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root/owl/trunk/src/owl/core/structure/vdw.radii
Revision: 1247
Committed: Fri Oct 1 12:53:40 2010 UTC (11 years, 9 months ago) by jmduarteg
File size: 8555 byte(s)
Log Message: 
Implemented our own ASA calculation! Taken from Bosco's python implementation, thanks again Bosco!
Line File contents
1 #vdw_start
2 # NACCESS standard residue library
3 #
4 # Format:
5 #
6 # RESIDUE starts off each residue. It must be followed by one of
7 # a) ATOM - amino acids
8 # b) NUCL - nucleic acids
9 # c) HETA - heteroatoms (e.g.HEMES)
10 # d) WATER - solvent (eg, HOH, WAT, MOH)
11 # After this label, a 3 letter residue name must be supplied. It must be
12 # 3 letters, and if it is preceded by spaces (see the nucleic acids for
13 # example) the spaces should be replaced by underscores (_).
14 #
15 # ATOM begins each atom of a residue. All ATOM records between residue
16 # statments are counted for each residue. The format of this line is
17 # important, and is *not* free format. After ATOM there should be one
18 # space followed by the 4-character atom name corresponding to the 13th
19 # to 16th column of a standard PDB file. After the atom name, format is
20 # free, and should contain a real number (the van der Waals radius) and
21 # a 1 digit integer (0 or 1) where 1 implies this atom is deemed to be
22 # polar.
23 #
24 RESIDUE ATOM ALA 5
25 ATOM N 1.65 1
26 ATOM CA 1.87 0
27 ATOM C 1.76 0
28 ATOM O 1.40 1
29 ATOM CB 1.87 0
30 RESIDUE ATOM ARG 11
31 ATOM N 1.65 1
32 ATOM CA 1.87 0
33 ATOM C 1.76 0
34 ATOM O 1.40 1
35 ATOM CB 1.87 0
36 ATOM CG 1.87 0
37 ATOM CD 1.87 0
38 ATOM NE 1.65 1
39 ATOM CZ 1.76 0
40 ATOM NH1 1.65 1
41 ATOM NH2 1.65 1
42 RESIDUE ATOM ASP 8
43 ATOM N 1.65 1
44 ATOM CA 1.87 0
45 ATOM C 1.76 0
46 ATOM O 1.40 1
47 ATOM CB 1.87 0
48 ATOM CG 1.76 0
49 ATOM OD1 1.40 1
50 ATOM OD2 1.40 1
51 RESIDUE ATOM ASN 8
52 ATOM N 1.65 1
53 ATOM CA 1.87 0
54 ATOM C 1.76 0
55 ATOM O 1.40 1
56 ATOM CB 1.87 0
57 ATOM CG 1.76 0
58 ATOM OD1 1.40 1
59 ATOM ND2 1.65 1
60 RESIDUE ATOM CYS 6
61 ATOM N 1.65 1
62 ATOM CA 1.87 0
63 ATOM C 1.76 0
64 ATOM O 1.40 1
65 ATOM CB 1.87 0
66 ATOM SG 1.85 0
67 RESIDUE ATOM GLU 9
68 ATOM N 1.65 1
69 ATOM CA 1.87 0
70 ATOM C 1.76 0
71 ATOM O 1.40 1
72 ATOM CB 1.87 0
73 ATOM CG 1.87 0
74 ATOM CD 1.76 0
75 ATOM OE1 1.40 1
76 ATOM OE2 1.40 1
77 RESIDUE ATOM GLN 9
78 ATOM N 1.65 1
79 ATOM CA 1.87 0
80 ATOM C 1.76 0
81 ATOM O 1.40 1
82 ATOM CB 1.87 0
83 ATOM CG 1.87 0
84 ATOM CD 1.76 0
85 ATOM OE1 1.40 1
86 ATOM NE2 1.65 1
87 RESIDUE ATOM GLY 4
88 ATOM N 1.65 1
89 ATOM CA 1.87 0
90 ATOM C 1.76 0
91 ATOM O 1.40 1
92 RESIDUE ATOM HIS 10
93 ATOM N 1.65 1
94 ATOM CA 1.87 0
95 ATOM C 1.76 0
96 ATOM O 1.40 1
97 ATOM CB 1.87 0
98 ATOM CG 1.76 0
99 ATOM ND1 1.65 1
100 ATOM CD2 1.76 0
101 ATOM CE1 1.76 0
102 ATOM NE2 1.65 1
103 RESIDUE ATOM ILE 8
104 ATOM N 1.65 1
105 ATOM CA 1.87 0
106 ATOM C 1.76 0
107 ATOM O 1.40 1
108 ATOM CB 1.87 0
109 ATOM CG1 1.87 0
110 ATOM CG2 1.87 0
111 ATOM CD1 1.87 0
112 RESIDUE ATOM LEU 8
113 ATOM N 1.65 1
114 ATOM CA 1.87 0
115 ATOM C 1.76 0
116 ATOM O 1.40 1
117 ATOM CB 1.87 0
118 ATOM CG 1.87 0
119 ATOM CD1 1.87 0
120 ATOM CD2 1.87 0
121 RESIDUE ATOM LYS 9
122 ATOM N 1.65 1
123 ATOM CA 1.87 0
124 ATOM C 1.76 0
125 ATOM O 1.40 1
126 ATOM CB 1.87 0
127 ATOM CG 1.87 0
128 ATOM CD 1.87 0
129 ATOM CE 1.87 0
130 ATOM NZ 1.50 1
131 RESIDUE ATOM MET 8
132 ATOM N 1.65 1
133 ATOM CA 1.87 0
134 ATOM C 1.76 0
135 ATOM O 1.40 1
136 ATOM CB 1.87 0
137 ATOM CG 1.87 0
138 ATOM SD 1.85 0
139 ATOM CE 1.87 0
140 RESIDUE ATOM PHE 11
141 ATOM N 1.65 1
142 ATOM CA 1.87 0
143 ATOM C 1.76 0
144 ATOM O 1.40 1
145 ATOM CB 1.87 0
146 ATOM CG 1.76 0
147 ATOM CD1 1.76 0
148 ATOM CD2 1.76 0
149 ATOM CE1 1.76 0
150 ATOM CE2 1.76 0
151 ATOM CZ 1.76 0
152 RESIDUE ATOM PRO 7
153 ATOM N 1.65 1
154 ATOM CA 1.87 0
155 ATOM C 1.76 0
156 ATOM O 1.40 1
157 ATOM CB 1.87 0
158 ATOM CG 1.87 0
159 ATOM CD 1.87 0
160 RESIDUE ATOM SER 6
161 ATOM N 1.65 1
162 ATOM CA 1.87 0
163 ATOM C 1.76 0
164 ATOM O 1.40 1
165 ATOM CB 1.87 0
166 ATOM OG 1.40 1
167 RESIDUE ATOM THR 7
168 ATOM N 1.65 1
169 ATOM CA 1.87 0
170 ATOM C 1.76 0
171 ATOM O 1.40 1
172 ATOM CB 1.87 0
173 ATOM OG1 1.40 1
174 ATOM CG2 1.87 0
175 RESIDUE ATOM TRP 14
176 ATOM N 1.65 1
177 ATOM CA 1.87 0
178 ATOM C 1.76 0
179 ATOM O 1.40 1
180 ATOM CB 1.87 0
181 ATOM CG 1.76 0
182 ATOM CD1 1.76 0
183 ATOM CD2 1.76 0
184 ATOM NE1 1.65 1
185 ATOM CE2 1.76 0
186 ATOM CE3 1.76 0
187 ATOM CZ2 1.76 0
188 ATOM CZ3 1.76 0
189 ATOM CH2 1.76 0
190 RESIDUE ATOM TYR 12
191 ATOM N 1.65 1
192 ATOM CA 1.87 0
193 ATOM C 1.76 0
194 ATOM O 1.40 1
195 ATOM CB 1.87 0
196 ATOM CG 1.76 0
197 ATOM CD1 1.76 0
198 ATOM CD2 1.76 0
199 ATOM CE1 1.76 0
200 ATOM CE2 1.76 0
201 ATOM CZ 1.76 0
202 ATOM OH 1.40 1
203 RESIDUE ATOM VAL 7
204 ATOM N 1.65 1
205 ATOM CA 1.87 0
206 ATOM C 1.76 0
207 ATOM O 1.40 1
208 ATOM CB 1.87 0
209 ATOM CG1 1.87 0
210 ATOM CG2 1.87 0
211 RESIDUE ATOM ASX 8
212 ATOM N 1.65 1
213 ATOM CA 1.87 0
214 ATOM C 1.76 0
215 ATOM O 1.40 1
216 ATOM CB 1.87 0
217 ATOM CG 1.76 0
218 ATOM AD1 1.50 0
219 ATOM AD2 1.50 0
220 RESIDUE ATOM GLX 9
221 ATOM N 1.65 1
222 ATOM CA 1.87 0
223 ATOM C 1.76 0
224 ATOM O 1.40 1
225 ATOM CB 1.87 0
226 ATOM CG 1.76 0
227 ATOM CD 1.87 0
228 ATOM AE1 1.50 0
229 ATOM AE2 1.50 0
230 RESIDUE ATOM ACE 3
231 ATOM C 1.76 0
232 ATOM O 1.40 1
233 ATOM CH3 1.87 0
234 RESIDUE NUCL __A 21
235 ATOM P 1.90 0
236 ATOM O1P 1.40 1
237 ATOM O2P 1.40 1
238 ATOM O5* 1.40 1
239 ATOM C5* 1.80 0
240 ATOM C4* 1.80 0
241 ATOM O4* 1.40 1
242 ATOM C3* 1.80 0
243 ATOM O3* 1.40 1
244 ATOM C2* 1.80 0
245 ATOM C1* 1.80 0
246 ATOM N9 1.60 1
247 ATOM C8 1.80 0
248 ATOM N7 1.60 1
249 ATOM C5 1.80 0
250 ATOM C6 1.80 0
251 ATOM N6 1.60 1
252 ATOM N1 1.60 1
253 ATOM C2 1.80 0
254 ATOM N3 1.60 1
255 ATOM C4 1.80 0
256 RESIDUE NUCL __C 19
257 ATOM P 1.90 0
258 ATOM O1P 1.40 1
259 ATOM O2P 1.40 1
260 ATOM O5* 1.40 1
261 ATOM C5* 1.80 0
262 ATOM C4* 1.80 0
263 ATOM O4* 1.40 1
264 ATOM C3* 1.80 0
265 ATOM O3* 1.40 1
266 ATOM C2* 1.80 0
267 ATOM C1* 1.80 0
268 ATOM N1 1.60 1
269 ATOM C2 1.80 0
270 ATOM O2 1.40 1
271 ATOM N3 1.60 1
272 ATOM C4 1.80 0
273 ATOM N4 1.60 1
274 ATOM C5 1.80 0
275 ATOM C6 1.80 0
276 RESIDUE NUCL __G 22
277 ATOM P 1.90 0
278 ATOM O1P 1.40 1
279 ATOM O2P 1.40 1
280 ATOM O5* 1.40 1
281 ATOM C5* 1.80 0
282 ATOM C4* 1.80 0
283 ATOM O4* 1.40 1
284 ATOM C3* 1.80 0
285 ATOM O3* 1.40 1
286 ATOM C2* 1.80 0
287 ATOM C1* 1.80 0
288 ATOM N9 1.60 1
289 ATOM C8 1.80 0
290 ATOM N7 1.60 1
291 ATOM C5 1.80 0
292 ATOM C6 1.80 0
293 ATOM O6 1.40 1
294 ATOM N1 1.60 1
295 ATOM C2 1.80 0
296 ATOM N2 1.60 1
297 ATOM N3 1.60 1
298 ATOM C4 1.80 0
299 RESIDUE NUCL __T 20
300 ATOM P 1.90 0
301 ATOM O1P 1.40 1
302 ATOM O2P 1.40 1
303 ATOM O5* 1.40 1
304 ATOM C5* 1.80 0
305 ATOM C4* 1.80 0
306 ATOM O4* 1.40 1
307 ATOM C3* 1.80 0
308 ATOM O3* 1.40 1
309 ATOM C2* 1.80 0
310 ATOM C1* 1.80 0
311 ATOM N1 1.60 1
312 ATOM C2 1.80 0
313 ATOM O2 1.40 1
314 ATOM N3 1.60 1
315 ATOM C4 1.80 0
316 ATOM O4 1.40 1
317 ATOM C5 1.80 0
318 ATOM C5M 1.80 0
319 ATOM C6 1.80 0
320 RESIDUE NUCL __U 20
321 ATOM P 1.90 0
322 ATOM O1P 1.40 1
323 ATOM O2P 1.40 1
324 ATOM O5* 1.40 1
325 ATOM C5* 1.80 0
326 ATOM C4* 1.80 0
327 ATOM O4* 1.40 1
328 ATOM C3* 1.80 0
329 ATOM O3* 1.40 1
330 ATOM C2* 1.80 0
331 ATOM O2* 1.40 1
332 ATOM C1* 1.80 0
333 ATOM N1 1.60 1
334 ATOM C2 1.80 0
335 ATOM O2 1.40 1
336 ATOM N3 1.60 1
337 ATOM C4 1.80 0
338 ATOM O4 1.40 1
339 ATOM C5 1.80 0
340 ATOM C6 1.80 0
341 RESIDUE NUCL 2MG 24
342 ATOM P 1.90 0
343 ATOM O1P 1.40 1
344 ATOM O2P 1.40 1
345 ATOM O5* 1.40 1
346 ATOM C5* 1.80 0
347 ATOM C4* 1.80 0
348 ATOM O4* 1.40 1
349 ATOM C3* 1.80 0
350 ATOM O3* 1.40 1
351 ATOM C2* 1.80 0
352 ATOM O2* 1.40 1
353 ATOM C1* 1.80 0
354 ATOM N9 1.60 1
355 ATOM C8 1.80 0
356 ATOM N7 1.60 1
357 ATOM C5 1.80 0
358 ATOM C6 1.80 0
359 ATOM O6 1.40 1
360 ATOM N1 1.60 1
361 ATOM C2 1.80 0
362 ATOM N2 1.60 1
363 ATOM C2A 1.80 0
364 ATOM N3 1.60 1
365 ATOM C4 1.80 0
366 RESIDUE NUCL H2U 20
367 ATOM P 1.90 0
368 ATOM O1P 1.40 1
369 ATOM O2P 1.40 1
370 ATOM O5* 1.40 1
371 ATOM C5* 1.80 0
372 ATOM C4* 1.80 0
373 ATOM O4* 1.40 1
374 ATOM C3* 1.80 0
375 ATOM O3* 1.40 1
376 ATOM C2* 1.80 0
377 ATOM O2* 1.40 1
378 ATOM C1* 1.80 0
379 ATOM N1 1.60 1
380 ATOM C2 1.80 0
381 ATOM O2 1.40 1
382 ATOM N3 1.60 1
383 ATOM C4 1.80 0
384 ATOM O4 1.40 1
385 ATOM C5 1.80 0
386 ATOM C6 1.80 0
387 RESIDUE HETATM HEM 43
388 ATOM FE 1.47 0
389 ATOM CHA 2.00 0
390 ATOM CHB 2.00 0
391 ATOM CHC 2.00 0
392 ATOM CHD 2.00 0
393 ATOM N A 1.55 1
394 ATOM C1A 1.78 0
395 ATOM C2A 1.78 0
396 ATOM C3A 1.78 0
397 ATOM C4A 1.78 0
398 ATOM CMA 1.90 0
399 ATOM CAA 1.90 0
400 ATOM CBA 1.90 0
401 ATOM CGA 1.90 0
402 ATOM N B 1.55 1
403 ATOM C1B 1.78 0
404 ATOM C2B 1.78 0
405 ATOM C3B 1.78 0
406 ATOM C4B 1.78 0
407 ATOM CMB 1.90 0
408 ATOM CAB 1.90 0
409 ATOM CBB 1.90 0
410 ATOM N C 1.55 1
411 ATOM C1C 1.78 0
412 ATOM C2C 1.78 0
413 ATOM C3C 1.78 0
414 ATOM C4C 1.78 0
415 ATOM CMC 1.90 0
416 ATOM CAC 1.90 0
417 ATOM CBC 1.90 0
418 ATOM N D 1.55 1
419 ATOM C1D 1.78 0
420 ATOM C2D 1.78 0
421 ATOM C3D 1.78 0
422 ATOM C4D 1.78 0
423 ATOM CMD 1.90 0
424 ATOM CAD 1.90 0
425 ATOM CBD 1.90 0
426 ATOM CGD 1.90 0
427 ATOM O1A 1.35 1
428 ATOM O2A 1.35 1
429 ATOM O1D 1.35 1
430 ATOM O2D 1.35 1
431 RESIDUE WATER HOH 1
432 ATOM O 1.40 1
433 #vdw_end