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 high
Native strong
SASA done
Strain ΔE
27.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.94, Jaccard 0.89, H-bond role recall 0.64
Reason: no major geometry red flags detected
2 protein-contact clashes
67% of hydrophobic surface is solvent-exposed (12/18 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 (-0.830 kcal/mol/HA)
✓ Good fit quality (FQ -7.74)
✓ Strong H-bond network (16 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (63%)
✗ High strain energy (27.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-22.407
kcal/mol
LE
-0.830
kcal/mol/HA
Fit Quality
-7.74
FQ (Leeson)
HAC
27
heavy atoms
MW
415
Da
LogP
1.19
cLogP
Interaction summary
HB 16
HY 1
PI 1
CLASH 2
⚠ Exposure 66%
Interaction summary
HB 16
HY 1
PI 1
CLASH 2
⚠ Exposure 66%
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
67% of hydrophobic surface is solvent-exposed (12/18 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 18
Buried (contacted) 6
Exposed 12
LogP 1.19
H-bonds 16
Exposed fragments:
phenyl (5/5 atoms exposed)phenyl (5/5 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 4.476 | Score | -22.407 |
|---|---|---|---|
| Inter norm | -1.038 | Intra norm | 0.209 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 16 |
| Artifact reason | geometry warning; 10 clashes; 3 protein clashes; moderate strain Δ 27.9 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
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 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 616 | 3.147423451270175 | -0.969471 | -24.0552 | 13 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 597 | 3.816956584422617 | -1.17655 | -29.6107 | 15 | 16 | 5 | 0.29 | 0.27 | - | no | Open |
| 609 | 3.9524670316859187 | -0.834271 | -21.0301 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 603 | 4.47613555924801 | -1.03848 | -22.4069 | 16 | 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
-22.407kcal/mol
Ligand efficiency (LE)
-0.8299kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.743
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
414.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.19
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-106.47kcal/mol
Minimised FF energy
-134.41kcal/mol
SASA & burial
✓ computed
SASA (unbound)
655.5Ų
Total solvent-accessible surface area of free ligand
BSA total
449.2Ų
Buried surface area upon binding
BSA apolar
284.0Ų
Hydrophobic contacts buried
BSA polar
165.2Ų
Polar contacts buried
Fraction buried
68.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
63.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2240.2Ų
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
653.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)