Update each ligands.yml file to include only ligands that could be …

…docked
openforcefield · Jun 23, 2022 · 089858c · 089858c
1 parent c420442
commit 089858c
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Showing 17 changed files with 13 additions and 756 deletions.
diff --git a/data/bace/00_data/ligands.yml b/data/bace/00_data/ligands.yml
@@ -152,17 +152,6 @@ lig_CAT-13o:
     value: 1200
   name: lig_CAT-13o
   smiles: '[H][C]1=[C]([H])[S][C]([C@@]2([C]3=[C]([H])[C]([H])=[C]([H])[C]([C]4=[C]([H])[C]([Cl])=[C]([H])[C]([H])=[C]4[H])=[C]3[H])[C](=[O])[N]([C]([H])([H])[H])[C]([N]([H])[H])=[N+]2[H])=[N]1'
-lig_CAT-17a:
-  charge: 1
-  measurement:
-    comment: Table 4, entry 17a
-    doi: 10.1016/j.bmcl.2012.02.013
-    error: -1
-    type: ki
-    unit: nM
-    value: 30
-  name: lig_CAT-17a
-  smiles: '[H][C]1=[C]([H])[C]([C]2=[C]([H])[C]([Cl])=[C]([H])[C]([Cl])=[C]2[H])=[C]([H])[C]([C@]2([C]3([H])[C]([H])([H])[C]3([H])[H])[C](=[O])[N]([C]([H])([H])[H])[C]([N]([H])[H])=[N+]2[H])=[C]1[H]'
 lig_CAT-17b:
   charge: 1
   measurement:
@@ -273,28 +262,6 @@ lig_CAT-4a:
     value: 3.3
   name: lig_CAT-4a
   smiles: '[H][C]1=[C]([H])[C]([H])=[C]([C]2=[C]([H])[C]([C@]3([C]4=[C]([H])[C]([H])=[C]([H])[C]([H])=[C]4[H])[C](=[O])[N]([C]([H])([H])[H])[C]([N]([H])[H])=[N+]3[H])=[C]([H])[C]([H])=[C]2[H])[C]([H])=[C]1[H]'
-lig_CAT-4b:
-  charge: 1
-  measurement:
-    comment: Table 1, entry 4b
-    doi: 10.1016/j.bmcl.2012.02.013
-    error: -1
-    type: ki
-    unit: uM
-    value: 0.19
-  name: lig_CAT-4b
-  smiles: '[H][C]1=[C]([H])[C]([H])=[C]([C@@]2([C]3=[C]([H])[C]([H])=[C]([H])[C]([C]4=[C]([H])[C]([O][C]([H])([H])[H])=[C]([H])[C]([H])=[C]4[H])=[C]3[H])[C](=[O])[N]([C]([H])([H])[H])[C]([N]([H])[H])=[N+]2[H])[C]([H])=[C]1[H]'
-lig_CAT-4c:
-  charge: 1
-  measurement:
-    comment: Table 1, entry 4c
-    doi: 10.1016/j.bmcl.2012.02.013
-    error: -1
-    type: ki
-    unit: uM
-    value: 3.8
-  name: lig_CAT-4c
-  smiles: '[H][C]1=[C]([H])[C]([H])=[C]([C@@]2([C]3=[C]([H])[C]([H])=[C]([H])[C]([C]4=[C]([H])[C]([H])=[C]([O][C]([H])([H])[H])[C]([H])=[C]4[H])=[C]3[H])[C](=[O])[N]([C]([H])([H])[H])[C]([N]([H])[H])=[N+]2[H])[C]([H])=[C]1[H]'
 lig_CAT-4d:
   charge: 1
   measurement:

diff --git a/data/bace_hunt/00_data/ligands.yml b/data/bace_hunt/00_data/ligands.yml
@@ -42,17 +42,6 @@ lig_14:
     value: 68
   name: lig_14
   smiles: '[H][C]1=[C]([H])[C]([C]2=[C]([H])[C]([H])=[C]3[O][C]([C]([H])([H])[H])([C]([H])([H])[H])[C]([H])([H])[C@]4([C](=[O])[N]([C]([H])([H])[H])[C]([N]([H])[H])=[N+]4[H])[C]3=[C]2[H])=[C]([H])[C]([O][C]([H])([H])[H])=[C]1[H]'
-lig_15:
-  charge: 1
-  measurement:
-    comment: Table 1, entry 15
-    doi: 10.1021/jm4002154
-    error: -1
-    type: ic50
-    unit: nM
-    value: 1701
-  name: lig_15
-  smiles: '[H][C]1=[C]([H])[C]([H])=[C]([C]2=[C]([H])[C]([H])=[C]3[O][C]([C]([H])([H])[H])([C]([H])([H])[H])[C]([H])([H])[C@]4([C](=[O])[N]([C]([H])([H])[H])[C]([N]([H])[H])=[N+]4[H])[C]3=[C]2[H])[C]([O][C]([H])([H])[H])=[C]1[H]'
 lig_16:
   charge: 1
   measurement:

diff --git a/data/bace_p2/00_data/ligands.yml b/data/bace_p2/00_data/ligands.yml
@@ -1,14 +1,3 @@
-lig_28_L:
-  charge: 1
-  measurement:
-    comment: Table 3, entry 37
-    doi: 10.1021/jm901414e
-    error: 0.01
-    type: ic50
-    unit: uM
-    value: 0.04
-  name: lig_28_L
-  smiles: '[H][C]1=[N][C]([H])=[C]([H])[C]([H])=[C]1[C]1=[C]([H])[C]([C@@]2([C]3=[C]([H])[C]([C]([H])([H])[H])=[C]([O][C]([H])([H])[H])[C]([H])=[C]3[H])[C](=[O])[N]([C]([H])([H])[H])[C]([N]([H])[H])=[N+]2[H])=[C]([H])[C]([H])=[C]1[H]'
 lig_29_L:
   charge: 1
   measurement:
@@ -42,17 +31,6 @@ lig_31_L:
     value: 0.05
   name: lig_31_L
   smiles: '[H][C]1=[N][C]([H])=[C]([H])[C]([H])=[C]1[C]1=[C]([H])[C]([C@]2([C]3=[C]([H])[C]([H])=[C]([O][C]([H])([H])[H])[C]([O][C]([H])([H])[C]([H])([H])[C]([H])([H])[H])=[C]3[H])[C](=[O])[N]([C]([H])([H])[H])[C]([N]([H])[H])=[N+]2[H])=[C]([H])[C]([H])=[C]1[H]'
-lig_32_L:
-  charge: 1
-  measurement:
-    comment: Table 3, entry 41
-    doi: 10.1021/jm901414e
-    error: 0.04
-    type: ic50
-    unit: uM
-    value: 0.05
-  name: lig_32_L
-  smiles: '[H][C]1=[N][C]([H])=[C]([H])[C]([H])=[C]1[C]1=[C]([H])[C]([C@]2([C]3=[C]([H])[C]([H])=[C]([O][C]([H])([H])[H])[C]([O][C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[H])=[C]3[H])[C](=[O])[N]([C]([H])([H])[H])[C]([N]([H])[H])=[N+]2[H])=[C]([H])[C]([H])=[C]1[H]'
 lig_33_L:
   charge: 1
   measurement:

diff --git a/data/cdk2/00_data/ligands.yml b/data/cdk2/00_data/ligands.yml
@@ -28,16 +28,6 @@ lig_1h1r:
     value: 2.3
   name: lig_1h1r
   smiles: '[H]c1c(c(c(c(c1[H])Cl)[H])N([H])c2nc3c(c(n2)OC([H])([H])C4(C(C(C(C(C4([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])N=C(N3[H])[H])[H]'
-lig_1h1s:
-  measurement:
-    comment: Table 2, entry 3
-    doi: 10.1021/jm0311442
-    error: 0.001
-    type: ic50
-    unit: uM
-    value: 0.0054
-  name: lig_1h1s
-  smiles: '[H][C]1=[N][C]2=[C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])[N]=[C]([N]([H])[C]3=[C]([H])[C]([H])=[C]([S](=[O])(=[O])[N]([H])[H])[C]([H])=[C]3[H])[N]=[C]2[N]1[H]'
 lig_1oi9:
   measurement:
     comment: Table 2, entry 25
@@ -108,54 +98,3 @@ lig_26:
     value: 0.65
   name: lig_26
   smiles: '[H][C]1=[N][C]2=[C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])[N]=[C]([N]([H])[C]3=[C]([H])[C]([H])=[C]([O][C]([H])([H])[H])[C]([H])=[C]3[H])[N]=[C]2[N]1[H]'
-lig_28:
-  measurement:
-    comment: Table 2, entry 28
-    doi: 10.1021/jm0311442
-    error: 0.0001
-    type: ic50
-    unit: uM
-    value: 0.007
-  name: lig_28
-  smiles: '[H][C]1=[N][C]2=[C]([O][C]([H])([H])[C]3([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]([H])([H])[C]3([H])[H])[N]=[C]([N]([H])[C]3=[C]([H])[C]([H])=[C]([S](=[O])(=[O])[N]([H])[C]([H])([H])[H])[C]([H])=[C]3[H])[N]=[C]2[N]1[H]'
-lig_29:
-  measurement:
-    comment: Table 3, entry 29
-    doi: 10.1021/jm0311442
-    error: 0.02
-    type: ic50
-    unit: uM
-    value: 0.056
-  name: lig_29
-  smiles: '[H]c1c(c(c(c(c1N([H])c2nc3c(c(n2)OC([H])([H])C4(C(C(C(C(C4([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])N=C(N3[H])[H])[H])[H])S(=O)(=O)N(C([H])([H])[H])C([H])([H])[H])[H]'
-lig_30:
-  measurement:
-    comment: Table 3, entry 30
-    doi: 10.1021/jm0311442
-    error: 0.007
-    type: ic50
-    unit: uM
-    value: 0.063
-  name: lig_30
-  smiles: '[H]c1c(c(c(c(c1N([H])c2nc3c(c(n2)OC([H])([H])C4(C(C(C(C(C4([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])N=C(N3[H])[H])[H])[H])S(=O)(=O)C([H])([H])[H])[H]'
-lig_31:
-  measurement:
-    comment: Table 3, entry 31; stereochemistry of sulfoxide not given in reference,
-      the configuration was manually specified as in DOI 10.1039/C9SC03754C
-    doi: 10.1021/jm0311442
-    error: 0.01
-    type: ic50
-    unit: uM
-    value: 0.1
-  name: lig_31
-  smiles: '[H]c1c(c(c(c(c1N([H])c2nc3c(c(n2)OC([H])([H])C4(C(C(C(C(C4([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])N=C(N3[H])[H])[H])[H])[S@@](=O)C([H])([H])[H])[H]'
-lig_32:
-  measurement:
-    comment: Table 3, entry 32
-    doi: 10.1021/jm0311442
-    error: 0.008
-    type: ic50
-    unit: uM
-    value: 0.07
-  name: lig_32
-  smiles: '[H]c1c(c(c(c(c1N([H])c2nc3c(c(n2)OC([H])([H])C4(C(C(C(C(C4([H])[H])([H])[H])([H])[H])([H])[H])([H])[H])[H])N=C(N3[H])[H])[H])OC([H])([H])[H])S(=O)(=O)N([H])[H])[H]'
diff --git a/data/cdk8/00_data/ligands.yml b/data/cdk8/00_data/ligands.yml
@@ -98,16 +98,6 @@ lig_22:
     value: 0.032
   name: lig_22
   smiles: '[H][C]1=[N][N]([C]([H])([H])[H])[C]([H])=[C]1[C]1=[C]([H])[C]([H])=[C]([C]([H])([H])[C]2=[N][N]([H])[C]3=[C]2[C]([H])=[C]([C]2=[N][C]([H])=[C]([H])[N]2[C]([H])([H])[H])[C]([H])=[C]3[H])[C]([H])=[C]1[H]'
-lig_23:
-  charge: 0
-  measurement:
-    doi: 10.1016/j.bmcl.2016.01.062
-    error: -1
-    type: ic50
-    unit: uM
-    value: 0.27
-  name: lig_23
-  smiles: '[H][C]1=[N][N]([C]([H])([H])[H])[C]([H])=[C]1[C]1=[C]([H])[C]([H])=[C]([C]([H])([H])[C]2=[N][N]([H])[C]3=[C]2[C]([H])=[C]([C]2=[N][C]([H])=[C]([H])[C]([N]([H])[H])=[C]2[H])[C]([H])=[C]3[H])[C]([H])=[C]1[H]'
 lig_24:
   charge: 0
   measurement:
@@ -178,16 +168,6 @@ lig_30:
     value: 0.003
   name: lig_30
   smiles: '[H][O][C@]1([H])[C]([H])([H])[N]([C](=[O])[C]2=[C]([H])[C]3=[C]([C]([H])=[C]2[H])[N]([H])[N]=[C]3[C]([H])([H])[C]2=[C]([H])[C]([H])=[C]([C]3=[C]([H])[N]([C]([H])([H])[H])[N]=[C]3[H])[C]([H])=[C]2[H])[C]([H])([H])[C]1([H])[H]'
-lig_31:
-  charge: 0
-  measurement:
-    doi: 10.1016/j.bmcl.2016.01.062
-    error: -1
-    type: ic50
-    unit: uM
-    value: 0.002
-  name: lig_31
-  smiles: '[H][O][C@@]1([H])[C]([H])([H])[N]([C](=[O])[C]2=[C]([H])[C]3=[C]([C]([H])=[C]2[H])[N]([H])[N]=[C]3[C]([H])([H])[C]2=[C]([H])[C]([H])=[C]([C]3=[C]([H])[N]([C]([H])([H])[H])[N]=[C]3[H])[C]([H])=[C]2[H])[C]([H])([H])[C]1([H])[H]'
 lig_32:
   charge: 0
   measurement:

diff --git a/data/cmet/00_data/ligands.yml b/data/cmet/00_data/ligands.yml
@@ -20,28 +20,6 @@ lig_CHEMBL3402745_200_5:
     value: 200
   name: lig_CHEMBL3402745_200_5
   smiles: '[H][C]1=[C]([H])[C]([c]2[c]([H])[c]([F])[c]([H])[c]([F])[c]2[H])=[N][N]([C]([H])([H])[c]2[c]([H])[c]([H])[c]([H])[c]([N]([H])[C](=[O])[O][C]([H])([H])[C]([H])([H])[H])[c]2[H])[C]1=[O]'
-lig_CHEMBL3402747_3400_7:
-  charge: 0.0
-  measurement:
-    doi:
-    - 10.1016/j.bmcl.2015.02.002
-    error: -1
-    type: ic50
-    unit: nM
-    value: 3400
-  name: lig_CHEMBL3402747_3400_7
-  smiles: '[H][C]1=[C]([H])[C]([c]2[c]([H])[c]([F])[c]([H])[c]([F])[c]2[H])=[N][N]([C]([H])([H])[c]2[c]([H])[c]([H])[c]([H])[c]([C]3=[N][C]([C]([H])([H])[H])=[N][O]3)[c]2[H])[C]1=[O]'
-lig_CHEMBL3402748_5300_8:
-  charge: 0.0
-  measurement:
-    doi:
-    - 10.1016/j.bmcl.2015.02.002
-    error: -1
-    type: ic50
-    unit: nM
-    value: 5300
-  name: lig_CHEMBL3402748_5300_8
-  smiles: '[H][C]1=[C]([C]([H])([H])[H])[N]([H])[C]([c]2[c]([H])[c]([H])[c]([H])[c]([C]([H])([H])[N]3[N]=[C]([c]4[c]([H])[c]([F])[c]([H])[c]([F])[c]4[H])[C]([H])=[C]([H])[C]3=[O])[c]2[H])=[N]1'
 lig_CHEMBL3402749_500_9:
   charge: 0.0
   measurement:
@@ -53,50 +31,6 @@ lig_CHEMBL3402749_500_9:
     value: 500
   name: lig_CHEMBL3402749_500_9
   smiles: '[H][C]1=[C]([C]([H])([H])[H])[O][C]([c]2[c]([H])[c]([H])[c]([H])[c]([C]([H])([H])[N]3[N]=[C]([c]4[c]([H])[c]([F])[c]([H])[c]([F])[c]4[H])[C]([H])=[C]([H])[C]3=[O])[c]2[H])=[N]1'
-lig_CHEMBL3402750_400_10:
-  charge: 0.0
-  measurement:
-    doi:
-    - 10.1016/j.bmcl.2015.02.002
-    error: -1
-    type: ic50
-    unit: nM
-    value: 400
-  name: lig_CHEMBL3402750_400_10
-  smiles: '[H][C]1=[C]([C]([H])([H])[H])[S][C]([c]2[c]([H])[c]([H])[c]([H])[c]([C]([H])([H])[N]3[N]=[C]([c]4[c]([H])[c]([F])[c]([H])[c]([F])[c]4[H])[C]([H])=[C]([H])[C]3=[O])[c]2[H])=[N]1'
-lig_CHEMBL3402751_2100_11:
-  charge: 0.0
-  measurement:
-    doi:
-    - 10.1016/j.bmcl.2015.02.002
-    error: -1
-    type: ic50
-    unit: nM
-    value: 2100
-  name: lig_CHEMBL3402751_2100_11
-  smiles: '[H][C]1=[C]([C]([H])([H])[H])[N]=[C]([c]2[c]([H])[c]([H])[c]([H])[c]([C]([H])([H])[N]3[N]=[C]([c]4[c]([H])[c]([F])[c]([H])[c]([F])[c]4[H])[C]([H])=[C]([H])[C]3=[O])[c]2[H])[S]1'
-lig_CHEMBL3402752_30000_12:
-  charge: 0.0
-  measurement:
-    doi:
-    - 10.1016/j.bmcl.2015.02.002
-    error: -1
-    type: ic50
-    unit: nM
-    value: 30000
-  name: lig_CHEMBL3402752_30000_12
-  smiles: '[H][C]1=[C]([c]2[c]([H])[c]([H])[c]([H])[c]([C]([H])([H])[N]3[N]=[C]([c]4[c]([H])[c]([F])[c]([H])[c]([F])[c]4[H])[C]([H])=[C]([H])[C]3=[O])[c]2[H])[N]=[C]([C]([H])([H])[H])[S]1'
-lig_CHEMBL3402753_200_13:
-  charge: 0.0
-  measurement:
-    doi:
-    - 10.1016/j.bmcl.2015.02.002
-    error: -1
-    type: ic50
-    unit: nM
-    value: 200
-  name: lig_CHEMBL3402753_200_13
-  smiles: '[H][C]1=[C]([H])[C]([c]2[c]([H])[c]([F])[c]([H])[c]([F])[c]2[H])=[N][N]([C]([H])([H])[c]2[c]([H])[c]([H])[c]([H])[c](-[c]3[n][c]([H])[c]([C]([H])([H])[H])[c]([H])[c]3[H])[c]2[H])[C]1=[O]'
 lig_CHEMBL3402754_40_14:
   charge: 0.0
   measurement:
@@ -108,17 +42,6 @@ lig_CHEMBL3402754_40_14:
     value: 40
   name: lig_CHEMBL3402754_40_14
   smiles: '[H][C]1=[C]([H])[C]([c]2[c]([H])[c]([F])[c]([H])[c]([F])[c]2[H])=[N][N]([C]([H])([H])[c]2[c]([H])[c]([H])[c]([H])[c](-[c]3[n][c]([H])[c]([C]([H])([H])[H])[c]([H])[n]3)[c]2[H])[C]1=[O]'
-lig_CHEMBL3402755_4200_15:
-  charge: 0.0
-  measurement:
-    doi:
-    - 10.1016/j.bmcl.2015.02.002
-    error: -1
-    type: ic50
-    unit: nM
-    value: 4200
-  name: lig_CHEMBL3402755_4200_15
-  smiles: '[H][C]1=[C]([H])[C]([c]2[c]([H])[c]([F])[c]([H])[c]([F])[c]2[H])=[N][N]([C]([H])([H])[c]2[c]([H])[c]([H])[c]([H])[c](-[c]3[n][n][c]([C]([H])([H])[H])[c]([H])[c]3[H])[c]2[H])[C]1=[O]'
 lig_CHEMBL3402761_1_21:
   charge: 0.0
   measurement:

diff --git a/data/eg5/00_data/ligands.yml b/data/eg5/00_data/ligands.yml
@@ -108,16 +108,6 @@ lig_CHEMBL1084143:
     value: 2
   name: lig_CHEMBL1084143
   smiles: '[H][C]1=[C]([H])[C]([H])=[C]([C@]2([H])[N]([H])[C]3=[C]([H])[C]([H])=[C]([C]([H])([C]([H])([H])[H])[C]([H])([H])[H])[C]([H])=[C]3[C@@]3([H])[O][C@@]([H])([C]([H])([H])[N]([H])[S](=[O])(=[O])[C]([H])([H])[C]([H])([H])[C]([H])([H])[N+]([H])([C]([H])([H])[H])[C]([H])([H])[H])[C]([H])([H])[C]([H])([H])[C@]32[H])[C]([H])=[C]1[H]'
-lig_CHEMBL1084431:
-  charge: 1
-  measurement:
-    doi: 10.1158/0008-5472.CAN-16-0473
-    error: -1
-    type: ic50
-    unit: nM
-    value: 65
-  name: lig_CHEMBL1084431
-  smiles: '[H][C]1=[C]([H])[C]([H])=[C]([C@]2([H])[N]([H])[C]3=[C]([H])[C]([H])=[C]([C]([F])([F])[F])[C]([H])=[C]3[C@@]3([H])[O][C@@]([H])([C]([H])([H])[N]([C](=[O])[C]4=[C]([H])[C]([H])=[C]([C]([H])([H])[H])[C]([H])=[C]4[H])[C]([H])([H])[C]([H])([H])[N+]([H])([H])[H])[C]([H])([H])[C]([H])([H])[C@]32[H])[C]([H])=[C]1[H]'
 lig_CHEMBL1084676:
   charge: 1
   measurement: