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
38.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.50, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
54% of hydrophobic surface appears solvent-exposed (7/13 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.138 kcal/mol/HA)
✓ Good fit quality (FQ -9.33)
✓ Strong H-bond network (7 bonds)
✓ Good burial (49% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Very high strain energy (38.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-21.621
kcal/mol
LE
-1.138
kcal/mol/HA
Fit Quality
-9.33
FQ (Leeson)
HAC
19
heavy atoms
MW
265
Da
LogP
-0.81
cLogP
Interaction summary
HB 7
HY 3
PI 0
CLASH 2
⚠ Exposure 53%
Interaction summary
HB 7
HY 3
PI 0
CLASH 2
⚠ Exposure 53%
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
Partial hydrophobic solvent exposure
54% of hydrophobic surface appears solvent-exposed (7/13 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 13
Buried (contacted) 6
Exposed 7
LogP -0.81
H-bonds 7
Exposed fragments:
cyclohexyl (3/5 atoms exposed)cyclohexyl (6/6 atoms exposed)
| Final rank | 2.147 | Score | -21.621 |
|---|---|---|---|
| Inter norm | -0.999 | Intra norm | -0.139 |
| Top1000 | no | Excluded | no |
| Contacts | 7 | H-bonds | 7 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash; high strain Δ 38.2 | ||
| Residues |
ASN402
LEU399
LYS407
LYS410
PHE396
PRO398
THR397
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 9IFH | Contacts | 8 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASN402
GLU467
LEU399
PHE396
PRO398
SER394
SER470
THR397
| ||
| Current overlap | 5 | Native recall | 0.62 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
Protein summary
492 residues
| Protein target | T20 | Atoms | 7539 |
|---|---|---|---|
| Residues | 492 | 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:221 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:FAD501
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 219 | -0.2890034272782563 | -1.33092 | -26.072 | 2 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 248 | 2.1468220711761954 | -0.999302 | -21.6209 | 7 | 7 | 5 | 0.62 | 0.00 | - | no | Current |
| 201 | 2.629379648213995 | -1.31314 | -24.7998 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 225 | 3.453819368784842 | -1.23301 | -24.7733 | 8 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 145 | 4.2835367831841324 | -1.26072 | -22.3371 | 9 | 12 | 0 | 0.00 | 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
-21.621kcal/mol
Ligand efficiency (LE)
-1.1379kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.327
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
265.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.81
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.16kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
138.54kcal/mol
Minimised FF energy
100.38kcal/mol
SASA & burial
✓ computed
SASA (unbound)
497.9Ų
Total solvent-accessible surface area of free ligand
BSA total
242.9Ų
Buried surface area upon binding
BSA apolar
199.4Ų
Hydrophobic contacts buried
BSA polar
43.5Ų
Polar contacts buried
Fraction buried
48.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3011.2Ų
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
4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1472.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)