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root/owl/trunk/src/owl/core/structure/vdw.radii
Revision: 1247
Committed: Fri Oct 1 12:53:40 2010 UTC (10 years, 11 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 User Rev File contents
1 jmduarteg 1247 #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