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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
33.4 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.77, Jaccard 0.50
Reason: 6 internal clashes
6 protein-contact clashes
6 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.701 kcal/mol/HA)
✓ Good fit quality (FQ -6.62)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Very high strain energy (33.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-19.623
kcal/mol
LE
-0.701
kcal/mol/HA
Fit Quality
-6.62
FQ (Leeson)
HAC
28
heavy atoms
MW
400
Da
LogP
1.13
cLogP
Interaction summary
HB 10
HY 24
PI 3
CLASH 6
Interaction summary
HB 10
HY 24
PI 3
CLASH 6
| Final rank | 4.490 | Score | -19.623 |
|---|---|---|---|
| Inter norm | -0.892 | Intra norm | 0.191 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 10 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; high strain Δ 33.4 | ||
| Residues |
CYS52
FAD501
GLU18
GLY13
GLY49
GLY50
ILE106
ILE339
LEU17
MET113
SER109
SER14
THR335
TRP21
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 | 10 | Native recall | 0.77 |
| Jaccard | 0.50 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 77 | 2.876430342267816 | -0.922413 | -22.2431 | 5 | 19 | 0 | 0.00 | - | - | no | Open |
| 114 | 2.883794498530214 | -1.02014 | -26.3795 | 3 | 17 | 0 | 0.00 | - | - | no | Open |
| 101 | 2.9293523248686655 | -0.843323 | -23.4699 | 7 | 17 | 0 | 0.00 | - | - | no | Open |
| 114 | 3.601961305920066 | -1.19695 | -28.055 | 4 | 21 | 0 | 0.00 | - | - | no | Open |
| 85 | 3.6319795394564807 | -0.83297 | -17.4434 | 6 | 19 | 0 | 0.00 | - | - | no | Open |
| 71 | 4.15022742952253 | -1.05998 | -23.809 | 15 | 20 | 0 | 0.00 | - | - | no | Open |
| 71 | 4.421576432535559 | -0.829435 | -18.9188 | 4 | 17 | 0 | 0.00 | - | - | no | Open |
| 89 | 4.489621695148427 | -0.89201 | -19.623 | 10 | 17 | 10 | 0.77 | - | - | no | Current |
| 92 | 4.6462206342733205 | -0.843229 | -22.0498 | 9 | 15 | 0 | 0.00 | - | - | no | Open |
| 64 | 4.727763877486028 | -1.16427 | -28.89 | 10 | 16 | 0 | 0.00 | - | - | no | Open |
| 44 | 6.009884957343629 | -1.02072 | -18.2378 | 15 | 15 | 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
-19.623kcal/mol
Ligand efficiency (LE)
-0.7008kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.616
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
400.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.13
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-93.83kcal/mol
Minimised FF energy
-127.24kcal/mol
SASA & burial
✓ computed
SASA (unbound)
677.4Ų
Total solvent-accessible surface area of free ligand
BSA total
487.7Ų
Buried surface area upon binding
BSA apolar
366.4Ų
Hydrophobic contacts buried
BSA polar
121.3Ų
Polar contacts buried
Fraction buried
72.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3164.3Ų
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
1456.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)