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
5.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.53, Jaccard 0.42, H-bond role recall 0.40
Reason: no major geometry red flags detected
1 protein-contact clashes
60% of hydrophobic surface is solvent-exposed (9/15 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.
✓ Low conformational strain (5.6 kcal/mol)
✓ Excellent LE (-1.202 kcal/mol/HA)
✓ Good fit quality (FQ -10.06)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-24.043
kcal/mol
LE
-1.202
kcal/mol/HA
Fit Quality
-10.06
FQ (Leeson)
HAC
20
heavy atoms
MW
270
Da
LogP
2.58
cLogP
Interaction summary
HB 7
HY 7
PI 0
CLASH 1
⚠ Exposure 60%
Interaction summary
HB 7
HY 7
PI 0
CLASH 1
⚠ Exposure 60%
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
60% of hydrophobic surface is solvent-exposed (9/15 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 15
Buried (contacted) 6
Exposed 9
LogP 2.58
H-bonds 7
Exposed fragments:
phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)
| Final rank | 3.406 | Score | -24.043 |
|---|---|---|---|
| Inter norm | -1.225 | Intra norm | 0.023 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 7 |
| Artifact reason | geometry warning; 8 clashes; 3 protein clashes | ||
| Residues |
ARG22
ARG342
ASN20
ASP44
GLN341
GLU384
LEU25
LEU339
LEU382
PRO340
THR21
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 | 8 | Native recall | 0.53 |
| Jaccard | 0.42 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 71 | -0.6425912787373339 | -1.5364 | -30.9434 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 69 | 1.694537518369985 | -1.21538 | -22.0621 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 59 | 2.771198386423646 | -1.45638 | -28.5775 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 80 | 3.406183505862583 | -1.22511 | -24.0434 | 7 | 12 | 8 | 0.53 | 0.40 | - | no | Current |
| 45 | 3.6208123248314377 | -1.33156 | -25.6337 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 75 | 4.1092730997855105 | -1.13353 | -20.6307 | 8 | 13 | 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
-24.043kcal/mol
Ligand efficiency (LE)
-1.2022kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.060
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
20HA
Physicochemical properties
Molecular weight
270.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.58
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
5.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
66.18kcal/mol
Minimised FF energy
60.55kcal/mol
SASA & burial
✓ computed
SASA (unbound)
471.6Ų
Total solvent-accessible surface area of free ligand
BSA total
386.6Ų
Buried surface area upon binding
BSA apolar
275.6Ų
Hydrophobic contacts buried
BSA polar
111.0Ų
Polar contacts buried
Fraction buried
82.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2291.8Ų
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
1398.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)