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
24.5 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.85, Jaccard 0.58
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.444 kcal/mol/HA)
✓ Good fit quality (FQ -4.48)
✓ Good H-bonds (3 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ High strain energy (24.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-15.549
kcal/mol
LE
-0.444
kcal/mol/HA
Fit Quality
-4.48
FQ (Leeson)
HAC
35
heavy atoms
MW
462
Da
LogP
6.37
cLogP
Interaction summary
HB 3
HY 24
PI 4
CLASH 4
Interaction summary
HB 3
HY 24
PI 4
CLASH 4
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 | 3.176 | Score | -15.549 |
|---|---|---|---|
| Inter norm | -0.596 | Intra norm | 0.151 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 3 |
| Artifact reason | geometry warning; 13 clashes; 1 protein clash; moderate strain Δ 24.5 | ||
| Residues |
ASP116
CYS52
GLU18
GLY112
GLY13
GLY49
GLY50
ILE339
LEU17
MET113
SER109
SER14
THR117
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 | 11 | Native recall | 0.85 |
| Jaccard | 0.58 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 360 | 1.9858794448475394 | -0.60587 | -22.5384 | 8 | 15 | 0 | 0.00 | - | - | no | Open |
| 310 | 2.215876786266132 | -0.810312 | -26.2423 | 7 | 20 | 0 | 0.00 | - | - | no | Open |
| 296 | 2.3735761215630813 | -0.974129 | -31.9318 | 5 | 22 | 0 | 0.00 | - | - | no | Open |
| 304 | 2.4109016880892273 | -0.837854 | -29.8668 | 7 | 13 | 0 | 0.00 | - | - | no | Open |
| 350 | 2.5106836985505296 | -0.819328 | -29.6374 | 5 | 17 | 0 | 0.00 | - | - | no | Open |
| 350 | 2.9414702362290113 | -0.751309 | -27.9819 | 5 | 17 | 0 | 0.00 | - | - | no | Open |
| 358 | 3.175808622050242 | -0.595751 | -15.5491 | 3 | 17 | 11 | 0.85 | - | - | no | Current |
| 421 | 3.3117905327030788 | -0.65678 | -23.4933 | 3 | 16 | 0 | 0.00 | - | - | no | Open |
| 340 | 3.408980607340969 | -0.695149 | -24.1764 | 7 | 10 | 0 | 0.00 | - | - | no | Open |
| 387 | 3.5593066442778185 | -0.749818 | -29.818 | 7 | 21 | 0 | 0.00 | - | - | no | Open |
| 384 | 3.6360066859245648 | -0.841444 | -26.102 | 8 | 16 | 0 | 0.00 | - | - | no | Open |
| 458 | 3.684952783737684 | -0.836742 | -25.2904 | 4 | 18 | 0 | 0.00 | - | - | no | Open |
| 341 | 4.458291848249892 | -0.632747 | -19.3542 | 9 | 19 | 0 | 0.00 | - | - | no | Open |
| 340 | 4.6006376252543095 | -0.940685 | -33.7094 | 11 | 24 | 0 | 0.00 | - | - | no | Open |
| 312 | 5.204738389636102 | -0.790161 | -23.6613 | 11 | 20 | 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
-15.549kcal/mol
Ligand efficiency (LE)
-0.4443kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.481
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
461.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.37
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.52kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
106.64kcal/mol
Minimised FF energy
82.12kcal/mol
SASA & burial
✓ computed
SASA (unbound)
767.1Ų
Total solvent-accessible surface area of free ligand
BSA total
519.4Ų
Buried surface area upon binding
BSA apolar
427.2Ų
Hydrophobic contacts buried
BSA polar
92.2Ų
Polar contacts buried
Fraction buried
67.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3230.5Ų
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
1487.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)