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
8.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.60, Jaccard 0.47, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
65% of hydrophobic surface is solvent-exposed (13/20 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 (-0.864 kcal/mol/HA)
✓ Good fit quality (FQ -7.96)
✓ Good H-bonds (4 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ Moderate strain (8.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-22.452
kcal/mol
LE
-0.864
kcal/mol/HA
Fit Quality
-7.96
FQ (Leeson)
HAC
26
heavy atoms
MW
344
Da
LogP
2.51
cLogP
Final rank
3.4642
rank score
Inter norm
-0.847
normalised
Contacts
13
H-bonds 5
Interaction summary
HBD 4
HY 1
PI 0
CLASH 1
Interaction summary
HBD 4
HY 1
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 | 0.47 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 37 | 0.1852878262268813 | -1.2388 | -31.1169 | 4 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 70 | 0.7477966718695047 | -1.02701 | -26.7733 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 50 | 1.3519053727924024 | -0.814557 | -22.3807 | 3 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 48 | 1.9396733670013004 | -1.01831 | -25.6436 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 65 | 3.4642084593295603 | -0.846966 | -22.4516 | 5 | 13 | 9 | 0.60 | 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
-22.452kcal/mol
Ligand efficiency (LE)
-0.8635kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.956
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
344.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.51
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
8.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-108.38kcal/mol
Minimised FF energy
-116.72kcal/mol
SASA & burial
✓ computed
SASA (unbound)
607.5Ų
Total solvent-accessible surface area of free ligand
BSA total
412.8Ų
Buried surface area upon binding
BSA apolar
366.8Ų
Hydrophobic contacts buried
BSA polar
46.0Ų
Polar contacts buried
Fraction buried
67.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2481.2Ų
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
1424.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)