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 medium
Native mixed
SASA done
Strain ΔE
10.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.33, Jaccard 0.26, H-bond role recall 0.40
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
83% of hydrophobic surface is solvent-exposed (15/18 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 (-1.026 kcal/mol/HA)
✓ Good fit quality (FQ -9.19)
✓ Good H-bonds (4 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Moderate strain (10.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-24.620
kcal/mol
LE
-1.026
kcal/mol/HA
Fit Quality
-9.19
FQ (Leeson)
HAC
24
heavy atoms
MW
324
Da
LogP
3.45
cLogP
Final rank
2.8079
rank score
Inter norm
-1.026
normalised
Contacts
9
H-bonds 7
Interaction summary
HBD 2
HBA 2
HY 2
PI 0
CLASH 3
Interaction summary
HBD 2
HBA 2
HY 2
PI 0
CLASH 3
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 | 5 | Native recall | 0.33 |
| Jaccard | 0.26 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 387 | 0.36051882321163314 | -1.34004 | -29.2797 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 417 | 1.8908796334170939 | -1.35793 | -33.9757 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 435 | 1.9004749194382002 | -1.02058 | -25.9903 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 419 | 2.807878564222623 | -1.0264 | -24.6204 | 7 | 9 | 5 | 0.33 | 0.40 | - | no | Current |
| 403 | 3.0441745044344053 | -1.17278 | -25.3923 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 401 | 3.272585015045708 | -1.014 | -21.3315 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 496 | 4.171712409869473 | -0.992234 | -24.6771 | 8 | 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
-24.620kcal/mol
Ligand efficiency (LE)
-1.0258kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.194
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
324.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.45
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.13kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
59.86kcal/mol
Minimised FF energy
49.73kcal/mol
SASA & burial
✓ computed
SASA (unbound)
549.7Ų
Total solvent-accessible surface area of free ligand
BSA total
399.6Ų
Buried surface area upon binding
BSA apolar
303.4Ų
Hydrophobic contacts buried
BSA polar
96.2Ų
Polar contacts buried
Fraction buried
72.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2405.9Ų
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
1368.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)