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 high
Native strong
SASA done
Strain ΔE
21.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 1.00, Jaccard 0.80, H-bond role recall 1.00
Reason: no major geometry red flags detected
2 protein-contact clashes
44% of hydrophobic surface appears solvent-exposed (11/25 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 (-0.595 kcal/mol/HA)
✓ Good fit quality (FQ -5.90)
✓ Strong H-bond network (6 bonds)
✓ Good burial (51% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ High strain energy (21.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-19.622
kcal/mol
LE
-0.595
kcal/mol/HA
Fit Quality
-5.90
FQ (Leeson)
HAC
33
heavy atoms
MW
445
Da
LogP
0.49
cLogP
Interaction summary
HB 6
HY 11
PI 1
CLASH 2
⚠ Exposure 44%
Interaction summary
HB 6
HY 11
PI 1
CLASH 2
⚠ Exposure 44%
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
44% of hydrophobic surface appears solvent-exposed (11/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 25
Buried (contacted) 14
Exposed 11
LogP 0.49
H-bonds 6
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (3/5 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 4.559 | Score | -19.622 |
|---|---|---|---|
| Inter norm | -0.566 | Intra norm | -0.029 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 6 |
| Artifact reason | geometry warning; 11 clashes; 3 protein clashes; moderate strain Δ 21.8 | ||
| Residues |
ASN402
GLU466
GLU467
GLY459
LEU399
PHE396
PRO398
SER394
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 | 8 | Native recall | 1.00 |
| Jaccard | 0.80 | RMSD | - |
| HB strict | 2 | Strict recall | 1.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 177 | 0.9335928737155703 | -0.806272 | -23.5274 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 174 | 2.1788249852577826 | -0.965098 | -32.8563 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 139 | 2.871926907728719 | -0.775301 | -24.5546 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 144 | 4.303930565578323 | -0.77024 | -22.4725 | 6 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 180 | 4.559341772558047 | -0.565902 | -19.6221 | 6 | 10 | 8 | 1.00 | 1.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.622kcal/mol
Ligand efficiency (LE)
-0.5946kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.900
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
444.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.49
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.81kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
36.97kcal/mol
Minimised FF energy
15.15kcal/mol
SASA & burial
✓ computed
SASA (unbound)
762.4Ų
Total solvent-accessible surface area of free ligand
BSA total
388.4Ų
Buried surface area upon binding
BSA apolar
313.7Ų
Hydrophobic contacts buried
BSA polar
74.7Ų
Polar contacts buried
Fraction buried
50.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3225.6Ų
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
1515.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)