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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native mixed
SASA done
Strain ΔE
9.5 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.40, Jaccard 0.30, H-bond role recall 0.40
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.902 kcal/mol/HA)
✓ Good fit quality (FQ -8.09)
✓ Good H-bonds (4 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Moderate strain (9.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-21.660
kcal/mol
LE
-0.902
kcal/mol/HA
Fit Quality
-8.09
FQ (Leeson)
HAC
24
heavy atoms
MW
338
Da
LogP
3.36
cLogP
Interaction summary
HB 4
HY 6
PI 0
CLASH 5
⚠ Exposure 35%
Interaction summary
HB 4
HY 6
PI 0
CLASH 5
⚠ Exposure 35%
Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 11
Exposed 6
LogP 3.36
H-bonds 4
Exposed fragments:
phenyl (6/6 atoms exposed)
| Final rank | 3.409 | Score | -21.660 |
|---|---|---|---|
| Inter norm | -0.909 | Intra norm | 0.006 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 4 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes | ||
| Residues |
ALA334
ARG337
ASP243
ASP385
GLU384
LEU339
MET386
PHE383
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 | 6 | Native recall | 0.40 |
| Jaccard | 0.30 | 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 114 | 1.5860172937477603 | -1.21455 | -24.4039 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 97 | 1.8505603394551924 | -1.16929 | -25.4341 | 9 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 93 | 2.19739498584036 | -1.11561 | -31.8453 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 70 | 2.7036207493563826 | -1.08888 | -29.501 | 12 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 157 | 3.4093172975048245 | -0.908923 | -21.6596 | 4 | 11 | 6 | 0.40 | 0.40 | - | no | Current |
| 118 | 3.6102345461159344 | -1.03637 | -23.389 | 4 | 15 | 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
-21.660kcal/mol
Ligand efficiency (LE)
-0.9025kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.088
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
337.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.36
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
9.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
90.82kcal/mol
Minimised FF energy
81.34kcal/mol
SASA & burial
✓ computed
SASA (unbound)
563.2Ų
Total solvent-accessible surface area of free ligand
BSA total
397.4Ų
Buried surface area upon binding
BSA apolar
317.4Ų
Hydrophobic contacts buried
BSA polar
79.9Ų
Polar contacts buried
Fraction buried
70.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2390.4Ų
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
1440.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)