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
30.5 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.88, Jaccard 0.83, H-bond role recall 0.45
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
74% of hydrophobic surface is solvent-exposed (17/23 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.518 kcal/mol/HA)
✓ Good fit quality (FQ -5.09)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (66% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Very high strain energy (30.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-16.573
kcal/mol
LE
-0.518
kcal/mol/HA
Fit Quality
-5.09
FQ (Leeson)
HAC
32
heavy atoms
MW
470
Da
LogP
4.51
cLogP
Interaction summary
HB 8
HY 2
PI 2
CLASH 5
⚠ Exposure 73%
Interaction summary
HB 8
HY 2
PI 2
CLASH 5
⚠ Exposure 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
Solvent-exposed hydrophobic surface — desolvation penalty likely
74% of hydrophobic surface is solvent-exposed (17/23 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) 6
Exposed 17
LogP 4.51
H-bonds 8
Exposed fragments:
phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)phenyl (4/5 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 4.584 | Score | -16.573 |
|---|---|---|---|
| Inter norm | -0.807 | Intra norm | 0.289 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 8 |
| Artifact reason | geometry warning; 10 clashes; 3 protein clashes; high strain Δ 30.5 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY77
HIS105
HIS14
HIS141
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 | 15 | Native recall | 0.88 |
| Jaccard | 0.83 | RMSD | - |
| HB strict | 6 | Strict recall | 0.46 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 124 | 2.209772416141404 | -0.7511 | -21.2566 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 80 | 4.583978725486131 | -0.806529 | -16.5729 | 8 | 16 | 15 | 0.88 | 0.45 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-16.573kcal/mol
Ligand efficiency (LE)
-0.5179kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.093
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
469.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.51
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.51kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
45.47kcal/mol
Minimised FF energy
14.96kcal/mol
SASA & burial
✓ computed
SASA (unbound)
759.8Ų
Total solvent-accessible surface area of free ligand
BSA total
503.5Ų
Buried surface area upon binding
BSA apolar
412.0Ų
Hydrophobic contacts buried
BSA polar
91.5Ų
Polar contacts buried
Fraction buried
66.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2334.0Ų
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
686.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)