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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
19.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.60, Jaccard 0.38, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
100% of hydrophobic surface is solvent-exposed (22/22 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
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.832 kcal/mol/HA)
✓ Good fit quality (FQ -8.18)
✓ Good H-bonds (5 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Moderate strain (19.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-26.632
kcal/mol
LE
-0.832
kcal/mol/HA
Fit Quality
-8.18
FQ (Leeson)
HAC
32
heavy atoms
MW
507
Da
LogP
6.08
cLogP
Final rank
2.0477
rank score
Inter norm
-0.692
normalised
Contacts
18
H-bonds 7
Interaction summary
HBA 5
HY 3
PI 0
CLASH 1
Interaction summary
HBA 5
HY 3
PI 0
CLASH 1
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 | 9 | Native recall | 0.60 |
| Jaccard | 0.38 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 395 | 2.0476526138597184 | -0.692476 | -26.6323 | 7 | 18 | 9 | 0.60 | 0.20 | - | no | Current |
| 424 | 2.5788501676058075 | -0.867463 | -23.2831 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 471 | 2.817505272993306 | -0.881199 | -31.297 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 347 | 2.9210948625874136 | -1.00306 | -36.752 | 6 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 405 | 3.8775466064868525 | -0.584181 | -18.6285 | 3 | 13 | 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
-26.632kcal/mol
Ligand efficiency (LE)
-0.8323kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.184
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
507.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.08
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-23.77kcal/mol
Minimised FF energy
-42.82kcal/mol
SASA & burial
✓ computed
SASA (unbound)
760.1Ų
Total solvent-accessible surface area of free ligand
BSA total
582.3Ų
Buried surface area upon binding
BSA apolar
465.6Ų
Hydrophobic contacts buried
BSA polar
116.7Ų
Polar contacts buried
Fraction buried
76.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2541.2Ų
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
1416.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)