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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
21.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.46, H-bond role recall 0.00
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.652 kcal/mol/HA)
✓ Good fit quality (FQ -6.35)
✓ Good H-bonds (5 bonds)
✓ Good burial (58% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ High strain energy (21.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-20.212
kcal/mol
LE
-0.652
kcal/mol/HA
Fit Quality
-6.35
FQ (Leeson)
HAC
31
heavy atoms
MW
458
Da
LogP
4.28
cLogP
Interaction summary
HB 5
HY 20
PI 1
CLASH 1
Interaction summary
HB 5
HY 20
PI 1
CLASH 1
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
| Final rank | 2.137 | Score | -20.212 |
|---|---|---|---|
| Inter norm | -0.666 | Intra norm | 0.014 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 5 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash; moderate strain Δ 21.8 | ||
| Residues |
ASN402
GLU467
LEU399
LYS410
MET400
PHE396
PRO398
SER395
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 | 6 | Native recall | 0.75 |
| Jaccard | 0.46 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 185 | 2.1374948191649445 | -0.665842 | -20.2122 | 5 | 11 | 6 | 0.75 | 0.00 | - | no | Current |
| 142 | 2.7772525615488326 | -0.783142 | -21.378 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 162 | 2.820679519399628 | -0.731697 | -22.2861 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 118 | 4.687977126069968 | -0.927754 | -27.9026 | 10 | 17 | 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
-20.212kcal/mol
Ligand efficiency (LE)
-0.6520kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.352
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
457.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.28
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.78kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-3.70kcal/mol
Minimised FF energy
-25.48kcal/mol
SASA & burial
✓ computed
SASA (unbound)
759.5Ų
Total solvent-accessible surface area of free ligand
BSA total
442.2Ų
Buried surface area upon binding
BSA apolar
361.5Ų
Hydrophobic contacts buried
BSA polar
80.7Ų
Polar contacts buried
Fraction buried
58.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3188.9Ų
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
1505.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)