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
69.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.60, Jaccard 0.53, H-bond role recall 0.40
Reason: strain 69.4 kcal/mol
strain ΔE 69.4 kcal/mol
3 protein-contact clashes
3 intramolecular clashes
100% of hydrophobic surface is solvent-exposed (27/27 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 (-0.637 kcal/mol/HA)
✓ Good fit quality (FQ -6.62)
✓ Strong H-bond network (9 bonds)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ Extreme strain energy (69.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (20)
Score
-24.862
kcal/mol
LE
-0.637
kcal/mol/HA
Fit Quality
-6.62
FQ (Leeson)
HAC
39
heavy atoms
MW
545
Da
LogP
-0.72
cLogP
Interaction summary
HB 9
HY 1
PI 0
CLASH 3
⚠ Exposure 100%
Interaction summary
HB 9
HY 1
PI 0
CLASH 3
⚠ Exposure 100%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (27/27 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 27
Buried (contacted) 0
Exposed 27
LogP -0.72
H-bonds 9
Exposed fragments:
phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 5.926 | Score | -24.862 |
|---|---|---|---|
| Inter norm | -0.671 | Intra norm | 0.033 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 9 |
| Artifact reason | geometry warning; 20 clashes; 3 protein clashes; high strain Δ 69.4 | ||
| Residues |
ARG242
ARG337
ASP243
ASP385
GLU384
LEU339
LEU382
PHE383
PRO338
SER282
THR241
| ||
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 | 0.53 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 3 | HB residue recall | 0.60 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 25 | 4.545849938916814 | -0.612181 | -23.1555 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 50 | 4.558542500238084 | -0.750709 | -26.6034 | 12 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 37 | 5.41903790277031 | -0.585366 | -22.3397 | 7 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 46 | 5.925882696488416 | -0.670681 | -24.862 | 9 | 11 | 9 | 0.60 | 0.40 | - | no | Current |
| 29 | 7.449320461081546 | -0.724751 | -26.6738 | 7 | 16 | 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
-24.862kcal/mol
Ligand efficiency (LE)
-0.6375kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.616
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
39HA
Physicochemical properties
Molecular weight
544.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.72
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
69.43kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
154.35kcal/mol
Minimised FF energy
84.92kcal/mol
SASA & burial
✓ computed
SASA (unbound)
786.5Ų
Total solvent-accessible surface area of free ligand
BSA total
485.8Ų
Buried surface area upon binding
BSA apolar
335.1Ų
Hydrophobic contacts buried
BSA polar
150.8Ų
Polar contacts buried
Fraction buried
61.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2522.0Ų
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
3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1411.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)