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
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
32.2 kcal/mol
Protein clashes
0
Internal clashes
7
Native overlap
contact recall 0.40, Jaccard 0.30, H-bond role recall 0.40
Reason: 7 internal clashes
7 intramolecular clashes
67% of hydrophobic surface is solvent-exposed (12/18 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.937 kcal/mol/HA)
✓ Good fit quality (FQ -8.63)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Very high strain energy (32.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-24.362
kcal/mol
LE
-0.937
kcal/mol/HA
Fit Quality
-8.63
FQ (Leeson)
HAC
26
heavy atoms
MW
376
Da
LogP
1.67
cLogP
Interaction summary
HB 7
HY 3
PI 0
CLASH 0
⚠ Exposure 66%
Interaction summary
HB 7
HY 3
PI 0
CLASH 0
⚠ Exposure 66%
Solvent-exposed hydrophobic surface — desolvation penalty likely
67% of hydrophobic surface is solvent-exposed (12/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 18
Buried (contacted) 6
Exposed 12
LogP 1.67
H-bonds 7
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (4/5 atoms exposed)phenyl (4/5 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 3.272 | Score | -24.362 |
|---|---|---|---|
| Inter norm | -1.075 | Intra norm | 0.138 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 7 |
| Artifact reason | geometry warning; 7 clashes; 3 protein clashes; high strain Δ 32.2 | ||
| Residues |
ARG22
ARG342
ASN20
CYS26
GLN341
GLU343
GLU384
LEU25
LEU382
THR21
THR285
| ||
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 | 6 | Native recall | 0.40 |
| Jaccard | 0.30 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 70 | 0.4524054852069909 | -1.07917 | -27.9146 | 11 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 57 | 1.7005212207923281 | -1.25072 | -29.5956 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 90 | 2.1934380486129053 | -0.867539 | -25.8518 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 85 | 2.849846612885325 | -1.21001 | -27.9116 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 104 | 3.2721200927153076 | -1.07499 | -24.3621 | 7 | 11 | 6 | 0.40 | 0.40 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.362kcal/mol
Ligand efficiency (LE)
-0.9370kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.633
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
375.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.67
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
126.34kcal/mol
Minimised FF energy
94.10kcal/mol
SASA & burial
✓ computed
SASA (unbound)
594.4Ų
Total solvent-accessible surface area of free ligand
BSA total
444.0Ų
Buried surface area upon binding
BSA apolar
364.5Ų
Hydrophobic contacts buried
BSA polar
79.5Ų
Polar contacts buried
Fraction buried
74.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2444.7Ų
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
1390.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)