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 medium
Native strong
SASA done
Strain ΔE
32.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.77, Jaccard 0.56
Reason: no major geometry red flags detected
2 protein-contact clashes
36% of hydrophobic surface appears solvent-exposed (9/25 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 (-0.528 kcal/mol/HA)
✓ Good fit quality (FQ -5.37)
✓ Good H-bonds (5 bonds)
✓ Good burial (63% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Very high strain energy (32.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-19.003
kcal/mol
LE
-0.528
kcal/mol/HA
Fit Quality
-5.37
FQ (Leeson)
HAC
36
heavy atoms
MW
506
Da
LogP
2.56
cLogP
Interaction summary
HB 5
HY 18
PI 2
CLASH 2
⚠ Exposure 36%
Interaction summary
HB 5
HY 18
PI 2
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 (9/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 25
Buried (contacted) 16
Exposed 9
LogP 2.56
H-bonds 5
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 3.383 | Score | -19.003 |
|---|---|---|---|
| Inter norm | -0.574 | Intra norm | 0.047 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 5 |
| Artifact reason | geometry warning; 16 clashes; 1 protein clash; high strain Δ 31.3 | ||
| Residues |
ASP116
CYS52
GLU111
GLU18
GLY112
ILE339
LYS108
MET113
SER109
SER14
THR117
THR335
TRP21
TYR110
VAL53
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6RB5 | Contacts | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASP116
GLU18
GLY112
ILE106
LEU17
MET113
SER109
THR117
THR335
TRP21
TYR110
VAL53
VAL58
| ||
| Current overlap | 10 | Native recall | 0.77 |
| Jaccard | 0.56 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
Protein summary
493 residues
| Protein target | T18 | Atoms | 7550 |
|---|---|---|---|
| Residues | 493 | 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:276; 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 341 | 1.9394069180733753 | -0.90515 | -27.8859 | 7 | 16 | 0 | 0.00 | - | - | no | Open |
| 392 | 2.1746272232538577 | -0.756766 | -14.0764 | 6 | 17 | 0 | 0.00 | - | - | no | Open |
| 324 | 2.4670867339205116 | -0.82953 | -27.8188 | 7 | 20 | 0 | 0.00 | - | - | no | Open |
| 366 | 3.3829700936881166 | -0.574398 | -19.0034 | 5 | 15 | 10 | 0.77 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.003kcal/mol
Ligand efficiency (LE)
-0.5279kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.365
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
506.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.56
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.12kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
182.91kcal/mol
Minimised FF energy
150.78kcal/mol
SASA & burial
✓ computed
SASA (unbound)
831.2Ų
Total solvent-accessible surface area of free ligand
BSA total
522.3Ų
Buried surface area upon binding
BSA apolar
449.4Ų
Hydrophobic contacts buried
BSA polar
72.9Ų
Polar contacts buried
Fraction buried
62.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
86.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3269.6Ų
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
4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1545.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)