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 strong
SASA done
Strain ΔE
16.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.62, Jaccard 0.42
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.924 kcal/mol/HA)
✓ Good fit quality (FQ -8.51)
✓ Good H-bonds (4 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Moderate strain (16.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-24.018
kcal/mol
LE
-0.924
kcal/mol/HA
Fit Quality
-8.51
FQ (Leeson)
HAC
26
heavy atoms
MW
390
Da
LogP
4.00
cLogP
Interaction summary
HB 4
HY 19
PI 2
CLASH 1
Interaction summary
HB 4
HY 19
PI 2
CLASH 1
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 | 2.428 | Score | -24.018 |
|---|---|---|---|
| Inter norm | -0.800 | Intra norm | -0.124 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 4 |
| Artifact reason | geometry warning; 11 clashes; 1 protein clash | ||
| Residues |
CYS52
GLU18
GLY13
GLY49
GLY50
ILE339
LEU17
MET113
SER109
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 | 8 | Native recall | 0.62 |
| Jaccard | 0.42 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 513 | -0.2908267176309925 | -1.19073 | -29.6003 | 7 | 13 | 0 | 0.00 | - | - | no | Open |
| 530 | 1.8386052021954522 | -1.05981 | -26.1272 | 6 | 14 | 0 | 0.00 | - | - | no | Open |
| 549 | 1.9584098801368803 | -1.07383 | -29.3381 | 5 | 12 | 0 | 0.00 | - | - | no | Open |
| 560 | 2.428087883165567 | -0.799576 | -24.0181 | 4 | 14 | 8 | 0.62 | - | - | no | Current |
| 552 | 2.7941902960594462 | -0.966006 | -17.0384 | 4 | 20 | 0 | 0.00 | - | - | no | Open |
| 530 | 3.472283433281198 | -1.06233 | -28.3109 | 9 | 14 | 0 | 0.00 | - | - | no | Open |
| 516 | 3.8612649837231396 | -1.20279 | -31.5508 | 4 | 13 | 0 | 0.00 | - | - | no | Open |
| 526 | 4.287644089881446 | -1.23726 | -27.9603 | 10 | 18 | 0 | 0.00 | - | - | no | Open |
| 530 | 5.1552079225695575 | -1.06931 | -25.3885 | 13 | 17 | 0 | 0.00 | - | - | no | Open |
| 550 | 5.633262955142708 | -1.10654 | -23.6606 | 16 | 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
-24.018kcal/mol
Ligand efficiency (LE)
-0.9238kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.511
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
389.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.00
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.60kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
42.60kcal/mol
Minimised FF energy
25.99kcal/mol
SASA & burial
✓ computed
SASA (unbound)
616.6Ų
Total solvent-accessible surface area of free ligand
BSA total
432.0Ų
Buried surface area upon binding
BSA apolar
332.4Ų
Hydrophobic contacts buried
BSA polar
99.6Ų
Polar contacts buried
Fraction buried
70.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3053.9Ų
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
1500.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)