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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
19.7 kcal/mol
Protein clashes
2
Internal clashes
18
Native overlap
contact recall 0.53, Jaccard 0.40, H-bond role recall 0.20
Reason: 18 internal clashes
2 protein-contact clashes
18 intramolecular clashes
78% of hydrophobic surface is solvent-exposed (18/23 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 (-0.878 kcal/mol/HA)
✓ Good fit quality (FQ -8.47)
✓ Good H-bonds (4 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Moderate strain (19.7 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (18)
Score
-26.352
kcal/mol
LE
-0.878
kcal/mol/HA
Fit Quality
-8.47
FQ (Leeson)
HAC
30
heavy atoms
MW
398
Da
LogP
3.86
cLogP
Interaction summary
HB 4
HY 1
PI 0
CLASH 0
⚠ Exposure 78%
Interaction summary
HB 4
HY 1
PI 0
CLASH 0
⚠ Exposure 78%
Solvent-exposed hydrophobic surface — desolvation penalty likely
78% of hydrophobic surface is solvent-exposed (18/23 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 23
Buried (contacted) 5
Exposed 18
LogP 3.86
H-bonds 4
Exposed fragments:
phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 1.530 | Score | -26.352 |
|---|---|---|---|
| Inter norm | -0.780 | Intra norm | -0.110 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 4 |
| Artifact reason | geometry warning; 18 clashes; 2 protein contact clashes | ||
| Residues |
ARG242
ARG337
ASP243
ASP385
ASP47
GLU384
GLY240
LEU339
LYS51
PHE383
SER282
THR241
VAL336
| ||
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
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 | 8 | Native recall | 0.53 |
| Jaccard | 0.40 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 2 | HB residue recall | 0.40 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 383 | 1.2287636357355942 | -1.0501 | -37.6676 | 7 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 420 | 1.5304501302166158 | -0.780324 | -26.3523 | 4 | 13 | 8 | 0.53 | 0.20 | - | no | Current |
| 436 | 2.785856035332341 | -0.980801 | -34.63 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 497 | 2.955093255524448 | -0.865923 | -27.6702 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 509 | 3.2491331708059237 | -0.794232 | -23.4452 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 465 | 4.004368900998721 | -0.799974 | -24.3755 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 391 | 4.4407993593659 | -1.07037 | -31.267 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 426 | 4.8004481778310115 | -0.756591 | -25.3759 | 10 | 12 | 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
-26.352kcal/mol
Ligand efficiency (LE)
-0.8784kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.473
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
398.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.86
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
114.14kcal/mol
Minimised FF energy
94.47kcal/mol
SASA & burial
✓ computed
SASA (unbound)
679.6Ų
Total solvent-accessible surface area of free ligand
BSA total
473.7Ų
Buried surface area upon binding
BSA apolar
381.7Ų
Hydrophobic contacts buried
BSA polar
92.0Ų
Polar contacts buried
Fraction buried
69.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2505.1Ų
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
1403.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)