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
44.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 1.00, Jaccard 0.73, H-bond role recall 1.00
Reason: strain 44.8 kcal/mol
strain ΔE 44.8 kcal/mol
1 protein-contact clashes
43% of hydrophobic surface appears solvent-exposed (13/30 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 (-0.492 kcal/mol/HA)
✓ Good fit quality (FQ -5.11)
✓ Strong H-bond network (8 bonds)
✓ Good burial (50% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Extreme strain energy (44.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-19.204
kcal/mol
LE
-0.492
kcal/mol/HA
Fit Quality
-5.11
FQ (Leeson)
HAC
39
heavy atoms
MW
532
Da
LogP
3.79
cLogP
Interaction summary
HB 8
HY 13
PI 2
CLASH 1
⚠ Exposure 43%
Interaction summary
HB 8
HY 13
PI 2
CLASH 1
⚠ Exposure 43%
Partial hydrophobic solvent exposure
43% of hydrophobic surface appears solvent-exposed (13/30 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 30
Buried (contacted) 17
Exposed 13
LogP 3.79
H-bonds 8
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (2/5 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 5.651 | Score | -19.204 |
|---|---|---|---|
| Inter norm | -0.575 | Intra norm | 0.083 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 8 |
| Artifact reason | geometry warning; 15 clashes; 4 protein clashes; high strain Δ 44.8 | ||
| Residues |
ASN402
GLU466
GLU467
HIS461
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 | 0.73 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 248 | 2.048813667607478 | -0.614374 | -9.73646 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 215 | 2.4577901811693255 | -0.623182 | -16.3266 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 206 | 2.7577601342615625 | -0.827558 | -20.9914 | 7 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 254 | 3.256604468418019 | -0.663495 | -10.5295 | 5 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 275 | 4.777589574511002 | -0.772139 | -25.8389 | 10 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 273 | 5.650594001336309 | -0.575422 | -19.2044 | 8 | 11 | 8 | 1.00 | 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
-19.204kcal/mol
Ligand efficiency (LE)
-0.4924kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.110
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
39HA
Physicochemical properties
Molecular weight
531.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.79
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
44.84kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
131.26kcal/mol
Minimised FF energy
86.42kcal/mol
SASA & burial
✓ computed
SASA (unbound)
774.4Ų
Total solvent-accessible surface area of free ligand
BSA total
386.0Ų
Buried surface area upon binding
BSA apolar
301.6Ų
Hydrophobic contacts buried
BSA polar
84.4Ų
Polar contacts buried
Fraction buried
49.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3204.6Ų
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
1519.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)