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
28.1 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.53, Jaccard 0.33, H-bond role recall 0.20
Reason: 7 internal clashes
7 protein-contact clashes
7 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Good LE (-0.335 kcal/mol/HA)
✓ Good fit quality (FQ -3.19)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ High strain energy (28.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-9.706
kcal/mol
LE
-0.335
kcal/mol/HA
Fit Quality
-3.19
FQ (Leeson)
HAC
29
heavy atoms
MW
386
Da
LogP
5.42
cLogP
Interaction summary
HB 7
HY 8
PI 0
CLASH 7
Interaction summary
HB 7
HY 8
PI 0
CLASH 7
| Final rank | 3.305 | Score | -9.706 |
|---|---|---|---|
| Inter norm | -0.822 | Intra norm | 0.488 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 7 |
| Artifact reason | geometry warning; 11 clashes; 1 protein clash; high raw intra; moderate strain Δ 27.4 | ||
| Residues |
ALA283
ALA43
ARG22
ARG342
ASP385
ASP44
CYS26
GLN341
GLU343
GLU384
LEU25
LEU382
PHE284
SER282
THR21
THR285
VAL42
| ||
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 | 8 | Native recall | 0.53 |
| Jaccard | 0.33 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 323 | 1.9880960137870662 | -1.21642 | -31.5302 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 420 | 2.548705262181661 | -0.798165 | -21.0698 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 357 | 3.147742695757834 | -0.711274 | -16.5493 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 340 | 3.304872371779209 | -0.822248 | -9.70627 | 7 | 17 | 8 | 0.53 | 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
-9.706kcal/mol
Ligand efficiency (LE)
-0.3347kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.195
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
386.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.42
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.14kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
101.99kcal/mol
Minimised FF energy
73.85kcal/mol
SASA & burial
✓ computed
SASA (unbound)
693.0Ų
Total solvent-accessible surface area of free ligand
BSA total
566.0Ų
Buried surface area upon binding
BSA apolar
459.9Ų
Hydrophobic contacts buried
BSA polar
106.1Ų
Polar contacts buried
Fraction buried
81.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2527.7Ų
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
1385.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)