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 high
Native mixed
SASA done
Strain ΔE
17.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.40, Jaccard 0.32, H-bond role recall 0.40
Reason: no major geometry red flags detected
1 protein-contact clashes
60% of hydrophobic surface is solvent-exposed (6/10 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 (-1.140 kcal/mol/HA)
✓ Good fit quality (FQ -9.34)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (62%)
✗ Moderate strain (17.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-21.659
kcal/mol
LE
-1.140
kcal/mol/HA
Fit Quality
-9.34
FQ (Leeson)
HAC
19
heavy atoms
MW
281
Da
LogP
-0.02
cLogP
Interaction summary
HB 8
HY 1
PI 0
CLASH 1
⚠ Exposure 60%
Interaction summary
HB 8
HY 1
PI 0
CLASH 1
⚠ Exposure 60%
Solvent-exposed hydrophobic surface — desolvation penalty likely
60% of hydrophobic surface is solvent-exposed (6/10 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 10
Buried (contacted) 4
Exposed 6
LogP -0.02
H-bonds 8
Exposed fragments:
phenyl (6/6 atoms exposed)
| Final rank | 2.242 | Score | -21.659 |
|---|---|---|---|
| Inter norm | -1.161 | Intra norm | 0.021 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 8 |
| Artifact reason | geometry warning; 6 clashes; 2 protein clashes | ||
| Residues |
ALA244
ARG337
ASP243
ASP385
GLU384
LEU339
PHE383
THR241
VAL335
VAL336
| ||
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 | 6 | Native recall | 0.40 |
| Jaccard | 0.32 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 290 | 1.1542235761146216 | -1.3133 | -22.9835 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 326 | 2.241892118278962 | -1.16101 | -21.6592 | 8 | 10 | 6 | 0.40 | 0.40 | - | no | Current |
| 408 | 2.3864433454440244 | -1.28783 | -23.0227 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 340 | 2.4224499674500235 | -1.52753 | -26.5605 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 242 | 2.5012839495939683 | -1.35686 | -25.553 | 12 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 344 | 2.970230030733658 | -1.42184 | -25.8069 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 277 | 3.3258278508067045 | -1.67804 | -30.7231 | 16 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 381 | 3.627532215524071 | -1.28108 | -23.2122 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 357 | 3.7791067382818606 | -1.42538 | -25.9702 | 8 | 15 | 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
-21.659kcal/mol
Ligand efficiency (LE)
-1.1400kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.344
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
281.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.02
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-55.81kcal/mol
Minimised FF energy
-73.44kcal/mol
SASA & burial
✓ computed
SASA (unbound)
468.6Ų
Total solvent-accessible surface area of free ligand
BSA total
375.8Ų
Buried surface area upon binding
BSA apolar
231.5Ų
Hydrophobic contacts buried
BSA polar
144.3Ų
Polar contacts buried
Fraction buried
80.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
61.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2279.4Ų
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
1379.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)