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 high
Native strong
SASA done
Strain ΔE
21.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.82, Jaccard 0.78, H-bond role recall 0.36
Reason: no major geometry red flags detected
2 protein-contact clashes
53% of hydrophobic surface appears solvent-exposed (8/15 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 (-0.878 kcal/mol/HA)
✓ Good fit quality (FQ -7.20)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ High strain energy (21.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-16.680
kcal/mol
LE
-0.878
kcal/mol/HA
Fit Quality
-7.20
FQ (Leeson)
HAC
19
heavy atoms
MW
254
Da
LogP
2.46
cLogP
Interaction summary
HB 10
HY 3
PI 1
CLASH 2
⚠ Exposure 53%
Interaction summary
HB 10
HY 3
PI 1
CLASH 2
⚠ Exposure 53%
Partial hydrophobic solvent exposure
53% of hydrophobic surface appears solvent-exposed (8/15 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 15
Buried (contacted) 7
Exposed 8
LogP 2.46
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 1.659 | Score | -16.680 |
|---|---|---|---|
| Inter norm | -1.280 | Intra norm | 0.403 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 10 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash; moderate strain Δ 21.6 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
CYS72
GLY73
GLY77
HIS105
HIS14
HIS141
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 | 14 | Native recall | 0.82 |
| Jaccard | 0.78 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 156 | 1.6594795680915473 | -1.28042 | -16.6805 | 10 | 15 | 14 | 0.82 | 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
-16.680kcal/mol
Ligand efficiency (LE)
-0.8779kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.196
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
254.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.46
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
95.06kcal/mol
Minimised FF energy
73.50kcal/mol
SASA & burial
✓ computed
SASA (unbound)
515.8Ų
Total solvent-accessible surface area of free ligand
BSA total
416.0Ų
Buried surface area upon binding
BSA apolar
344.5Ų
Hydrophobic contacts buried
BSA polar
71.5Ų
Polar contacts buried
Fraction buried
80.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2203.5Ų
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
658.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)