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
38.0 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.71, Jaccard 0.60, H-bond role recall 0.45
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
56% of hydrophobic surface appears solvent-exposed (15/27 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 (-0.834 kcal/mol/HA)
✓ Good fit quality (FQ -8.34)
✓ Strong H-bond network (16 bonds)
✓ Good burial (64% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Very high strain energy (38.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-28.347
kcal/mol
LE
-0.834
kcal/mol/HA
Fit Quality
-8.34
FQ (Leeson)
HAC
34
heavy atoms
MW
467
Da
LogP
5.71
cLogP
Interaction summary
HB 16
HY 4
PI 2
CLASH 4
⚠ Exposure 55%
Interaction summary
HB 16
HY 4
PI 2
CLASH 4
⚠ Exposure 55%
Partial hydrophobic solvent exposure
56% of hydrophobic surface appears solvent-exposed (15/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 27
Buried (contacted) 12
Exposed 15
LogP 5.71
H-bonds 16
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 4.562 | Score | -28.347 |
|---|---|---|---|
| Inter norm | -0.886 | Intra norm | 0.052 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 16 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; high strain Δ 38.0 | ||
| Residues |
ARG116
ARG140
ARG144
ASN106
CYS72
GLN104
GLY73
HIS105
HIS14
HIS141
LEU101
LEU136
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 | 12 | Native recall | 0.71 |
| Jaccard | 0.60 | RMSD | - |
| HB strict | 7 | Strict recall | 0.54 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 5 | HB residue recall | 0.45 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 576 | 0.6352292789363421 | -0.986887 | -31.8198 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 593 | 2.139321928797725 | -0.590921 | -17.8316 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 579 | 2.680199327253876 | -0.644737 | -23.3603 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 584 | 3.932188150368959 | -0.99912 | -33.0857 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 591 | 4.5623805146338885 | -0.885953 | -28.347 | 16 | 15 | 12 | 0.71 | 0.45 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-28.347kcal/mol
Ligand efficiency (LE)
-0.8337kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.342
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
466.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.71
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
109.20kcal/mol
Minimised FF energy
71.16kcal/mol
SASA & burial
✓ computed
SASA (unbound)
733.2Ų
Total solvent-accessible surface area of free ligand
BSA total
466.1Ų
Buried surface area upon binding
BSA apolar
364.9Ų
Hydrophobic contacts buried
BSA polar
101.2Ų
Polar contacts buried
Fraction buried
63.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2320.1Ų
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
725.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)