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
20.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.62, Jaccard 0.53
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.646 kcal/mol/HA)
✓ Good fit quality (FQ -6.41)
✓ Good H-bonds (3 bonds)
✓ Good burial (64% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ High strain energy (20.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-21.309
kcal/mol
LE
-0.646
kcal/mol/HA
Fit Quality
-6.41
FQ (Leeson)
HAC
33
heavy atoms
MW
587
Da
LogP
6.59
cLogP
Interaction summary
HB 3
HY 24
PI 3
CLASH 3
Interaction summary
HB 3
HY 24
PI 3
CLASH 3
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 | 2.313 | Score | -21.309 |
|---|---|---|---|
| Inter norm | -0.654 | Intra norm | 0.008 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 3 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash; moderate strain Δ 20.3 | ||
| Residues |
GLU18
ILE106
ILE339
LEU17
MET113
SER109
SER14
THR335
TRP21
TYR110
| ||
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 | 8 | Native recall | 0.62 |
| Jaccard | 0.53 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 675 | 0.7365778015741843 | -0.722297 | -22.475 | 0 | 16 | 0 | 0.00 | - | - | no | Open |
| 675 | 0.9222024432790271 | -0.780298 | -20.7138 | 1 | 13 | 0 | 0.00 | - | - | no | Open |
| 675 | 1.3318990393087835 | -0.784455 | -23.5259 | 2 | 21 | 0 | 0.00 | - | - | no | Open |
| 673 | 1.8257988947562371 | -0.780003 | -25.6147 | 1 | 19 | 0 | 0.00 | - | - | no | Open |
| 677 | 2.185754577570499 | -0.707577 | -22.2139 | 3 | 17 | 0 | 0.00 | - | - | no | Open |
| 679 | 2.313050101027019 | -0.653709 | -21.3095 | 3 | 10 | 8 | 0.62 | - | - | no | Current |
| 673 | 3.0051206271132003 | -0.799552 | -28.209 | 3 | 14 | 0 | 0.00 | - | - | no | Open |
| 674 | 3.2471955707314253 | -0.731831 | -19.575 | 7 | 14 | 0 | 0.00 | - | - | no | Open |
| 668 | 3.304781108763105 | -0.829561 | -25.784 | 7 | 18 | 0 | 0.00 | - | - | no | Open |
| 671 | 3.426665874948449 | -0.751822 | -23.221 | 6 | 16 | 0 | 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
-21.309kcal/mol
Ligand efficiency (LE)
-0.6457kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.407
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
587.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.59
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.29kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-3.69kcal/mol
Minimised FF energy
-23.98kcal/mol
SASA & burial
✓ computed
SASA (unbound)
730.1Ų
Total solvent-accessible surface area of free ligand
BSA total
466.9Ų
Buried surface area upon binding
BSA apolar
397.0Ų
Hydrophobic contacts buried
BSA polar
69.9Ų
Polar contacts buried
Fraction buried
64.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3148.7Ų
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
1573.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)