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
24.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.44, H-bond role recall 0.40
Reason: no major geometry red flags detected
2 protein-contact clashes
100% of hydrophobic surface is solvent-exposed (11/11 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 (-1.141 kcal/mol/HA)
✓ Good fit quality (FQ -9.35)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ High strain energy (24.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-21.671
kcal/mol
LE
-1.141
kcal/mol/HA
Fit Quality
-9.35
FQ (Leeson)
HAC
19
heavy atoms
MW
281
Da
LogP
1.69
cLogP
Interaction summary
HB 9
HY 0
PI 0
CLASH 2
⚠ Exposure 100%
Interaction summary
HB 9
HY 0
PI 0
CLASH 2
⚠ Exposure 100%
Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (11/11 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 11
Buried (contacted) 0
Exposed 11
LogP 1.69
H-bonds 9
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.966 | Score | -21.671 |
|---|---|---|---|
| Inter norm | -1.530 | Intra norm | 0.389 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 9 |
| Artifact reason | geometry warning; 7 clashes; 3 protein clashes; moderate strain Δ 24.5 | ||
| Residues |
ARG242
ARG337
ASP243
ASP385
GLU384
LEU339
PHE383
PRO338
SER282
THR241
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 | 8 | Native recall | 0.53 |
| Jaccard | 0.44 | 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 |
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
No hy · hydrophobic contacts detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 536 | -1.2117718742022974 | -2.27302 | -41.2505 | 13 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 543 | -0.4617272198664007 | -1.92622 | -35.1793 | 12 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 553 | 0.7901052041183204 | -1.64895 | -25.0906 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 574 | 1.9197835489469466 | -1.27997 | -22.0242 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 539 | 2.834875949212269 | -1.96567 | -32.6489 | 13 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 574 | 2.938359789590277 | -1.13258 | -19.6979 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 542 | 3.36456591187264 | -1.66906 | -29.2551 | 16 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 544 | 3.597282871221922 | -1.55687 | -25.5432 | 13 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 546 | 3.9655058659124927 | -1.52952 | -21.6706 | 9 | 11 | 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
-21.671kcal/mol
Ligand efficiency (LE)
-1.1406kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.349
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
280.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.69
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
94.19kcal/mol
Minimised FF energy
69.66kcal/mol
SASA & burial
✓ computed
SASA (unbound)
484.0Ų
Total solvent-accessible surface area of free ligand
BSA total
388.8Ų
Buried surface area upon binding
BSA apolar
272.6Ų
Hydrophobic contacts buried
BSA polar
116.2Ų
Polar contacts buried
Fraction buried
80.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2317.9Ų
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
1385.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)