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
30.8 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.71, Jaccard 0.67, H-bond role recall 0.36
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
57% of hydrophobic surface appears solvent-exposed (8/14 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 (-0.995 kcal/mol/HA)
✓ Good fit quality (FQ -8.92)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (66% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Very high strain energy (30.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-23.886
kcal/mol
LE
-0.995
kcal/mol/HA
Fit Quality
-8.92
FQ (Leeson)
HAC
24
heavy atoms
MW
369
Da
LogP
1.63
cLogP
Interaction summary
HB 11
HY 1
PI 2
CLASH 5
⚠ Exposure 57%
Interaction summary
HB 11
HY 1
PI 2
CLASH 5
⚠ Exposure 57%
Partial hydrophobic solvent exposure
57% of hydrophobic surface appears solvent-exposed (8/14 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 14
Buried (contacted) 6
Exposed 8
LogP 1.63
H-bonds 11
Exposed fragments:
phenyl (4/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 4.253 | Score | -23.886 |
|---|---|---|---|
| Inter norm | -1.053 | Intra norm | 0.057 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 11 |
| Artifact reason | geometry warning; 7 clashes; 2 protein clashes; high strain Δ 30.8 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
HIS105
HIS14
HIS141
SER46
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 | 12 | Native recall | 0.71 |
| Jaccard | 0.67 | RMSD | - |
| HB strict | 5 | Strict recall | 0.38 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 351 | 1.2852977530047394 | -0.957895 | -23.319 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 292 | 1.902635354240016 | -1.14634 | -26.9779 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 331 | 2.674262462609744 | -0.875618 | -21.4239 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 382 | 2.825206801835356 | -1.232 | -28.397 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 427 | 3.7629889484629113 | -1.16817 | -29.4909 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 273 | 4.110967070037996 | -1.22237 | -25.3696 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 257 | 4.2528487823810615 | -1.05268 | -23.8857 | 11 | 13 | 12 | 0.71 | 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
-23.886kcal/mol
Ligand efficiency (LE)
-0.9952kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.919
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
369.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.63
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.80kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-52.62kcal/mol
Minimised FF energy
-83.41kcal/mol
SASA & burial
✓ computed
SASA (unbound)
605.6Ų
Total solvent-accessible surface area of free ligand
BSA total
402.9Ų
Buried surface area upon binding
BSA apolar
291.5Ų
Hydrophobic contacts buried
BSA polar
111.4Ų
Polar contacts buried
Fraction buried
66.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2209.4Ų
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
650.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)