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 mixed
SASA done
Strain ΔE
24.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.53, Jaccard 0.32, H-bond role recall 0.40
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.734 kcal/mol/HA)
✓ Good fit quality (FQ -7.01)
✓ Good H-bonds (5 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ High strain energy (24.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-21.298
kcal/mol
LE
-0.734
kcal/mol/HA
Fit Quality
-7.01
FQ (Leeson)
HAC
29
heavy atoms
MW
408
Da
LogP
3.56
cLogP
Interaction summary
HB 5
HY 18
PI 0
CLASH 1
Interaction summary
HB 5
HY 18
PI 0
CLASH 1
| Final rank | 2.443 | Score | -21.298 |
|---|---|---|---|
| Inter norm | -0.800 | Intra norm | 0.066 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 5 |
| Artifact reason | geometry warning; 11 clashes; 1 protein clash; moderate strain Δ 24.2 | ||
| Residues |
ARG22
ARG342
ASN20
CYS26
GLN341
GLU343
LEU25
LEU339
LEU350
LEU372
LEU382
PRO338
PRO340
PRO344
PRO373
THR21
TYR370
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 | 8 | Native recall | 0.53 |
| Jaccard | 0.32 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 611 | 1.6858718437942672 | -0.784032 | -24.4732 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 617 | 2.3411592116053694 | -0.856245 | -22.0048 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 598 | 2.4430336134887645 | -0.800422 | -21.2984 | 5 | 18 | 8 | 0.53 | 0.40 | - | no | Current |
| 633 | 2.8693333061383006 | -1.14047 | -28.4808 | 7 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 614 | 3.423589934689467 | -0.728846 | -19.561 | 7 | 11 | 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
-21.298kcal/mol
Ligand efficiency (LE)
-0.7344kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.011
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
408.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.56
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
59.82kcal/mol
Minimised FF energy
35.64kcal/mol
SASA & burial
✓ computed
SASA (unbound)
706.4Ų
Total solvent-accessible surface area of free ligand
BSA total
562.0Ų
Buried surface area upon binding
BSA apolar
428.8Ų
Hydrophobic contacts buried
BSA polar
133.2Ų
Polar contacts buried
Fraction buried
79.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2519.6Ų
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
1382.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)