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 strong
SASA done
Strain ΔE
29.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.40, H-bond role recall 0.60
Reason: no major geometry red flags detected
2 protein-contact clashes
95% of hydrophobic surface is solvent-exposed (19/20 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.755 kcal/mol/HA)
✓ Good fit quality (FQ -6.87)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ High strain energy (29.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-18.887
kcal/mol
LE
-0.755
kcal/mol/HA
Fit Quality
-6.87
FQ (Leeson)
HAC
25
heavy atoms
MW
340
Da
LogP
3.91
cLogP
Final rank
3.5207
rank score
Inter norm
-1.022
normalised
Contacts
13
H-bonds 8
Interaction summary
HBD 3
HBA 3
HY 3
PI 0
CLASH 2
Interaction summary
HBD 3
HBA 3
HY 3
PI 0
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.
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: permissive.
| 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 | 0.40 | RMSD | - |
| HB strict | 3 | Strict recall | 0.50 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 3 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 66 | 0.8305093453479375 | -0.860099 | -15.002 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 74 | 2.1373659912864653 | -0.970433 | -20.7683 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 29 | 2.600107939307177 | -1.01846 | -24.5258 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 65 | 2.6022736026417634 | -0.939392 | -18.7025 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 54 | 3.0349276914671437 | -1.1562 | -26.1336 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 43 | 3.222270151018671 | -1.10798 | -20.2889 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 79 | 3.5206894931967216 | -1.022 | -18.8867 | 8 | 13 | 8 | 0.53 | 0.60 | - | no | Current |
| 90 | 3.7209462673393525 | -1.01938 | -22.3114 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 64 | 4.14130884921673 | -1.0316 | -21.4621 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 77 | 4.326743905642506 | -0.753896 | -17.6426 | 7 | 12 | 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
-18.887kcal/mol
Ligand efficiency (LE)
-0.7555kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.868
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
340.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.91
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.39kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
88.66kcal/mol
Minimised FF energy
59.27kcal/mol
SASA & burial
✓ computed
SASA (unbound)
635.3Ų
Total solvent-accessible surface area of free ligand
BSA total
497.2Ų
Buried surface area upon binding
BSA apolar
394.3Ų
Hydrophobic contacts buried
BSA polar
102.9Ų
Polar contacts buried
Fraction buried
78.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2458.6Ų
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
1396.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)