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
31.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.93, Jaccard 0.81, H-bond role recall 0.67
Reason: no major geometry red flags detected
2 protein-contact clashes
67% of hydrophobic surface is solvent-exposed (14/21 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 (-0.806 kcal/mol/HA)
✓ Good fit quality (FQ -7.69)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (66% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Very high strain energy (31.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-23.367
kcal/mol
LE
-0.806
kcal/mol/HA
Fit Quality
-7.69
FQ (Leeson)
HAC
29
heavy atoms
MW
410
Da
LogP
2.78
cLogP
Interaction summary
HB 12
HY 4
PI 2
CLASH 2
⚠ Exposure 66%
Interaction summary
HB 12
HY 4
PI 2
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 (14/21 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 21
Buried (contacted) 7
Exposed 14
LogP 2.78
H-bonds 12
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 3.347 | Score | -23.367 |
|---|---|---|---|
| Inter norm | -0.865 | Intra norm | 0.059 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 12 |
| Artifact reason | geometry warning; 14 clashes; 1 protein clash; high strain Δ 31.2 | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
HIS138
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
PRO12
SER43
SER71
TYR46
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3K7O | Contacts | 14 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG137
ARG141
ASN103
HIS102
HIS138
ASP10
CYS69
GLY70
GLY74
HIS11
ILE73
PRO12
SER71
TYR46
| ||
| Current overlap | 13 | Native recall | 0.93 |
| Jaccard | 0.81 | RMSD | - |
| HB strict | 8 | Strict recall | 0.67 |
| HB same residue+role | 6 | HB role recall | 0.67 |
| HB same residue | 6 | HB residue recall | 0.75 |
Protein summary
305 residues
| Protein target | T21 | Atoms | 4646 |
|---|---|---|---|
| Residues | 305 | Chains | 2 |
| Residue summary | ARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 620 | 0.8780322138855498 | -0.904267 | -23.3199 | 0 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 642 | 2.9075729189780244 | -0.7654 | -21.3765 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 642 | 3.259827785463704 | -0.711603 | -19.7334 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 639 | 3.3149430830984703 | -1.0974 | -32.3995 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 642 | 3.347272408076479 | -0.865048 | -23.3667 | 12 | 15 | 13 | 0.93 | 0.67 | - | no | Current |
| 623 | 3.4158599517817776 | -0.786036 | -21.3729 | 4 | 14 | 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
-23.367kcal/mol
Ligand efficiency (LE)
-0.8057kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.691
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
410.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.78
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
35.17kcal/mol
Minimised FF energy
4.00kcal/mol
SASA & burial
✓ computed
SASA (unbound)
628.0Ų
Total solvent-accessible surface area of free ligand
BSA total
411.7Ų
Buried surface area upon binding
BSA apolar
298.3Ų
Hydrophobic contacts buried
BSA polar
113.4Ų
Polar contacts buried
Fraction buried
65.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2202.3Ų
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
2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
786.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)