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
16.3 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.47, Jaccard 0.32, H-bond role recall 0.20
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
76% of hydrophobic surface is solvent-exposed (19/25 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 (-0.945 kcal/mol/HA)
✓ Good fit quality (FQ -9.38)
✓ Good H-bonds (4 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (87%)
✗ Moderate strain (16.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (17)
Score
-31.185
kcal/mol
LE
-0.945
kcal/mol/HA
Fit Quality
-9.38
FQ (Leeson)
HAC
33
heavy atoms
MW
438
Da
LogP
0.96
cLogP
Final rank
3.7670
rank score
Inter norm
-0.675
normalised
Contacts
14
H-bonds 6
Interaction summary
HBD 3
HBA 1
HY 3
PI 0
CLASH 5
Interaction summary
HBD 3
HBA 1
HY 3
PI 0
CLASH 5
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| 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 | 7 | Native recall | 0.47 |
| Jaccard | 0.32 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 76 | 3.1897557631650058 | -0.698458 | -30.0565 | 7 | 14 | 8 | 0.53 | 0.20 | - | no | Open |
| 20 | 3.7669580872675072 | -0.674503 | -31.1854 | 6 | 14 | 7 | 0.47 | 0.20 | - | no | Current |
| 18 | 4.282458672808017 | -0.860278 | -31.4408 | 6 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 64 | 4.566891821002441 | -0.625556 | -22.4241 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 84 | 5.195621716119195 | -0.873675 | -30.0327 | 5 | 20 | 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
-31.185kcal/mol
Ligand efficiency (LE)
-0.9450kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.376
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
437.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.96
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
120.15kcal/mol
Minimised FF energy
103.87kcal/mol
SASA & burial
✓ computed
SASA (unbound)
753.5Ų
Total solvent-accessible surface area of free ligand
BSA total
569.3Ų
Buried surface area upon binding
BSA apolar
497.7Ų
Hydrophobic contacts buried
BSA polar
71.7Ų
Polar contacts buried
Fraction buried
75.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
87.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2611.5Ų
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
1403.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)