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
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
19.0 kcal/mol
Protein clashes
0
Internal clashes
14
Native overlap
contact recall 0.53, Jaccard 0.40, H-bond role recall 0.00
Reason: 14 internal clashes
14 intramolecular clashes
59% of hydrophobic surface appears solvent-exposed (10/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.931 kcal/mol/HA)
✓ Good fit quality (FQ -8.69)
✓ Good H-bonds (3 bonds)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ Moderate strain (19.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-25.145
kcal/mol
LE
-0.931
kcal/mol/HA
Fit Quality
-8.69
FQ (Leeson)
HAC
27
heavy atoms
MW
381
Da
LogP
1.83
cLogP
Interaction summary
HB 3
HY 7
PI 0
CLASH 0
⚠ Exposure 58%
Interaction summary
HB 3
HY 7
PI 0
CLASH 0
⚠ Exposure 58%
Partial hydrophobic solvent exposure
59% of hydrophobic surface appears solvent-exposed (10/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 7
Exposed 10
LogP 1.83
H-bonds 3
Exposed fragments:
phenyl (1/5 atoms exposed)phenyl (3/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 2.387 | Score | -25.145 |
|---|---|---|---|
| Inter norm | -0.876 | Intra norm | -0.055 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 3 |
| Artifact reason | geometry warning; 14 clashes; 1 protein clash | ||
| Residues |
ARG242
ARG337
ASP243
ASP385
GLU384
LEU339
MET386
PHE326
PHE383
SER282
THR241
VAL335
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 | 0.40 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 1 | HB residue recall | 0.20 |
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
No clash · clashes detected for this pose.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 662 | 2.387234550870066 | -0.875978 | -25.1448 | 3 | 13 | 8 | 0.53 | 0.00 | - | no | Current |
| 676 | 2.7504368620559965 | -1.1322 | -31.8335 | 10 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 665 | 2.9348303597234553 | -1.04997 | -30.5922 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 668 | 3.054569518894309 | -1.19774 | -32.9591 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 667 | 3.994413850524842 | -0.746194 | -21.7975 | 6 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 661 | 5.153622008531141 | -1.22703 | -35.7123 | 13 | 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
-25.145kcal/mol
Ligand efficiency (LE)
-0.9313kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.689
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
381.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.83
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.02kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
62.18kcal/mol
Minimised FF energy
43.16kcal/mol
SASA & burial
✓ computed
SASA (unbound)
605.6Ų
Total solvent-accessible surface area of free ligand
BSA total
472.4Ų
Buried surface area upon binding
BSA apolar
325.1Ų
Hydrophobic contacts buried
BSA polar
147.3Ų
Polar contacts buried
Fraction buried
78.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2403.0Ų
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
1383.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)