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
55.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 1.00, Jaccard 0.80, H-bond role recall 1.00
Reason: strain 55.3 kcal/mol
strain ΔE 55.3 kcal/mol
1 protein-contact clashes
54% of hydrophobic surface appears solvent-exposed (14/26 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.
✓ Good LE (-0.378 kcal/mol/HA)
✓ Good fit quality (FQ -3.81)
✓ Strong H-bond network (6 bonds)
✓ Good burial (46% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Extreme strain energy (55.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-13.238
kcal/mol
LE
-0.378
kcal/mol/HA
Fit Quality
-3.81
FQ (Leeson)
HAC
35
heavy atoms
MW
503
Da
LogP
2.03
cLogP
Interaction summary
HB 6
HY 12
PI 1
CLASH 1
⚠ Exposure 53%
Interaction summary
HB 6
HY 12
PI 1
CLASH 1
⚠ Exposure 53%
Partial hydrophobic solvent exposure
54% of hydrophobic surface appears solvent-exposed (14/26 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 26
Buried (contacted) 12
Exposed 14
LogP 2.03
H-bonds 6
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 4.857 | Score | -13.238 |
|---|---|---|---|
| Inter norm | -0.590 | Intra norm | 0.212 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 6 |
| Artifact reason | geometry warning; 16 clashes; 3 protein clashes; high strain Δ 55.3 | ||
| Residues |
ASN402
GLU466
GLU467
LEU399
PHE396
PRO398
SER394
SER395
SER470
THR397
| ||
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
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 | 8 | Native recall | 1.00 |
| Jaccard | 0.80 | RMSD | - |
| HB strict | 2 | Strict recall | 1.00 |
| HB same residue+role | 1 | HB role recall | 1.00 |
| HB same residue | 1 | HB residue recall | 1.00 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 280 | 3.072939621275057 | -0.652326 | -26.0627 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 262 | 4.357606610843862 | -0.719793 | -20.2471 | 13 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 352 | 4.377816770020476 | -0.688479 | -23.3913 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 299 | 4.8568129299279565 | -0.590291 | -13.2375 | 6 | 10 | 8 | 1.00 | 1.00 | - | no | Current |
| 221 | 5.152576031245613 | -0.894038 | -31.6518 | 8 | 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
-13.238kcal/mol
Ligand efficiency (LE)
-0.3782kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.815
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
502.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.03
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
55.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
113.22kcal/mol
Minimised FF energy
57.89kcal/mol
SASA & burial
✓ computed
SASA (unbound)
802.2Ų
Total solvent-accessible surface area of free ligand
BSA total
371.4Ų
Buried surface area upon binding
BSA apolar
267.3Ų
Hydrophobic contacts buried
BSA polar
104.2Ų
Polar contacts buried
Fraction buried
46.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3246.5Ų
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
1499.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)