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
46.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.94, Jaccard 0.89, H-bond role recall 0.36
Reason: strain 46.9 kcal/mol
strain ΔE 46.9 kcal/mol
2 protein-contact clashes
48% of hydrophobic surface appears solvent-exposed (11/23 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 (-0.545 kcal/mol/HA)
✓ Good fit quality (FQ -5.31)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (65% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Extreme strain energy (46.9 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (10)
✗ Many internal clashes (17)
Score
-16.893
kcal/mol
LE
-0.545
kcal/mol/HA
Fit Quality
-5.31
FQ (Leeson)
HAC
31
heavy atoms
MW
438
Da
LogP
4.68
cLogP
Interaction summary
HB 9
HY 2
PI 3
CLASH 2
⚠ Exposure 47%
Interaction summary
HB 9
HY 2
PI 3
CLASH 2
⚠ Exposure 47%
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
Partial hydrophobic solvent exposure
48% of hydrophobic surface appears solvent-exposed (11/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 23
Buried (contacted) 12
Exposed 11
LogP 4.68
H-bonds 9
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 2.704 | Score | -16.893 |
|---|---|---|---|
| Inter norm | -0.840 | Intra norm | 0.296 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 9 |
| Artifact reason | geometry warning; 17 clashes; 10 protein contact clashes; high strain Δ 46.9 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
SER46
THR74
TYR49
| ||
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 | 16 | Native recall | 0.94 |
| Jaccard | 0.89 | RMSD | - |
| HB strict | 6 | Strict recall | 0.46 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 7 | HB residue recall | 0.64 |
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 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 408 | 1.553284776421913 | -1.08218 | -20.9256 | 9 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 385 | 2.7035990479878067 | -0.840458 | -16.8933 | 9 | 17 | 16 | 0.94 | 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
-16.893kcal/mol
Ligand efficiency (LE)
-0.5449kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.309
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
437.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.68
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
46.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
13.94kcal/mol
Minimised FF energy
-32.96kcal/mol
SASA & burial
✓ computed
SASA (unbound)
708.5Ų
Total solvent-accessible surface area of free ligand
BSA total
461.2Ų
Buried surface area upon binding
BSA apolar
378.9Ų
Hydrophobic contacts buried
BSA polar
82.3Ų
Polar contacts buried
Fraction buried
65.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2271.2Ų
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
750.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)