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 mixed
SASA done
Strain ΔE
18.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.53, Jaccard 0.47, H-bond role recall 0.20
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
77% of hydrophobic surface is solvent-exposed (20/26 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 (-0.759 kcal/mol/HA)
✓ Good fit quality (FQ -7.40)
✓ Good H-bonds (4 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ Moderate strain (18.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (17)
Score
-23.533
kcal/mol
LE
-0.759
kcal/mol/HA
Fit Quality
-7.40
FQ (Leeson)
HAC
31
heavy atoms
MW
409
Da
LogP
4.57
cLogP
Interaction summary
HB 4
HY 2
PI 0
CLASH 3
⚠ Exposure 76%
Interaction summary
HB 4
HY 2
PI 0
CLASH 3
⚠ Exposure 76%
Solvent-exposed hydrophobic surface — desolvation penalty likely
77% of hydrophobic surface is solvent-exposed (20/26 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 26
Buried (contacted) 6
Exposed 20
LogP 4.57
H-bonds 4
Exposed fragments:
phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.309 | Score | -23.533 |
|---|---|---|---|
| Inter norm | -0.719 | Intra norm | -0.040 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 4 |
| Artifact reason | geometry warning; 17 clashes; 1 protein clash | ||
| Residues |
ARG242
ARG337
ASP243
ASP385
GLU384
LEU339
SER282
THR21
THR241
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 | 8 | Native recall | 0.53 |
| Jaccard | 0.47 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| 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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 560 | 1.5524363376816304 | -0.743418 | -20.5292 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 529 | 1.815148662072829 | -0.62049 | -19.2224 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 516 | 1.8766063905365975 | -0.821197 | -24.9157 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 550 | 2.5648728586241805 | -0.720981 | -21.2854 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 517 | 3.30870723637248 | -0.718914 | -23.5334 | 4 | 10 | 8 | 0.53 | 0.20 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.533kcal/mol
Ligand efficiency (LE)
-0.7591kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.396
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
409.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.57
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
138.13kcal/mol
Minimised FF energy
119.37kcal/mol
SASA & burial
✓ computed
SASA (unbound)
689.2Ų
Total solvent-accessible surface area of free ligand
BSA total
496.4Ų
Buried surface area upon binding
BSA apolar
440.4Ų
Hydrophobic contacts buried
BSA polar
56.0Ų
Polar contacts buried
Fraction buried
72.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2578.8Ų
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
1401.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)