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
35.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.53, Jaccard 0.35, H-bond role recall 0.40
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
100% of hydrophobic surface is solvent-exposed (21/21 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 (-0.730 kcal/mol/HA)
✓ Good fit quality (FQ -7.11)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Very high strain energy (35.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-22.623
kcal/mol
LE
-0.730
kcal/mol/HA
Fit Quality
-7.11
FQ (Leeson)
HAC
31
heavy atoms
MW
460
Da
LogP
2.49
cLogP
Interaction summary
HB 6
HY 1
PI 0
CLASH 3
⚠ Exposure 100%
Interaction summary
HB 6
HY 1
PI 0
CLASH 3
⚠ Exposure 100%
Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (21/21 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 21
Buried (contacted) 0
Exposed 21
LogP 2.49
H-bonds 6
Exposed fragments:
phenyl (4/5 atoms exposed)phenyl (4/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 3.932 | Score | -22.623 |
|---|---|---|---|
| Inter norm | -0.716 | Intra norm | -0.019 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 6 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; high strain Δ 35.3 | ||
| Residues |
ARG242
ARG337
ARG50
ASP243
ASP385
ASP47
GLU384
GLY240
LEU339
LYS51
MET386
PHE383
SER282
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 | 8 | Native recall | 0.53 |
| Jaccard | 0.35 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| 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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 517 | 0.8033075431695811 | -0.824519 | -27.514 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 480 | 1.1073605408917213 | -0.835412 | -27.7086 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 486 | 2.3443851257078063 | -0.674504 | -21.9468 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 518 | 2.663920897533413 | -0.857198 | -27.5751 | 10 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 480 | 3.9319423886939506 | -0.715958 | -22.623 | 6 | 16 | 8 | 0.53 | 0.40 | - | no | Current |
| 480 | 4.82598670924582 | -0.976122 | -30.1806 | 9 | 23 | 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
-22.623kcal/mol
Ligand efficiency (LE)
-0.7298kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.110
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
459.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.49
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-117.15kcal/mol
Minimised FF energy
-152.52kcal/mol
SASA & burial
✓ computed
SASA (unbound)
726.6Ų
Total solvent-accessible surface area of free ligand
BSA total
529.3Ų
Buried surface area upon binding
BSA apolar
372.5Ų
Hydrophobic contacts buried
BSA polar
156.8Ų
Polar contacts buried
Fraction buried
72.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2510.2Ų
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
1380.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)