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
34.6 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.59, Jaccard 0.56, H-bond role recall 0.27
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
40% of hydrophobic surface appears solvent-exposed (4/10 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.188 kcal/mol/HA)
✓ Good fit quality (FQ -9.74)
✓ Strong H-bond network (14 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Very high strain energy (34.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-22.576
kcal/mol
LE
-1.188
kcal/mol/HA
Fit Quality
-9.74
FQ (Leeson)
HAC
19
heavy atoms
MW
281
Da
LogP
-0.26
cLogP
Interaction summary
HB 14
HY 2
PI 1
CLASH 4
⚠ Exposure 40%
Interaction summary
HB 14
HY 2
PI 1
CLASH 4
⚠ Exposure 40%
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
Partial hydrophobic solvent exposure
40% of hydrophobic surface appears solvent-exposed (4/10 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 10
Buried (contacted) 6
Exposed 4
LogP -0.26
H-bonds 14
Exposed fragments:
phenyl (4/6 atoms exposed)
| Final rank | 4.247 | Score | -22.576 |
|---|---|---|---|
| Inter norm | -1.258 | Intra norm | 0.070 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 14 |
| Artifact reason | geometry warning; 6 clashes; 3 protein clashes; high strain Δ 34.6 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASP13
CYS72
GLY73
HIS105
HIS14
HIS141
SER46
| ||
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 | 10 | Native recall | 0.59 |
| Jaccard | 0.56 | RMSD | - |
| HB strict | 4 | Strict recall | 0.31 |
| HB same residue+role | 3 | HB role recall | 0.27 |
| HB same residue | 3 | HB residue recall | 0.27 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 305 | 1.0227578376082587 | -1.63221 | -29.0736 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 339 | 1.0977752334667914 | -1.50379 | -27.2444 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 364 | 1.3242847920907537 | -1.42014 | -26.0848 | 7 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 318 | 1.677371121731007 | -1.19289 | -20.0023 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 404 | 2.029490729260137 | -1.22908 | -23.3088 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 305 | 2.6817761148920427 | -1.69453 | -29.2684 | 16 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 264 | 4.247124566588215 | -1.25775 | -22.5757 | 14 | 11 | 10 | 0.59 | 0.27 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.576kcal/mol
Ligand efficiency (LE)
-1.1882kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.739
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
281.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.26
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
34.63kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-130.22kcal/mol
Minimised FF energy
-164.84kcal/mol
SASA & burial
✓ computed
SASA (unbound)
474.1Ų
Total solvent-accessible surface area of free ligand
BSA total
341.6Ų
Buried surface area upon binding
BSA apolar
240.5Ų
Hydrophobic contacts buried
BSA polar
101.0Ų
Polar contacts buried
Fraction buried
72.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2103.9Ų
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
650.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)