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
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
40.1 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.53, Jaccard 0.31, H-bond role recall 0.20
Reason: 6 internal clashes
6 protein-contact clashes
6 intramolecular clashes
76% of hydrophobic surface is solvent-exposed (19/25 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 (-0.690 kcal/mol/HA)
✓ Good fit quality (FQ -7.06)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Extreme strain energy (40.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (17)
Score
-25.527
kcal/mol
LE
-0.690
kcal/mol/HA
Fit Quality
-7.06
FQ (Leeson)
HAC
37
heavy atoms
MW
493
Da
LogP
3.67
cLogP
Interaction summary
HB 11
HY 1
PI 0
CLASH 6
⚠ Exposure 76%
Interaction summary
HB 11
HY 1
PI 0
CLASH 6
⚠ Exposure 76%
Solvent-exposed hydrophobic surface — desolvation penalty likely
76% of hydrophobic surface is solvent-exposed (19/25 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 25
Buried (contacted) 6
Exposed 19
LogP 3.67
H-bonds 11
Exposed fragments:
phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 6.093 | Score | -25.527 |
|---|---|---|---|
| Inter norm | -0.763 | Intra norm | 0.073 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 11 |
| Artifact reason | geometry warning; 17 clashes; 3 protein clashes; high strain Δ 40.0 | ||
| Residues |
ARG242
ARG337
ARG50
ASP243
ASP385
ASP44
ASP47
GLU384
LEU339
LYS51
MET386
PHE383
PRO338
SER282
THR21
THR241
THR285
VAL335
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 | 0.31 | 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 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 353 | 2.015098068419916 | -0.644222 | -12.4849 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 422 | 3.344179847059429 | -0.757789 | -22.5673 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 385 | 3.613721224243601 | -0.745122 | -17.8461 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 324 | 3.7829752552443856 | -1.101 | -35.0187 | 10 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 359 | 3.9698352490279074 | -0.644073 | -22.3155 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 313 | 4.694947483235921 | -0.98281 | -33.8871 | 13 | 24 | 0 | 0.00 | 0.00 | - | no | Open |
| 388 | 4.821725173570794 | -0.777024 | -25.3326 | 12 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 342 | 6.092894906155297 | -0.763123 | -25.5269 | 11 | 19 | 8 | 0.53 | 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
-25.527kcal/mol
Ligand efficiency (LE)
-0.6899kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.063
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
493.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.67
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
40.13kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
113.44kcal/mol
Minimised FF energy
73.31kcal/mol
SASA & burial
✓ computed
SASA (unbound)
788.0Ų
Total solvent-accessible surface area of free ligand
BSA total
615.0Ų
Buried surface area upon binding
BSA apolar
461.7Ų
Hydrophobic contacts buried
BSA polar
153.3Ų
Polar contacts buried
Fraction buried
78.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2537.9Ų
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
1411.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)