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
38.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.47, Jaccard 0.35, H-bond role recall 0.20
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.683 kcal/mol/HA)
✓ Good fit quality (FQ -6.52)
✓ Good H-bonds (5 bonds)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Very high strain energy (38.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-19.794
kcal/mol
LE
-0.683
kcal/mol/HA
Fit Quality
-6.52
FQ (Leeson)
HAC
29
heavy atoms
MW
404
Da
LogP
4.67
cLogP
Interaction summary
HB 5
HY 12
PI 0
CLASH 3
Interaction summary
HB 5
HY 12
PI 0
CLASH 3
| Final rank | 4.087 | Score | -19.794 |
|---|---|---|---|
| Inter norm | -0.836 | Intra norm | 0.153 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 5 |
| Artifact reason | geometry warning; 15 clashes; 2 protein clashes; high strain Δ 37.8 | ||
| Residues |
ARG22
ARG342
ASN20
CYS26
GLN341
GLU343
GLU384
LEU25
LEU382
PRO340
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 | 7 | Native recall | 0.47 |
| Jaccard | 0.35 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 494 | 1.1577042796268664 | -0.806499 | -20.9573 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 452 | 1.5916735758417686 | -1.10999 | -27.3548 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 476 | 1.697784199305133 | -0.945349 | -17.4477 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 429 | 1.9753143606479693 | -0.828598 | -16.278 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 437 | 2.7071296605498025 | -1.02096 | -25.3626 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 463 | 3.0485298790569324 | -0.939335 | -24.8709 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 436 | 3.9486253783950946 | -1.03556 | -23.1969 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 454 | 4.0865649410255696 | -0.835591 | -19.7943 | 5 | 12 | 7 | 0.47 | 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
-19.794kcal/mol
Ligand efficiency (LE)
-0.6826kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.516
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
404.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.67
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.46kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
77.45kcal/mol
Minimised FF energy
38.99kcal/mol
SASA & burial
✓ computed
SASA (unbound)
638.4Ų
Total solvent-accessible surface area of free ligand
BSA total
497.1Ų
Buried surface area upon binding
BSA apolar
388.7Ų
Hydrophobic contacts buried
BSA polar
108.3Ų
Polar contacts buried
Fraction buried
77.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2468.9Ų
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
1376.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)