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 medium
Native strong
SASA done
Strain ΔE
31.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.47, H-bond role recall 1.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.567 kcal/mol/HA)
✓ Good fit quality (FQ -5.71)
✓ Strong H-bond network (8 bonds)
✓ Good burial (57% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Very high strain energy (31.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-19.832
kcal/mol
LE
-0.567
kcal/mol/HA
Fit Quality
-5.71
FQ (Leeson)
HAC
35
heavy atoms
MW
472
Da
LogP
4.29
cLogP
Interaction summary
HB 8
HY 21
PI 2
CLASH 2
Interaction summary
HB 8
HY 21
PI 2
CLASH 2
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 | 3.212 | Score | -19.832 |
|---|---|---|---|
| Inter norm | -0.570 | Intra norm | 0.004 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 8 |
| Artifact reason | geometry warning; 11 clashes; 1 protein clash; moderate strain Δ 28.2 | ||
| Residues |
ASN402
GLU466
GLU467
HIS461
LEU399
MET393
MET400
PHE396
PRO398
PRO462
SER394
SER395
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 | 7 | Native recall | 0.88 |
| Jaccard | 0.47 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 454 | 1.0192895051419053 | -0.741241 | -21.3513 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 390 | 1.5052202304832685 | -0.955819 | -24.3858 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 440 | 2.74160670505527 | -0.6624 | -22.2468 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 422 | 2.771361240009014 | -0.81133 | -22.6994 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 470 | 2.9114764992761053 | -0.725292 | -24.2896 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 401 | 3.2119656626153703 | -0.570175 | -19.8317 | 8 | 14 | 7 | 0.88 | 1.00 | - | no | Current |
| 467 | 3.3645717008842215 | -0.793299 | -24.0163 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 341 | 4.94938367910771 | -0.802078 | -26.3534 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 374 | 5.096813064147079 | -0.883803 | -25.7507 | 11 | 22 | 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
-19.832kcal/mol
Ligand efficiency (LE)
-0.5666kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.715
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
471.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.29
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
130.98kcal/mol
Minimised FF energy
99.34kcal/mol
SASA & burial
✓ computed
SASA (unbound)
741.9Ų
Total solvent-accessible surface area of free ligand
BSA total
419.8Ų
Buried surface area upon binding
BSA apolar
330.9Ų
Hydrophobic contacts buried
BSA polar
89.0Ų
Polar contacts buried
Fraction buried
56.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3168.3Ų
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
1501.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)