update terminal_group molecule bank

daico007 · Oct 22, 2021 · c0d77b6 · c0d77b6
1 parent 541a559
commit c0d77b6
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Showing 52 changed files with 429 additions and 642 deletions.
diff --git a/surface_coatings/molecules/one_port/pdbs/2pyrrole.pdb b/surface_coatings/molecules/one_port/pdbs/2pyrrole.pdb
@@ -0,0 +1,22 @@
+COMPND    UNNAMED
+AUTHOR    GENERATED BY OPEN BABEL 2.3.90
+HETATM    1  C   UNL     1      -0.464  -0.403  -0.000  1.00  0.00           C  
+HETATM    2  C   UNL     1       0.906   0.495  -0.000  1.00  0.00           C  
+HETATM    3  N   UNL     1      -1.789   0.434  -0.000  1.00  0.00           N  
+HETATM    4  C   UNL     1      -1.241   2.017  -0.000  1.00  0.00           C  
+HETATM    5  C   UNL     1       0.510   2.047  -0.000  1.00  0.00           C  
+HETATM    6  H   UNL     1      -2.900   0.129  -0.000  1.00  0.00           H  
+HETATM    7  H   UNL     1      -2.002   2.976  -0.000  1.00  0.00           H  
+HETATM    8  H   UNL     1       1.149   3.006  -0.000  1.00  0.00           H  
+HETATM    9  H   UNL     1       1.971  -0.008  -0.000  1.00  0.00           H  
+CONECT    1    2    3                                                 
+CONECT    2    1    5    9                                            
+CONECT    3    1    4    6                                            
+CONECT    4    3    5    7                                            
+CONECT    5    2    4    8                                            
+CONECT    6    3                                                      
+CONECT    7    4                                                      
+CONECT    8    5                                                      
+CONECT    9    2                                                      
+MASTER        0    0    0    0    0    0    0    0    9    0    9    0
+END
diff --git a/surface_coatings/molecules/one_port/pdbs/acetyl-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/acetyl-ch3.pdb
diff --git a/surface_coatings/molecules/one_port/pdbs/acetyl-h.pdb b/surface_coatings/molecules/one_port/pdbs/acetyl-h.pdb
diff --git a/.../molecules/one_port/pdbs/hydroxyl-ch3.pdb → ...atings/molecules/one_port/pdbs/acetyl.pdb b/.../molecules/one_port/pdbs/hydroxyl-ch3.pdb → ...atings/molecules/one_port/pdbs/acetyl.pdb
@@ -1,11 +1,11 @@
 COMPND    UNNAMED
 AUTHOR    GENERATED BY OPEN BABEL 2.3.90
-HETATM    1  O   UNL     1      -0.176  -0.103   1.047  1.00  0.00           O  
-HETATM    2  H   UNL     1      -0.052  -0.030   0.065  1.00  0.00           H  
-HETATM    3  C   UNL     1      -1.373  -0.802   1.233  1.00  0.00           C  
-HETATM    4  H   UNL     1      -1.559  -0.911   2.321  1.00  0.00           H  
-HETATM    5  H   UNL     1      -2.222  -0.238   0.790  1.00  0.00           H  
-HETATM    6  H   UNL     1      -1.298  -1.819   0.790  1.00  0.00           H  
+HETATM    1  C   UNL     1       0.008  -1.332  -0.000  1.00  0.00           C  
+HETATM    2  O   UNL     1      -1.393  -1.317  -0.000  1.00  0.00           O  
+HETATM    3  C   UNL     1       0.830  -0.023  -0.000  1.00  0.00           C  
+HETATM    4  H   UNL     1      -0.419  -0.008  -0.000  1.00  0.00           H  
+HETATM    5  H   UNL     1       0.814   1.164  -0.000  1.00  0.00           H  
+HETATM    6  H   UNL     1       2.032  -0.008  -0.000  1.00  0.00           H  
 CONECT    1    2    3                                                 
 CONECT    2    1                                                      
 CONECT    3    1    4    5    6                                       

diff --git a/surface_coatings/molecules/one_port/pdbs/amino-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/amino-ch3.pdb
diff --git a/...gs/molecules/one_port/pdbs/hydroxyl-h.pdb → ...oatings/molecules/one_port/pdbs/amino.pdb b/...gs/molecules/one_port/pdbs/hydroxyl-h.pdb → ...oatings/molecules/one_port/pdbs/amino.pdb
@@ -1,8 +1,8 @@
 COMPND    UNNAMED
 AUTHOR    GENERATED BY OPEN BABEL 2.3.90
-HETATM    1  O   HOH     1      -1.521   0.548  -0.009  1.00  0.00           O  
-HETATM    2  H   HOH     0      -1.786   1.497  -0.108  1.00  0.00           H  
-HETATM    3  H   HOH     0      -2.270   0.038  -0.406  1.00  0.00           H  
+HETATM    1  N   UNL     1      -0.342   0.038  -0.000  1.00  0.00           N  
+HETATM    2  H   UNL     1       0.647   0.784  -0.000  1.00  0.00           H  
+HETATM    3  H   UNL     1      -1.378   0.693  -0.000  1.00  0.00           H  
 CONECT    1    2    3                                                 
 CONECT    2    1                                                      
 CONECT    3    1                                                      

diff --git a/surface_coatings/molecules/one_port/pdbs/benzoicacid.pdb b/surface_coatings/molecules/one_port/pdbs/benzoicacid.pdb
@@ -0,0 +1,34 @@
+COMPND    UNNAMED
+AUTHOR    GENERATED BY OPEN BABEL 2.3.90
+HETATM    1  O   UNL     1       1.065   0.556  -0.054  1.00  0.00           O  
+HETATM    2  C   UNL     1       2.245   0.091  -0.026  1.00  0.00           C  
+HETATM    3  O   UNL     1       2.835  -0.542  -0.953  1.00  0.00           O  
+HETATM    4  C   UNL     1       3.025   0.309   1.230  1.00  0.00           C  
+HETATM    5  C   UNL     1       2.993   1.550   1.869  1.00  0.00           C  
+HETATM    6  C   UNL     1       3.726   1.759   3.035  1.00  0.00           C  
+HETATM    7  C   UNL     1       4.476   0.720   3.581  1.00  0.00           C  
+HETATM    8  C   UNL     1       4.499  -0.524   2.956  1.00  0.00           C  
+HETATM    9  C   UNL     1       3.782  -0.723   1.779  1.00  0.00           C  
+HETATM   10  H   UNL     1       3.713  -0.844  -0.829  1.00  0.00           H  
+HETATM   11  H   UNL     1       2.424   2.316   1.476  1.00  0.00           H  
+HETATM   12  H   UNL     1       3.714   2.683   3.493  1.00  0.00           H  
+HETATM   13  H   UNL     1       5.014   0.872   4.449  1.00  0.00           H  
+HETATM   14  H   UNL     1       5.046  -1.298   3.364  1.00  0.00           H  
+HETATM   15  H   UNL     1       3.812  -1.642   1.309  1.00  0.00           H  
+CONECT    1    2                                                      
+CONECT    2    1    3    4                                            
+CONECT    3    2   10                                                 
+CONECT    4    2    5    9                                            
+CONECT    5    4    6   11                                            
+CONECT    6    5    7   12                                            
+CONECT    7    6    8   13                                            
+CONECT    8    7    9   14                                            
+CONECT    9    8    4   15                                            
+CONECT   10    3                                                      
+CONECT   11    5                                                      
+CONECT   12    6                                                      
+CONECT   13    7                                                      
+CONECT   14    8                                                      
+CONECT   15    9                                                      
+MASTER        0    0    0    0    0    0    0    0   15    0   15    0
+END
diff --git a/surface_coatings/molecules/one_port/pdbs/carboxyl-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/carboxyl-ch3.pdb
diff --git a/surface_coatings/molecules/one_port/pdbs/carboxyl-h.pdb b/surface_coatings/molecules/one_port/pdbs/carboxyl-h.pdb
diff --git a/surface_coatings/molecules/one_port/pdbs/carboxyl.pdb b/surface_coatings/molecules/one_port/pdbs/carboxyl.pdb
@@ -0,0 +1,12 @@
+COMPND    UNNAMED
+AUTHOR    GENERATED BY OPEN BABEL 2.3.90
+HETATM    1  C   UNL     1      -0.251   0.023  -0.000  1.00  0.00           C  
+HETATM    2  O   UNL     1      -1.712   0.053  -0.000  1.00  0.00           O  
+HETATM    3  O   UNL     1       0.632   1.362  -0.000  1.00  0.00           O  
+HETATM    4  H   UNL     1       0.601   2.519  -0.000  1.00  0.00           H  
+CONECT    1    2    3                                                 
+CONECT    2    1                                                      
+CONECT    3    1    4                                                 
+CONECT    4    3                                                      
+MASTER        0    0    0    0    0    0    0    0    4    0    4    0
+END
diff --git a/...tings/molecules/one_port/pdbs/amino-h.pdb → ..._coatings/molecules/one_port/pdbs/ch3.pdb b/...tings/molecules/one_port/pdbs/amino-h.pdb → ..._coatings/molecules/one_port/pdbs/ch3.pdb
@@ -1,9 +1,9 @@
 COMPND    UNNAMED
-AUTHOR    GENERATED BY OPEN BABEL 2.3.90
-HETATM    1  N   UNL     1      -0.806   0.349  -0.012  1.00  0.00           N  
-HETATM    2  H   UNL     1      -0.773   0.952  -0.865  1.00  0.00           H  
-HETATM    3  H   UNL     1      -1.767   0.380   0.396  1.00  0.00           H  
-HETATM    4  H   UNL     1      -0.575  -0.635  -0.277  1.00  0.00           H  
+AUTHOR    GENERATED BY OPEN BABEL 
+ATOM      1  C   LIG A   1      -1.750   1.662   0.000  1.00  0.00           C  
+ATOM      2  H   LIG A   1      -0.680   1.662   0.000  1.00  0.00           H  
+ATOM      3  H   LIG A   1      -2.107   2.431   0.653  1.00  0.00           H  
+ATOM      4  H   LIG A   1      -2.107   1.843  -0.993  1.00  0.00           H  
 CONECT    1    2    3    4                                            
 CONECT    2    1                                                      
 CONECT    3    1                                                      

diff --git a/surface_coatings/molecules/one_port/pdbs/cyano-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/cyano-ch3.pdb
diff --git a/surface_coatings/molecules/one_port/pdbs/cyano.pdb b/surface_coatings/molecules/one_port/pdbs/cyano.pdb
@@ -0,0 +1,8 @@
+COMPND    UNNAMED
+AUTHOR    GENERATED BY OPEN BABEL 2.3.90
+HETATM    1  C   UNL     1      -0.358  -0.906  -0.000  1.00  0.00           C  
+HETATM    2  N   UNL     1      -0.358   0.388  -0.000  1.00  0.00           N  
+CONECT    1    2                                                      
+CONECT    2    1                                                      
+MASTER        0    0    0    0    0    0    0    0    2    0    2    0
+END
diff --git a/surface_coatings/molecules/one_port/pdbs/cyclopropyl-ch3.pdb b/surface_coatings/molecules/one_port/pdbs/cyclopropyl-ch3.pdb
diff --git a/surface_coatings/molecules/one_port/pdbs/cyclopropyl-h.pdb b/surface_coatings/molecules/one_port/pdbs/cyclopropyl-h.pdb