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
Reject
SASA cached
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
40.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.80, Jaccard 0.60, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
75% of hydrophobic surface is solvent-exposed (33/44 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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.421 kcal/mol/HA)
✓ Good fit quality (FQ -4.60)
✓ Deep burial (67% SASA buried)
✓ Lipophilic contacts well-matched (100%)
✗ Extreme strain energy (40.5 kcal/mol)
✗ No H-bonds detected
✗ Geometry warnings
✗ Many internal clashes (22)
Score
-20.612
kcal/mol
LE
-0.421
kcal/mol/HA
Fit Quality
-4.60
FQ (Leeson)
HAC
49
heavy atoms
MW
656
Da
LogP
7.02
cLogP
Final rank
2.0234
rank score
Inter norm
-0.456
normalised
Contacts
17
H-bonds 1
Interaction summary
HB 0
HY 3
PI 0
CLASH 1
Interaction summary
HB 0
HY 3
PI 0
CLASH 1
HBD/HBA · H-bonds (geometric)
No hbd/hba · h-bonds (geometric) detected for this pose.
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 | 12 | Native recall | 0.80 |
| Jaccard | 0.60 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 161 | 1.7046483196384499 | -0.543317 | -26.7988 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 187 | 2.0233650628257442 | -0.455594 | -20.612 | 1 | 17 | 12 | 0.80 | 0.20 | - | no | Current |
| 284 | 3.0793514184073816 | -0.498436 | -24.0733 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 279 | 3.291236765499163 | -0.508086 | -25.1692 | 1 | 16 | 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
-20.612kcal/mol
Ligand efficiency (LE)
-0.4207kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.603
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
49HA
Physicochemical properties
Molecular weight
656.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
7.02
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
40.53kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
129.76kcal/mol
Minimised FF energy
89.22kcal/mol
SASA & burial
✓ computed
SASA (unbound)
1039.3Ų
Total solvent-accessible surface area of free ligand
BSA total
698.1Ų
Buried surface area upon binding
BSA apolar
694.4Ų
Hydrophobic contacts buried
BSA polar
3.7Ų
Polar contacts buried
Fraction buried
67.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
99.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2952.6Ų
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
1412.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)