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
80.3 kcal/mol
Protein clashes
0
Internal clashes
23
Native overlap
contact recall 0.47, Jaccard 0.30, H-bond role recall 0.40
Reason: 23 internal clashes, strain 80.3 kcal/mol
strain ΔE 80.3 kcal/mol
23 intramolecular clashes
77% of hydrophobic surface is solvent-exposed (20/26 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 (-0.707 kcal/mol/HA)
✓ Good fit quality (FQ -7.18)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (65% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Extreme strain energy (80.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (23)
Score
-25.434
kcal/mol
LE
-0.707
kcal/mol/HA
Fit Quality
-7.18
FQ (Leeson)
HAC
36
heavy atoms
MW
499
Da
LogP
0.30
cLogP
Interaction summary
HB 9
HY 2
PI 0
CLASH 0
⚠ Exposure 76%
Interaction summary
HB 9
HY 2
PI 0
CLASH 0
⚠ Exposure 76%
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.
Solvent-exposed hydrophobic surface — desolvation penalty likely
77% of hydrophobic surface is solvent-exposed (20/26 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) 6
Exposed 20
LogP 0.3
H-bonds 9
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 5.184 | Score | -25.434 |
|---|---|---|---|
| Inter norm | -0.682 | Intra norm | -0.025 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 9 |
| Artifact reason | geometry warning; 23 clashes; 3 protein clashes; high strain Δ 80.3 | ||
| Residues |
ALA283
ARG22
ARG50
ASP385
ASP44
ASP47
CYS26
GLN341
GLU384
LEU25
LEU382
PHE284
SER282
THR21
THR285
| ||
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 | 0.30 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 36 | 3.754760107297694 | -0.70587 | -27.3156 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 43 | 5.184386456076703 | -0.681665 | -25.4339 | 9 | 15 | 7 | 0.47 | 0.40 | - | no | Current |
| 23 | 5.87747965905087 | -0.654866 | -26.2231 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 40 | 5.921196088162966 | -0.755699 | -26.9022 | 8 | 13 | 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
-25.434kcal/mol
Ligand efficiency (LE)
-0.7065kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.181
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
498.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.30
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
80.29kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
142.03kcal/mol
Minimised FF energy
61.74kcal/mol
SASA & burial
✓ computed
SASA (unbound)
719.4Ų
Total solvent-accessible surface area of free ligand
BSA total
470.2Ų
Buried surface area upon binding
BSA apolar
379.4Ų
Hydrophobic contacts buried
BSA polar
90.8Ų
Polar contacts buried
Fraction buried
65.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2517.6Ų
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
1388.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)