Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
24.9 kcal/mol
Protein clashes
0
Internal clashes
13
Native overlap
contact recall 0.60, Jaccard 0.36, H-bond role recall 0.20
Reason: 13 internal clashes
13 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.669 kcal/mol/HA)
✓ Good fit quality (FQ -6.52)
✓ Good H-bonds (3 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ High strain energy (24.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-20.749
kcal/mol
LE
-0.669
kcal/mol/HA
Fit Quality
-6.52
FQ (Leeson)
HAC
31
heavy atoms
MW
406
Da
LogP
4.85
cLogP
Interaction summary
HB 3
HY 24
PI 1
CLASH 0
Interaction summary
HB 3
HY 24
PI 1
CLASH 0
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
| Final rank | 2.333 | Score | -20.749 |
|---|---|---|---|
| Inter norm | -0.796 | Intra norm | 0.122 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 3 |
| Artifact reason | geometry warning; 13 clashes; 1 protein clash; moderate strain Δ 24.9 | ||
| Residues |
ARG22
ARG342
ASN20
GLN341
GLU343
GLU348
GLU384
LEU25
LEU339
LEU350
LEU372
LEU382
PRO338
PRO340
PRO344
PRO373
THR21
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 | 9 | Native recall | 0.60 |
| Jaccard | 0.36 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 457 | 2.3334579004819758 | -0.796377 | -20.7486 | 3 | 19 | 9 | 0.60 | 0.20 | - | no | Current |
| 497 | 3.5983764184525246 | -0.777505 | -23.4879 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 425 | 3.8222514009867794 | -1.05411 | -30.6961 | 4 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 518 | 4.0410304952851 | -0.765173 | -23.1476 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 467 | 6.791932017520767 | -0.670596 | -20.6493 | 8 | 8 | 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
-20.749kcal/mol
Ligand efficiency (LE)
-0.6693kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.521
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
406.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.85
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.88kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
164.67kcal/mol
Minimised FF energy
139.79kcal/mol
SASA & burial
✓ computed
SASA (unbound)
707.0Ų
Total solvent-accessible surface area of free ligand
BSA total
564.9Ų
Buried surface area upon binding
BSA apolar
477.8Ų
Hydrophobic contacts buried
BSA polar
87.0Ų
Polar contacts buried
Fraction buried
79.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2554.5Ų
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
1395.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)