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 high
Native strong
SASA done
Strain ΔE
24.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.67, Jaccard 0.43, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
82% of hydrophobic surface is solvent-exposed (28/34 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 (-0.640 kcal/mol/HA)
✓ Good fit quality (FQ -6.81)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (95%)
✗ High strain energy (24.1 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Many internal clashes (21)
Score
-27.536
kcal/mol
LE
-0.640
kcal/mol/HA
Fit Quality
-6.81
FQ (Leeson)
HAC
43
heavy atoms
MW
654
Da
LogP
7.33
cLogP
Final rank
2.1689
rank score
Inter norm
-0.587
normalised
Contacts
18
H-bonds 3
Interaction summary
HBD 1
HY 2
PI 0
CLASH 1
Interaction summary
HBD 1
HY 2
PI 0
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 1.
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 | 10 | Native recall | 0.67 |
| Jaccard | 0.43 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 26 | 2.1688970873774895 | -0.58667 | -27.5364 | 3 | 18 | 10 | 0.67 | 0.20 | - | no | Current |
| 9 | 2.3190570076294623 | -0.603254 | -21.9181 | 1 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 21 | 2.872325018187148 | -0.635792 | -24.439 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 18 | 3.3402080092915787 | -0.686468 | -26.5185 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 13 | 3.9691236791986175 | -0.521697 | -21.5427 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 9 | 4.4414998865683915 | -0.646675 | -23.9393 | 6 | 18 | 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
-27.536kcal/mol
Ligand efficiency (LE)
-0.6404kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.806
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
43HA
Physicochemical properties
Molecular weight
654.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
7.33
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
275.89kcal/mol
Minimised FF energy
251.80kcal/mol
SASA & burial
✓ computed
SASA (unbound)
945.0Ų
Total solvent-accessible surface area of free ligand
BSA total
684.3Ų
Buried surface area upon binding
BSA apolar
649.6Ų
Hydrophobic contacts buried
BSA polar
34.7Ų
Polar contacts buried
Fraction buried
72.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
94.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2770.4Ų
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
1484.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)