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 strong
SASA done
Strain ΔE
28.2 kcal/mol
Protein clashes
9
Internal clashes
9
Native overlap
contact recall 0.76, Jaccard 0.62, H-bond role recall 0.27
Reason: 9 protein-contact clashes, 9 internal clashes
9 protein-contact clashes
9 intramolecular clashes
53% of hydrophobic surface appears solvent-exposed (9/17 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 (-0.909 kcal/mol/HA)
✓ Good fit quality (FQ -8.58)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ High strain energy (28.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-25.459
kcal/mol
LE
-0.909
kcal/mol/HA
Fit Quality
-8.58
FQ (Leeson)
HAC
28
heavy atoms
MW
430
Da
LogP
4.21
cLogP
Interaction summary
HB 9
HY 6
PI 3
CLASH 9
⚠ Exposure 52%
Interaction summary
HB 9
HY 6
PI 3
CLASH 9
⚠ Exposure 52%
Partial hydrophobic solvent exposure
53% of hydrophobic surface appears solvent-exposed (9/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 8
Exposed 9
LogP 4.21
H-bonds 9
Exposed fragments:
phenyl (1/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 3.427 | Score | -25.459 |
|---|---|---|---|
| Inter norm | -0.865 | Intra norm | -0.054 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 9 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash; moderate strain Δ 28.2 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
ASP44
CYS72
GLY73
GLY77
HIS105
HIS14
HIS141
SER46
THR45
TYR17
TYR49
| ||
Protein summary
155 residues
| Protein target | T10 | Atoms | 4590 |
|---|---|---|---|
| Residues | 155 | Chains | 1 |
| Residue summary | ILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6FXW | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
THR74
TYR49
| ||
| Current overlap | 13 | Native recall | 0.76 |
| Jaccard | 0.62 | RMSD | - |
| HB strict | 4 | Strict recall | 0.31 |
| HB same residue+role | 3 | HB role recall | 0.27 |
| HB same residue | 3 | HB residue recall | 0.27 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 381 | 0.4678678754036258 | -1.1526 | -33.9568 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 360 | 0.5197055751298865 | -0.90829 | -27.5829 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 447 | 1.219696433124539 | -0.981399 | -29.5048 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 355 | 1.3063524923317955 | -1.04791 | -30.2735 | 11 | 20 | 5 | 0.29 | 0.18 | - | no | Open |
| 408 | 1.743798155616244 | -1.05333 | -31.9361 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 329 | 1.7650189558589326 | -1.04283 | -32.4787 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 379 | 1.969342891855111 | -0.889133 | -24.5333 | 2 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 325 | 2.125064930305446 | -1.21138 | -36.9499 | 9 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 370 | 2.6577378078182576 | -0.783465 | -23.9328 | 5 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 401 | 2.8276500106851037 | -0.751507 | -24.4635 | 10 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 339 | 3.4270672992810502 | -0.865213 | -25.4592 | 9 | 17 | 13 | 0.76 | 0.27 | - | no | Current |
| 388 | 3.555555808287048 | -0.931199 | -26.8835 | 15 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 360 | 3.9357191430534906 | -1.02887 | -25.0561 | 14 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 385 | 4.556515282102343 | -0.781229 | -24.3789 | 8 | 11 | 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
-25.459kcal/mol
Ligand efficiency (LE)
-0.9093kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.584
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
429.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.21
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
50.81kcal/mol
Minimised FF energy
22.59kcal/mol
SASA & burial
✓ computed
SASA (unbound)
674.9Ų
Total solvent-accessible surface area of free ligand
BSA total
515.6Ų
Buried surface area upon binding
BSA apolar
399.7Ų
Hydrophobic contacts buried
BSA polar
115.9Ų
Polar contacts buried
Fraction buried
76.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2226.8Ų
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
2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
656.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)