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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
43.0 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.62, Jaccard 0.36, H-bond role recall 0.00
Reason: strain 43.0 kcal/mol
strain ΔE 43.0 kcal/mol
3 protein-contact clashes
3 intramolecular clashes
36% of hydrophobic surface appears solvent-exposed (10/28 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 (-0.481 kcal/mol/HA)
✓ Good fit quality (FQ -4.93)
✓ Good H-bonds (5 bonds)
✓ Good burial (53% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Extreme strain energy (43.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-17.816
kcal/mol
LE
-0.481
kcal/mol/HA
Fit Quality
-4.93
FQ (Leeson)
HAC
37
heavy atoms
MW
526
Da
LogP
6.67
cLogP
Interaction summary
HB 5
HY 16
PI 1
CLASH 3
⚠ Exposure 35%
Interaction summary
HB 5
HY 16
PI 1
CLASH 3
⚠ Exposure 35%
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
36% of hydrophobic surface appears solvent-exposed (10/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 28
Buried (contacted) 18
Exposed 10
LogP 6.67
H-bonds 5
Exposed fragments:
phenyl (2/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 3.405 | Score | -17.816 |
|---|---|---|---|
| Inter norm | -0.545 | Intra norm | 0.063 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 5 |
| Artifact reason | geometry warning; 15 clashes; 1 protein clash; high strain Δ 41.7 | ||
| Residues |
ASN402
HIS461
LEU399
LYS407
MET400
PHE396
PRO398
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 546 | 1.762147411304352 | -0.688299 | -26.4287 | 0 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 557 | 1.889460363131821 | -0.685334 | -23.8587 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 535 | 2.469004843643862 | -0.756544 | -27.8503 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 523 | 3.4046233442825438 | -0.544599 | -17.8162 | 5 | 11 | 5 | 0.62 | 0.00 | - | no | Current |
| 519 | 6.081198947712167 | -0.646973 | -22.4977 | 12 | 13 | 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
-17.816kcal/mol
Ligand efficiency (LE)
-0.4815kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.930
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
525.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.67
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
43.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
75.41kcal/mol
Minimised FF energy
32.41kcal/mol
SASA & burial
✓ computed
SASA (unbound)
839.2Ų
Total solvent-accessible surface area of free ligand
BSA total
443.4Ų
Buried surface area upon binding
BSA apolar
328.9Ų
Hydrophobic contacts buried
BSA polar
114.5Ų
Polar contacts buried
Fraction buried
52.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3181.7Ų
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
1518.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)