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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
38.6 kcal/mol
Protein clashes
0
Internal clashes
8
Native overlap
contact recall 0.60, Jaccard 0.39, H-bond role recall 0.20
Reason: 8 internal clashes
8 intramolecular clashes
44% of hydrophobic surface appears solvent-exposed (7/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.074 kcal/mol/HA)
✓ Good fit quality (FQ -9.62)
✓ Good H-bonds (5 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Very high strain energy (38.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-25.771
kcal/mol
LE
-1.074
kcal/mol/HA
Fit Quality
-9.62
FQ (Leeson)
HAC
24
heavy atoms
MW
366
Da
LogP
2.66
cLogP
Interaction summary
HB 5
HY 13
PI 0
CLASH 0
⚠ Exposure 43%
Interaction summary
HB 5
HY 13
PI 0
CLASH 0
⚠ Exposure 43%
Partial hydrophobic solvent exposure
44% of hydrophobic surface appears solvent-exposed (7/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 16
Buried (contacted) 9
Exposed 7
LogP 2.66
H-bonds 5
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 2.032 | Score | -25.771 |
|---|---|---|---|
| Inter norm | -0.918 | Intra norm | -0.156 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 5 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash; high strain Δ 38.6 | ||
| Residues |
ALA283
ARG22
ARG50
ASN20
ASP385
ASP44
ASP47
CYS26
GLN341
GLU384
LEU25
LEU339
LEU382
PRO340
SER282
THR21
THR285
| ||
Protein summary
398 residues
| Protein target | T14 | Atoms | 6140 |
|---|---|---|---|
| Residues | 398 | Chains | 1 |
| Residue summary | VAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:ORX602
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1NJJ | Contacts | 15 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG22
ARG242
ARG337
ARG342
ASP243
ASP385
GLN341
GLU384
LEU25
LEU339
LEU382
PRO340
PRO344
SER282
THR241
| ||
| Current overlap | 9 | Native recall | 0.60 |
| Jaccard | 0.39 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
All stored poses for this docking hit
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.771kcal/mol
Ligand efficiency (LE)
-1.0738kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.623
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
365.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.66
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
5.47kcal/mol
Minimised FF energy
-33.15kcal/mol
SASA & burial
✓ computed
SASA (unbound)
585.7Ų
Total solvent-accessible surface area of free ligand
BSA total
500.0Ų
Buried surface area upon binding
BSA apolar
408.1Ų
Hydrophobic contacts buried
BSA polar
91.9Ų
Polar contacts buried
Fraction buried
85.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2434.5Ų
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
3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1389.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)