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
7.7 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.76, Jaccard 0.68, H-bond role recall 0.45
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
53% of hydrophobic surface appears solvent-exposed (9/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Low conformational strain (7.7 kcal/mol)
✓ Excellent LE (-1.207 kcal/mol/HA)
✓ Good fit quality (FQ -10.81)
✓ Strong H-bond network (13 bonds)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-28.960
kcal/mol
LE
-1.207
kcal/mol/HA
Fit Quality
-10.81
FQ (Leeson)
HAC
24
heavy atoms
MW
321
Da
LogP
2.85
cLogP
Interaction summary
HB 13
HY 4
PI 2
CLASH 3
⚠ Exposure 52%
Interaction summary
HB 13
HY 4
PI 2
CLASH 3
⚠ Exposure 52%
Partial hydrophobic solvent exposure
53% of hydrophobic surface appears solvent-exposed (9/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 8
Exposed 9
LogP 2.85
H-bonds 13
Exposed fragments:
phenyl (2/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 2.888 | Score | -28.960 |
|---|---|---|---|
| Inter norm | -1.018 | Intra norm | -0.188 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 13 |
| Artifact reason | geometry warning; 11 clashes; 1 protein clash | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
HIS105
HIS14
HIS141
SER46
THR45
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 | 13 | Native recall | 0.76 |
| Jaccard | 0.68 | RMSD | - |
| HB strict | 7 | Strict recall | 0.54 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 103 | 1.6777422230515087 | -1.12899 | -22.7159 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 148 | 2.4084950130068776 | -1.09591 | -26.5384 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 62 | 2.888449860517804 | -1.01834 | -28.9604 | 13 | 15 | 13 | 0.76 | 0.45 | - | no | Current |
| 114 | 3.487018371197951 | -1.00669 | -22.768 | 4 | 15 | 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
-28.960kcal/mol
Ligand efficiency (LE)
-1.2067kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.814
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
321.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.85
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
7.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
110.58kcal/mol
Minimised FF energy
102.84kcal/mol
SASA & burial
✓ computed
SASA (unbound)
550.3Ų
Total solvent-accessible surface area of free ligand
BSA total
435.4Ų
Buried surface area upon binding
BSA apolar
340.3Ų
Hydrophobic contacts buried
BSA polar
95.2Ų
Polar contacts buried
Fraction buried
79.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2183.6Ų
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
687.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)