Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native mixed
SASA done
Strain ΔE
15.4 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.53, Jaccard 0.42, H-bond role recall 0.00
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
94% of hydrophobic surface is solvent-exposed (16/17 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 (-0.968 kcal/mol/HA)
✓ Good fit quality (FQ -8.26)
✓ Good H-bonds (5 bonds)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Moderate strain (15.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-20.335
kcal/mol
LE
-0.968
kcal/mol/HA
Fit Quality
-8.26
FQ (Leeson)
HAC
21
heavy atoms
MW
282
Da
LogP
3.06
cLogP
Interaction summary
HB 5
HY 1
PI 0
CLASH 4
⚠ Exposure 94%
Interaction summary
HB 5
HY 1
PI 0
CLASH 4
⚠ Exposure 94%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
94% of hydrophobic surface is solvent-exposed (16/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 17
Buried (contacted) 1
Exposed 16
LogP 3.06
H-bonds 5
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 2.586 | Score | -20.335 |
|---|---|---|---|
| Inter norm | -1.084 | Intra norm | 0.116 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 5 |
| Artifact reason | geometry warning; 10 clashes; 1 protein clash | ||
| Residues |
ARG242
ARG337
ASP243
ASP385
GLU384
LEU339
PHE383
PRO338
SER282
THR241
VAL335
VAL336
| ||
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 | 0.42 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 555 | 2.5855112669062192 | -1.08433 | -20.3351 | 5 | 12 | 8 | 0.53 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.335kcal/mol
Ligand efficiency (LE)
-0.9683kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.260
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
282.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.06
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.39kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
60.67kcal/mol
Minimised FF energy
45.28kcal/mol
SASA & burial
✓ computed
SASA (unbound)
513.5Ų
Total solvent-accessible surface area of free ligand
BSA total
407.3Ų
Buried surface area upon binding
BSA apolar
335.1Ų
Hydrophobic contacts buried
BSA polar
72.2Ų
Polar contacts buried
Fraction buried
79.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2391.2Ų
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
1392.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)