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
Reject
SASA cached
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
40.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.50, Jaccard 0.29, H-bond role recall 1.00
Reason: no major geometry red flags detected
2 protein-contact clashes
50% of hydrophobic surface appears solvent-exposed (10/20 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 (-0.572 kcal/mol/HA)
✓ Good fit quality (FQ -5.34)
✓ Strong H-bond network (7 bonds)
✓ Good burial (56% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ Extreme strain energy (40.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-15.452
kcal/mol
LE
-0.572
kcal/mol/HA
Fit Quality
-5.34
FQ (Leeson)
HAC
27
heavy atoms
MW
378
Da
LogP
2.27
cLogP
Interaction summary
HB 7
HY 7
PI 2
CLASH 2
⚠ Exposure 50%
Interaction summary
HB 7
HY 7
PI 2
CLASH 2
⚠ Exposure 50%
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
Partial hydrophobic solvent exposure
50% of hydrophobic surface appears solvent-exposed (10/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20
Buried (contacted) 10
Exposed 10
LogP 2.27
H-bonds 7
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 4.332 | Score | -15.452 |
|---|---|---|---|
| Inter norm | -0.711 | Intra norm | 0.139 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 7 |
| Artifact reason | geometry warning; 7 clashes; 3 protein clashes; high strain Δ 40.6 | ||
| Residues |
GLU466
GLU467
HIS461
MET393
PHE396
SER394
SER395
SER464
SER470
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 | 4 | Native recall | 0.50 |
| Jaccard | 0.29 | RMSD | - |
| HB strict | 1 | Strict recall | 0.50 |
| HB same residue+role | 1 | HB role recall | 1.00 |
| HB same residue | 1 | HB residue recall | 1.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 83 | 0.2926960968942545 | -1.21859 | -25.5241 | 5 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 105 | 0.7752453917590536 | -0.897078 | -15.3685 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 63 | 2.434070692638824 | -1.0614 | -21.37 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 74 | 2.711650149851395 | -1.07125 | -23.2545 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 116 | 4.331959399363628 | -0.71141 | -15.4524 | 7 | 10 | 4 | 0.50 | 1.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-15.452kcal/mol
Ligand efficiency (LE)
-0.5723kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.339
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
378.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.27
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
40.65kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
51.44kcal/mol
Minimised FF energy
10.79kcal/mol
SASA & burial
✓ computed
SASA (unbound)
627.4Ų
Total solvent-accessible surface area of free ligand
BSA total
347.9Ų
Buried surface area upon binding
BSA apolar
308.4Ų
Hydrophobic contacts buried
BSA polar
39.6Ų
Polar contacts buried
Fraction buried
55.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3072.8Ų
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
1513.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)