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 high
Native mixed
SASA done
Strain ΔE
29.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.47, Jaccard 0.29, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.887 kcal/mol/HA)
✓ Good fit quality (FQ -7.95)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (64%)
✗ High strain energy (29.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-21.287
kcal/mol
LE
-0.887
kcal/mol/HA
Fit Quality
-7.95
FQ (Leeson)
HAC
24
heavy atoms
MW
369
Da
LogP
0.38
cLogP
Interaction summary
HB 11
HY 3
PI 0
CLASH 2
⚠ Exposure 60%
Interaction summary
HB 11
HY 3
PI 0
CLASH 2
⚠ Exposure 60%
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 0.38
H-bonds 11
Exposed fragments:
thienyl (4/6 atoms exposed)thienyl (2/5 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 2.694 | Score | -21.287 |
|---|---|---|---|
| Inter norm | -0.984 | Intra norm | 0.094 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 11 |
| Artifact reason | geometry warning; 5 clashes; 2 protein clashes; moderate strain Δ 29.7 | ||
| Residues |
ALA283
ALA43
ARG22
ASN20
ASP385
ASP44
GLN341
GLU343
GLU384
LEU25
LEU382
PHE284
SER282
THR21
THR285
VAL42
| ||
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 | 7 | Native recall | 0.47 |
| Jaccard | 0.29 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 374 | 2.0865146822246143 | -1.38198 | -34.324 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 413 | 2.6943961769928566 | -0.984124 | -21.2873 | 11 | 16 | 7 | 0.47 | 0.20 | - | no | Current |
| 410 | 2.7399256456858576 | -1.07947 | -26.8497 | 10 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 459 | 3.458566031907076 | -1.03078 | -25.5076 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 392 | 3.7441207624658626 | -1.27643 | -28.7503 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 387 | 4.41582415185168 | -1.27937 | -27.7085 | 14 | 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
-21.287kcal/mol
Ligand efficiency (LE)
-0.8870kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.949
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
369.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.38
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.65kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-17.91kcal/mol
Minimised FF energy
-47.56kcal/mol
SASA & burial
✓ computed
SASA (unbound)
603.8Ų
Total solvent-accessible surface area of free ligand
BSA total
487.0Ų
Buried surface area upon binding
BSA apolar
313.5Ų
Hydrophobic contacts buried
BSA polar
173.5Ų
Polar contacts buried
Fraction buried
80.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2365.1Ų
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
1364.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)