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
7.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.47, Jaccard 0.35, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
56% of hydrophobic surface appears solvent-exposed (9/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Low conformational strain (7.9 kcal/mol)
✓ Excellent LE (-1.135 kcal/mol/HA)
✓ Good fit quality (FQ -9.68)
✓ Good H-bonds (3 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ Geometry warnings
✗ Protein-contact clashes (5)
✗ Internal clashes (8)
Score
-23.827
kcal/mol
LE
-1.135
kcal/mol/HA
Fit Quality
-9.68
FQ (Leeson)
HAC
21
heavy atoms
MW
301
Da
LogP
4.12
cLogP
Final rank
0.7798
rank score
Inter norm
-1.039
normalised
Contacts
12
H-bonds 6
Interaction summary
HBD 2
HBA 1
HY 3
PI 0
CLASH 2
Interaction summary
HBD 2
HBA 1
HY 3
PI 0
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
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 | 0 | Strict recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 635 | 0.7797543063660407 | -1.03864 | -23.8267 | 6 | 12 | 7 | 0.47 | 0.20 | - | no | Current |
| 629 | 1.4429483420959466 | -1.27465 | -24.7705 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 651 | 2.2720410504418993 | -1.07823 | -21.4419 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 651 | 3.201970499986924 | -1.26973 | -25.8745 | 6 | 16 | 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
-23.827kcal/mol
Ligand efficiency (LE)
-1.1346kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.678
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
300.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.12
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
7.85kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
57.45kcal/mol
Minimised FF energy
49.60kcal/mol
SASA & burial
✓ computed
SASA (unbound)
507.8Ų
Total solvent-accessible surface area of free ligand
BSA total
383.3Ų
Buried surface area upon binding
BSA apolar
317.0Ų
Hydrophobic contacts buried
BSA polar
66.3Ų
Polar contacts buried
Fraction buried
75.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2369.7Ų
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
1407.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)