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
36.8 kcal/mol
Protein clashes
0
Internal clashes
5
Native overlap
contact recall 0.62, Jaccard 0.36, H-bond role recall 0.00
Reason: no major geometry red flags detected
5 intramolecular clashes
39% of hydrophobic surface appears solvent-exposed (11/28 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 (-0.498 kcal/mol/HA)
✓ Good fit quality (FQ -5.06)
✓ Good H-bonds (4 bonds)
✓ Good burial (52% SASA buried)
✓ Lipophilic contacts well-matched (98%)
✗ Very high strain energy (36.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-17.927
kcal/mol
LE
-0.498
kcal/mol/HA
Fit Quality
-5.06
FQ (Leeson)
HAC
36
heavy atoms
MW
505
Da
LogP
-1.64
cLogP
Interaction summary
HB 4
HY 10
PI 0
CLASH 0
⚠ Exposure 39%
Interaction summary
HB 4
HY 10
PI 0
CLASH 0
⚠ Exposure 39%
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
No clash · clashes detected for this pose.
Partial hydrophobic solvent exposure
39% of hydrophobic surface appears solvent-exposed (11/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 28
Buried (contacted) 17
Exposed 11
LogP -1.64
H-bonds 4
Exposed fragments:
phenyl (10/14 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 1.684 | Score | -17.927 |
|---|---|---|---|
| Inter norm | -0.537 | Intra norm | 0.039 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 4 |
| Artifact reason | geometry warning; 5 clashes; 1 protein clash; high strain Δ 36.7 | ||
| Residues |
ASN402
GLU466
GLU467
HIS461
LEU399
LYS407
PHE396
PRO462
SER464
THR397
THR463
| ||
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 | 0.36 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 462 | -0.2924236749244264 | -0.897491 | -30.3221 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 529 | 0.2266800236437038 | -0.763306 | -24.8595 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 535 | 0.510708423527471 | -0.726438 | -24.7716 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 506 | 0.6125424365817946 | -0.750888 | -22.9192 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 496 | 1.6838300499446746 | -0.537129 | -17.9266 | 4 | 11 | 5 | 0.62 | 0.00 | - | no | Current |
| 524 | 1.9630116217514917 | -0.66271 | -20.2398 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 521 | 2.0654308346565085 | -0.584516 | -20.0515 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 552 | 2.3810170928493584 | -0.702076 | -24.8734 | 6 | 16 | 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
-17.927kcal/mol
Ligand efficiency (LE)
-0.4980kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.061
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
504.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-1.64
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
36.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
140.71kcal/mol
Minimised FF energy
103.95kcal/mol
SASA & burial
✓ computed
SASA (unbound)
814.5Ų
Total solvent-accessible surface area of free ligand
BSA total
421.9Ų
Buried surface area upon binding
BSA apolar
414.4Ų
Hydrophobic contacts buried
BSA polar
7.5Ų
Polar contacts buried
Fraction buried
51.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
98.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3406.8Ų
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
4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1463.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)