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 high
Native strong
SASA done
Strain ΔE
24.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.60, Jaccard 0.39, H-bond role recall 0.60
Reason: no major geometry red flags detected
2 protein-contact clashes
45% of hydrophobic surface appears solvent-exposed (9/20 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 (-0.687 kcal/mol/HA)
✓ Good fit quality (FQ -6.88)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ High strain energy (24.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-23.366
kcal/mol
LE
-0.687
kcal/mol/HA
Fit Quality
-6.88
FQ (Leeson)
HAC
34
heavy atoms
MW
473
Da
LogP
3.62
cLogP
Interaction summary
HB 8
HY 23
PI 0
CLASH 2
⚠ Exposure 45%
Interaction summary
HB 8
HY 23
PI 0
CLASH 2
⚠ Exposure 45%
Partial hydrophobic solvent exposure
45% of hydrophobic surface appears solvent-exposed (9/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20
Buried (contacted) 11
Exposed 9
LogP 3.62
H-bonds 8
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (2/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 5.221 | Score | -23.366 |
|---|---|---|---|
| Inter norm | -0.655 | Intra norm | -0.033 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 8 |
| Artifact reason | geometry warning; 15 clashes; 3 protein clashes; moderate strain Δ 24.5 | ||
| Residues |
ARG22
ARG342
CYS26
GLN341
GLU343
GLU384
LEU25
LEU339
LEU350
LEU372
LEU382
PRO340
PRO344
PRO373
THR21
THR285
TYR371
| ||
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 | 9 | Native recall | 0.60 |
| Jaccard | 0.39 | RMSD | - |
| HB strict | 3 | Strict recall | 0.50 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 3 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 402 | 2.532635380183973 | -0.78869 | -18.0267 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 354 | 3.6788985161070658 | -0.702287 | -14.6877 | 9 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 374 | 3.7377674173523148 | -0.920885 | -26.0731 | 14 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 386 | 4.7673793828367055 | -0.60447 | -2.74681 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 418 | 4.819316264563223 | -0.688052 | -11.396 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 363 | 5.2213655928055065 | -0.654564 | -23.366 | 8 | 17 | 9 | 0.60 | 0.60 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.366kcal/mol
Ligand efficiency (LE)
-0.6872kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.876
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
473.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.62
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
98.37kcal/mol
Minimised FF energy
73.83kcal/mol
SASA & burial
✓ computed
SASA (unbound)
705.4Ų
Total solvent-accessible surface area of free ligand
BSA total
567.6Ų
Buried surface area upon binding
BSA apolar
450.9Ų
Hydrophobic contacts buried
BSA polar
116.7Ų
Polar contacts buried
Fraction buried
80.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2502.0Ų
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
1390.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)