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
12.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.69, Jaccard 0.69
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.931 kcal/mol/HA)
✓ Good fit quality (FQ -8.08)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (66% SASA buried)
✓ Lipophilic contacts well-matched (62%)
✗ Moderate strain (12.3 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Internal clashes (8)
Score
-20.482
kcal/mol
LE
-0.931
kcal/mol/HA
Fit Quality
-8.08
FQ (Leeson)
HAC
22
heavy atoms
MW
302
Da
LogP
1.99
cLogP
Interaction summary
HB 6
HY 21
PI 2
CLASH 1
Interaction summary
HB 6
HY 21
PI 2
CLASH 1
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 | 0.720 | Score | -20.482 |
|---|---|---|---|
| Inter norm | -0.933 | Intra norm | 0.002 |
| Top1000 | no | Excluded | no |
| Contacts | 9 | H-bonds | 6 |
| Artifact reason | geometry warning; 8 clashes; 4 protein contact clashes | ||
| Residues |
ASP116
GLU18
GLY112
LEU17
MET113
SER109
THR117
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 | 9 | Native recall | 0.69 |
| Jaccard | 0.69 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 559 | 0.7198418180090042 | -0.933488 | -20.4818 | 6 | 9 | 9 | 0.69 | - | - | no | Current |
| 525 | 2.4172194168614993 | -1.48041 | -32.0363 | 9 | 18 | 0 | 0.00 | - | - | no | Open |
| 512 | 2.545937422647049 | -1.61802 | -34.0323 | 11 | 17 | 0 | 0.00 | - | - | no | Open |
| 567 | 2.9952729829901434 | -1.24945 | -25.8165 | 9 | 18 | 0 | 0.00 | - | - | no | Open |
| 524 | 3.422947619134114 | -1.36673 | -26.6001 | 13 | 17 | 0 | 0.00 | - | - | no | Open |
| 550 | 3.750956682432338 | -1.21808 | -25.8403 | 6 | 12 | 0 | 0.00 | - | - | no | Open |
| 582 | 4.472569139535506 | -1.15982 | -25.4195 | 9 | 12 | 0 | 0.00 | - | - | no | Open |
| 529 | 4.491059808940537 | -1.52163 | -29.8977 | 11 | 17 | 0 | 0.00 | - | - | no | Open |
| 541 | 5.152210004952779 | -1.44518 | -30.0794 | 11 | 18 | 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
-20.482kcal/mol
Ligand efficiency (LE)
-0.9310kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.083
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
302.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.99
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.28kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
88.02kcal/mol
Minimised FF energy
75.74kcal/mol
SASA & burial
✓ computed
SASA (unbound)
493.9Ų
Total solvent-accessible surface area of free ligand
BSA total
328.3Ų
Buried surface area upon binding
BSA apolar
204.3Ų
Hydrophobic contacts buried
BSA polar
124.0Ų
Polar contacts buried
Fraction buried
66.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
62.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2915.5Ų
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
1470.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)