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 mixed
SASA done
Strain ΔE
7.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.46, Jaccard 0.26
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Low conformational strain (7.1 kcal/mol)
✓ Excellent LE (-1.011 kcal/mol/HA)
✓ Good fit quality (FQ -8.78)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-22.250
kcal/mol
LE
-1.011
kcal/mol/HA
Fit Quality
-8.78
FQ (Leeson)
HAC
22
heavy atoms
MW
335
Da
LogP
3.13
cLogP
Interaction summary
HB 8
HY 24
PI 0
CLASH 2
Interaction summary
HB 8
HY 24
PI 0
CLASH 2
| Final rank | 2.071 | Score | -22.250 |
|---|---|---|---|
| Inter norm | -1.020 | Intra norm | 0.008 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 8 |
| Artifact reason | geometry warning; 10 clashes; 1 protein clash | ||
| Residues |
CYS52
CYS57
FAD501
GLU18
GLY13
GLY49
GLY50
ILE339
LEU17
LYS61
PRO336
SER14
THR335
TYR110
VAL53
VAL58
| ||
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 | 6 | Native recall | 0.46 |
| Jaccard | 0.26 | 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
No pi · π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 78 | -0.20912994509114985 | -1.75118 | -36.1308 | 6 | 18 | 0 | 0.00 | - | - | no | Open |
| 84 | 0.5438443585937882 | -1.2573 | -27.98 | 5 | 15 | 0 | 0.00 | - | - | no | Open |
| 80 | 0.6506929664465294 | -1.24509 | -27.1953 | 5 | 16 | 0 | 0.00 | - | - | no | Open |
| 68 | 0.7497043112738141 | -1.73014 | -35.9228 | 6 | 16 | 0 | 0.00 | - | - | no | Open |
| 75 | 1.5541187281168434 | -1.03619 | -21.9615 | 5 | 15 | 0 | 0.00 | - | - | no | Open |
| 77 | 1.9234445748383517 | -1.24712 | -26.67 | 7 | 19 | 0 | 0.00 | - | - | no | Open |
| 60 | 2.0098157272063952 | -1.10131 | -20.5867 | 5 | 15 | 0 | 0.00 | - | - | no | Open |
| 62 | 2.071239823785125 | -1.01983 | -22.2505 | 8 | 16 | 6 | 0.46 | - | - | no | Current |
| 67 | 2.518150442780698 | -1.30567 | -25.2304 | 6 | 21 | 0 | 0.00 | - | - | no | Open |
| 73 | 3.396519251747581 | -0.9275 | -16.5183 | 6 | 12 | 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
-22.250kcal/mol
Ligand efficiency (LE)
-1.0114kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.781
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
335.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.13
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
7.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-7.94kcal/mol
Minimised FF energy
-14.99kcal/mol
SASA & burial
✓ computed
SASA (unbound)
561.5Ų
Total solvent-accessible surface area of free ligand
BSA total
434.2Ų
Buried surface area upon binding
BSA apolar
384.9Ų
Hydrophobic contacts buried
BSA polar
49.3Ų
Polar contacts buried
Fraction buried
77.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3072.8Ų
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
1513.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)