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 mixed
SASA done
Strain ΔE
11.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.54, Jaccard 0.54
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.799 kcal/mol/HA)
✓ Good fit quality (FQ -7.27)
✓ Good H-bonds (4 bonds)
✓ Good burial (64% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Moderate strain (11.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-19.981
kcal/mol
LE
-0.799
kcal/mol/HA
Fit Quality
-7.27
FQ (Leeson)
HAC
25
heavy atoms
MW
344
Da
LogP
2.08
cLogP
Interaction summary
HB 4
HY 21
PI 2
CLASH 2
Interaction summary
HB 4
HY 21
PI 2
CLASH 2
| Final rank | 1.935 | Score | -19.981 |
|---|---|---|---|
| Inter norm | -0.836 | Intra norm | 0.037 |
| Top1000 | no | Excluded | no |
| Contacts | 7 | H-bonds | 4 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash | ||
| Residues |
GLU18
ILE106
LEU17
MET113
SER109
TRP21
TYR110
| ||
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
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 | 7 | Native recall | 0.54 |
| Jaccard | 0.54 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 86 | 0.2818935574711993 | -1.36988 | -33.4963 | 9 | 15 | 0 | 0.00 | - | - | no | Open |
| 74 | 0.8008377470094211 | -1.4479 | -35.08 | 9 | 16 | 0 | 0.00 | - | - | no | Open |
| 86 | 1.0357506165953647 | -0.942392 | -21.3933 | 9 | 13 | 0 | 0.00 | - | - | no | Open |
| 68 | 1.934786202958034 | -0.836158 | -19.9807 | 4 | 7 | 7 | 0.54 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.981kcal/mol
Ligand efficiency (LE)
-0.7992kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.266
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
344.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.08
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
11.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
74.52kcal/mol
Minimised FF energy
63.49kcal/mol
SASA & burial
✓ computed
SASA (unbound)
537.4Ų
Total solvent-accessible surface area of free ligand
BSA total
344.6Ų
Buried surface area upon binding
BSA apolar
239.6Ų
Hydrophobic contacts buried
BSA polar
105.0Ų
Polar contacts buried
Fraction buried
64.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2996.5Ų
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
1460.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)