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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
53.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.93, Jaccard 0.87, H-bond role recall 0.67
Reason: strain 53.2 kcal/mol
strain ΔE 53.2 kcal/mol
1 protein-contact clashes
62% of hydrophobic surface is solvent-exposed (10/16 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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.153 kcal/mol/HA)
✓ Good fit quality (FQ -10.34)
✓ Strong H-bond network (14 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Extreme strain energy (53.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-27.681
kcal/mol
LE
-1.153
kcal/mol/HA
Fit Quality
-10.34
FQ (Leeson)
HAC
24
heavy atoms
MW
327
Da
LogP
1.78
cLogP
Interaction summary
HB 14
HY 5
PI 2
CLASH 1
⚠ Exposure 62%
Interaction summary
HB 14
HY 5
PI 2
CLASH 1
⚠ Exposure 62%
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
62% of hydrophobic surface is solvent-exposed (10/16 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 16
Buried (contacted) 6
Exposed 10
LogP 1.78
H-bonds 14
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 3.449 | Score | -27.681 |
|---|---|---|---|
| Inter norm | -1.265 | Intra norm | 0.111 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 14 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; high strain Δ 53.2 | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
ASP10
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
PRO12
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 | 0.87 | RMSD | - |
| HB strict | 8 | Strict recall | 0.67 |
| HB same residue+role | 6 | HB role recall | 0.67 |
| HB same residue | 7 | HB residue recall | 0.88 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 221 | 2.0077812066392657 | -1.17383 | -28.7197 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 241 | 2.3528098974898835 | -0.863335 | -23.523 | 8 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 240 | 3.2412632912082957 | -1.01964 | -23.5904 | 9 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 210 | 3.449396824714685 | -1.26484 | -27.6814 | 14 | 14 | 13 | 0.93 | 0.67 | - | no | Current |
| 257 | 3.5567855665101447 | -1.42321 | -33.4356 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 150 | 4.302305108254698 | -1.30222 | -27.4863 | 14 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 267 | 4.3230268269514776 | -0.796912 | -19.6092 | 9 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 162 | 4.726542041013789 | -1.23245 | -28.9868 | 12 | 13 | 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
-27.681kcal/mol
Ligand efficiency (LE)
-1.1534kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.337
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
327.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.78
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
53.16kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
124.22kcal/mol
Minimised FF energy
71.07kcal/mol
SASA & burial
✓ computed
SASA (unbound)
563.5Ų
Total solvent-accessible surface area of free ligand
BSA total
390.7Ų
Buried surface area upon binding
BSA apolar
272.2Ų
Hydrophobic contacts buried
BSA polar
118.5Ų
Polar contacts buried
Fraction buried
69.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2145.1Ų
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
769.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)