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
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
22.7 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.53, Jaccard 0.36, H-bond role recall 0.20
Reason: 6 internal clashes
6 protein-contact clashes
6 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.767 kcal/mol/HA)
✓ Good fit quality (FQ -7.48)
✓ Good H-bonds (4 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (92%)
✗ High strain energy (22.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-23.791
kcal/mol
LE
-0.767
kcal/mol/HA
Fit Quality
-7.48
FQ (Leeson)
HAC
31
heavy atoms
MW
464
Da
LogP
3.89
cLogP
Interaction summary
HB 4
HY 24
PI 0
CLASH 6
Interaction summary
HB 4
HY 24
PI 0
CLASH 6
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
| Final rank | 3.187 | Score | -23.791 |
|---|---|---|---|
| Inter norm | -0.797 | Intra norm | 0.030 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 4 |
| Artifact reason | geometry warning; 12 clashes; 1 protein clash; moderate strain Δ 22.7 | ||
| Residues |
ARG22
ARG342
CYS26
GLN341
GLU343
GLU348
LEU25
LEU339
LEU350
LEU372
LEU382
PRO340
PRO344
PRO373
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 | 8 | Native recall | 0.53 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 149 | 3.186636741914792 | -0.797165 | -23.7914 | 4 | 15 | 8 | 0.53 | 0.20 | - | no | Current |
| 143 | 3.599525627754173 | -0.647312 | -17.7174 | 3 | 13 | 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
-23.791kcal/mol
Ligand efficiency (LE)
-0.7675kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.477
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
464.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.89
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
78.63kcal/mol
Minimised FF energy
55.98kcal/mol
SASA & burial
✓ computed
SASA (unbound)
721.0Ų
Total solvent-accessible surface area of free ligand
BSA total
600.2Ų
Buried surface area upon binding
BSA apolar
554.4Ų
Hydrophobic contacts buried
BSA polar
45.8Ų
Polar contacts buried
Fraction buried
83.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
92.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2648.1Ų
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
1369.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)