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 medium
Native strong
SASA done
Strain ΔE
32.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.67, Jaccard 0.56, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
71% of hydrophobic surface is solvent-exposed (15/21 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 (-1.472 kcal/mol/HA)
✓ Good fit quality (FQ -14.47)
✓ Good H-bonds (5 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Very high strain energy (32.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-47.100
kcal/mol
LE
-1.472
kcal/mol/HA
Fit Quality
-14.47
FQ (Leeson)
HAC
32
heavy atoms
MW
492
Da
LogP
2.75
cLogP
Interaction summary
HB 5
HY 7
PI 0
CLASH 2
⚠ Exposure 71%
Interaction summary
HB 5
HY 7
PI 0
CLASH 2
⚠ Exposure 71%
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
71% of hydrophobic surface is solvent-exposed (15/21 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 21
Buried (contacted) 6
Exposed 15
LogP 2.75
H-bonds 5
Exposed fragments:
phenyl (4/5 atoms exposed)phenyl (4/5 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 3.179 | Score | -47.100 |
|---|---|---|---|
| Inter norm | -0.732 | Intra norm | -0.739 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 5 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes; very favorable intra outlier; high strain Δ 32.6 | ||
| Residues |
ARG22
ARG242
ASP243
ASP385
CYS26
GLN341
GLU384
LEU25
LEU382
SER282
THR21
THR241
THR285
| ||
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 | 10 | Native recall | 0.67 |
| Jaccard | 0.56 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 647 | 1.1847930015500647 | -0.884942 | -49.0529 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 632 | 1.4951936856465549 | -0.821422 | -31.1479 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 632 | 1.7612227019476687 | -0.793129 | -46.3282 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 659 | 3.075408860119218 | -0.786972 | -46.8966 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 641 | 3.178654702339341 | -0.732381 | -47.0997 | 5 | 13 | 10 | 0.67 | 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
-47.100kcal/mol
Ligand efficiency (LE)
-1.4719kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-14.474
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
491.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.75
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
67.03kcal/mol
Minimised FF energy
34.47kcal/mol
SASA & burial
✓ computed
SASA (unbound)
740.1Ų
Total solvent-accessible surface area of free ligand
BSA total
524.0Ų
Buried surface area upon binding
BSA apolar
405.3Ų
Hydrophobic contacts buried
BSA polar
118.7Ų
Polar contacts buried
Fraction buried
70.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2511.3Ų
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
1374.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)