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
49.2 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.88, Jaccard 0.50, H-bond role recall 0.00
Reason: strain 49.2 kcal/mol
strain ΔE 49.2 kcal/mol
5 protein-contact clashes
5 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.478 kcal/mol/HA)
✓ Good fit quality (FQ -5.08)
✓ Good burial (54% SASA buried)
✓ Lipophilic contacts well-matched (96%)
✗ Extreme strain energy (49.2 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (6)
✗ Many internal clashes (21)
Score
-20.544
kcal/mol
LE
-0.478
kcal/mol/HA
Fit Quality
-5.08
FQ (Leeson)
HAC
43
heavy atoms
MW
654
Da
LogP
7.33
cLogP
Interaction summary
HB 1
HY 14
PI 2
CLASH 5
Interaction summary
HB 1
HY 14
PI 2
CLASH 5
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 | 2.858 | Score | -20.544 |
|---|---|---|---|
| Inter norm | -0.480 | Intra norm | 0.003 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 1 |
| Artifact reason | geometry warning; 21 clashes; 6 protein contact clashes; high strain Δ 48.9 | ||
| Residues |
ASN402
GLU466
GLU467
GLY459
HIS461
LEU399
LYS407
LYS410
PHE396
PRO398
SER395
SER470
THR397
| ||
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 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 17 | 2.8583517843052655 | -0.480348 | -20.5442 | 1 | 13 | 7 | 0.88 | 0.00 | - | no | Current |
| 26 | 3.260679601160878 | -0.760166 | -29.0923 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 8 | 3.4006655898136917 | -0.530249 | -19.8543 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 23 | 4.018701128647769 | -0.785627 | -29.6147 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 12 | 4.471718256580671 | -0.517338 | -17.9095 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 20 | 5.128692228900877 | -0.670586 | -22.7951 | 6 | 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
-20.544kcal/mol
Ligand efficiency (LE)
-0.4778kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.078
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
43HA
Physicochemical properties
Molecular weight
654.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
7.33
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
49.16kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
293.13kcal/mol
Minimised FF energy
243.97kcal/mol
SASA & burial
✓ computed
SASA (unbound)
957.9Ų
Total solvent-accessible surface area of free ligand
BSA total
516.3Ų
Buried surface area upon binding
BSA apolar
496.6Ų
Hydrophobic contacts buried
BSA polar
19.8Ų
Polar contacts buried
Fraction buried
53.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
96.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3373.8Ų
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
1617.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)