Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native mixed
SASA done
Strain ΔE
23.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.47, Jaccard 0.37, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
70% of hydrophobic surface is solvent-exposed (16/23 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Daphnia EC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Algae IC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Bioaccum.
B — Bioaccumulative (BCF>2000)
Persistent
Yes
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.862 kcal/mol/HA)
✓ Good fit quality (FQ -8.23)
✓ Good H-bonds (3 bonds)
✓ Good burial (61% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ High strain energy (23.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-25.010
kcal/mol
LE
-0.862
kcal/mol/HA
Fit Quality
-8.23
FQ (Leeson)
HAC
29
heavy atoms
MW
417
Da
LogP
6.21
cLogP
Final rank
3.7399
rank score
Inter norm
-0.896
normalised
Contacts
11
H-bonds 4
Interaction summary
HBD 1
HBA 2
HY 3
PI 0
CLASH 2
Interaction summary
HBD 1
HBA 2
HY 3
PI 0
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
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: 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 | 7 | Native recall | 0.47 |
| Jaccard | 0.37 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 619 | 1.0357649891295575 | -0.712271 | -20.5399 | 2 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 598 | 1.1609293363911366 | -0.916148 | -28.6471 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 613 | 1.3510130234537063 | -1.24287 | -36.6547 | 2 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 604 | 3.739881015500972 | -0.895706 | -25.0102 | 4 | 11 | 7 | 0.47 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.010kcal/mol
Ligand efficiency (LE)
-0.8624kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.232
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
416.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.21
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.60kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
96.26kcal/mol
Minimised FF energy
72.66kcal/mol
SASA & burial
✓ computed
SASA (unbound)
665.5Ų
Total solvent-accessible surface area of free ligand
BSA total
408.8Ų
Buried surface area upon binding
BSA apolar
330.9Ų
Hydrophobic contacts buried
BSA polar
77.9Ų
Polar contacts buried
Fraction buried
61.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2463.3Ų
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
1427.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)