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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
36.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.47, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
36% of hydrophobic surface appears solvent-exposed (8/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.658 kcal/mol/HA)
✓ Good fit quality (FQ -6.41)
✓ Good H-bonds (3 bonds)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (90%)
✗ Very high strain energy (36.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-20.391
kcal/mol
LE
-0.658
kcal/mol/HA
Fit Quality
-6.41
FQ (Leeson)
HAC
31
heavy atoms
MW
418
Da
LogP
3.00
cLogP
Interaction summary
HB 3
HY 9
PI 1
CLASH 2
⚠ Exposure 36%
Interaction summary
HB 3
HY 9
PI 1
CLASH 2
⚠ Exposure 36%
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
Partial hydrophobic solvent exposure
36% of hydrophobic surface appears solvent-exposed (8/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 22
Buried (contacted) 14
Exposed 8
LogP 3.0
H-bonds 3
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 3.035 | Score | -20.391 |
|---|---|---|---|
| Inter norm | -0.640 | Intra norm | -0.018 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 3 |
| Artifact reason | geometry warning; 15 clashes; 1 protein clash; high strain Δ 36.4 | ||
| Residues |
ASN402
CYS469
GLU466
GLU467
GLY459
HIS461
LEU399
PHE396
PRO398
PRO462
SER464
SER470
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 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 142 | 1.7134112149889114 | -1.03446 | -29.5939 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 108 | 1.832549972618827 | -0.994641 | -28.9981 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 30 | 3.0354158862778213 | -0.639517 | -20.3913 | 3 | 14 | 7 | 0.88 | 0.00 | - | no | Current |
| 143 | 3.036003608320648 | -0.844612 | -23.4937 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 26 | 3.204939574247354 | -0.888832 | -28.2398 | 6 | 19 | 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
-20.391kcal/mol
Ligand efficiency (LE)
-0.6578kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.408
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
418.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.00
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
36.42kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-144.91kcal/mol
Minimised FF energy
-181.33kcal/mol
SASA & burial
✓ computed
SASA (unbound)
724.6Ų
Total solvent-accessible surface area of free ligand
BSA total
452.1Ų
Buried surface area upon binding
BSA apolar
407.2Ų
Hydrophobic contacts buried
BSA polar
44.9Ų
Polar contacts buried
Fraction buried
62.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3219.1Ų
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
1479.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)