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
26.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.76, Jaccard 0.72, H-bond role recall 0.45
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
50% of hydrophobic surface appears solvent-exposed (6/12 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 (-0.899 kcal/mol/HA)
✓ Good fit quality (FQ -7.37)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ High strain energy (26.1 kcal/mol)
✗ Geometry warnings
Score
-17.079
kcal/mol
LE
-0.899
kcal/mol/HA
Fit Quality
-7.37
FQ (Leeson)
HAC
19
heavy atoms
MW
279
Da
LogP
1.39
cLogP
Interaction summary
HB 11
HY 4
PI 2
CLASH 3
⚠ Exposure 50%
Interaction summary
HB 11
HY 4
PI 2
CLASH 3
⚠ Exposure 50%
Partial hydrophobic solvent exposure
50% of hydrophobic surface appears solvent-exposed (6/12 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 12
Buried (contacted) 6
Exposed 6
LogP 1.39
H-bonds 11
Exposed fragments:
phenyl (3/5 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 1.586 | Score | -17.079 |
|---|---|---|---|
| Inter norm | -1.296 | Intra norm | 0.398 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 11 |
| Artifact reason | geometry warning; 4 clashes; 1 protein clash; moderate strain Δ 26.1 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY77
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 | 13 | Native recall | 0.76 |
| Jaccard | 0.72 | RMSD | - |
| HB strict | 6 | Strict recall | 0.46 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 6 | HB residue recall | 0.55 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 534 | 1.586258691401532 | -1.29645 | -17.0786 | 11 | 14 | 13 | 0.76 | 0.45 | - | no | Current |
| 533 | 3.165423383602174 | -1.53038 | -22.5993 | 10 | 16 | 0 | 0.00 | 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
-17.079kcal/mol
Ligand efficiency (LE)
-0.8989kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.368
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
279.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.39
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.14kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
87.51kcal/mol
Minimised FF energy
61.37kcal/mol
SASA & burial
✓ computed
SASA (unbound)
510.2Ų
Total solvent-accessible surface area of free ligand
BSA total
395.1Ų
Buried surface area upon binding
BSA apolar
293.5Ų
Hydrophobic contacts buried
BSA polar
101.6Ų
Polar contacts buried
Fraction buried
77.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2145.7Ų
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
650.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)