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
Likely artefact or unreliable pose
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
24.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.50, H-bond role recall 1.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.549 kcal/mol/HA)
✓ Good fit quality (FQ -5.62)
✓ Good H-bonds (5 bonds)
✓ Good burial (52% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ High strain energy (24.7 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (6)
✗ Many internal clashes (15)
Score
-20.330
kcal/mol
LE
-0.549
kcal/mol/HA
Fit Quality
-5.62
FQ (Leeson)
HAC
37
heavy atoms
MW
517
Da
LogP
4.43
cLogP
Interaction summary
HB 5
HY 17
PI 2
CLASH 2
Interaction summary
HB 5
HY 17
PI 2
CLASH 2
| Final rank | 2.078 | Score | -20.330 |
|---|---|---|---|
| Inter norm | -0.572 | Intra norm | 0.022 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 5 |
| Artifact reason | geometry warning; 15 clashes; 6 protein contact clashes; moderate strain Δ 24.7 | ||
| Residues |
ASN402
GLU466
GLU467
LEU399
MET393
MET400
PHE396
PRO398
PRO462
SER394
SER395
THR397
THR463
| ||
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 | 7 | Native recall | 0.88 |
| Jaccard | 0.50 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 673 | 2.078483895529641 | -0.571527 | -20.3299 | 5 | 13 | 7 | 0.88 | 1.00 | - | no | Current |
| 670 | 2.7261617430122502 | -0.947385 | -30.4389 | 4 | 25 | 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
-20.330kcal/mol
Ligand efficiency (LE)
-0.5495kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.625
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
516.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.43
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.65kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
50.96kcal/mol
Minimised FF energy
26.31kcal/mol
SASA & burial
✓ computed
SASA (unbound)
823.2Ų
Total solvent-accessible surface area of free ligand
BSA total
425.5Ų
Buried surface area upon binding
BSA apolar
358.7Ų
Hydrophobic contacts buried
BSA polar
66.8Ų
Polar contacts buried
Fraction buried
51.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3255.4Ų
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
1533.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)