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
24.0 kcal/mol
Protein clashes
0
Internal clashes
22
Native overlap
contact recall 0.53, Jaccard 0.36, H-bond role recall 0.20
Reason: 22 internal clashes
22 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.689 kcal/mol/HA)
✓ Good fit quality (FQ -6.89)
✓ Good H-bonds (4 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ High strain energy (24.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (22)
Score
-23.431
kcal/mol
LE
-0.689
kcal/mol/HA
Fit Quality
-6.89
FQ (Leeson)
HAC
34
heavy atoms
MW
476
Da
LogP
3.33
cLogP
Interaction summary
HB 4
HY 4
PI 0
CLASH 0
⚠ Exposure 76%
Interaction summary
HB 4
HY 4
PI 0
CLASH 0
⚠ 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 3.33
H-bonds 4
Exposed fragments:
phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 4.421 | Score | -23.431 |
|---|---|---|---|
| Inter norm | -0.682 | Intra norm | -0.007 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 4 |
| Artifact reason | geometry warning; 22 clashes; 2 protein clashes; moderate strain Δ 24.0 | ||
| Residues |
ARG22
ARG242
ARG50
ASN20
ASP385
ASP44
GLU384
GLY240
LEU25
LEU382
LYS51
SER282
THR21
THR241
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 | 8 | Native recall | 0.53 |
| Jaccard | 0.36 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 520 | 1.6424782003672744 | -1.00249 | -34.1913 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 519 | 4.421420834376208 | -0.682309 | -23.4308 | 4 | 15 | 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
-23.431kcal/mol
Ligand efficiency (LE)
-0.6891kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.895
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
475.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.33
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.01kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
159.36kcal/mol
Minimised FF energy
135.35kcal/mol
SASA & burial
✓ computed
SASA (unbound)
732.4Ų
Total solvent-accessible surface area of free ligand
BSA total
545.7Ų
Buried surface area upon binding
BSA apolar
451.1Ų
Hydrophobic contacts buried
BSA polar
94.7Ų
Polar contacts buried
Fraction buried
74.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2571.4Ų
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
1400.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)