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
38.2 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.94, Jaccard 0.89, H-bond role recall 0.36
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
70% of hydrophobic surface is solvent-exposed (23/33 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.802 kcal/mol/HA)
✓ Good fit quality (FQ -8.43)
✓ Strong H-bond network (10 bonds)
✓ Good burial (60% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Very high strain energy (38.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-32.878
kcal/mol
LE
-0.802
kcal/mol/HA
Fit Quality
-8.43
FQ (Leeson)
HAC
41
heavy atoms
MW
560
Da
LogP
4.89
cLogP
Interaction summary
HB 10
HY 5
PI 2
CLASH 4
⚠ Exposure 69%
Interaction summary
HB 10
HY 5
PI 2
CLASH 4
⚠ Exposure 69%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
70% of hydrophobic surface is solvent-exposed (23/33 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 33
Buried (contacted) 10
Exposed 23
LogP 4.89
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (9 atoms exposed)
| Final rank | 3.867 | Score | -32.878 |
|---|---|---|---|
| Inter norm | -0.774 | Intra norm | -0.028 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 10 |
| Artifact reason | geometry warning; 14 clashes; 1 protein clash; high strain Δ 37.3 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
SER46
THR74
TYR49
| ||
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 | 16 | Native recall | 0.94 |
| Jaccard | 0.89 | RMSD | - |
| HB strict | 5 | Strict recall | 0.38 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 6 | HB residue recall | 0.55 |
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 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 259 | 1.9112823406497645 | -0.61835 | -20.835 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 263 | 3.2150630446791273 | -0.61661 | -25.6406 | 6 | 24 | 0 | 0.00 | 0.00 | - | no | Open |
| 369 | 3.5556749477823884 | -0.615241 | -22.2717 | 6 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 342 | 3.8265450347153354 | -0.56122 | -21.9549 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 171 | 3.8667762534557513 | -0.774095 | -32.8776 | 10 | 17 | 16 | 0.94 | 0.36 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-32.878kcal/mol
Ligand efficiency (LE)
-0.8019kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.426
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
41HA
Physicochemical properties
Molecular weight
559.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.89
Lipinski: ≤ 5
Rotatable bonds
12
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
120.08kcal/mol
Minimised FF energy
81.85kcal/mol
SASA & burial
✓ computed
SASA (unbound)
893.6Ų
Total solvent-accessible surface area of free ligand
BSA total
535.4Ų
Buried surface area upon binding
BSA apolar
441.3Ų
Hydrophobic contacts buried
BSA polar
94.0Ų
Polar contacts buried
Fraction buried
59.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2517.7Ų
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
691.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)