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
26.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.56, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.724 kcal/mol/HA)
✓ Good fit quality (FQ -6.67)
✓ Strong H-bond network (6 bonds)
✓ Good burial (47% SASA buried)
✓ Lipophilic contacts well-matched (90%)
✗ High strain energy (26.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-18.815
kcal/mol
LE
-0.724
kcal/mol/HA
Fit Quality
-6.67
FQ (Leeson)
HAC
26
heavy atoms
MW
362
Da
LogP
5.19
cLogP
Interaction summary
HB 6
HY 15
PI 1
CLASH 2
Interaction summary
HB 6
HY 15
PI 1
CLASH 2
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 | 5.019 | Score | -18.815 |
|---|---|---|---|
| Inter norm | -0.730 | Intra norm | 0.006 |
| Top1000 | no | Excluded | no |
| Contacts | 6 | H-bonds | 6 |
| Artifact reason | geometry warning; 14 clashes; 3 protein clashes; moderate strain Δ 26.8 | ||
| Residues |
ASN402
LEU399
LYS407
PHE396
PRO398
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 | 5 | Native recall | 0.62 |
| Jaccard | 0.56 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 660 | 1.809275051757592 | -1.26339 | -31.3028 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 650 | 2.7376015591993794 | -0.900122 | -22.8247 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 650 | 2.768098212242029 | -1.23361 | -28.2306 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 656 | 5.018600851908217 | -0.730113 | -18.8151 | 6 | 6 | 5 | 0.62 | 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
-18.815kcal/mol
Ligand efficiency (LE)
-0.7237kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.667
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
361.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.19
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.85kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
88.47kcal/mol
Minimised FF energy
61.62kcal/mol
SASA & burial
✓ computed
SASA (unbound)
594.5Ų
Total solvent-accessible surface area of free ligand
BSA total
280.5Ų
Buried surface area upon binding
BSA apolar
252.4Ų
Hydrophobic contacts buried
BSA polar
28.1Ų
Polar contacts buried
Fraction buried
47.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3067.2Ų
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
1548.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)