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
24.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.71, Jaccard 0.67, H-bond role recall 0.27
Reason: no major geometry red flags detected
3 protein-contact clashes
3 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 (-1.345 kcal/mol/HA)
✓ Good fit quality (FQ -11.02)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ High strain energy (24.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-25.553
kcal/mol
LE
-1.345
kcal/mol/HA
Fit Quality
-11.02
FQ (Leeson)
HAC
19
heavy atoms
MW
281
Da
LogP
-0.02
cLogP
Interaction summary
HB 12
HY 2
PI 1
CLASH 3
⚠ Exposure 40%
Interaction summary
HB 12
HY 2
PI 1
CLASH 3
⚠ Exposure 40%
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 -0.02
H-bonds 12
Exposed fragments:
phenyl (4/6 atoms exposed)
| Final rank | 2.501 | Score | -25.553 |
|---|---|---|---|
| Inter norm | -1.357 | Intra norm | 0.012 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 12 |
| Artifact reason | geometry warning; 6 clashes; 1 protein clash; moderate strain Δ 24.1 | ||
| 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 | 3 | Strict recall | 0.23 |
| HB same residue+role | 3 | HB role recall | 0.27 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 290 | 1.1542235761146216 | -1.3133 | -22.9835 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 326 | 2.241892118278962 | -1.16101 | -21.6592 | 8 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 408 | 2.3864433454440244 | -1.28783 | -23.0227 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 340 | 2.4224499674500235 | -1.52753 | -26.5605 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 242 | 2.5012839495939683 | -1.35686 | -25.553 | 12 | 13 | 12 | 0.71 | 0.27 | - | no | Current |
| 344 | 2.970230030733658 | -1.42184 | -25.8069 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 277 | 3.3258278508067045 | -1.67804 | -30.7231 | 16 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 381 | 3.627532215524071 | -1.28108 | -23.2122 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 357 | 3.7791067382818606 | -1.42538 | -25.9702 | 8 | 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
-25.553kcal/mol
Ligand efficiency (LE)
-1.3449kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.024
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
281.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.02
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.11kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-45.37kcal/mol
Minimised FF energy
-69.48kcal/mol
SASA & burial
✓ computed
SASA (unbound)
476.7Ų
Total solvent-accessible surface area of free ligand
BSA total
363.4Ų
Buried surface area upon binding
BSA apolar
255.4Ų
Hydrophobic contacts buried
BSA polar
108.0Ų
Polar contacts buried
Fraction buried
76.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2092.7Ų
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
653.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)