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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
15.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.33, Jaccard 0.26, H-bond role recall 0.60
Reason: no major geometry red flags detected
1 protein-contact clashes
100% of hydrophobic surface is solvent-exposed (4/4 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 (-2.183 kcal/mol/HA)
✓ Good fit quality (FQ -13.07)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Moderate strain (15.8 kcal/mol)
✗ Geometry warnings
Score
-21.834
kcal/mol
LE
-2.183
kcal/mol/HA
Fit Quality
-13.07
FQ (Leeson)
HAC
10
heavy atoms
MW
205
Da
LogP
-0.18
cLogP
Interaction summary
HB 10
HY 1
PI 0
CLASH 1
⚠ Exposure 100%
Interaction summary
HB 10
HY 1
PI 0
CLASH 1
⚠ Exposure 100%
Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (4/4 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 4
Buried (contacted) 0
Exposed 4
LogP -0.18
H-bonds 10
Exposed fragments:
aromatic ring (4/6 atoms exposed)
| Final rank | 2.283 | Score | -21.834 |
|---|---|---|---|
| Inter norm | -2.210 | Intra norm | 0.027 |
| Top1000 | no | Excluded | no |
| Contacts | 9 | H-bonds | 10 |
| Artifact reason | geometry warning; 4 clashes; 3 protein clashes | ||
| Residues |
ARG337
ASP243
ASP385
GLU384
LEU339
MET386
PHE383
PRO338
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 | 5 | Native recall | 0.33 |
| Jaccard | 0.26 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 3 | HB residue recall | 0.60 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 210 | 2.283223533985376 | -2.21009 | -21.8338 | 10 | 9 | 5 | 0.33 | 0.60 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.834kcal/mol
Ligand efficiency (LE)
-2.1834kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.074
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
10HA
Physicochemical properties
Molecular weight
205.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.18
Lipinski: ≤ 5
Rotatable bonds
2
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.81kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
121.66kcal/mol
Minimised FF energy
105.85kcal/mol
SASA & burial
✓ computed
SASA (unbound)
313.2Ų
Total solvent-accessible surface area of free ligand
BSA total
271.7Ų
Buried surface area upon binding
BSA apolar
212.2Ų
Hydrophobic contacts buried
BSA polar
59.5Ų
Polar contacts buried
Fraction buried
86.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2195.8Ų
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
1371.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)