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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
39.9 kcal/mol
Protein clashes
10
Internal clashes
10
Native overlap
contact recall 0.94, Jaccard 0.76, H-bond role recall 0.45
Reason: 10 protein-contact clashes, 10 internal clashes
10 protein-contact clashes
10 intramolecular clashes
65% of hydrophobic surface is solvent-exposed (13/20 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.630 kcal/mol/HA)
✓ Good fit quality (FQ -6.25)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (88%)
✗ Very high strain energy (39.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-20.804
kcal/mol
LE
-0.630
kcal/mol/HA
Fit Quality
-6.25
FQ (Leeson)
HAC
33
heavy atoms
MW
476
Da
LogP
4.87
cLogP
Interaction summary
HB 8
HY 6
PI 1
CLASH 10
⚠ Exposure 65%
Interaction summary
HB 8
HY 6
PI 1
CLASH 10
⚠ Exposure 65%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
65% of hydrophobic surface is solvent-exposed (13/20 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 20
Buried (contacted) 7
Exposed 13
LogP 4.87
H-bonds 8
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 4.590 | Score | -20.804 |
|---|---|---|---|
| Inter norm | -0.748 | Intra norm | 0.117 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 8 |
| Artifact reason | geometry warning; 16 clashes; 1 protein clash; high strain Δ 39.9 | ||
| Residues |
ALA15
ALA18
ARG116
ARG140
ARG144
ASN106
ASP44
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
SER46
THR74
TYR17
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 | 0.76 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 401 | 1.848147612243246 | -0.822861 | -16.3223 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 383 | 3.3295964245493788 | -0.696111 | -18.717 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 362 | 3.4157576199808495 | -0.687364 | -20.5018 | 7 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 416 | 3.989968891561393 | -0.676669 | -21.4174 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 318 | 4.590233008105476 | -0.747743 | -20.8037 | 8 | 20 | 16 | 0.94 | 0.45 | - | no | Current |
| 317 | 4.948774694239921 | -0.85615 | -27.0558 | 9 | 18 | 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
-20.804kcal/mol
Ligand efficiency (LE)
-0.6304kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.255
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
475.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.87
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
39.92kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
103.32kcal/mol
Minimised FF energy
63.39kcal/mol
SASA & burial
✓ computed
SASA (unbound)
702.2Ų
Total solvent-accessible surface area of free ligand
BSA total
544.3Ų
Buried surface area upon binding
BSA apolar
478.1Ų
Hydrophobic contacts buried
BSA polar
66.3Ų
Polar contacts buried
Fraction buried
77.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
87.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2333.7Ų
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
681.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)