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
29.1 kcal/mol
Protein clashes
0
Internal clashes
8
Native overlap
contact recall 0.53, Jaccard 0.38, H-bond role recall 0.00
Reason: 8 internal clashes
8 intramolecular clashes
41% of hydrophobic surface appears solvent-exposed (7/17 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 (-1.001 kcal/mol/HA)
✓ Good fit quality (FQ -9.23)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ High strain energy (29.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-26.037
kcal/mol
LE
-1.001
kcal/mol/HA
Fit Quality
-9.23
FQ (Leeson)
HAC
26
heavy atoms
MW
351
Da
LogP
0.96
cLogP
Interaction summary
HB 7
HY 9
PI 0
CLASH 0
⚠ Exposure 41%
Interaction summary
HB 7
HY 9
PI 0
CLASH 0
⚠ Exposure 41%
Partial hydrophobic solvent exposure
41% of hydrophobic surface appears solvent-exposed (7/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 10
Exposed 7
LogP 0.96
H-bonds 7
Exposed fragments:
pyridyl (4/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 3.776 | Score | -26.037 |
|---|---|---|---|
| Inter norm | -1.049 | Intra norm | 0.047 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 7 |
| Artifact reason | geometry warning; 8 clashes; 3 protein clashes; moderate strain Δ 29.1 | ||
| Residues |
ALA334
ARG242
ARG337
ASP243
ASP385
GLU384
GLY240
LEU339
MET386
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 | 0.38 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 242 | 0.013117550346434954 | -1.27485 | -32.1304 | 9 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 247 | 0.34940278881708586 | -0.995743 | -23.256 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 235 | 1.7531652320878486 | -1.16928 | -29.5525 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 168 | 2.7555481195899034 | -1.09563 | -21.4154 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 260 | 3.7764900594995785 | -1.04939 | -26.037 | 7 | 14 | 8 | 0.53 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-26.037kcal/mol
Ligand efficiency (LE)
-1.0014kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.226
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
351.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.96
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.08kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
39.10kcal/mol
Minimised FF energy
10.02kcal/mol
SASA & burial
✓ computed
SASA (unbound)
619.6Ų
Total solvent-accessible surface area of free ligand
BSA total
501.0Ų
Buried surface area upon binding
BSA apolar
380.1Ų
Hydrophobic contacts buried
BSA polar
120.9Ų
Polar contacts buried
Fraction buried
80.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2440.6Ų
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
1384.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)