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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
54.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.38, H-bond role recall 0.40
Reason: strain 54.2 kcal/mol
strain ΔE 54.2 kcal/mol
2 protein-contact clashes
100% of hydrophobic surface is solvent-exposed (26/26 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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.407 kcal/mol/HA)
✓ Good fit quality (FQ -4.20)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Extreme strain energy (54.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-15.483
kcal/mol
LE
-0.407
kcal/mol/HA
Fit Quality
-4.20
FQ (Leeson)
HAC
38
heavy atoms
MW
553
Da
LogP
5.30
cLogP
Interaction summary
HB 6
HY 0
PI 0
CLASH 2
⚠ Exposure 100%
Interaction summary
HB 6
HY 0
PI 0
CLASH 2
⚠ Exposure 100%
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
No hy · hydrophobic contacts detected for this pose.
CLASH · Clashes
Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (26/26 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 26
Buried (contacted) 0
Exposed 26
LogP 5.3
H-bonds 6
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (4/5 atoms exposed)phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 4.087 | Score | -15.483 |
|---|---|---|---|
| Inter norm | -0.610 | Intra norm | 0.203 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 6 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes; high strain Δ 54.2 | ||
| Residues |
ALA283
ARG22
ARG242
ASN20
ASP243
ASP385
ASP44
ASP47
GLU384
GLY240
LEU339
SER282
THR21
THR241
| ||
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 | 0.38 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 376 | 2.38538977685145 | -0.748088 | -29.5979 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 410 | 2.531002620908655 | -0.839942 | -30.6602 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 507 | 2.6120830374456596 | -0.623331 | -12.3829 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 437 | 2.794037718136994 | -0.604459 | -17.8959 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 488 | 2.9134037039057636 | -0.631802 | -20.1678 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 397 | 3.0484229827099503 | -0.655948 | -18.9257 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 405 | 3.297389648705711 | -0.985362 | -27.5835 | 12 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 412 | 4.086860697814478 | -0.610123 | -15.4834 | 6 | 14 | 8 | 0.53 | 0.40 | - | no | Current |
| 428 | 4.3700864456086075 | -0.792431 | -28.084 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 397 | 4.945488414768248 | -0.750799 | -21.5195 | 9 | 20 | 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
-15.483kcal/mol
Ligand efficiency (LE)
-0.4075kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.201
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
38HA
Physicochemical properties
Molecular weight
552.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.30
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
54.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
65.65kcal/mol
Minimised FF energy
11.43kcal/mol
SASA & burial
✓ computed
SASA (unbound)
858.0Ų
Total solvent-accessible surface area of free ligand
BSA total
599.4Ų
Buried surface area upon binding
BSA apolar
431.4Ų
Hydrophobic contacts buried
BSA polar
168.0Ų
Polar contacts buried
Fraction buried
69.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2550.3Ų
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
1462.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)