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 mixed
SASA done
Strain ΔE
42.0 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.53, Jaccard 0.44, H-bond role recall 0.20
Reason: strain 42.0 kcal/mol
strain ΔE 42.0 kcal/mol
4 protein-contact clashes
4 intramolecular clashes
100% of hydrophobic surface is solvent-exposed (19/19 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
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.624 kcal/mol/HA)
✓ Good fit quality (FQ -5.82)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Extreme strain energy (42.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (17)
Score
-16.842
kcal/mol
LE
-0.624
kcal/mol/HA
Fit Quality
-5.82
FQ (Leeson)
HAC
27
heavy atoms
MW
363
Da
LogP
0.09
cLogP
Final rank
5.3421
rank score
Inter norm
-0.886
normalised
Contacts
11
H-bonds 7
Interaction summary
HBD 2
HBA 4
HY 0
PI 0
CLASH 4
Interaction summary
HBD 2
HBA 4
HY 0
PI 0
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
No hy · hydrophobic contacts detected for this pose.
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 | 8 | Native recall | 0.53 |
| Jaccard | 0.44 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 568 | 5.342081703171574 | -0.886349 | -16.8416 | 7 | 11 | 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
-16.842kcal/mol
Ligand efficiency (LE)
-0.6238kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.819
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
363.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.09
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
42.02kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
183.63kcal/mol
Minimised FF energy
141.61kcal/mol
SASA & burial
✓ computed
SASA (unbound)
612.7Ų
Total solvent-accessible surface area of free ligand
BSA total
441.6Ų
Buried surface area upon binding
BSA apolar
338.0Ų
Hydrophobic contacts buried
BSA polar
103.6Ų
Polar contacts buried
Fraction buried
72.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2428.7Ų
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
1413.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)