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
Weak or marginal quality
Binding strong
Geometry high
Native mixed
SASA done
Strain ΔE
16.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.40, Jaccard 0.27, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
47% of hydrophobic surface appears solvent-exposed (9/19 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 (-0.897 kcal/mol/HA)
✓ Good fit quality (FQ -8.16)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Moderate strain (16.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-22.432
kcal/mol
LE
-0.897
kcal/mol/HA
Fit Quality
-8.16
FQ (Leeson)
HAC
25
heavy atoms
MW
348
Da
LogP
4.03
cLogP
Interaction summary
HB 8
HY 1
PI 0
CLASH 2
⚠ Exposure 47%
Interaction summary
HB 8
HY 1
PI 0
CLASH 2
⚠ Exposure 47%
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
Partial hydrophobic solvent exposure
47% of hydrophobic surface appears solvent-exposed (9/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19
Buried (contacted) 10
Exposed 9
LogP 4.03
H-bonds 8
Exposed fragments:
phenyl (4/5 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 3.443 | Score | -22.432 |
|---|---|---|---|
| Inter norm | -0.888 | Intra norm | -0.010 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 8 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes | ||
| Residues |
ARG242
ARG50
ASP243
ASP385
ASP44
ASP47
GLU384
LYS51
PHE284
SER282
THR21
THR241
THR285
| ||
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 | 0.27 | 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 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 602 | 0.11430096132212113 | -1.27135 | -29.7382 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 616 | 0.8791360147483075 | -0.830152 | -18.6899 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 601 | 1.2194364801494049 | -1.02909 | -25.5113 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 612 | 1.5874584481341056 | -1.13378 | -28.2176 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 595 | 1.8006179207427564 | -1.05666 | -24.4722 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 599 | 3.4431675101061257 | -0.887757 | -22.4323 | 8 | 13 | 6 | 0.40 | 0.20 | - | no | Current |
| 611 | 4.478348342907414 | -1.13978 | -27.4314 | 7 | 9 | 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
-22.432kcal/mol
Ligand efficiency (LE)
-0.8973kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.157
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
348.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.03
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
25.27kcal/mol
Minimised FF energy
9.21kcal/mol
SASA & burial
✓ computed
SASA (unbound)
554.3Ų
Total solvent-accessible surface area of free ligand
BSA total
425.6Ų
Buried surface area upon binding
BSA apolar
326.8Ų
Hydrophobic contacts buried
BSA polar
98.8Ų
Polar contacts buried
Fraction buried
76.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2403.7Ų
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
1390.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)