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
67.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.50, H-bond role recall 0.00
Reason: strain 67.3 kcal/mol
strain ΔE 67.3 kcal/mol
1 protein-contact clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.471 kcal/mol/HA)
✓ Good fit quality (FQ -4.71)
✓ Good H-bonds (4 bonds)
✓ Good burial (57% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Extreme strain energy (67.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-16.013
kcal/mol
LE
-0.471
kcal/mol/HA
Fit Quality
-4.71
FQ (Leeson)
HAC
34
heavy atoms
MW
481
Da
LogP
4.53
cLogP
Interaction summary
HB 4
HY 19
PI 2
CLASH 1
Interaction summary
HB 4
HY 19
PI 2
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 | 4.120 | Score | -16.013 |
|---|---|---|---|
| Inter norm | -0.563 | Intra norm | 0.092 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 4 |
| Artifact reason | geometry warning; 14 clashes; 2 protein clashes; high strain Δ 67.3 | ||
| Residues |
ASN402
GLU467
HIS461
LEU399
PHE396
PRO398
PRO462
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 | 0.50 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 599 | 1.4196484638659015 | -0.939239 | -28.1464 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 613 | 2.5558035847312244 | -0.816482 | -25.0979 | 11 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 621 | 4.119991031040839 | -0.563275 | -16.0134 | 4 | 10 | 6 | 0.75 | 0.00 | - | no | Current |
| 623 | 5.234710793187857 | -0.741743 | -19.4364 | 15 | 14 | 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
-16.013kcal/mol
Ligand efficiency (LE)
-0.4710kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.713
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
480.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.53
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
67.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
88.89kcal/mol
Minimised FF energy
21.62kcal/mol
SASA & burial
✓ computed
SASA (unbound)
712.7Ų
Total solvent-accessible surface area of free ligand
BSA total
405.8Ų
Buried surface area upon binding
BSA apolar
340.4Ų
Hydrophobic contacts buried
BSA polar
65.4Ų
Polar contacts buried
Fraction buried
56.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3169.1Ų
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
1483.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)