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
16.5 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.47, Jaccard 0.33, H-bond role recall 0.20
Reason: 6 internal clashes
6 protein-contact clashes
6 intramolecular clashes
44% of hydrophobic surface appears solvent-exposed (8/18 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 (-0.743 kcal/mol/HA)
✓ Good fit quality (FQ -6.85)
✓ Good H-bonds (5 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Moderate strain (16.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-19.323
kcal/mol
LE
-0.743
kcal/mol/HA
Fit Quality
-6.85
FQ (Leeson)
HAC
26
heavy atoms
MW
367
Da
LogP
3.69
cLogP
Interaction summary
HB 5
HY 9
PI 1
CLASH 6
⚠ Exposure 44%
Interaction summary
HB 5
HY 9
PI 1
CLASH 6
⚠ Exposure 44%
Partial hydrophobic solvent exposure
44% of hydrophobic surface appears solvent-exposed (8/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 18
Buried (contacted) 10
Exposed 8
LogP 3.69
H-bonds 5
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 4.169 | Score | -19.323 |
|---|---|---|---|
| Inter norm | -0.946 | Intra norm | 0.201 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 5 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes | ||
| Residues |
ALA244
ARG337
ASP243
ASP385
GLU384
LEU339
LEU382
MET386
PHE383
PRO338
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 | 7 | Native recall | 0.47 |
| Jaccard | 0.33 | 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
Native π–π recall is disabled because no explicit native π–π reference was stored.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 151 | 0.32172865327613354 | -1.26883 | -25.9434 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 120 | 1.4182620796154546 | -0.869502 | -18.8868 | 0 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 159 | 1.6639623900139582 | -1.07838 | -24.547 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 115 | 2.052194704544698 | -1.01732 | -26.0095 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 155 | 2.6074809669883345 | -0.786201 | -16.7503 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 98 | 2.6369590614426244 | -1.2378 | -24.8459 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 88 | 3.6279790838447203 | -1.06416 | -18.492 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 158 | 4.168810452369634 | -0.945702 | -19.3234 | 5 | 13 | 7 | 0.47 | 0.20 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.323kcal/mol
Ligand efficiency (LE)
-0.7432kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.847
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
366.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.69
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.51kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
33.85kcal/mol
Minimised FF energy
17.34kcal/mol
SASA & burial
✓ computed
SASA (unbound)
616.4Ų
Total solvent-accessible surface area of free ligand
BSA total
442.7Ų
Buried surface area upon binding
BSA apolar
354.0Ų
Hydrophobic contacts buried
BSA polar
88.7Ų
Polar contacts buried
Fraction buried
71.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2451.2Ų
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
1417.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)