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
Weak or marginal quality
Binding strong
Geometry medium
Native mixed
SASA done
Strain ΔE
24.9 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.47, Jaccard 0.39, H-bond role recall 0.20
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
67% of hydrophobic surface is solvent-exposed (16/24 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 (-0.660 kcal/mol/HA)
✓ Good fit quality (FQ -6.37)
✓ Good H-bonds (5 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ High strain energy (24.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (17)
Score
-19.813
kcal/mol
LE
-0.660
kcal/mol/HA
Fit Quality
-6.37
FQ (Leeson)
HAC
30
heavy atoms
MW
410
Da
LogP
4.77
cLogP
Interaction summary
HB 5
HY 3
PI 0
CLASH 5
⚠ Exposure 66%
Interaction summary
HB 5
HY 3
PI 0
CLASH 5
⚠ Exposure 66%
Solvent-exposed hydrophobic surface — desolvation penalty likely
67% of hydrophobic surface is solvent-exposed (16/24 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 24
Buried (contacted) 8
Exposed 16
LogP 4.77
H-bonds 5
Exposed fragments:
phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.244 | Score | -19.813 |
|---|---|---|---|
| Inter norm | -0.727 | Intra norm | 0.066 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 5 |
| Artifact reason | geometry warning; 17 clashes; 1 protein clash; moderate strain Δ 24.9 | ||
| Residues |
ARG242
ARG337
ASP243
ASP385
GLU384
LEU339
PHE383
THR241
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 | 7 | Native recall | 0.47 |
| Jaccard | 0.39 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| 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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 40 | 3.2438954404894225 | -0.726884 | -19.8134 | 5 | 10 | 7 | 0.47 | 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
-19.813kcal/mol
Ligand efficiency (LE)
-0.6604kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.371
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
410.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.77
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.93kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
153.86kcal/mol
Minimised FF energy
128.93kcal/mol
SASA & burial
✓ computed
SASA (unbound)
645.7Ų
Total solvent-accessible surface area of free ligand
BSA total
450.6Ų
Buried surface area upon binding
BSA apolar
355.8Ų
Hydrophobic contacts buried
BSA polar
94.8Ų
Polar contacts buried
Fraction buried
69.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2483.2Ų
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)