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
25.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.54, Jaccard 0.35
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.016 kcal/mol/HA)
✓ Good fit quality (FQ -8.97)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ High strain energy (25.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-23.372
kcal/mol
LE
-1.016
kcal/mol/HA
Fit Quality
-8.97
FQ (Leeson)
HAC
23
heavy atoms
MW
355
Da
LogP
1.65
cLogP
Interaction summary
HB 9
HY 15
PI 2
CLASH 2
Interaction summary
HB 9
HY 15
PI 2
CLASH 2
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
| Final rank | 1.652 | Score | -23.372 |
|---|---|---|---|
| Inter norm | -0.923 | Intra norm | -0.093 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 9 |
| Artifact reason | geometry warning; 6 clashes; 1 protein clash; moderate strain Δ 25.0 | ||
| Residues |
ASN22
CYS52
GLU18
GLY13
GLY49
GLY50
ILE339
LEU17
MET113
SER14
THR335
TRP21
TYR110
VAL53
| ||
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 | 0.35 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 310 | 1.6517756537347557 | -0.923016 | -23.3717 | 9 | 14 | 7 | 0.54 | - | - | no | Current |
| 270 | 1.6639064795267455 | -1.1777 | -26.9612 | 10 | 12 | 0 | 0.00 | - | - | no | Open |
| 411 | 1.842210776941111 | -1.08583 | -23.896 | 8 | 16 | 0 | 0.00 | - | - | no | Open |
| 334 | 1.8998383924810274 | -0.888361 | -20.4444 | 8 | 10 | 0 | 0.00 | - | - | no | Open |
| 343 | 2.0334518639712758 | -1.24284 | -25.2174 | 8 | 14 | 0 | 0.00 | - | - | no | Open |
| 256 | 2.5392554407387005 | -1.19497 | -26.3836 | 12 | 12 | 0 | 0.00 | - | - | no | Open |
| 293 | 2.906929042751237 | -1.06321 | -21.6989 | 6 | 18 | 0 | 0.00 | - | - | no | Open |
| 346 | 2.9842050902607964 | -1.22311 | -28.2689 | 8 | 15 | 0 | 0.00 | - | - | no | Open |
| 361 | 3.3942738138361097 | -1.12993 | -22.908 | 7 | 15 | 0 | 0.00 | - | - | no | Open |
| 281 | 3.5581070657350717 | -1.33462 | -33.5911 | 16 | 20 | 0 | 0.00 | - | - | no | Open |
| 244 | 4.77291506171667 | -1.19294 | -25.9697 | 11 | 14 | 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
-23.372kcal/mol
Ligand efficiency (LE)
-1.0162kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.968
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
355.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.65
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-59.89kcal/mol
Minimised FF energy
-84.92kcal/mol
SASA & burial
✓ computed
SASA (unbound)
583.7Ų
Total solvent-accessible surface area of free ligand
BSA total
401.6Ų
Buried surface area upon binding
BSA apolar
279.4Ų
Hydrophobic contacts buried
BSA polar
122.2Ų
Polar contacts buried
Fraction buried
68.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3052.0Ų
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
1443.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)