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 strong
SASA done
Strain ΔE
57.1 kcal/mol
Protein clashes
0
Internal clashes
22
Native overlap
contact recall 0.67, Jaccard 0.34, H-bond role recall 0.40
Reason: 22 internal clashes, strain 57.1 kcal/mol
strain ΔE 57.1 kcal/mol
22 intramolecular clashes
50% of hydrophobic surface appears solvent-exposed (17/34 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Good LE (-0.378 kcal/mol/HA)
✓ Good fit quality (FQ -4.00)
✓ Good H-bonds (5 bonds)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (87%)
✗ Extreme strain energy (57.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (22)
Score
-15.880
kcal/mol
LE
-0.378
kcal/mol/HA
Fit Quality
-4.00
FQ (Leeson)
HAC
42
heavy atoms
MW
565
Da
LogP
2.57
cLogP
Interaction summary
HB 5
HY 20
PI 0
CLASH 0
⚠ Exposure 50%
Interaction summary
HB 5
HY 20
PI 0
CLASH 0
⚠ Exposure 50%
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.
Partial hydrophobic solvent exposure
50% of hydrophobic surface appears solvent-exposed (17/34 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 34
Buried (contacted) 17
Exposed 17
LogP 2.57
H-bonds 5
Exposed fragments:
phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 6.289 | Score | -15.880 |
|---|---|---|---|
| Inter norm | -0.562 | Intra norm | 0.170 |
| Top1000 | no | Excluded | no |
| Contacts | 24 | H-bonds | 5 |
| Artifact reason | geometry warning; 22 clashes; 4 protein clashes; high strain Δ 57.1 | ||
| Residues |
ALA283
ARG22
ARG342
ARG50
ASN20
ASP44
ASP47
CYS26
GLN341
GLU343
GLU384
LEU25
LEU339
LEU350
LEU372
LEU382
PRO340
PRO344
PRO373
SER282
THR21
THR285
TYR370
TYR371
| ||
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 | 10 | Native recall | 0.67 |
| Jaccard | 0.34 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 675 | 2.3439420748985156 | -0.651185 | -19.6259 | 1 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 672 | 6.28885401762623 | -0.562054 | -15.8803 | 5 | 24 | 10 | 0.67 | 0.40 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-15.880kcal/mol
Ligand efficiency (LE)
-0.3781kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.996
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
42HA
Physicochemical properties
Molecular weight
564.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.57
Lipinski: ≤ 5
Rotatable bonds
13
Conformational strain (MMFF94s)
Strain energy (ΔE)
57.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
62.27kcal/mol
Minimised FF energy
5.20kcal/mol
SASA & burial
✓ computed
SASA (unbound)
938.3Ų
Total solvent-accessible surface area of free ligand
BSA total
704.2Ų
Buried surface area upon binding
BSA apolar
614.1Ų
Hydrophobic contacts buried
BSA polar
90.0Ų
Polar contacts buried
Fraction buried
75.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
87.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2750.9Ų
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
1427.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)