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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
81.9 kcal/mol
Protein clashes
13
Internal clashes
13
Native overlap
contact recall 0.88, Jaccard 0.83, H-bond role recall 0.64
Reason: 13 protein-contact clashes, 13 internal clashes, strain 81.9 kcal/mol
strain ΔE 81.9 kcal/mol
13 protein-contact clashes
13 intramolecular clashes
38% of hydrophobic surface appears solvent-exposed (8/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.778 kcal/mol/HA)
✓ Good fit quality (FQ -7.51)
✓ Strong H-bond network (14 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Extreme strain energy (81.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-23.355
kcal/mol
LE
-0.778
kcal/mol/HA
Fit Quality
-7.51
FQ (Leeson)
HAC
30
heavy atoms
MW
425
Da
LogP
2.49
cLogP
Interaction summary
HB 14
HY 8
PI 2
CLASH 13
⚠ Exposure 38%
Interaction summary
HB 14
HY 8
PI 2
CLASH 13
⚠ Exposure 38%
Partial hydrophobic solvent exposure
38% of hydrophobic surface appears solvent-exposed (8/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 21
Buried (contacted) 13
Exposed 8
LogP 2.49
H-bonds 14
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 6.548 | Score | -23.355 |
|---|---|---|---|
| Inter norm | -0.844 | Intra norm | 0.065 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 14 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; high strain Δ 81.9 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
HIS105
HIS14
HIS141
LEU101
THR117
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 | 15 | Native recall | 0.88 |
| Jaccard | 0.83 | RMSD | - |
| HB strict | 9 | Strict recall | 0.69 |
| HB same residue+role | 7 | HB role recall | 0.64 |
| HB same residue | 8 | HB residue recall | 0.73 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 558 | 3.05726253765378 | -0.884139 | -24.1066 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 552 | 6.547617658563305 | -0.843929 | -23.3554 | 14 | 16 | 15 | 0.88 | 0.64 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.355kcal/mol
Ligand efficiency (LE)
-0.7785kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.510
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
425.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.49
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
81.93kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
97.23kcal/mol
Minimised FF energy
15.30kcal/mol
SASA & burial
✓ computed
SASA (unbound)
657.8Ų
Total solvent-accessible surface area of free ligand
BSA total
462.6Ų
Buried surface area upon binding
BSA apolar
359.8Ų
Hydrophobic contacts buried
BSA polar
102.8Ų
Polar contacts buried
Fraction buried
70.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2259.8Ų
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
680.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)