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
Reject
SASA cached
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
41.3 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 1.00, Jaccard 0.94, H-bond role recall 0.55
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
68% of hydrophobic surface is solvent-exposed (13/19 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.789 kcal/mol/HA)
✓ Good fit quality (FQ -7.61)
✓ Strong H-bond network (9 bonds)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Extreme strain energy (41.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-23.668
kcal/mol
LE
-0.789
kcal/mol/HA
Fit Quality
-7.61
FQ (Leeson)
HAC
30
heavy atoms
MW
428
Da
LogP
0.73
cLogP
Interaction summary
HB 9
HY 6
PI 1
CLASH 5
⚠ Exposure 68%
Interaction summary
HB 9
HY 6
PI 1
CLASH 5
⚠ Exposure 68%
Solvent-exposed hydrophobic surface — desolvation penalty likely
68% of hydrophobic surface is solvent-exposed (13/19 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 19
Buried (contacted) 6
Exposed 13
LogP 0.73
H-bonds 9
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.784 | Score | -23.668 |
|---|---|---|---|
| Inter norm | -0.943 | Intra norm | 0.154 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 9 |
| Artifact reason | geometry warning; 14 clashes; 1 protein clash; high strain Δ 41.3 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
SER46
THR74
TYR49
| ||
Protein summary
155 residues
| Protein target | T10 | Atoms | 4590 |
|---|---|---|---|
| Residues | 155 | Chains | 1 |
| Residue summary | ILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6FXW | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
THR74
TYR49
| ||
| Current overlap | 17 | Native recall | 1.00 |
| Jaccard | 0.94 | RMSD | - |
| HB strict | 6 | Strict recall | 0.46 |
| HB same residue+role | 6 | HB role recall | 0.55 |
| HB same residue | 8 | HB residue recall | 0.73 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 343 | 3.3806032224084737 | -1.02576 | -27.2232 | 8 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 368 | 3.660113442346769 | -0.743051 | -17.1971 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 344 | 3.680388032224625 | -1.41134 | -32.5815 | 8 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 305 | 3.7841109715598766 | -0.942594 | -23.6684 | 9 | 18 | 17 | 1.00 | 0.55 | - | no | Current |
| 367 | 3.801123320082061 | -0.687097 | -19.2302 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 331 | 4.968164464318635 | -1.07715 | -29.0268 | 11 | 18 | 5 | 0.29 | 0.18 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.668kcal/mol
Ligand efficiency (LE)
-0.7889kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.610
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
427.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.73
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
41.28kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
168.34kcal/mol
Minimised FF energy
127.05kcal/mol
SASA & burial
✓ computed
SASA (unbound)
674.3Ų
Total solvent-accessible surface area of free ligand
BSA total
414.9Ų
Buried surface area upon binding
BSA apolar
308.3Ų
Hydrophobic contacts buried
BSA polar
106.6Ų
Polar contacts buried
Fraction buried
61.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2200.9Ų
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
2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
775.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)