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 mixed
SASA done
Strain ΔE
26.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.53, Jaccard 0.36, H-bond role recall 0.40
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
68% of hydrophobic surface is solvent-exposed (15/22 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 (-0.883 kcal/mol/HA)
✓ Good fit quality (FQ -8.77)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ High strain energy (26.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-29.156
kcal/mol
LE
-0.883
kcal/mol/HA
Fit Quality
-8.77
FQ (Leeson)
HAC
33
heavy atoms
MW
477
Da
LogP
3.74
cLogP
Interaction summary
HB 8
HY 2
PI 0
CLASH 3
⚠ Exposure 68%
Interaction summary
HB 8
HY 2
PI 0
CLASH 3
⚠ Exposure 68%
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
68% of hydrophobic surface is solvent-exposed (15/22 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 22
Buried (contacted) 7
Exposed 15
LogP 3.74
H-bonds 8
Exposed fragments:
phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
| Final rank | 5.037 | Score | -29.156 |
|---|---|---|---|
| Inter norm | -0.872 | Intra norm | -0.012 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 8 |
| Artifact reason | geometry warning; 12 clashes; 3 protein clashes; moderate strain Δ 26.3 | ||
| Residues |
ALA244
ARG242
ARG337
ASP243
ASP385
GLU384
GLY240
LEU339
LYS247
LYS51
PHE383
SER282
THR241
VAL335
VAL336
| ||
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 | 0.36 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 513 | 3.9808127535607634 | -0.687926 | -22.8398 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 446 | 5.03721171803602 | -0.871649 | -29.1557 | 8 | 15 | 8 | 0.53 | 0.40 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.156kcal/mol
Ligand efficiency (LE)
-0.8835kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.766
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
477.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.74
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
72.15kcal/mol
Minimised FF energy
45.80kcal/mol
SASA & burial
✓ computed
SASA (unbound)
758.0Ų
Total solvent-accessible surface area of free ligand
BSA total
532.1Ų
Buried surface area upon binding
BSA apolar
445.7Ų
Hydrophobic contacts buried
BSA polar
86.4Ų
Polar contacts buried
Fraction buried
70.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2569.3Ų
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
1402.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)