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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
6.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.55, H-bond role recall 0.00
Reason: no major geometry red flags detected
1 protein-contact clashes
47% of hydrophobic surface appears solvent-exposed (8/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (6.5 kcal/mol)
✓ Excellent LE (-0.754 kcal/mol/HA)
✓ Good fit quality (FQ -6.54)
✓ Good H-bonds (4 bonds)
✓ Good burial (59% SASA buried)
✓ Lipophilic contacts well-matched (95%)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-16.586
kcal/mol
LE
-0.754
kcal/mol/HA
Fit Quality
-6.54
FQ (Leeson)
HAC
22
heavy atoms
MW
314
Da
LogP
2.49
cLogP
Interaction summary
HB 4
HY 14
PI 1
CLASH 1
⚠ Exposure 47%
Interaction summary
HB 4
HY 14
PI 1
CLASH 1
⚠ Exposure 47%
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
47% of hydrophobic surface appears solvent-exposed (8/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 9
Exposed 8
LogP 2.49
H-bonds 4
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 4.046 | Score | -16.586 |
|---|---|---|---|
| Inter norm | -0.879 | Intra norm | 0.125 |
| Top1000 | no | Excluded | no |
| Contacts | 9 | H-bonds | 4 |
| Artifact reason | geometry warning; 8 clashes; 3 protein clashes | ||
| Residues |
ASN402
GLU467
LEU399
LYS407
PHE396
PRO398
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 | 0.55 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 544 | -0.16898207418400796 | -1.34578 | -27.6688 | 1 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 549 | 4.046147766041832 | -0.878836 | -16.5857 | 4 | 9 | 6 | 0.75 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-16.586kcal/mol
Ligand efficiency (LE)
-0.7539kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.545
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
314.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.49
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
6.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
1.10kcal/mol
Minimised FF energy
-5.37kcal/mol
SASA & burial
✓ computed
SASA (unbound)
590.9Ų
Total solvent-accessible surface area of free ligand
BSA total
349.7Ų
Buried surface area upon binding
BSA apolar
333.3Ų
Hydrophobic contacts buried
BSA polar
16.3Ų
Polar contacts buried
Fraction buried
59.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
95.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3068.1Ų
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
1506.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)