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
40.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.75, Jaccard 0.35, H-bond role recall 1.00
Reason: no major geometry red flags detected
2 protein-contact clashes
38% of hydrophobic surface appears solvent-exposed (9/24 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 (-0.440 kcal/mol/HA)
✓ Good fit quality (FQ -4.44)
✓ Strong H-bond network (6 bonds)
✓ Good burial (57% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Extreme strain energy (40.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (18)
Score
-15.398
kcal/mol
LE
-0.440
kcal/mol/HA
Fit Quality
-4.44
FQ (Leeson)
HAC
35
heavy atoms
MW
476
Da
LogP
0.67
cLogP
Interaction summary
HB 6
HY 18
PI 1
CLASH 2
⚠ Exposure 37%
Interaction summary
HB 6
HY 18
PI 1
CLASH 2
⚠ Exposure 37%
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
38% of hydrophobic surface appears solvent-exposed (9/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 24
Buried (contacted) 15
Exposed 9
LogP 0.67
H-bonds 6
Exposed fragments:
phenyl (5/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 5.452 | Score | -15.398 |
|---|---|---|---|
| Inter norm | -0.558 | Intra norm | 0.118 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 6 |
| Artifact reason | geometry warning; 18 clashes; 3 protein clashes; high strain Δ 40.9 | ||
| Residues |
ARG472
GLU466
GLU467
LEU399
MET393
MET400
MET471
PHE396
PRO398
SER394
SER395
SER464
SER470
THR463
THR473
| ||
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 | 6 | Native recall | 0.75 |
| Jaccard | 0.35 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 6 | 1.8442758454334953 | -1.1484 | -34.8941 | 9 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 6 | 3.2140927104793953 | -0.844147 | -29.4225 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 4 | 4.098665573912961 | -0.588615 | -21.8858 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 9 | 4.256826637465723 | -0.886547 | -26.2953 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 4 | 5.177059448137301 | -0.83407 | -25.8189 | 8 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 7 | 5.451739153191316 | -0.558397 | -15.3983 | 6 | 15 | 6 | 0.75 | 1.00 | - | no | Current |
| 5 | 5.606622137177629 | -0.887957 | -28.3698 | 11 | 19 | 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
-15.398kcal/mol
Ligand efficiency (LE)
-0.4400kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.438
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
475.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.67
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
40.87kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-36.38kcal/mol
Minimised FF energy
-77.25kcal/mol
SASA & burial
✓ computed
SASA (unbound)
792.8Ų
Total solvent-accessible surface area of free ligand
BSA total
455.9Ų
Buried surface area upon binding
BSA apolar
328.8Ų
Hydrophobic contacts buried
BSA polar
127.2Ų
Polar contacts buried
Fraction buried
57.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3160.7Ų
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
1538.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)