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
20.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.58, Jaccard 0.33
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 (-1.129 kcal/mol/HA)
✓ Good fit quality (FQ -9.25)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ High strain energy (20.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-21.452
kcal/mol
LE
-1.129
kcal/mol/HA
Fit Quality
-9.25
FQ (Leeson)
HAC
19
heavy atoms
MW
280
Da
LogP
0.02
cLogP
Interaction summary
HB 9
HY 19
PI 1
CLASH 3
Interaction summary
HB 9
HY 19
PI 1
CLASH 3
| Final rank | 3.820 | Score | -21.452 |
|---|---|---|---|
| Inter norm | -1.269 | Intra norm | 0.115 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 9 |
| Artifact reason | geometry warning; 6 clashes; 3 protein clashes; moderate strain Δ 20.4 | ||
| Residues |
ALA209
ALA67
ALA90
ASN208
GLY214
GLY215
GLY66
LEU73
LYS211
LYS89
MET70
PRO212
PRO213
TYR210
TYR69
VAL88
| ||
Protein summary
493 residues
| Protein target | T16 | Atoms | 7551 |
|---|---|---|---|
| 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 | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA90
ARG74
GLY85
LEU73
LYS89
MET70
PHE83
PRO212
PRO213
SER86
SER87
VAL88
| ||
| Current overlap | 7 | Native recall | 0.58 |
| Jaccard | 0.33 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 312 | -0.12698051497752788 | -1.4099 | -25.1999 | 5 | 13 | 0 | 0.00 | - | - | no | Open |
| 409 | 1.5618486583435398 | -1.25392 | -19.5039 | 8 | 16 | 0 | 0.00 | - | - | no | Open |
| 329 | 1.810958723850599 | -1.17778 | -21.5875 | 6 | 14 | 0 | 0.00 | - | - | no | Open |
| 267 | 3.3656450884601203 | -1.63439 | -30.9104 | 5 | 17 | 0 | 0.00 | - | - | no | Open |
| 265 | 3.3810319513898386 | -1.35166 | -24.7621 | 11 | 18 | 0 | 0.00 | - | - | no | Open |
| 341 | 3.5339212025300557 | -1.51737 | -27.3765 | 9 | 15 | 0 | 0.00 | - | - | no | Open |
| 382 | 3.8196564752012465 | -1.26937 | -21.4516 | 9 | 16 | 7 | 0.58 | - | - | no | Current |
| 288 | 4.003072569334565 | -1.34735 | -23.6626 | 10 | 17 | 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
-21.452kcal/mol
Ligand efficiency (LE)
-1.1290kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.254
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
280.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.02
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.39kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-120.89kcal/mol
Minimised FF energy
-141.28kcal/mol
SASA & burial
✓ computed
SASA (unbound)
483.1Ų
Total solvent-accessible surface area of free ligand
BSA total
400.2Ų
Buried surface area upon binding
BSA apolar
282.4Ų
Hydrophobic contacts buried
BSA polar
117.7Ų
Polar contacts buried
Fraction buried
82.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2968.6Ų
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
1438.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)