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 medium
Native mixed
SASA done
Strain ΔE
16.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.33, Jaccard 0.20
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.864 kcal/mol/HA)
✓ Good fit quality (FQ -7.63)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Moderate strain (16.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-19.881
kcal/mol
LE
-0.864
kcal/mol/HA
Fit Quality
-7.63
FQ (Leeson)
HAC
23
heavy atoms
MW
314
Da
LogP
1.19
cLogP
Interaction summary
HB 8
HY 17
PI 0
CLASH 3
Interaction summary
HB 8
HY 17
PI 0
CLASH 3
| Final rank | 4.311 | Score | -19.881 |
|---|---|---|---|
| Inter norm | -1.063 | Intra norm | 0.198 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 8 |
| Artifact reason | geometry warning; 9 clashes; 3 protein clashes | ||
| Residues |
ALA90
ASN91
GLY214
GLY215
LYS211
LYS89
LYS93
PRO187
PRO212
PRO213
TRP92
TYR210
| ||
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 | 4 | Native recall | 0.33 |
| Jaccard | 0.20 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 628 | 0.18702354902015306 | -1.17891 | -22.6406 | 4 | 15 | 0 | 0.00 | - | - | no | Open |
| 616 | 0.6285692150163996 | -1.03442 | -15.6318 | 7 | 18 | 0 | 0.00 | - | - | no | Open |
| 617 | 2.579057013340084 | -1.22393 | -23.9439 | 9 | 13 | 0 | 0.00 | - | - | no | Open |
| 636 | 2.6212597648646407 | -1.27144 | -23.7154 | 7 | 19 | 1 | 0.08 | - | - | no | Open |
| 635 | 2.628679045735035 | -1.08796 | -19.974 | 6 | 13 | 0 | 0.00 | - | - | no | Open |
| 639 | 2.942909683415412 | -1.07862 | -18.8879 | 7 | 12 | 0 | 0.00 | - | - | no | Open |
| 626 | 4.096418414128663 | -1.32544 | -25.1928 | 10 | 18 | 0 | 0.00 | - | - | no | Open |
| 622 | 4.311340728481773 | -1.06258 | -19.8805 | 8 | 12 | 4 | 0.33 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.881kcal/mol
Ligand efficiency (LE)
-0.8644kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.629
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
314.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.19
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
42.81kcal/mol
Minimised FF energy
26.25kcal/mol
SASA & burial
✓ computed
SASA (unbound)
597.2Ų
Total solvent-accessible surface area of free ligand
BSA total
407.2Ų
Buried surface area upon binding
BSA apolar
305.0Ų
Hydrophobic contacts buried
BSA polar
102.2Ų
Polar contacts buried
Fraction buried
68.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3074.5Ų
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
1473.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)