Fix internal contacts in OR models. (#501)

* Models. * Protonation functions. * Stays flexions cause side chain clashes. #415 * Spacefill UI.
primaryodors · Dec 31, 2024 · 53ab5f3 · 53ab5f3
1 parent 8d72c7c
commit 53ab5f3
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diff --git a/data/odorant.json b/data/odorant.json
@@ -1991,6 +1991,7 @@
     "091f953d9bb4d63af4021067222dda72":
     {
         "full_name": "2-octanol",
+        "iupac": "octan-2-ol",
         "smiles": "CCCCCCC(O)C",
         "isomers":
         {
@@ -12264,6 +12265,8 @@
     "53593b4a71638a116082eded92de4ced":
     {
         "full_name": "1-heptanol",
+        "name1": "1-heptanol",
+        "iupac": "heptan-1-ol",
         "smiles": "CCCCCCCO",
         "aroma":
         {
@@ -14897,6 +14900,7 @@
     "65cfa7a59e60c0559bf67cc7b63b31cb":
     {
         "full_name": "3-octanol",
+        "iupac": "octan-3-ol",
         "smiles": "CCCCCC(O)CC",
         "isomers":
         {
@@ -15728,7 +15732,9 @@
     },
     "674758039c98a44c54365f229e82d544":
     {
-        "full_name": "1-hexanol",
+        "full_name": "hexanol",
+        "name1": "1-hexanol",
+        "iupac": "hexan-1-ol",
         "smiles": "CCCCCCO",
         "aroma":
         {
@@ -20808,6 +20814,8 @@
     "85c4b8225f8b7fdda3b8c213b33e6350":
     {
         "full_name": "propanol",
+        "name1": "1-propanol",
+        "iupac": "propan-1-ol",
         "smiles": "CCCO",
         "aroma":
         {
@@ -34428,6 +34436,7 @@
     "e54aaff9566be026b54a962f0a397dbc":
     {
         "full_name": "4-octanol",
+        "iupac": "octan-4-ol",
         "smiles": "CCCCC(O)CCC",
         "isomers":
         {
@@ -35272,7 +35281,9 @@
     },
     "ebf0d0b3c02b378d6567c12c068c75f4":
     {
-        "full_name": "1-butanol",
+        "full_name": "butanol",
+        "name1": "1-butanol",
+        "iupac": "butan-1-ol",
         "smiles": "CCCCO",
         "aroma":
         {
@@ -35530,6 +35541,7 @@
     "ee4dd2290d52c459c35d7b6c3203f231":
     {
         "full_name": "1-octanol",
+        "iupac": "octan-1-ol",
         "smiles": "CCCCCCCCO",
         "aroma":
         {

diff --git a/data/receptor.json b/data/receptor.json
diff --git a/pdbs/OR1/OR1B1.active.pdb b/pdbs/OR1/OR1B1.active.pdb
diff --git a/pdbs/OR1/OR1C1.active.pdb b/pdbs/OR1/OR1C1.active.pdb
diff --git a/pdbs/OR1/OR1D2.active.pdb b/pdbs/OR1/OR1D2.active.pdb
diff --git a/pdbs/OR1/OR1D4.active.pdb b/pdbs/OR1/OR1D4.active.pdb
diff --git a/pdbs/OR1/OR1D5.active.pdb b/pdbs/OR1/OR1D5.active.pdb
diff --git a/pdbs/OR1/OR1E1.active.pdb b/pdbs/OR1/OR1E1.active.pdb
diff --git a/pdbs/OR1/OR1E2.active.pdb b/pdbs/OR1/OR1E2.active.pdb
diff --git a/pdbs/OR1/OR1E3.active.pdb b/pdbs/OR1/OR1E3.active.pdb
diff --git a/pdbs/OR1/OR1F1.active.pdb b/pdbs/OR1/OR1F1.active.pdb
diff --git a/pdbs/OR1/OR1F12.active.pdb b/pdbs/OR1/OR1F12.active.pdb
diff --git a/pdbs/OR1/OR1F2.active.pdb b/pdbs/OR1/OR1F2.active.pdb
diff --git a/pdbs/OR1/OR1G1.active.pdb b/pdbs/OR1/OR1G1.active.pdb
diff --git a/pdbs/OR1/OR1I1.active.pdb b/pdbs/OR1/OR1I1.active.pdb
diff --git a/pdbs/OR1/OR1J1.active.pdb b/pdbs/OR1/OR1J1.active.pdb
diff --git a/pdbs/OR1/OR1J2.active.pdb b/pdbs/OR1/OR1J2.active.pdb
diff --git a/pdbs/OR1/OR1J4.active.pdb b/pdbs/OR1/OR1J4.active.pdb
diff --git a/pdbs/OR1/OR1K1.active.pdb b/pdbs/OR1/OR1K1.active.pdb
diff --git a/pdbs/OR1/OR1L1.active.pdb b/pdbs/OR1/OR1L1.active.pdb
diff --git a/pdbs/OR1/OR1L3.active.pdb b/pdbs/OR1/OR1L3.active.pdb
diff --git a/pdbs/OR1/OR1L4.active.pdb b/pdbs/OR1/OR1L4.active.pdb
diff --git a/pdbs/OR1/OR1L6.active.pdb b/pdbs/OR1/OR1L6.active.pdb
diff --git a/pdbs/OR1/OR1L8.active.pdb b/pdbs/OR1/OR1L8.active.pdb
diff --git a/pdbs/OR1/OR1M1.active.pdb b/pdbs/OR1/OR1M1.active.pdb
diff --git a/pdbs/OR1/OR1N1.active.pdb b/pdbs/OR1/OR1N1.active.pdb
diff --git a/pdbs/OR1/OR1N2.active.pdb b/pdbs/OR1/OR1N2.active.pdb
diff --git a/pdbs/OR1/OR1Q1.active.pdb b/pdbs/OR1/OR1Q1.active.pdb
diff --git a/pdbs/OR1/OR1S1.active.pdb b/pdbs/OR1/OR1S1.active.pdb
diff --git a/pdbs/OR1/OR1S2.active.pdb b/pdbs/OR1/OR1S2.active.pdb
diff --git a/pdbs/OR10/OR10A2.active.pdb b/pdbs/OR10/OR10A2.active.pdb
diff --git a/pdbs/OR10/OR10A3.active.pdb b/pdbs/OR10/OR10A3.active.pdb
diff --git a/pdbs/OR10/OR10A4.active.pdb b/pdbs/OR10/OR10A4.active.pdb
diff --git a/pdbs/OR10/OR10A5.active.pdb b/pdbs/OR10/OR10A5.active.pdb
diff --git a/pdbs/OR10/OR10A6.active.pdb b/pdbs/OR10/OR10A6.active.pdb
diff --git a/pdbs/OR10/OR10A7.active.pdb b/pdbs/OR10/OR10A7.active.pdb
diff --git a/pdbs/OR10/OR10AC1.active.pdb b/pdbs/OR10/OR10AC1.active.pdb
diff --git a/pdbs/OR10/OR10AD1.active.pdb b/pdbs/OR10/OR10AD1.active.pdb
diff --git a/pdbs/OR10/OR10AG1.active.pdb b/pdbs/OR10/OR10AG1.active.pdb
diff --git a/pdbs/OR10/OR10C1.active.pdb b/pdbs/OR10/OR10C1.active.pdb
diff --git a/pdbs/OR10/OR10D3.active.pdb b/pdbs/OR10/OR10D3.active.pdb
diff --git a/pdbs/OR10/OR10D4.active.pdb b/pdbs/OR10/OR10D4.active.pdb
diff --git a/pdbs/OR10/OR10G2.active.pdb b/pdbs/OR10/OR10G2.active.pdb
diff --git a/pdbs/OR10/OR10G3.active.pdb b/pdbs/OR10/OR10G3.active.pdb
diff --git a/pdbs/OR10/OR10G4.active.pdb b/pdbs/OR10/OR10G4.active.pdb
diff --git a/pdbs/OR10/OR10G6.active.pdb b/pdbs/OR10/OR10G6.active.pdb
diff --git a/pdbs/OR10/OR10G7.active.pdb b/pdbs/OR10/OR10G7.active.pdb
diff --git a/pdbs/OR10/OR10G8.active.pdb b/pdbs/OR10/OR10G8.active.pdb
diff --git a/pdbs/OR10/OR10G9.active.pdb b/pdbs/OR10/OR10G9.active.pdb
diff --git a/pdbs/OR10/OR10H1.active.pdb b/pdbs/OR10/OR10H1.active.pdb
diff --git a/pdbs/OR10/OR10H2.active.pdb b/pdbs/OR10/OR10H2.active.pdb
diff --git a/pdbs/OR10/OR10H3.active.pdb b/pdbs/OR10/OR10H3.active.pdb
diff --git a/pdbs/OR10/OR10H4.active.pdb b/pdbs/OR10/OR10H4.active.pdb
diff --git a/pdbs/OR10/OR10H5.active.pdb b/pdbs/OR10/OR10H5.active.pdb
diff --git a/pdbs/OR10/OR10J1.active.pdb b/pdbs/OR10/OR10J1.active.pdb
diff --git a/pdbs/OR10/OR10J3.active.pdb b/pdbs/OR10/OR10J3.active.pdb
diff --git a/pdbs/OR10/OR10J4.active.pdb b/pdbs/OR10/OR10J4.active.pdb
diff --git a/pdbs/OR10/OR10J5.active.pdb b/pdbs/OR10/OR10J5.active.pdb
diff --git a/pdbs/OR10/OR10K1.active.pdb b/pdbs/OR10/OR10K1.active.pdb
diff --git a/pdbs/OR10/OR10K2.active.pdb b/pdbs/OR10/OR10K2.active.pdb
diff --git a/pdbs/OR10/OR10P1.active.pdb b/pdbs/OR10/OR10P1.active.pdb
diff --git a/pdbs/OR10/OR10Q1.active.pdb b/pdbs/OR10/OR10Q1.active.pdb
diff --git a/pdbs/OR10/OR10R2.active.pdb b/pdbs/OR10/OR10R2.active.pdb
diff --git a/pdbs/OR10/OR10S1.active.pdb b/pdbs/OR10/OR10S1.active.pdb
diff --git a/pdbs/OR10/OR10T2.active.pdb b/pdbs/OR10/OR10T2.active.pdb
diff --git a/pdbs/OR10/OR10V1.active.pdb b/pdbs/OR10/OR10V1.active.pdb
diff --git a/pdbs/OR10/OR10W1.active.pdb b/pdbs/OR10/OR10W1.active.pdb
diff --git a/pdbs/OR10/OR10X1.active.pdb b/pdbs/OR10/OR10X1.active.pdb
diff --git a/pdbs/OR10/OR10Z1.active.pdb b/pdbs/OR10/OR10Z1.active.pdb
diff --git a/pdbs/OR11/OR11A1.active.pdb b/pdbs/OR11/OR11A1.active.pdb
diff --git a/pdbs/OR11/OR11G2.active.pdb b/pdbs/OR11/OR11G2.active.pdb
diff --git a/pdbs/OR11/OR11H1.active.pdb b/pdbs/OR11/OR11H1.active.pdb
diff --git a/pdbs/OR11/OR11H12.active.pdb b/pdbs/OR11/OR11H12.active.pdb
diff --git a/pdbs/OR11/OR11H2.active.pdb b/pdbs/OR11/OR11H2.active.pdb
diff --git a/pdbs/OR11/OR11H4.active.pdb b/pdbs/OR11/OR11H4.active.pdb
diff --git a/pdbs/OR11/OR11H6.active.pdb b/pdbs/OR11/OR11H6.active.pdb
diff --git a/pdbs/OR11/OR11H7.active.pdb b/pdbs/OR11/OR11H7.active.pdb
diff --git a/pdbs/OR11/OR11L1.active.pdb b/pdbs/OR11/OR11L1.active.pdb
diff --git a/pdbs/OR12/OR12D2.active.pdb b/pdbs/OR12/OR12D2.active.pdb
diff --git a/pdbs/OR12/OR12D3.active.pdb b/pdbs/OR12/OR12D3.active.pdb
diff --git a/pdbs/OR13/OR13A1.active.pdb b/pdbs/OR13/OR13A1.active.pdb
diff --git a/pdbs/OR13/OR13C2.active.pdb b/pdbs/OR13/OR13C2.active.pdb
diff --git a/pdbs/OR13/OR13C3.active.pdb b/pdbs/OR13/OR13C3.active.pdb
diff --git a/pdbs/OR13/OR13C4.active.pdb b/pdbs/OR13/OR13C4.active.pdb
diff --git a/pdbs/OR13/OR13C5.active.pdb b/pdbs/OR13/OR13C5.active.pdb
diff --git a/pdbs/OR13/OR13C8.active.pdb b/pdbs/OR13/OR13C8.active.pdb
diff --git a/pdbs/OR13/OR13C9.active.pdb b/pdbs/OR13/OR13C9.active.pdb
diff --git a/pdbs/OR13/OR13D1.active.pdb b/pdbs/OR13/OR13D1.active.pdb
diff --git a/pdbs/OR13/OR13F1.active.pdb b/pdbs/OR13/OR13F1.active.pdb
diff --git a/pdbs/OR13/OR13G1.active.pdb b/pdbs/OR13/OR13G1.active.pdb
diff --git a/pdbs/OR13/OR13H1.active.pdb b/pdbs/OR13/OR13H1.active.pdb
diff --git a/pdbs/OR13/OR13J1.active.pdb b/pdbs/OR13/OR13J1.active.pdb
diff --git a/pdbs/OR14/OR14A16.active.pdb b/pdbs/OR14/OR14A16.active.pdb
diff --git a/pdbs/OR14/OR14A2.active.pdb b/pdbs/OR14/OR14A2.active.pdb
diff --git a/pdbs/OR14/OR14C36.active.pdb b/pdbs/OR14/OR14C36.active.pdb
diff --git a/pdbs/OR14/OR14I1.active.pdb b/pdbs/OR14/OR14I1.active.pdb
diff --git a/pdbs/OR14/OR14J1.active.pdb b/pdbs/OR14/OR14J1.active.pdb
diff --git a/pdbs/OR14/OR14K1.active.pdb b/pdbs/OR14/OR14K1.active.pdb
diff --git a/pdbs/OR14/OR14L1.active.pdb b/pdbs/OR14/OR14L1.active.pdb
diff --git a/pdbs/OR2/OR2A1.active.pdb b/pdbs/OR2/OR2A1.active.pdb
diff --git a/pdbs/OR2/OR2A12.active.pdb b/pdbs/OR2/OR2A12.active.pdb
diff --git a/pdbs/OR2/OR2A14.active.pdb b/pdbs/OR2/OR2A14.active.pdb
diff --git a/pdbs/OR2/OR2A2.active.pdb b/pdbs/OR2/OR2A2.active.pdb
diff --git a/pdbs/OR2/OR2A25.active.pdb b/pdbs/OR2/OR2A25.active.pdb
diff --git a/pdbs/OR2/OR2A5.active.pdb b/pdbs/OR2/OR2A5.active.pdb
diff --git a/pdbs/OR2/OR2A7.active.pdb b/pdbs/OR2/OR2A7.active.pdb
diff --git a/pdbs/OR2/OR2AE1.active.pdb b/pdbs/OR2/OR2AE1.active.pdb
diff --git a/pdbs/OR2/OR2AG1.active.pdb b/pdbs/OR2/OR2AG1.active.pdb
diff --git a/pdbs/OR2/OR2AG1.upright.pdb b/pdbs/OR2/OR2AG1.upright.pdb
@@ -45,7 +45,7 @@ REMARK 800 SITE BW 3.50 122
 REMARK 800 SITE BW 34.50 129
 REMARK 800 SITE BW 4.50 149
 REMARK 800 SITE BW 45.50 179
-REMARK 800 SITE BW 5.50 209
+REMARK 800 SITE BW 5.50 210
 REMARK 800 SITE BW 56.50 230
 REMARK 800 SITE BW 6.50 254
 REMARK 800 SITE BW 7.50 287

diff --git a/pdbs/OR2/OR2AG2.active.pdb b/pdbs/OR2/OR2AG2.active.pdb
diff --git a/pdbs/OR2/OR2AJ1.active.pdb b/pdbs/OR2/OR2AJ1.active.pdb
diff --git a/pdbs/OR2/OR2AK2.active.pdb b/pdbs/OR2/OR2AK2.active.pdb
diff --git a/pdbs/OR2/OR2AP1.active.pdb b/pdbs/OR2/OR2AP1.active.pdb
diff --git a/pdbs/OR2/OR2AT4.active.pdb b/pdbs/OR2/OR2AT4.active.pdb
diff --git a/pdbs/OR2/OR2AT4.upright.pdb b/pdbs/OR2/OR2AT4.upright.pdb
@@ -41,15 +41,15 @@ REMARK 650
 REMARK 800
 REMARK 800 SITE BW 1.50 47
 REMARK 800 SITE BW 2.50 75
-REMARK 800 SITE BW 3.50 126
-REMARK 800 SITE BW 34.50 133
-REMARK 800 SITE BW 4.50 153
-REMARK 800 SITE BW 45.50 183
-REMARK 800 SITE BW 5.50 214
-REMARK 800 SITE BW 56.50 234
-REMARK 800 SITE BW 6.50 258
-REMARK 800 SITE BW 7.50 291
-REMARK 800 SITE BW 8.50 305
+REMARK 800 SITE BW 3.50 127
+REMARK 800 SITE BW 4.50 154
+REMARK 800 SITE BW 5.50 215
+REMARK 800 SITE BW 6.50 259
+REMARK 800 SITE BW 7.50 292
+REMARK 800 SITE BW 8.50 306
+REMARK 800 SITE BW 34.50 134
+REMARK 800 SITE BW 45.50 184
+REMARK 800 SITE BW 56.50 235
 REMARK 800 SITE LIGAND_BINDING 64
 REMARK 800 SITE LIGAND_BINDING 78
 REMARK 800 SITE LIGAND_BINDING 105
@@ -1276,7 +1276,6 @@ ATOM   1190  HB2 ASP A  75     -4.313  -4.168  -4.324   1.00001.00           H
 ATOM   1191  CG  ASP A  75     -2.233  -3.919  -3.990   1.00001.00           C 
 ATOM   1192  OD1 ASP A  75     -1.496  -3.324  -3.186   1.00001.00           O-
 ATOM   1193  OD2 ASP A  75     -1.869  -4.931  -4.633   1.00001.00           O-
-ATOM   1194  HD2 ASP A  75     -1.025  -5.398  -4.531   1.00001.00           H 
 ATOM   1195  C   ASP A  75     -5.205  -1.413  -3.954   1.00001.00           C 
 ATOM   1196  O   ASP A  75     -4.974  -0.263  -4.342   1.00001.00           O 
 ATOM   1197  N   ILE A  76     -6.435  -1.938  -4.029   1.00001.00           N 
@@ -2102,7 +2101,6 @@ ATOM   2016  HB2 ASP A 126      0.390 -17.708   5.757   1.00001.00           H
 ATOM   2017  CG  ASP A 126      0.762 -19.179   4.247   1.00001.00           C 
 ATOM   2018  OD1 ASP A 126      0.032 -20.105   4.665   1.00001.00           O-
 ATOM   2019  OD2 ASP A 126      1.133 -19.075   3.057   1.00001.00           O-
-ATOM   2020  HD2 ASP A 126      0.894 -19.680   2.337   1.00001.00           H 
 ATOM   2021  C   ASP A 126      3.283 -19.576   5.557   1.00001.00           C 
 ATOM   2022  O   ASP A 126      3.308 -20.789   5.776   1.00001.00           O 
 ATOM   2023  N   ARG A 127      4.186 -18.979   4.770   1.00001.00           N 
@@ -3023,7 +3021,6 @@ ATOM   2937  HB2 ASP A 185      1.592  12.717   1.073   1.00001.00           H
 ATOM   2938  CG  ASP A 185      2.853  12.625   2.821   1.00001.00           C 
 ATOM   2939  OD1 ASP A 185      2.728  11.412   3.093   1.00001.00           O-
 ATOM   2940  OD2 ASP A 185      3.688  13.388   3.357   1.00001.00           O-
-ATOM   2941  HD2 ASP A 185      4.445  13.114   3.898   1.00001.00           H 
 ATOM   2942  C   ASP A 185      0.652  13.771   4.244   1.00001.00           C 
 ATOM   2943  O   ASP A 185      0.554  14.981   4.458   1.00001.00           O 
 ATOM   2944  N   HIS A 186      0.974  12.906   5.211   1.00001.00           N 
@@ -4384,7 +4381,6 @@ ATOM   4298  HB2 ASP A 274     10.547  18.143  -8.808   1.00001.00           H
 ATOM   4299  CG  ASP A 274      9.034  19.636  -8.936   1.00001.00           C 
 ATOM   4300  OD1 ASP A 274      7.817  19.909  -9.010   1.00001.00           O-
 ATOM   4301  OD2 ASP A 274      9.944  20.480  -9.064   1.00001.00           O-
-ATOM   4302  HD2 ASP A 274      9.808  21.427  -9.226   1.00001.00           H 
 ATOM   4303  C   ASP A 274      9.513  16.236  -7.136   1.00001.00           C 
 ATOM   4304  O   ASP A 274      8.704  15.335  -7.356   1.00001.00           O 
 ATOM   4305  N   PHE A 275     10.755  15.971  -6.712   1.00001.00           N 
@@ -4836,7 +4832,6 @@ ATOM   4750  HB2 ASP A 301     -1.793 -21.183  -7.373   1.00001.00           H
 ATOM   4751  CG  ASP A 301     -1.076 -23.156  -7.294   1.00001.00           C 
 ATOM   4752  OD1 ASP A 301     -0.546 -24.039  -8.003   1.00001.00           O-
 ATOM   4753  OD2 ASP A 301     -0.954 -23.106  -6.041   1.00001.00           O-
-ATOM   4754  HD2 ASP A 301     -0.425 -23.715  -5.503   1.00001.00           H 
 ATOM   4755  C   ASP A 301     -2.655 -20.601  -9.846   1.00001.00           C 
 ATOM   4756  O   ASP A 301     -3.682 -20.787 -10.494   1.00001.00           O 
 ATOM   4757  N   VAL A 302     -2.229 -19.367  -9.536   1.00001.00           N