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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
33.1 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.82, Jaccard 0.70, H-bond role recall 0.45
Reason: 6 internal clashes
6 protein-contact clashes
6 intramolecular clashes
54% of hydrophobic surface appears solvent-exposed (14/26 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 (-0.519 kcal/mol/HA)
✓ Good fit quality (FQ -5.32)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Very high strain energy (33.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (20)
Score
-19.219
kcal/mol
LE
-0.519
kcal/mol/HA
Fit Quality
-5.32
FQ (Leeson)
HAC
37
heavy atoms
MW
496
Da
LogP
2.38
cLogP
Interaction summary
HB 10
HY 14
PI 1
CLASH 6
⚠ Exposure 53%
Interaction summary
HB 10
HY 14
PI 1
CLASH 6
⚠ Exposure 53%
Partial hydrophobic solvent exposure
54% of hydrophobic surface appears solvent-exposed (14/26 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 26
Buried (contacted) 12
Exposed 14
LogP 2.38
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 5.279 | Score | -19.219 |
|---|---|---|---|
| Inter norm | -0.678 | Intra norm | 0.159 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 10 |
| Artifact reason | geometry warning; 20 clashes; 2 protein clashes; high strain Δ 33.1 | ||
| Residues |
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY77
HIS105
HIS14
HIS141
LEU101
SER46
THR117
THR74
TYR49
VAL97
| ||
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 | 14 | Native recall | 0.82 |
| Jaccard | 0.70 | RMSD | - |
| HB strict | 5 | Strict recall | 0.38 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 420 | 2.202040043426332 | -0.761594 | -21.5322 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 386 | 2.7607078051406773 | -0.726203 | -14.8438 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 405 | 3.2841898246993426 | -0.771985 | -25.082 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 315 | 4.768441194813837 | -0.998446 | -31.3873 | 15 | 20 | 5 | 0.29 | 0.09 | - | no | Open |
| 298 | 5.279426456791999 | -0.678437 | -19.2188 | 10 | 17 | 14 | 0.82 | 0.45 | - | no | Current |
| 364 | 5.49298592197989 | -0.518654 | -12.2869 | 7 | 10 | 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
-19.219kcal/mol
Ligand efficiency (LE)
-0.5194kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.318
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
495.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.38
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
119.76kcal/mol
Minimised FF energy
86.70kcal/mol
SASA & burial
✓ computed
SASA (unbound)
756.5Ų
Total solvent-accessible surface area of free ligand
BSA total
510.6Ų
Buried surface area upon binding
BSA apolar
415.6Ų
Hydrophobic contacts buried
BSA polar
95.0Ų
Polar contacts buried
Fraction buried
67.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2340.1Ų
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
690.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)