Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
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
53.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.94, Jaccard 0.89, H-bond role recall 0.64
Reason: strain 53.9 kcal/mol
strain ΔE 53.9 kcal/mol
3 protein-contact clashes
3 intramolecular clashes
70% of hydrophobic surface is solvent-exposed (16/23 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.500 kcal/mol/HA)
✓ Good fit quality (FQ -5.00)
✓ Strong H-bond network (13 bonds)
✓ Good burial (64% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Extreme strain energy (53.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-17.001
kcal/mol
LE
-0.500
kcal/mol/HA
Fit Quality
-5.00
FQ (Leeson)
HAC
34
heavy atoms
MW
461
Da
LogP
3.08
cLogP
Interaction summary
HB 13
HY 1
PI 1
CLASH 3
⚠ Exposure 69%
Interaction summary
HB 13
HY 1
PI 1
CLASH 3
⚠ Exposure 69%
Solvent-exposed hydrophobic surface — desolvation penalty likely
70% of hydrophobic surface is solvent-exposed (16/23 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 23
Buried (contacted) 7
Exposed 16
LogP 3.08
H-bonds 13
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 5.569 | Score | -17.001 |
|---|---|---|---|
| Inter norm | -0.762 | Intra norm | 0.242 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 13 |
| Artifact reason | geometry warning; 13 clashes; 3 protein clashes; high strain Δ 53.7 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
LEU101
THR74
TYR49
VAL115
| ||
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 | 16 | Native recall | 0.94 |
| Jaccard | 0.89 | RMSD | - |
| HB strict | 8 | Strict recall | 0.62 |
| HB same residue+role | 7 | HB role recall | 0.64 |
| HB same residue | 7 | HB residue recall | 0.64 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 427 | 1.3468576735481605 | -0.808417 | -18.675 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 372 | 1.6823460811845725 | -0.78016 | -19.7888 | 7 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 411 | 2.2104857339584942 | -0.669199 | -19.1927 | 12 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 444 | 2.4534108204004426 | -0.764614 | -17.3765 | 9 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 378 | 3.765478119320939 | -0.643558 | -19.7646 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 337 | 5.369926118840396 | -0.895866 | -25.0991 | 15 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 313 | 5.56934551442081 | -0.761521 | -17.001 | 13 | 17 | 16 | 0.94 | 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
-17.001kcal/mol
Ligand efficiency (LE)
-0.5000kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.003
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
461.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.08
Lipinski: ≤ 5
Rotatable bonds
12
Conformational strain (MMFF94s)
Strain energy (ΔE)
53.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
120.70kcal/mol
Minimised FF energy
66.81kcal/mol
SASA & burial
✓ computed
SASA (unbound)
753.2Ų
Total solvent-accessible surface area of free ligand
BSA total
479.6Ų
Buried surface area upon binding
BSA apolar
367.9Ų
Hydrophobic contacts buried
BSA polar
111.7Ų
Polar contacts buried
Fraction buried
63.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2324.4Ų
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
693.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)