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 high
Native mixed
SASA done
Strain ΔE
4.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.54, Jaccard 0.32
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Low conformational strain (4.7 kcal/mol)
✓ Excellent LE (-0.887 kcal/mol/HA)
✓ Good fit quality (FQ -8.17)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (90%)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (12)
Score
-23.051
kcal/mol
LE
-0.887
kcal/mol/HA
Fit Quality
-8.17
FQ (Leeson)
HAC
26
heavy atoms
MW
340
Da
LogP
5.70
cLogP
Interaction summary
HB 1
HY 24
PI 2
CLASH 1
Interaction summary
HB 1
HY 24
PI 2
CLASH 1
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 | 0.846 | Score | -23.051 |
|---|---|---|---|
| Inter norm | -0.904 | Intra norm | 0.017 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 1 |
| Artifact reason | geometry warning; 12 clashes; 2 protein contact clashes | ||
| Residues |
ALA209
ALA67
ALA77
ALA90
ARG74
GLU82
GLY66
GLY85
LEU73
MET70
PHE83
SER76
TRP81
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 | 7 | Native recall | 0.54 |
| Jaccard | 0.32 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 456 | 0.8463456003839415 | -0.903914 | -23.0506 | 1 | 16 | 7 | 0.54 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.051kcal/mol
Ligand efficiency (LE)
-0.8866kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.168
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
340.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.70
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
4.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
61.86kcal/mol
Minimised FF energy
57.13kcal/mol
SASA & burial
✓ computed
SASA (unbound)
624.6Ų
Total solvent-accessible surface area of free ligand
BSA total
489.9Ų
Buried surface area upon binding
BSA apolar
441.2Ų
Hydrophobic contacts buried
BSA polar
48.8Ų
Polar contacts buried
Fraction buried
78.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3020.0Ų
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
1533.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)