -0.777386 | -23.7652 | 9 | 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
-23.061kcal/mol
Ligand efficiency (LE)
-0.7207kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.087
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
483.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.98
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
60.60kcal/mol
Minimised FF energy
36.84kcal/mol
SASA & burial
✓ computed
SASA (unbound)
715.0Ų
Total solvent-accessible surface area of free ligand
BSA total
544.0Ų
Buried surface area upon binding
BSA apolar
460.9Ų
Hydrophobic contacts buried
BSA polar
83.2Ų
Polar contacts buried
Fraction buried
76.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3034.6Ų
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
1567.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)