ptm-parameters 0.1.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (29) hide show
  1. ptm_parameters/GROMACS/README.md +7 -0
  2. ptm_parameters/GROMACS/gromos54a8.ff/aminoacids.c.tdb +106 -0
  3. ptm_parameters/GROMACS/gromos54a8.ff/aminoacids.hdb +626 -0
  4. ptm_parameters/GROMACS/gromos54a8.ff/aminoacids.n.tdb +750 -0
  5. ptm_parameters/GROMACS/gromos54a8.ff/aminoacids.r2b +8 -0
  6. ptm_parameters/GROMACS/gromos54a8.ff/aminoacids.rtp +21240 -0
  7. ptm_parameters/GROMACS/gromos54a8.ff/aminoacids.vsd +169 -0
  8. ptm_parameters/GROMACS/gromos54a8.ff/atomtypes.atp +57 -0
  9. ptm_parameters/GROMACS/gromos54a8.ff/dppc.itp +284 -0
  10. ptm_parameters/GROMACS/gromos54a8.ff/ff_dum.itp +35 -0
  11. ptm_parameters/GROMACS/gromos54a8.ff/ffbonded.itp +549 -0
  12. ptm_parameters/GROMACS/gromos54a8.ff/ffnonbonded.itp +3091 -0
  13. ptm_parameters/GROMACS/gromos54a8.ff/forcefield.doc +1 -0
  14. ptm_parameters/GROMACS/gromos54a8.ff/forcefield.itp +10 -0
  15. ptm_parameters/GROMACS/gromos54a8.ff/ions.itp +55 -0
  16. ptm_parameters/GROMACS/gromos54a8.ff/popc.itp +293 -0
  17. ptm_parameters/GROMACS/gromos54a8.ff/spc.itp +35 -0
  18. ptm_parameters/GROMACS/gromos54a8.ff/spce.itp +35 -0
  19. ptm_parameters/GROMACS/gromos54a8.ff/tip3p.itp +30 -0
  20. ptm_parameters/GROMACS/gromos54a8.ff/tip4p.itp +52 -0
  21. ptm_parameters/GROMACS/gromos54a8.ff/tmcl.itp +481 -0
  22. ptm_parameters/GROMACS/gromos54a8.ff/watermodels.dat +2 -0
  23. ptm_parameters/GROMACS/residuetypes.dat +259 -0
  24. ptm_parameters/__init__.py +0 -0
  25. ptm_parameters-0.1.0.dist-info/METADATA +86 -0
  26. ptm_parameters-0.1.0.dist-info/RECORD +29 -0
  27. ptm_parameters-0.1.0.dist-info/WHEEL +5 -0
  28. ptm_parameters-0.1.0.dist-info/licenses/LICENSE +395 -0
  29. ptm_parameters-0.1.0.dist-info/top_level.txt +1 -0
ptm_parameters/GROMACS/README.md ADDED
@@ -0,0 +1,7 @@
1
+ # GROMOS force field parameters for protein post-translational modifications (GROMACS format)
2
+
3
+ Use together with the [GROMACS simulation package](https://www.gromacs.org/)
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+
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+ Copy the folder of choice ("gromosXXXX.ff") and the file "residuetypes.dat" to $GMXLIB/share/gromacs/top
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+
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+ Alternatively, to keep the GROMACS installation unchanged, create symbolic links of the folder of choice ("gromosXXXX.ff") and the file "residuetypes.dat" in the working directory when executing GROMACS programs (e.g. `pdb2gmx`).
ptm_parameters/GROMACS/gromos54a8.ff/aminoacids.c.tdb ADDED
@@ -0,0 +1,106 @@
1
+ [ None ]
2
+
3
+ [ COO- ]
4
+ [ replace ]
5
+ CA C 13.019 0.16
6
+ C C 12.011 0.27
7
+ O O1 OM 15.9994 -0.715
8
+ OXT O2 OM 15.9994 -0.715
9
+ [ add ]
10
+ 2 8 O C CA N
11
+ OM 15.9994 -0.715
12
+ [ delete ]
13
+ O
14
+ [ bonds ]
15
+ C O1 gb_6
16
+ C O2 gb_6
17
+ [ angles ]
18
+ O1 C O2 ga_38
19
+ CA C O1 ga_22
20
+ CA C O2 ga_22
21
+ [ dihedrals ]
22
+ N CA C O2 gd_45
23
+ N CA C O2 gd_42
24
+ [ impropers ]
25
+ C CA O2 O1 gi_1
26
+
27
+ [ COOH ]
28
+ [ replace ]
29
+ C C 12.011 0.33
30
+ O OA 15.9994 -0.288
31
+ OXT OT O 15.9994 -0.45
32
+ [ add ]
33
+ 1 2 OT C CA N
34
+ O 15.9994 -0.45
35
+ 1 2 HO O C CA
36
+ H 1.008 0.408
37
+ [ bonds ]
38
+ C O gb_13
39
+ C OT gb_5
40
+ O HO gb_1
41
+ [ angles ]
42
+ O C OT ga_33
43
+ C O HO ga_12
44
+ CA C O ga_19
45
+ CA C OT ga_30
46
+ [ dihedrals ]
47
+ N CA C O gd_45
48
+ N CA C O gd_42
49
+ CA C O HO gd_12
50
+ [ impropers ]
51
+ C CA OT O gi_1
52
+
53
+ ; AA-amide
54
+ [ AMD ]
55
+ [ replace ]
56
+ C C 12.011 0.29
57
+ [ add ]
58
+ 1 1 NC1 C N O
59
+ NT 14.00670 -0.7200
60
+ 1 1 HC11 C CA N
61
+ H 1.008 0.4400
62
+ 1 2 HC12 C CA N
63
+ H 1.008 0.4400
64
+ [ bonds ]
65
+ C NC1 gb_9
66
+ NC1 HC11 gb_2
67
+ NC1 HC12 gb_2
68
+ [ angles ]
69
+ O C NC1 ga_33
70
+ CA C O ga_30
71
+ CA C NC1 ga_19
72
+ C NC1 HC11 ga_23
73
+ C NC1 HC12 ga_23
74
+ HC11 NC1 HC12 ga_24
75
+ [ impropers ]
76
+ C CA O NC1 gi_1
77
+ NC1 C HC11 HC12 gi_1
78
+ [ dihedrals ]
79
+ N CA C NC1 gd_40
80
+ CA C NC1 HC11 gd_14
81
+
82
+ ; AA-methyl ester
83
+ [ CME ]
84
+ [ replace ]
85
+ C C 12.011 0.253
86
+ O OE 15.9994 -0.069
87
+ [ add ]
88
+ 1 2 OC1 C CA N
89
+ O 15.9994 -0.45
90
+ 1 2 CC2 O C CA
91
+ CH3 15.035 0.266
92
+ [ bonds ]
93
+ C O gb_13
94
+ C OC1 gb_5
95
+ O CC2 gb_18
96
+ [ angles ]
97
+ O C OC1 ga_33
98
+ C O CC2 ga_22
99
+ CA C O ga_19
100
+ CA C OC1 ga_30
101
+ [ impropers ]
102
+ C CA OC1 O gi_1
103
+ [ dihedrals ]
104
+ N CA C O gd_40
105
+ CA C O CC2 gd_12
106
+
ptm_parameters/GROMACS/gromos54a8.ff/aminoacids.hdb ADDED
@@ -0,0 +1,626 @@
1
+ ABU 1
2
+ 1 1 H N -C CA
3
+ ACEH 1
4
+ 3 4 HA CA C O
5
+ AIB 1
6
+ 1 1 H N -C CA
7
+ ALA 1
8
+ 1 1 H N -C CA
9
+ ARG 4
10
+ 1 1 H N -C CA
11
+ 1 1 HE NE CD CZ
12
+ 2 3 HH1 NH1 CZ NE
13
+ 2 3 HH2 NH2 CZ NE
14
+ ARGN 4
15
+ 1 1 H N -C CA
16
+ 1 1 HE NE CD CZ
17
+ 1 2 HH1 NH1 CZ NE
18
+ 2 3 HH2 NH2 CZ NE
19
+ ASN 2
20
+ 1 1 H N -C CA
21
+ 2 3 HD2 ND2 CG CB
22
+ ASP 1
23
+ 1 1 H N -C CA
24
+ ASP1 2
25
+ 1 1 H N -C CA
26
+ 1 2 HD1 OD1 CG CB
27
+ ASPH 2
28
+ 1 1 H N -C CA
29
+ 1 2 HD2 OD2 CG CB
30
+ BEN 7
31
+ 1 1 H2 C2 C1 C3
32
+ 1 1 H3 C3 C2 C4
33
+ 1 1 H4 C4 C3 C5
34
+ 1 1 H5 C5 C4 C6
35
+ 1 1 H6 C6 C5 C1
36
+ 2 3 H1 N1 C7 C1
37
+ 2 3 H2 N2 C7 C1
38
+ CYS2 1
39
+ 1 1 H N -C CA
40
+ CYSH 2
41
+ 1 1 H N -C CA
42
+ 1 2 HG SG CB CA
43
+ FAD 7
44
+ 2 3 HN6 AN6 AC6 AC5
45
+ 1 2 HO2* AO2* AC2* AC1*
46
+ 1 2 HO3* AO3* AC3* AC2*
47
+ 1 2 H4* O4* C4* C5*
48
+ 1 2 H3* O3* C3* C4*
49
+ 1 2 H2* O2* C2* C3*
50
+ 1 2 H3 N3 C4 C4A
51
+ GLN 2
52
+ 1 1 H N -C CA
53
+ 2 3 HE2 NE2 CD CG
54
+ GLU 1
55
+ 1 1 H N -C CA
56
+ GLUH 2
57
+ 1 1 H N -C CA
58
+ 1 2 HE2 OE2 CD CG
59
+ GLY 1
60
+ 1 1 H N -C CA
61
+ HEME 4
62
+ 1 1 HHA CHA C1A C4D
63
+ 1 1 HHB CHB C1B C4A
64
+ 1 1 HHC CHC C1C C4B
65
+ 1 1 HHD CHD C1D C4C
66
+ HIS1 4
67
+ 1 1 H N -C CA
68
+ 1 1 HD1 ND1 CG CE1
69
+ 1 1 HD2 CD2 CG NE2
70
+ 1 1 HE1 CE1 ND1 NE2
71
+ HIS2 4
72
+ 1 1 H N -C CA
73
+ 1 1 HD1 ND1 CG CE1
74
+ 1 1 HD2 CD2 CG NE2
75
+ 1 1 HE1 CE1 ND1 NE2
76
+ HISA 4
77
+ 1 1 H N -C CA
78
+ 1 1 HD1 ND1 CG CE1
79
+ 1 1 HD2 CD2 CG NE2
80
+ 1 1 HE1 CE1 ND1 NE2
81
+ HISB 4
82
+ 1 1 H N -C CA
83
+ 1 1 HD2 CD2 CG NE2
84
+ 1 1 HE1 CE1 ND1 NE2
85
+ 1 1 HE2 NE2 CE1 CD2
86
+ HISH 5
87
+ 1 1 H N -C CA
88
+ 1 1 HD1 ND1 CG CE1
89
+ 1 1 HD2 CD2 CG NE2
90
+ 1 1 HE1 CE1 ND1 NE2
91
+ 1 1 HE2 NE2 CE1 CD2
92
+ HOH 1
93
+ 2 7 HW OW
94
+ HYP 1
95
+ 1 2 HD1 OD1 CG CB
96
+ ILE 1
97
+ 1 1 H N -C CA
98
+ LEU 1
99
+ 1 1 H N -C CA
100
+ LYS 2
101
+ 1 1 H N -C CA
102
+ 2 4 HZ NZ CE CD
103
+ LYSH 2
104
+ 1 1 H N -C CA
105
+ 3 4 HZ NZ CE CD
106
+ MET 1
107
+ 1 1 H N -C CA
108
+ NAC 1
109
+ 1 1 H N -C CA
110
+ NACH 2
111
+ 1 1 H N -C CA
112
+ 3 4 HA CA N NH
113
+ NH2 1
114
+ 2 3 H N -C -CA
115
+ PHE 6
116
+ 1 1 H N -C CA
117
+ 1 1 HD1 CD1 CG CE1
118
+ 1 1 HD2 CD2 CG CE2
119
+ 1 1 HE1 CE1 CD1 CZ
120
+ 1 1 HE2 CE2 CD2 CZ
121
+ 1 1 HZ CZ CE1 CE2
122
+ PHEU 1
123
+ 1 1 H N -C CA
124
+ PHL 7
125
+ 1 1 H N -C CA
126
+ 1 1 HD1 CD1 CG CE1
127
+ 1 1 HD2 CD2 CG CE2
128
+ 1 1 HE1 CE1 CD1 CZ
129
+ 1 1 HE2 CE2 CD2 CZ
130
+ 1 1 HZ CZ CE1 CE2
131
+ 1 2 HY OY CX CA
132
+ SER 2
133
+ 1 1 H N -C CA
134
+ 1 2 HG OG CB CA
135
+ TFE 1
136
+ 1 2 H O CH2 C
137
+ THR 2
138
+ 1 1 H N -C CA
139
+ 1 2 HG1 OG1 CB CA
140
+ TRP 7
141
+ 1 1 H N -C CA
142
+ 1 1 HD1 CD1 CG NE1
143
+ 1 1 HE1 NE1 CD1 CE2
144
+ 1 1 HE3 CE3 CD2 CZ3
145
+ 1 1 HZ3 CZ3 CE3 CH2
146
+ 1 1 HH2 CH2 CZ3 CZ2
147
+ 1 1 HZ2 CZ2 CE2 CH2
148
+ TRPU 2
149
+ 1 1 H N -C CA
150
+ 1 1 HE1 NE1 CD1 CE2
151
+ TYR 6
152
+ 1 1 H N -C CA
153
+ 1 1 HD1 CD1 CG CE1
154
+ 1 1 HD2 CD2 CG CE2
155
+ 1 1 HE1 CE1 CD1 CZ
156
+ 1 1 HE2 CE2 CD2 CZ
157
+ 1 2 HH OH CZ CE1
158
+ TYRU 2
159
+ 1 1 H N -C CA
160
+ 1 2 HH OH CZ CE1
161
+ VAL 1
162
+ 1 1 H N -C CA
163
+ S1P 2
164
+ 1 1 H N -C CA
165
+ 1 2 HE3 OE3 PD OG
166
+ S2P 1
167
+ 1 1 H N -C CA
168
+ T1P 2
169
+ 1 1 H N -C CA
170
+ 1 2 HE3 OE3 PD OG1
171
+ T2P 1
172
+ 1 1 H N -C CA
173
+ Y1P 6
174
+ 1 1 H N -C CA
175
+ 1 1 HD1 CD1 CG CE1
176
+ 1 1 HD2 CD2 CG CE2
177
+ 1 1 HE1 CE1 CD1 CZ
178
+ 1 1 HE2 CE2 CD2 CZ
179
+ 1 2 HI3 OI3 PT OH
180
+ Y2P 5
181
+ 1 1 H N -C CA
182
+ 1 1 HD1 CD1 CG CE1
183
+ 1 1 HD2 CD2 CG CE2
184
+ 1 1 HE1 CE1 CD1 CZ
185
+ 1 1 HE2 CE2 CD2 CZ
186
+ D1P 2
187
+ 1 1 H N -C CA
188
+ 1 2 HZ3 OZ3 PE OD2
189
+ D2P 1
190
+ 1 1 H N -C CA
191
+ K1P 3
192
+ 1 1 H N -C CA
193
+ 1 1 HZ NZ PH CE
194
+ 1 2 HI3 OI3 PH NZ
195
+ K2P 2
196
+ 1 1 H N -C CA
197
+ 1 1 HZ NZ PH CE
198
+ R0P 5
199
+ 1 1 H N -C CA
200
+ 1 1 HE NE CD CZ
201
+ 2 3 HH1 NH1 CZ NE
202
+ 1 1 HH2 NH2 PT CZ
203
+ 1 2 HI3 OI3 PT NH2
204
+ R1P 4
205
+ 1 1 H N -C CA
206
+ 1 1 HE NE CD CZ
207
+ 2 3 HH1 NH1 CZ NE
208
+ 1 1 HH2 NH2 PT CZ
209
+ H11 4
210
+ 1 1 H N -C CA
211
+ 1 1 HD2 CD2 CG NE2
212
+ 1 1 HE1 CE1 ND1 NE2
213
+ 1 2 HH3 OH3 PZ NE2
214
+ H12 3
215
+ 1 1 H N -C CA
216
+ 1 1 HD2 CD2 CG NE2
217
+ 1 1 HE1 CE1 ND1 NE2
218
+ H31 4
219
+ 1 1 H N -C CA
220
+ 1 1 HD2 CD2 CG NE2
221
+ 1 1 HE1 CE1 ND1 NE2
222
+ 1 2 HZ3 OZ3 PE3 ND1
223
+ H32 3
224
+ 1 1 H N -C CA
225
+ 1 1 HD2 CD2 CG NE2
226
+ 1 1 HE1 CE1 ND1 NE2
227
+ KMN 2
228
+ 1 1 H N -C CA
229
+ 1 2 HZ NZ CE CD
230
+ KMC 2
231
+ 1 1 H N -C CA
232
+ 2 4 HZ NZ CE CD
233
+ K2M 1
234
+ 1 1 H N -C CA
235
+ K2C 2
236
+ 1 1 H N -C CA
237
+ 1 2 HZ NZ CE CD
238
+ K3C 1
239
+ 1 1 H N -C CA
240
+ RMN 3
241
+ 1 1 H N -C CA
242
+ 1 1 HE NE CD CZ
243
+ 2 3 HH2 NH2 CZ NE
244
+ RMC 4
245
+ 1 1 H N -C CA
246
+ 1 1 HE NE CD CZ
247
+ 2 3 HH1 NH1 CZ NE
248
+ 1 1 HH2 NH2 CT CZ
249
+ RSM 3
250
+ 1 1 H N -C CA
251
+ 1 1 HE NE CD CZ
252
+ 1 1 HH2 NH2 CT2 CZ
253
+ RMS 4
254
+ 1 1 H N -C CA
255
+ 1 1 HE NE CD CZ
256
+ 1 1 HH1 NH1 CT1 CZ
257
+ 1 1 HH2 NH2 CT2 CZ
258
+ RAM 3
259
+ 1 1 H N -C CA
260
+ 1 1 HE NE CD CZ
261
+ 1 2 HH1 NH1 CZ NE
262
+ RMA 3
263
+ 1 1 H N -C CA
264
+ 1 1 HE NE CD CZ
265
+ 2 3 HH1 NH1 CZ NE
266
+ H1M 3
267
+ 1 1 H N -C CA
268
+ 1 1 HD2 CD2 CG NE2
269
+ 1 1 HE1 CE1 ND1 NE2
270
+ H1C 4
271
+ 1 1 H N -C CA
272
+ 1 1 HD1 ND1 CG CE1
273
+ 1 1 HD2 CD2 CG NE2
274
+ 1 1 HE1 CE1 ND1 NE2
275
+ H3M 3
276
+ 1 1 H N -C CA
277
+ 1 1 HD2 CD2 CG NE2
278
+ 1 1 HE1 CE1 ND1 NE2
279
+ H3C 4
280
+ 1 1 H N -C CA
281
+ 1 1 HD2 CD2 CG NE2
282
+ 1 1 HE1 CE1 ND1 NE2
283
+ 1 1 HE2 NE2 CE1 CD2
284
+ QME 2
285
+ 1 1 H N -C CA
286
+ 1 1 HE2 NE2 CZ CD
287
+ NME 2
288
+ 1 1 H N -C CA
289
+ 1 1 HD2 ND2 CE CG
290
+ EME 1
291
+ 1 1 H N -C CA
292
+ DMA 1
293
+ 1 1 H N -C CA
294
+ CYM 1
295
+ 1 1 H N -C CA
296
+ KAC 2
297
+ 1 1 H N -C CA
298
+ 1 1 HZ NZ CE CH
299
+ KHR 5
300
+ 1 1 H N -C CA
301
+ 1 1 HZ1 NZ CE CH
302
+ 1 1 HZ2 NZ CE CD
303
+ 1 1 HI1 OI1 CT CH
304
+ 3 4 HL NL CK CI2
305
+ KHS 5
306
+ 1 1 H N -C CA
307
+ 1 1 HZ1 NZ CE CH
308
+ 1 1 HZ2 NZ CE CD
309
+ 1 1 HI1 OI1 CT CH
310
+ 3 4 HL NL CK CI2
311
+ KLA 8
312
+ 1 1 H N -C CA
313
+ 1 1 HZ NZ CE CH
314
+ 1 1 HI11 NI1 CT2 CH
315
+ 1 1 HI12 NI1 CT2 CI2
316
+ 1 1 HI13 NI1 CT2 CK
317
+ 1 1 HN1 NN CM CL
318
+ 1 1 HN2 NN CM CK
319
+ 1 1 HN3 NN CM CI2
320
+ KLB 8
321
+ 1 1 H N -C CA
322
+ 1 1 HZ NZ CE CH
323
+ 1 1 HK11 NK1 CI CT2
324
+ 1 1 HK12 NK1 CI CK2
325
+ 1 1 HK13 NK1 CI CH
326
+ 1 1 HN1 NN CM CL
327
+ 1 1 HN2 NN CM CK2
328
+ 1 1 HN3 NN CM CI
329
+ PH3 1
330
+ 1 2 HG1 OG1 CB CA
331
+ P3H 1
332
+ 1 2 HG1 OG1 CB CA
333
+ HY2 1
334
+ 1 2 HD1 OD1 CG CB
335
+ PHH 2
336
+ 1 2 HG1 OG1 CB CA
337
+ 1 2 HD1 OD1 CG2 CB
338
+ KH5 3
339
+ 1 1 H N -C CA
340
+ 1 2 HE1 OE1 CD CB
341
+ 2 4 HZ NZ CE2 CD
342
+ K5H 3
343
+ 1 1 H N -C CA
344
+ 1 2 HE1 OE1 CD CB
345
+ 2 4 HZ NZ CE2 CD
346
+ KPH 3
347
+ 1 1 H N -C CA
348
+ 1 2 HE1 OE1 CD CB
349
+ 3 4 HZ NZ CE2 CD
350
+ KHP 3
351
+ 1 1 H N -C CA
352
+ 1 2 HE1 OE1 CD CB
353
+ 3 4 HZ NZ CE2 CD
354
+ K2B 3
355
+ 1 1 H N -C CA
356
+ 1 1 HZ NZ CE CH
357
+ 1 2 HI1 OI1 CT1 CH
358
+ KB2 3
359
+ 1 1 H N -C CA
360
+ 1 1 HZ NZ CE CH
361
+ 1 2 HI1 OI1 CT1 CH
362
+ KHB 3
363
+ 1 1 H N -C CA
364
+ 1 1 HZ NZ CE CH
365
+ 1 2 HI1 OI1 CT1 CH
366
+ HTY 6
367
+ 1 1 H N -C CA
368
+ 1 1 HD1 CD1 CG CE1
369
+ 1 1 HD2 CD2 CG CE2
370
+ 1 2 HZ1 OZ1 CE1 CD1
371
+ 1 1 HE2 CE2 CD2 CZ2
372
+ 1 2 HH OH CZ2 CE1
373
+ W7H 7
374
+ 1 1 H N -C CA
375
+ 1 1 HD1 CD1 CG NE1
376
+ 1 1 HE1 NE1 CD1 CE2
377
+ 1 1 HE3 CE3 CD2 CZ3
378
+ 1 1 HZ3 CZ3 CE3 CH3
379
+ 1 1 HH3 CH3 CZ3 CZ2
380
+ 1 2 HH2 OH2 CZ2 CE2
381
+ DH3 2
382
+ 1 1 H N -C CA
383
+ 1 2 HG1 OG1 CB CA
384
+ D3H 2
385
+ 1 1 H N -C CA
386
+ 1 2 HG1 OG1 CB CA
387
+ DN3 3
388
+ 1 1 H N -C CA
389
+ 1 2 HG1 OG1 CB CA
390
+ 1 2 HD2 OD2 CG2 CB
391
+ D3N 3
392
+ 1 1 H N -C CA
393
+ 1 2 HG1 OG1 CB CA
394
+ 1 2 HD2 OD2 CG2 CB
395
+ N3H 3
396
+ 1 1 H N -C CA
397
+ 1 2 HG1 OG1 CB CA
398
+ 2 3 HD2 ND2 CG2 CB
399
+ NH3 3
400
+ 1 1 H N -C CA
401
+ 1 2 HG1 OG1 CB CA
402
+ 2 3 HD2 ND2 CG2 CB
403
+ Q4H 3
404
+ 1 1 H N -C CA
405
+ 1 2 HD1 OD1 CG CB
406
+ 2 3 HE2 NE2 CD2 CG
407
+ QH4 3
408
+ 1 1 H N -C CA
409
+ 1 2 HD1 OD1 CG CB
410
+ 2 3 HE2 NE2 CD2 CG
411
+ ECA 1
412
+ 1 1 H N -C CA
413
+ ECN 2
414
+ 1 1 H N -C CA
415
+ 1 2 HE2 OE2 CD1 CG
416
+ YSU 5
417
+ 1 1 H N -C CA
418
+ 1 1 HD1 CD1 CG CE1
419
+ 1 1 HD2 CD2 CG CE2
420
+ 1 1 HE1 CE1 CD1 CZ
421
+ 1 1 HE2 CE2 CD2 CZ
422
+ SDH 1
423
+ 1 1 H N -C CA
424
+ TDH 1
425
+ 1 1 H N -C CA
426
+ WBR 6
427
+ 1 1 H N -C CA
428
+ 1 1 HD1 CD1 CG NE1
429
+ 1 1 HE1 NE1 CD1 CE2
430
+ 1 1 HE3 CE3 CD2 CZ3
431
+ 1 1 HZ3 CZ3 CE3 CH2
432
+ 1 1 HZ2 CZ2 CE2 CH2
433
+ CSN 1
434
+ 1 1 H N -C CA
435
+ RCI 3
436
+ 1 1 H N -C CA
437
+ 1 1 HE NE CD CZ
438
+ 2 3 HH2 NH2 CZ NE
439
+ KAL 2
440
+ 1 1 H N -C CA
441
+ 1 1 HE CE OZ CD
442
+ NNG 6
443
+ 1 1 H N -C CA
444
+ 1 2 HO3 O3 C3 C2
445
+ 1 2 HO4 O4 C4 C3
446
+ 1 2 HO6 O6 C6 C5
447
+ 1 2 HN2 N2 C2 C1
448
+ 1 2 HD2 ND2 C1 C2
449
+ SOG 5
450
+ 1 1 H N -C CA
451
+ 1 2 HO3 O3 C3 C2
452
+ 1 2 HO4 O4 C4 C3
453
+ 1 2 HO6 O6 C6 C5
454
+ 1 2 HN2 N2 C2 C1
455
+ TOG 5
456
+ 1 1 H N -C CA
457
+ 1 2 HO3 O3 C3 C2
458
+ 1 2 HO4 O4 C4 C3
459
+ 1 2 HO6 O6 C6 C5
460
+ 1 2 HN2 N2 C2 C1
461
+ F23 6
462
+ 1 1 H N -C CA
463
+ 1 2 HE3 OE3 CD1 CG
464
+ 1 1 HD2 CD2 CG CE2
465
+ 1 2 HZ1 OZ1 CE1 CD1
466
+ 1 1 HE2 CE2 CD2 CZ2
467
+ 1 1 HZ2 CZ2 CE1 CE2
468
+ F2H 6
469
+ 1 1 H N -C CA
470
+ 1 2 HE3 OE3 CD1 CG
471
+ 1 1 HD2 CD2 CG CE2
472
+ 1 1 HE1 CE1 CD1 CZ
473
+ 1 1 HE2 CE2 CD2 CZ
474
+ 1 1 HZ CZ CE1 CE2
475
+ F3H 6
476
+ 1 1 H N -C CA
477
+ 1 1 HD1 CD1 CG CE1
478
+ 1 1 HD2 CD2 CG CE2
479
+ 1 2 HZ1 OZ1 CE1 CD1
480
+ 1 1 HE2 CE2 CD2 CZ2
481
+ 1 1 HZ2 CZ2 CE1 CE2
482
+ W6H 7
483
+ 1 1 H N -C CA
484
+ 1 1 HD1 CD1 CG NE1
485
+ 1 1 HE1 NE1 CD1 CE2
486
+ 1 1 HE3 CE3 CD2 CZ3
487
+ 1 1 HZ3 CZ3 CE3 CH2
488
+ 1 2 HI OI CH2 CZ2
489
+ 1 1 HZ2 CZ2 CE2 CH2
490
+ W5H 7
491
+ 1 1 H N -C CA
492
+ 1 1 HD1 CD1 CG NE1
493
+ 1 1 HE1 NE1 CD1 CE2
494
+ 1 1 HE3 CE3 CD2 CZ3
495
+ 1 2 HH3 OH3 CZ3 CE2
496
+ 1 1 HH2 CH2 CZ3 CZ2
497
+ 1 1 HZ2 CZ2 CE2 CH2
498
+ W4H 7
499
+ 1 1 H N -C CA
500
+ 1 1 HD1 CD1 CG NE1
501
+ 1 1 HE1 NE1 CD1 CE2
502
+ 1 2 HZ4 OZ4 CE3 CD2
503
+ 1 1 HZ3 CZ3 CE3 CH2
504
+ 1 1 HH2 CH2 CZ3 CZ2
505
+ 1 1 HZ2 CZ2 CE2 CH2
506
+ W2H 7
507
+ 1 1 H N -C CA
508
+ 1 2 HE4 OE4 CD1 CG
509
+ 1 1 HE1 NE1 CD1 CE2
510
+ 1 1 HE3 CE3 CD2 CZ3
511
+ 1 1 HZ3 CZ3 CE3 CH2
512
+ 1 1 HH2 CH2 CZ3 CZ2
513
+ 1 1 HZ2 CZ2 CE2 CH2
514
+ L3H 2
515
+ 1 1 H N -C CA
516
+ 1 2 HG1 OG1 CB CA
517
+ LH3 2
518
+ 1 1 H N -C CA
519
+ 1 2 HG1 OG1 CB CA
520
+ L4H 2
521
+ 1 1 H N -C CA
522
+ 1 2 HD3 OD3 CG CB
523
+ L5H 2
524
+ 1 1 H N -C CA
525
+ 1 2 HE OE CD2 CG
526
+ LH5 2
527
+ 1 1 H N -C CA
528
+ 1 2 HE OE CD2 CG
529
+ V3H 2
530
+ 1 1 H N -C CA
531
+ 1 2 HG3 OG3 CB CA
532
+ CYH 2
533
+ 1 1 H N -C CA
534
+ 1 2 HD OD SG CB
535
+ PH5 1
536
+ 1 2 HE OE CD CG
537
+ P5H 1
538
+ 1 2 HE OE CD CG
539
+ GSA 2
540
+ 1 1 H N -C CA
541
+ 1 1 HD CD OE CG
542
+ TOX 1
543
+ 1 1 H N -C CA
544
+ H2X 4
545
+ 1 1 H N -C CA
546
+ 1 1 HD1 ND1 CG CE1
547
+ 1 1 HD2 CD2 CG NE2
548
+ 1 1 HE2 NE2 CE1 CD2
549
+ MSX 1
550
+ 1 1 H N -C CA
551
+ MXS 1
552
+ 1 1 H N -C CA
553
+ MES 1
554
+ 1 1 H N -C CA
555
+ CSA 1
556
+ 1 1 H N -C CA
557
+ CSE 1
558
+ 1 1 H N -C CA
559
+ YNI 4
560
+ 1 1 H N -C CA
561
+ 1 1 HD1 CD1 CG CE1
562
+ 1 1 HD2 CD2 CG CE2
563
+ 1 1 HE2 CE2 CD2 CZ2
564
+ YNN 5
565
+ 1 1 H N -C CA
566
+ 1 1 HD1 CD1 CG CE1
567
+ 1 1 HD2 CD2 CG CE2
568
+ 1 1 HE2 CE2 CD2 CZ2
569
+ 1 2 HH3 OH3 CZ2 CE1
570
+ YNB 5
571
+ 1 1 H N -C CA
572
+ 1 1 HD1 CD1 CG CE1
573
+ 1 1 HD2 CD2 CG CE2
574
+ 1 1 HE2 CE2 CD2 CZ2
575
+ 1 2 HH3 OH3 CZ2 CE1
576
+ WNI 6
577
+ 1 1 H N -C CA
578
+ 1 1 HD1 CD1 CG NE1
579
+ 1 1 HE1 NE1 CD1 CE2
580
+ 1 1 HE3 CE3 CD2 CZ3
581
+ 1 1 HZ3 CZ3 CE3 CH2
582
+ 1 1 HZ2 CZ2 CE2 CH2
583
+ WKY 6
584
+ 1 1 H N -C CA
585
+ 1 1 HE2 CE2 CD2 CZ3
586
+ 2 3 HZ1 NZ1 CE1 CD2
587
+ 1 1 HZ2 CZ2 CE1 CH
588
+ 1 1 HZ3 CZ3 CE2 CH
589
+ 1 1 HH CH CZ2 CZ3
590
+ WKH 6
591
+ 1 1 H N -C CA
592
+ 1 1 HE2 CE2 CD2 CZ3
593
+ 2 3 HZ1 NZ1 CE1 CD2
594
+ 1 1 HZ3 CZ3 CE2 CH2
595
+ 1 2 HH1 OH1 CZ2 CE1
596
+ 1 1 HH2 CH2 CZ2 CZ3
597
+ WKF 7
598
+ 1 1 H N -C CA
599
+ 1 1 HE2 CE2 CD2 CZ3
600
+ 1 1 HZ1 NZ1 CE1 CH1
601
+ 1 1 HZ2 CZ2 CE1 CH2
602
+ 1 1 HZ3 CZ3 CE2 CH2
603
+ 1 1 HH1 CH1 NZ1 OI
604
+ 1 1 HH2 CH2 CZ2 CZ3
605
+ YCH 5
606
+ 1 1 H N -C CA
607
+ 1 1 HD1 CD1 CG CE1
608
+ 1 1 HD2 CD2 CG CE2
609
+ 1 1 HE2 CE2 CD2 CZ2
610
+ 1 2 HH OH CZ2 CE1
611
+ KAM 3
612
+ 1 1 H N -C CA
613
+ 1 1 HZ NZ CH CE
614
+ 2 4 HI2 NI2 CH NZ
615
+ KCA 2
616
+ 1 1 H N -C CA
617
+ 1 1 HZ NZ CH CE
618
+ KCN 3
619
+ 1 1 H N -C CA
620
+ 1 1 HZ NZ CH CE
621
+ 1 2 HI2 OI2 CH NZ
622
+ CAM 2
623
+ 1 1 H N -C CA
624
+ 2 3 HE2 NE2 CD SG
625
+ LNO 1
626
+ 1 1 H N -C CA