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 high
Native mixed
SASA done
Strain ΔE
23.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.47, Jaccard 0.37, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
87% of hydrophobic surface is solvent-exposed (13/15 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 (-0.973 kcal/mol/HA)
✓ Good fit quality (FQ -8.30)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ High strain energy (23.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-20.439
kcal/mol
LE
-0.973
kcal/mol/HA
Fit Quality
-8.30
FQ (Leeson)
HAC
21
heavy atoms
MW
298
Da
LogP
2.88
cLogP
Interaction summary
HB 10
HY 2
PI 0
CLASH 1
⚠ Exposure 86%
Interaction summary
HB 10
HY 2
PI 0
CLASH 1
⚠ Exposure 86%
Solvent-exposed hydrophobic surface — desolvation penalty likely
87% of hydrophobic surface is solvent-exposed (13/15 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 15
Buried (contacted) 2
Exposed 13
LogP 2.88
H-bonds 10
Exposed fragments:
phenyl (4/5 atoms exposed)phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 1.810 | Score | -20.439 |
|---|---|---|---|
| Inter norm | -1.121 | Intra norm | 0.148 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 10 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash; moderate strain Δ 23.9 | ||
| Residues |
ARG22
ASN20
ASP385
GLU384
LEU25
LEU339
LEU382
PHE284
SER282
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 | 7 | Native recall | 0.47 |
| Jaccard | 0.37 | 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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 335 | -0.1986468320773188 | -1.38789 | -26.622 | 6 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 378 | 1.8102537151256433 | -1.12124 | -20.439 | 10 | 11 | 7 | 0.47 | 0.20 | - | no | Current |
| 332 | 2.4659844951824543 | -1.54318 | -32.8627 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 395 | 3.0226348704806103 | -0.917889 | -18.9715 | 6 | 11 | 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
-20.439kcal/mol
Ligand efficiency (LE)
-0.9733kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.302
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
298.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.88
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
13.96kcal/mol
Minimised FF energy
-9.90kcal/mol
SASA & burial
✓ computed
SASA (unbound)
507.8Ų
Total solvent-accessible surface area of free ligand
BSA total
376.8Ų
Buried surface area upon binding
BSA apolar
272.9Ų
Hydrophobic contacts buried
BSA polar
103.9Ų
Polar contacts buried
Fraction buried
74.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2360.1Ų
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
1378.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)