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
Reject
SASA cached
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native mixed
SASA done
Strain ΔE
41.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.33, Jaccard 0.24, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
52% of hydrophobic surface appears solvent-exposed (13/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.682 kcal/mol/HA)
✓ Good fit quality (FQ -6.77)
✓ Strong H-bond network (7 bonds)
✓ Good burial (58% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ Extreme strain energy (41.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-22.523
kcal/mol
LE
-0.682
kcal/mol/HA
Fit Quality
-6.77
FQ (Leeson)
HAC
33
heavy atoms
MW
455
Da
LogP
4.38
cLogP
Interaction summary
HB 7
HY 3
PI 0
CLASH 2
⚠ Exposure 52%
Interaction summary
HB 7
HY 3
PI 0
CLASH 2
⚠ Exposure 52%
Partial hydrophobic solvent exposure
52% of hydrophobic surface appears solvent-exposed (13/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 25
Buried (contacted) 12
Exposed 13
LogP 4.38
H-bonds 7
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 4.441 | Score | -22.523 |
|---|---|---|---|
| Inter norm | -0.758 | Intra norm | 0.076 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 7 |
| Artifact reason | geometry warning; 13 clashes; 3 protein clashes; high strain Δ 41.2 | ||
| Residues |
ALA334
ARG337
ASP243
ASP385
GLU384
LEU339
MET386
PHE383
PRO338
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 | 5 | Native recall | 0.33 |
| Jaccard | 0.24 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| 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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 5 | 0.6548724046132871 | -0.965976 | -33.2103 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 7 | 0.9116591125750627 | -0.833168 | -30.5499 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2 | 1.9798119759158557 | -0.914597 | -32.5335 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 5 | 4.440878567887839 | -0.758066 | -22.5234 | 7 | 11 | 5 | 0.33 | 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
-22.523kcal/mol
Ligand efficiency (LE)
-0.6825kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.772
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
454.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.38
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
41.24kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
86.29kcal/mol
Minimised FF energy
45.06kcal/mol
SASA & burial
✓ computed
SASA (unbound)
741.9Ų
Total solvent-accessible surface area of free ligand
BSA total
430.7Ų
Buried surface area upon binding
BSA apolar
365.9Ų
Hydrophobic contacts buried
BSA polar
64.9Ų
Polar contacts buried
Fraction buried
58.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2545.8Ų
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
1478.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)