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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native mixed
SASA done
Strain ΔE
8.9 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.27, Jaccard 0.16, H-bond role recall 0.00
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
100% of hydrophobic surface is solvent-exposed (18/18 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
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.890 kcal/mol/HA)
✓ Good fit quality (FQ -7.85)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (98%)
✗ Moderate strain (8.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-20.467
kcal/mol
LE
-0.890
kcal/mol/HA
Fit Quality
-7.85
FQ (Leeson)
HAC
23
heavy atoms
MW
345
Da
LogP
4.33
cLogP
Interaction summary
HB 6
HY 0
PI 0
CLASH 4
⚠ Exposure 100%
Interaction summary
HB 6
HY 0
PI 0
CLASH 4
⚠ Exposure 100%
Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (18/18 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 18
Buried (contacted) 0
Exposed 18
LogP 4.33
H-bonds 6
Exposed fragments:
phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 2.322 | Score | -20.467 |
|---|---|---|---|
| Inter norm | -0.949 | Intra norm | 0.058 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 6 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash | ||
| Residues |
ALA283
ALA43
ARG22
ARG50
ASN20
ASP385
ASP44
ASP47
GLU384
PHE284
SER282
THR21
THR285
VAL42
| ||
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 | 4 | Native recall | 0.27 |
| Jaccard | 0.16 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
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
No hy · hydrophobic contacts detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 673 | -0.2870957527735501 | -1.47119 | -32.8162 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 662 | 0.692809738121724 | -1.43211 | -31.3557 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 666 | 0.8249783486502428 | -1.05017 | -21.57 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 658 | 1.2691902380682223 | -1.11054 | -25.1576 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 664 | 2.3219346743576095 | -0.948762 | -20.4673 | 6 | 14 | 4 | 0.27 | 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
-20.467kcal/mol
Ligand efficiency (LE)
-0.8899kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.854
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
345.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.33
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
8.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
62.98kcal/mol
Minimised FF energy
54.09kcal/mol
SASA & burial
✓ computed
SASA (unbound)
546.4Ų
Total solvent-accessible surface area of free ligand
BSA total
414.7Ų
Buried surface area upon binding
BSA apolar
405.5Ų
Hydrophobic contacts buried
BSA polar
9.2Ų
Polar contacts buried
Fraction buried
75.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
97.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2425.7Ų
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
1454.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)