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
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
26.5 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.82, Jaccard 0.82, H-bond role recall 0.73
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
65% of hydrophobic surface is solvent-exposed (11/17 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 (-0.805 kcal/mol/HA)
✓ Good fit quality (FQ -7.42)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ High strain energy (26.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-20.944
kcal/mol
LE
-0.805
kcal/mol/HA
Fit Quality
-7.42
FQ (Leeson)
HAC
26
heavy atoms
MW
366
Da
LogP
2.33
cLogP
Interaction summary
HB 9
HY 1
PI 2
CLASH 5
⚠ Exposure 64%
Interaction summary
HB 9
HY 1
PI 2
CLASH 5
⚠ Exposure 64%
Solvent-exposed hydrophobic surface — desolvation penalty likely
65% of hydrophobic surface is solvent-exposed (11/17 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 17
Buried (contacted) 6
Exposed 11
LogP 2.33
H-bonds 9
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (3/5 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.955 | Score | -20.944 |
|---|---|---|---|
| Inter norm | -0.943 | Intra norm | 0.137 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 9 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes; moderate strain Δ 26.5 | ||
| Residues |
ARG116
ARG140
ARG144
ASN106
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
LEU101
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 | 14 | Native recall | 0.82 |
| Jaccard | 0.82 | RMSD | - |
| HB strict | 8 | Strict recall | 0.62 |
| HB same residue+role | 8 | HB role recall | 0.73 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 132 | 0.6034787560662435 | -0.986253 | -17.9228 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 138 | 1.4476132232114785 | -1.32116 | -31.3906 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 60 | 1.8348160871656356 | -1.07441 | -21.076 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 85 | 3.5037539024917495 | -1.26397 | -32.0923 | 10 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 61 | 3.9546360904873596 | -0.94287 | -20.9441 | 9 | 14 | 14 | 0.82 | 0.73 | - | no | Current |
| 123 | 4.331751406084817 | -0.886047 | -18.545 | 6 | 15 | 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
-20.944kcal/mol
Ligand efficiency (LE)
-0.8055kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.422
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
366.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.33
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-51.90kcal/mol
Minimised FF energy
-78.43kcal/mol
SASA & burial
✓ computed
SASA (unbound)
605.4Ų
Total solvent-accessible surface area of free ligand
BSA total
424.5Ų
Buried surface area upon binding
BSA apolar
315.2Ų
Hydrophobic contacts buried
BSA polar
109.3Ų
Polar contacts buried
Fraction buried
70.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2187.6Ų
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
676.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)