Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
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
48.1 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 1.00, Jaccard 0.57, H-bond role recall 1.00
Reason: strain 48.1 kcal/mol
strain ΔE 48.1 kcal/mol
4 protein-contact clashes
4 intramolecular clashes
68% of hydrophobic surface is solvent-exposed (27/40 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Good LE (-0.328 kcal/mol/HA)
✓ Good fit quality (FQ -3.68)
✓ Strong H-bond network (7 bonds)
✓ Good burial (48% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Extreme strain energy (48.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (19)
Score
-18.060
kcal/mol
LE
-0.328
kcal/mol/HA
Fit Quality
-3.68
FQ (Leeson)
HAC
55
heavy atoms
MW
809
Da
LogP
7.38
cLogP
Interaction summary
HB 7
HY 20
PI 1
CLASH 4
⚠ Exposure 67%
Interaction summary
HB 7
HY 20
PI 1
CLASH 4
⚠ Exposure 67%
Solvent-exposed hydrophobic surface — desolvation penalty likely
68% of hydrophobic surface is solvent-exposed (27/40 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 40
Buried (contacted) 13
Exposed 27
LogP 7.38
H-bonds 7
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 6.302 | Score | -18.060 |
|---|---|---|---|
| Inter norm | -0.405 | Intra norm | 0.076 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 7 |
| Artifact reason | geometry warning; 19 clashes; 3 protein clashes; high strain Δ 44.9 | ||
| Residues |
ASN402
CYS469
GLU466
GLU467
GLY459
HIS461
LEU399
LYS407
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 | 0.57 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 45 | 3.74401282107407 | -0.439367 | -18.1354 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 52 | 4.0274688575957995 | -0.411645 | -19.2807 | 3 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 54 | 4.379236070520798 | -0.505874 | -16.948 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 52 | 6.302001767606716 | -0.404816 | -18.0604 | 7 | 14 | 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
-18.060kcal/mol
Ligand efficiency (LE)
-0.3284kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.678
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
55HA
Physicochemical properties
Molecular weight
809.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
7.38
Lipinski: ≤ 5
Rotatable bonds
16
Conformational strain (MMFF94s)
Strain energy (ΔE)
48.13kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
6.98kcal/mol
Minimised FF energy
-41.15kcal/mol
SASA & burial
✓ computed
SASA (unbound)
1150.4Ų
Total solvent-accessible surface area of free ligand
BSA total
557.3Ų
Buried surface area upon binding
BSA apolar
450.1Ų
Hydrophobic contacts buried
BSA polar
107.2Ų
Polar contacts buried
Fraction buried
48.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3401.3Ų
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
1606.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)