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
35.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.40, Jaccard 0.30, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
53% of hydrophobic surface appears solvent-exposed (9/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.107 kcal/mol/HA)
✓ Good fit quality (FQ -10.06)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ Very high strain energy (35.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-27.664
kcal/mol
LE
-1.107
kcal/mol/HA
Fit Quality
-10.06
FQ (Leeson)
HAC
25
heavy atoms
MW
351
Da
LogP
3.77
cLogP
Interaction summary
HB 7
HY 7
PI 0
CLASH 2
⚠ Exposure 52%
Interaction summary
HB 7
HY 7
PI 0
CLASH 2
⚠ Exposure 52%
Partial hydrophobic solvent exposure
53% of hydrophobic surface appears solvent-exposed (9/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 8
Exposed 9
LogP 3.77
H-bonds 7
Exposed fragments:
phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 2.705 | Score | -27.664 |
|---|---|---|---|
| Inter norm | -0.958 | Intra norm | -0.149 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 7 |
| Artifact reason | geometry warning; 6 clashes; 2 protein clashes; high strain Δ 35.5 | ||
| Residues |
ARG22
ARG342
ASN20
CYS26
GLN341
GLU343
GLU384
LEU25
LEU382
THR21
THR285
| ||
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 | 6 | Native recall | 0.40 |
| Jaccard | 0.30 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 589 | 2.7052767419044574 | -0.957704 | -27.664 | 7 | 11 | 6 | 0.40 | 0.20 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.664kcal/mol
Ligand efficiency (LE)
-1.1066kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.060
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
351.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.77
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
33.02kcal/mol
Minimised FF energy
-2.47kcal/mol
SASA & burial
✓ computed
SASA (unbound)
602.1Ų
Total solvent-accessible surface area of free ligand
BSA total
477.2Ų
Buried surface area upon binding
BSA apolar
331.1Ų
Hydrophobic contacts buried
BSA polar
146.1Ų
Polar contacts buried
Fraction buried
79.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2401.6Ų
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
1385.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)