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
Reject
SASA cached
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
31.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.60, Jaccard 0.41, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
100% of hydrophobic surface is solvent-exposed (23/23 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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.696 kcal/mol/HA)
✓ Good fit quality (FQ -6.78)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ Very high strain energy (31.7 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (6)
✗ Many internal clashes (13)
Score
-21.566
kcal/mol
LE
-0.696
kcal/mol/HA
Fit Quality
-6.78
FQ (Leeson)
HAC
31
heavy atoms
MW
426
Da
LogP
3.08
cLogP
Interaction summary
HB 6
HY 2
PI 0
CLASH 1
⚠ Exposure 100%
Interaction summary
HB 6
HY 2
PI 0
CLASH 1
⚠ Exposure 100%
Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (23/23 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 23
Buried (contacted) 0
Exposed 23
LogP 3.08
H-bonds 6
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 1.792 | Score | -21.566 |
|---|---|---|---|
| Inter norm | -0.727 | Intra norm | 0.031 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 6 |
| Artifact reason | geometry warning; 13 clashes; 6 protein contact clashes; high strain Δ 31.7 | ||
| Residues |
ARG22
ARG242
ARG50
ASN20
ASP243
ASP385
ASP47
GLU384
GLY240
LEU25
LEU382
LYS51
SER282
THR21
THR241
THR285
| ||
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 | 9 | Native recall | 0.60 |
| Jaccard | 0.41 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 590 | 1.7921677220287922 | -0.727153 | -21.5664 | 6 | 16 | 9 | 0.60 | 0.20 | - | no | Current |
| 618 | 2.5205346310719405 | -1.00267 | -28.7297 | 10 | 16 | 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
-21.566kcal/mol
Ligand efficiency (LE)
-0.6957kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.778
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
426.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.08
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
30.21kcal/mol
Minimised FF energy
-1.47kcal/mol
SASA & burial
✓ computed
SASA (unbound)
683.5Ų
Total solvent-accessible surface area of free ligand
BSA total
527.3Ų
Buried surface area upon binding
BSA apolar
446.2Ų
Hydrophobic contacts buried
BSA polar
81.1Ų
Polar contacts buried
Fraction buried
77.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2563.5Ų
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
1378.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)