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 strong
SASA done
Strain ΔE
37.4 kcal/mol
Protein clashes
0
Internal clashes
4
Native overlap
contact recall 0.60, Jaccard 0.50, H-bond role recall 0.40
Reason: no major geometry red flags detected
4 intramolecular clashes
65% of hydrophobic surface is solvent-exposed (11/17 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 (-1.040 kcal/mol/HA)
✓ Good fit quality (FQ -9.45)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ Very high strain energy (37.4 kcal/mol)
✗ Geometry warnings
Score
-25.990
kcal/mol
LE
-1.040
kcal/mol/HA
Fit Quality
-9.45
FQ (Leeson)
HAC
25
heavy atoms
MW
376
Da
LogP
1.67
cLogP
Interaction summary
HB 8
HY 2
PI 0
CLASH 0
⚠ Exposure 64%
Interaction summary
HB 8
HY 2
PI 0
CLASH 0
⚠ Exposure 64%
Solvent-exposed hydrophobic surface — desolvation penalty likely
65% of hydrophobic surface is solvent-exposed (11/17 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 17
Buried (contacted) 6
Exposed 11
LogP 1.67
H-bonds 8
Exposed fragments:
phenyl (3/5 atoms exposed)phenyl (4/5 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 1.610 | Score | -25.990 |
|---|---|---|---|
| Inter norm | -1.076 | Intra norm | 0.037 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 8 |
| Artifact reason | geometry warning; 4 clashes; 1 protein clash; high strain Δ 37.4 | ||
| Residues |
ARG242
ARG337
ASP243
ASP385
GLU384
LEU339
LEU382
PHE383
PRO338
SER282
THR241
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 | 9 | Native recall | 0.60 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 395 | 0.10927334712649962 | -1.0296 | -21.6302 | 11 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 422 | 0.14692465670760751 | -1.36126 | -25.1177 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 393 | 0.2333073319917216 | -1.41845 | -29.1095 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 423 | 1.6098485630425021 | -1.07617 | -25.9897 | 8 | 12 | 9 | 0.60 | 0.40 | - | no | Current |
| 466 | 2.1741307385320137 | -0.984654 | -21.2362 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 499 | 3.024266895819682 | -0.977796 | -21.3529 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 485 | 3.395760459171136 | -1.21637 | -25.8565 | 4 | 19 | 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
-25.990kcal/mol
Ligand efficiency (LE)
-1.0396kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.451
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
376.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.67
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.36kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
82.42kcal/mol
Minimised FF energy
45.06kcal/mol
SASA & burial
✓ computed
SASA (unbound)
624.5Ų
Total solvent-accessible surface area of free ligand
BSA total
426.2Ų
Buried surface area upon binding
BSA apolar
294.3Ų
Hydrophobic contacts buried
BSA polar
131.9Ų
Polar contacts buried
Fraction buried
68.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2414.3Ų
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
1398.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)