modules/chempy/champ/amber99.py (1,694 lines of code) (raw):
amber99_dict = {
'NHE': [
(
'N<0>([H]<1>)([H]<2>)',
{
0: ('N' , 'N' , -0.4630, 1.8240),
1: ('HN1' , 'H' , 0.2315, 0.6000),
2: ('HN2' , 'H' , 0.2315, 0.6000),
},
),
],
'NME': [
(
'N<0>([H]<1>)[C@]<2>([H]<3>)([H]<4>)[H]<5>',
{
0: ('N' , 'N' , -0.4157, 1.8240),
1: ('H' , 'H' , 0.2719, 0.6000),
2: ('CH3' , 'CT' , -0.1490, 1.9080),
3: ('HH31', 'HC' , 0.0976, 1.3870),
4: ('HH32', 'HC' , 0.0976, 1.3870),
5: ('HH33', 'HC' , 0.0976, 1.3870),
},
),
],
'ACE': [
(
'C<0>(=O<1>)[C@]<2>([H]<3>)([H]<4>)[H]<5>',
{
0: ('C' , 'C' , 0.5972, 1.9080),
1: ('O' , 'O' , -0.5679, 1.6612),
2: ('CH3' , 'CT' , -0.3662, 1.9080),
3: ('HH31', 'HC' , 0.1123, 1.4870),
4: ('HH32', 'HC' , 0.1123, 1.4870),
5: ('HH33', 'HC' , 0.1123, 1.4870),
},
),
],
'ALA': [
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@]<4>([H]<5>)([H]<6>)[H]<7>)C<8>=O<9>',
{
0: ('N' , 'N' , -0.4157, 1.8240),
1: ('H' , 'H' , 0.2719, 0.6000),
2: ('CA' , 'CT' , 0.0337, 1.9080),
3: ('HA' , 'H1' , 0.0823, 1.3870),
4: ('CB' , 'CT' , -0.1825, 1.9080),
5: ('HB3' , 'HC' , 0.0603, 1.4870),
6: ('HB2' , 'HC' , 0.0603, 1.4870),
7: ('HB1' , 'HC' , 0.0603, 1.4870),
8: ('C' , 'C' , 0.5973, 1.9080),
9: ('O' , 'O' , -0.5679, 1.6612),
},
),
(
'C<0>(=O<1>)[C@]<2>([H]<3>)([C@]<4>([H]<5>)([H]<6>)[H]<7>)[N@+]<8>([H]<9>)([H]<10>)[H]<11>',
{
0: ('C' , 'C' , 0.6163, 1.9080),
1: ('O' , 'O' , -0.5722, 1.6612),
2: ('CA' , 'CT' , 0.0962, 1.9080),
3: ('HA' , 'HP' , 0.0889, 1.1000),
4: ('CB' , 'CT' , -0.0597, 1.9080),
5: ('HB3' , 'HC' , 0.0300, 1.4870),
6: ('HB2' , 'HC' , 0.0300, 1.4870),
7: ('HB1' , 'HC' , 0.0300, 1.4870),
8: ('N' , 'N3' , 0.1414, 1.8240),
9: ('H3' , 'H' , 0.1997, 0.6000),
10: ('H2' , 'H' , 0.1997, 0.6000),
11: ('H1' , 'H' , 0.1997, 0.6000),
},
),
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@]<4>([H]<5>)([H]<6>)[H]<7>)C<8>([O-]<9>)=O<10>',
{
0: ('N' , 'N' , -0.3821, 1.8240),
1: ('H' , 'H' , 0.2681, 0.6000),
2: ('CA' , 'CT' , -0.1747, 1.9080),
3: ('HA' , 'H1' , 0.1067, 1.3870),
4: ('CB' , 'CT' , -0.2093, 1.9080),
5: ('HB3' , 'HC' , 0.0764, 1.4870),
6: ('HB2' , 'HC' , 0.0764, 1.4870),
7: ('HB1' , 'HC' , 0.0764, 1.4870),
8: ('C' , 'C' , 0.7731, 1.9080),
9: ('OXT' , 'O2' , -0.8055, 1.6612),
10: ('O' , 'O2' , -0.8055, 1.6612),
},
),
],
'ARG': [
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)[C@@]<7>([H]<8>)([H]<9>)[C@@]<10>([H]<11>)([H]<12>)N<13>([H]<14>)C<15>(N<16>([H]<17>)[H]<18>)=[N+]<19>([H]<20>)[H]<21>)C<22>=O<23>',
{
0: ('N' , 'N' , -0.3479, 1.8240),
1: ('H' , 'H' , 0.2747, 0.6000),
2: ('CA' , 'CT' , -0.2637, 1.9080),
3: ('HA' , 'H1' , 0.1560, 1.3870),
4: ('CB' , 'CT' , -0.0007, 1.9080),
5: ('HB3' , 'HC' , 0.0327, 1.4870),
6: ('HB2' , 'HC' , 0.0327, 1.4870),
7: ('CG' , 'CT' , 0.0390, 1.9080),
8: ('HG3' , 'HC' , 0.0285, 1.4870),
9: ('HG2' , 'HC' , 0.0285, 1.4870),
10: ('CD' , 'CT' , 0.0486, 1.9080),
11: ('HD3' , 'H1' , 0.0687, 1.3870),
12: ('HD2' , 'H1' , 0.0687, 1.3870),
13: ('NE' , 'N2' , -0.5295, 1.8240),
14: ('HE' , 'H' , 0.3456, 0.6000),
15: ('CZ' , 'CA' , 0.8076, 1.9080),
16: ('NH2' , 'N2' , -0.8627, 1.8240),
17: ('HH22', 'H' , 0.4478, 0.6000),
18: ('HH21', 'H' , 0.4478, 0.6000),
19: ('NH1' , 'N2' , -0.8627, 1.8240),
20: ('HH12', 'H' , 0.4478, 0.6000),
21: ('HH11', 'H' , 0.4478, 0.6000),
22: ('C' , 'C' , 0.7341, 1.9080),
23: ('O' , 'O' , -0.5894, 1.6612),
},
),
(
'C<0>(=O<1>)[C@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)[C@@]<7>([H]<8>)([H]<9>)[C@@]<10>([H]<11>)([H]<12>)N<13>([H]<14>)C<15>(N<16>([H]<17>)[H]<18>)=[N+]<19>([H]<20>)[H]<21>)[N@+]<22>([H]<23>)([H]<24>)[H]<25>',
{
0: ('C' , 'C' , 0.7214, 1.9080),
1: ('O' , 'O' , -0.6013, 1.6612),
2: ('CA' , 'CT' , -0.0223, 1.9080),
3: ('HA' , 'HP' , 0.1242, 1.1000),
4: ('CB' , 'CT' , 0.0118, 1.9080),
5: ('HB3' , 'HC' , 0.0226, 1.4870),
6: ('HB2' , 'HC' , 0.0226, 1.4870),
7: ('CG' , 'CT' , 0.0236, 1.9080),
8: ('HG3' , 'HC' , 0.0309, 1.4870),
9: ('HG2' , 'HC' , 0.0309, 1.4870),
10: ('CD' , 'CT' , 0.0935, 1.9080),
11: ('HD3' , 'H1' , 0.0527, 1.3870),
12: ('HD2' , 'H1' , 0.0527, 1.3870),
13: ('NE' , 'N2' , -0.5650, 1.8240),
14: ('HE' , 'H' , 0.3592, 0.6000),
15: ('CZ' , 'CA' , 0.8281, 1.9080),
16: ('NH2' , 'N2' , -0.8693, 1.8240),
17: ('HH22', 'H' , 0.4494, 0.6000),
18: ('HH21', 'H' , 0.4494, 0.6000),
19: ('NH1' , 'N2' , -0.8693, 1.8240),
20: ('HH12', 'H' , 0.4494, 0.6000),
21: ('HH11', 'H' , 0.4494, 0.6000),
22: ('N' , 'N3' , 0.1305, 1.8240),
23: ('H3' , 'H' , 0.2083, 0.6000),
24: ('H2' , 'H' , 0.2083, 0.6000),
25: ('H1' , 'H' , 0.2083, 0.6000),
},
),
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)[C@@]<7>([H]<8>)([H]<9>)[C@@]<10>([H]<11>)([H]<12>)N<13>([H]<14>)C<15>(N<16>([H]<17>)[H]<18>)=[N+]<19>([H]<20>)[H]<21>)C<22>([O-]<23>)=O<24>',
{
0: ('N' , 'N' , -0.3481, 1.8240),
1: ('H' , 'H' , 0.2764, 0.6000),
2: ('CA' , 'CT' , -0.3068, 1.9080),
3: ('HA' , 'H1' , 0.1447, 1.3870),
4: ('CB' , 'CT' , -0.0374, 1.9080),
5: ('HB3' , 'HC' , 0.0371, 1.4870),
6: ('HB2' , 'HC' , 0.0371, 1.4870),
7: ('CG' , 'CT' , 0.0744, 1.9080),
8: ('HG3' , 'HC' , 0.0185, 1.4870),
9: ('HG2' , 'HC' , 0.0185, 1.4870),
10: ('CD' , 'CT' , 0.1114, 1.9080),
11: ('HD3' , 'H1' , 0.0468, 1.3870),
12: ('HD2' , 'H1' , 0.0468, 1.3870),
13: ('NE' , 'N2' , -0.5564, 1.8240),
14: ('HE' , 'H' , 0.3479, 0.6000),
15: ('CZ' , 'CA' , 0.8368, 1.9080),
16: ('NH2' , 'N2' , -0.8737, 1.8240),
17: ('HH22', 'H' , 0.4493, 0.6000),
18: ('HH21', 'H' , 0.4493, 0.6000),
19: ('NH1' , 'N2' , -0.8737, 1.8240),
20: ('HH12', 'H' , 0.4493, 0.6000),
21: ('HH11', 'H' , 0.4493, 0.6000),
22: ('C' , 'C' , 0.8557, 1.9080),
23: ('OXT' , 'O2' , -0.8266, 1.6612),
24: ('O' , 'O2' , -0.8266, 1.6612),
},
),
],
'ASP': [
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)C<7>([O-]<8>)=O<9>)C<10>=O<11>',
{
0: ('N' , 'N' , -0.5163, 1.8240),
1: ('H' , 'H' , 0.2936, 0.6000),
2: ('CA' , 'CT' , 0.0381, 1.9080),
3: ('HA' , 'H1' , 0.0880, 1.3870),
4: ('CB' , 'CT' , -0.0303, 1.9080),
5: ('HB3' , 'HC' , -0.0122, 1.4870),
6: ('HB2' , 'HC' , -0.0122, 1.4870),
7: ('CG' , 'C' , 0.7994, 1.9080),
8: ('OD2' , 'O2' , -0.8014, 1.6612),
9: ('OD1' , 'O2' , -0.8014, 1.6612),
10: ('C' , 'C' , 0.5366, 1.9080),
11: ('O' , 'O' , -0.5819, 1.6612),
},
),
(
'C<0>(=O<1>)[C@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)C<7>([O-]<8>)=O<9>)[N@+]<10>([H]<11>)([H]<12>)[H]<13>',
{
0: ('C' , 'C' , 0.5621, 1.9080),
1: ('O' , 'O' , -0.5889, 1.6612),
2: ('CA' , 'CT' , 0.0292, 1.9080),
3: ('HA' , 'HP' , 0.1141, 1.1000),
4: ('CB' , 'CT' , -0.0235, 1.9080),
5: ('HB3' , 'HC' , -0.0169, 1.4870),
6: ('HB2' , 'HC' , -0.0169, 1.4870),
7: ('CG' , 'C' , 0.8194, 1.9080),
8: ('OD2' , 'O2' , -0.8084, 1.6612),
9: ('OD1' , 'O2' , -0.8084, 1.6612),
10: ('N' , 'N3' , 0.0782, 1.8240),
11: ('H3' , 'H' , 0.2200, 0.6000),
12: ('H2' , 'H' , 0.2200, 0.6000),
13: ('H1' , 'H' , 0.2200, 0.6000),
},
),
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)C<7>([O-]<8>)=O<9>)C<10>([O-]<11>)=O<12>',
{
0: ('N' , 'N' , -0.5192, 1.8240),
1: ('H' , 'H' , 0.3055, 0.6000),
2: ('CA' , 'CT' , -0.1817, 1.9080),
3: ('HA' , 'H1' , 0.1046, 1.3870),
4: ('CB' , 'CT' , -0.0677, 1.9080),
5: ('HB3' , 'HC' , -0.0212, 1.4870),
6: ('HB2' , 'HC' , -0.0212, 1.4870),
7: ('CG' , 'C' , 0.8851, 1.9080),
8: ('OD2' , 'O2' , -0.8162, 1.6612),
9: ('OD1' , 'O2' , -0.8162, 1.6612),
10: ('C' , 'C' , 0.7256, 1.9080),
11: ('OXT' , 'O2' , -0.7887, 1.6612),
12: ('O' , 'O2' , -0.7887, 1.6612),
},
),
],
'ASN': [
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)C<7>(=O<8>)N<9>([H]<10>)[H]<11>)C<12>=O<13>',
{
0: ('N' , 'N' , -0.4157, 1.8240),
1: ('H' , 'H' , 0.2719, 0.6000),
2: ('CA' , 'CT' , 0.0143, 1.9080),
3: ('HA' , 'H1' , 0.1048, 1.3870),
4: ('CB' , 'CT' , -0.2041, 1.9080),
5: ('HB3' , 'HC' , 0.0797, 1.4870),
6: ('HB2' , 'HC' , 0.0797, 1.4870),
7: ('CG' , 'C' , 0.7130, 1.9080),
8: ('OD1' , 'O' , -0.5931, 1.6612),
9: ('ND2' , 'N' , -0.9191, 1.8240),
10: ('HD22', 'H' , 0.4196, 0.6000),
11: ('HD21', 'H' , 0.4196, 0.6000),
12: ('C' , 'C' , 0.5973, 1.9080),
13: ('O' , 'O' , -0.5679, 1.6612),
},
),
(
'C<0>(=O<1>)[C@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)C<7>(=O<8>)N<9>([H]<10>)[H]<11>)[N@+]<12>([H]<13>)([H]<14>)[H]<15>',
{
0: ('C' , 'C' , 0.6163, 1.9080),
1: ('O' , 'O' , -0.5722, 1.6612),
2: ('CA' , 'CT' , 0.0368, 1.9080),
3: ('HA' , 'HP' , 0.1231, 1.1000),
4: ('CB' , 'CT' , -0.0283, 1.9080),
5: ('HB3' , 'HC' , 0.0515, 1.4870),
6: ('HB2' , 'HC' , 0.0515, 1.4870),
7: ('CG' , 'C' , 0.5833, 1.9080),
8: ('OD1' , 'O' , -0.5744, 1.6612),
9: ('ND2' , 'N' , -0.8634, 1.8240),
10: ('HD22', 'H' , 0.4097, 0.6000),
11: ('HD21', 'H' , 0.4097, 0.6000),
12: ('N' , 'N3' , 0.1801, 1.8240),
13: ('H3' , 'H' , 0.1921, 0.6000),
14: ('H2' , 'H' , 0.1921, 0.6000),
15: ('H1' , 'H' , 0.1921, 0.6000),
},
),
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)C<7>(=O<8>)N<9>([H]<10>)[H]<11>)C<12>([O-]<13>)=O<14>',
{
0: ('N' , 'N' , -0.3821, 1.8240),
1: ('H' , 'H' , 0.2681, 0.6000),
2: ('CA' , 'CT' , -0.2080, 1.9080),
3: ('HA' , 'H1' , 0.1358, 1.3870),
4: ('CB' , 'CT' , -0.2299, 1.9080),
5: ('HB3' , 'HC' , 0.1023, 1.4870),
6: ('HB2' , 'HC' , 0.1023, 1.4870),
7: ('CG' , 'C' , 0.7153, 1.9080),
8: ('OD1' , 'O' , -0.6010, 1.6612),
9: ('ND2' , 'N' , -0.9084, 1.8240),
10: ('HD22', 'H' , 0.4150, 0.6000),
11: ('HD21', 'H' , 0.4150, 0.6000),
12: ('C' , 'C' , 0.8050, 1.9080),
13: ('OXT' , 'O2' , -0.8147, 1.6612),
14: ('O' , 'O2' , -0.8147, 1.6612),
},
),
],
'CYS': [
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)S<7>[H]<8>)C<9>=O<10>',
{
0: ('N' , 'N' , -0.4157, 1.8240),
1: ('H' , 'H' , 0.2719, 0.6000),
2: ('CA' , 'CT' , 0.0213, 1.9080),
3: ('HA' , 'H1' , 0.1124, 1.3870),
4: ('CB' , 'CT' , -0.1231, 1.9080),
5: ('HB3' , 'H1' , 0.1112, 1.3870),
6: ('HB2' , 'H1' , 0.1112, 1.3870),
7: ('SG' , 'SH' , -0.3119, 2.0000),
8: ('HG' , 'HS' , 0.1933, 0.6000),
9: ('C' , 'C' , 0.5973, 1.9080),
10: ('O' , 'O' , -0.5679, 1.6612),
},
),
(
'C<0>(=O<1>)[C@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)S<7>[H]<8>)[N@+]<9>([H]<10>)([H]<11>)[H]<12>',
{
0: ('C' , 'C' , 0.6123, 1.9080),
1: ('O' , 'O' , -0.5713, 1.6612),
2: ('CA' , 'CT' , 0.0927, 1.9080),
3: ('HA' , 'HP' , 0.1411, 1.1000),
4: ('CB' , 'CT' , -0.1195, 1.9080),
5: ('HB3' , 'H1' , 0.1188, 1.3870),
6: ('HB2' , 'H1' , 0.1188, 1.3870),
7: ('SG' , 'SH' , -0.3298, 2.0000),
8: ('HG' , 'HS' , 0.1975, 0.6000),
9: ('N' , 'N3' , 0.1325, 1.8240),
10: ('H3' , 'H' , 0.2023, 0.6000),
11: ('H2' , 'H' , 0.2023, 0.6000),
12: ('H1' , 'H' , 0.2023, 0.6000),
},
),
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)S<7>[H]<8>)C<9>([O-]<10>)=O<11>',
{
0: ('N' , 'N' , -0.3821, 1.8240),
1: ('H' , 'H' , 0.2681, 0.6000),
2: ('CA' , 'CT' , -0.1635, 1.9080),
3: ('HA' , 'H1' , 0.1396, 1.3870),
4: ('CB' , 'CT' , -0.1996, 1.9080),
5: ('HB3' , 'H1' , 0.1437, 1.3870),
6: ('HB2' , 'H1' , 0.1437, 1.3870),
7: ('SG' , 'SH' , -0.3102, 2.0000),
8: ('HG' , 'HS' , 0.2068, 0.6000),
9: ('C' , 'C' , 0.7497, 1.9080),
10: ('OXT' , 'O2' , -0.7981, 1.6612),
11: ('O' , 'O2' , -0.7981, 1.6612),
},
),
( # disulfide bonded
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)S<7>S<7>)C<9>=O<10>',
{
0: ('N' , 'N' , -0.4157, 1.8240),
1: ('H' , 'H' , 0.2719, 0.6000),
2: ('CA' , 'CT' , 0.0429, 1.9080),
3: ('HA' , 'H1' , 0.0766, 1.3870),
4: ('CB' , 'CT' , -0.0790, 1.9080),
5: ('HB3' , 'H1' , 0.0910, 1.3870),
6: ('HB2' , 'H1' , 0.0910, 1.3870),
7: ('SG' , 'S' , -0.1081, 2.0000),
9: ('C' , 'C' , 0.5973, 1.9080),
10: ('O' , 'O' , -0.5679, 1.6612),
},
),
(
'C<0>(=O<1>)[C@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)S<7>S<7>)[N@+]<9>([H]<10>)([H]<11>)[H]<12>',
{
0: ('C' , 'C' , 0.6123, 1.9080),
1: ('O' , 'O' , -0.5713, 1.6612),
2: ('CA' , 'CT' , 0.1055, 1.9080),
3: ('HA' , 'HP' , 0.0922, 1.1000),
4: ('CB' , 'CT' , -0.0277, 1.9080),
5: ('HB3' , 'H1' , 0.0680, 1.3870),
6: ('HB2' , 'H1' , 0.0680, 1.3870),
7: ('SG' , 'S' , -0.0984, 2.0000),
9: ('N' , 'N3' , 0.2069, 1.8240),
10: ('H3' , 'H' , 0.1815, 0.6000),
11: ('H2' , 'H' , 0.1815, 0.6000),
12: ('H1' , 'H' , 0.1815, 0.6000),
},
),
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)S<7>S<7>)C<9>([O-]<10>)=O<11>',
{
0: ('N' , 'N' , -0.3821, 1.8240),
1: ('H' , 'H' , 0.2681, 0.6000),
2: ('CA' , 'CT' , -0.1318, 1.9080),
3: ('HA' , 'H1' , 0.0938, 1.3870),
4: ('CB' , 'CT' , -0.1934, 1.9080),
5: ('HB3' , 'H1' , 0.1228, 1.3870),
6: ('HB2' , 'H1' , 0.1228, 1.3870),
7: ('SG' , 'S' , -0.0529, 2.0000),
9: ('C' , 'C' , 0.7618, 1.9080),
10: ('OXT' , 'O2' , -0.8041, 1.6612),
11: ('O' , 'O2' , -0.8041, 1.6612),
},
),
],
'CYX': [
( # disulfide bonded
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)S<7>S<7>)C<9>=O<10>',
{
0: ('N' , 'N' , -0.4157, 1.8240),
1: ('H' , 'H' , 0.2719, 0.6000),
2: ('CA' , 'CT' , 0.0429, 1.9080),
3: ('HA' , 'H1' , 0.0766, 1.3870),
4: ('CB' , 'CT' , -0.0790, 1.9080),
5: ('HB3' , 'H1' , 0.0910, 1.3870),
6: ('HB2' , 'H1' , 0.0910, 1.3870),
7: ('SG' , 'S' , -0.1081, 2.0000),
9: ('C' , 'C' , 0.5973, 1.9080),
10: ('O' , 'O' , -0.5679, 1.6612),
},
),
(
'C<0>(=O<1>)[C@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)S<7>S<7>)[N@+]<9>([H]<10>)([H]<11>)[H]<12>',
{
0: ('C' , 'C' , 0.6123, 1.9080),
1: ('O' , 'O' , -0.5713, 1.6612),
2: ('CA' , 'CT' , 0.1055, 1.9080),
3: ('HA' , 'HP' , 0.0922, 1.1000),
4: ('CB' , 'CT' , -0.0277, 1.9080),
5: ('HB3' , 'H1' , 0.0680, 1.3870),
6: ('HB2' , 'H1' , 0.0680, 1.3870),
7: ('SG' , 'S' , -0.0984, 2.0000),
9: ('N' , 'N3' , 0.2069, 1.8240),
10: ('H3' , 'H' , 0.1815, 0.6000),
11: ('H2' , 'H' , 0.1815, 0.6000),
12: ('H1' , 'H' , 0.1815, 0.6000),
},
),
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)S<7>S<7>)C<9>([O-]<10>)=O<11>',
{
0: ('N' , 'N' , -0.3821, 1.8240),
1: ('H' , 'H' , 0.2681, 0.6000),
2: ('CA' , 'CT' , -0.1318, 1.9080),
3: ('HA' , 'H1' , 0.0938, 1.3870),
4: ('CB' , 'CT' , -0.1934, 1.9080),
5: ('HB3' , 'H1' , 0.1228, 1.3870),
6: ('HB2' , 'H1' , 0.1228, 1.3870),
7: ('SG' , 'S' , -0.0529, 2.0000),
9: ('C' , 'C' , 0.7618, 1.9080),
10: ('OXT' , 'O2' , -0.8041, 1.6612),
11: ('O' , 'O2' , -0.8041, 1.6612),
},
),
],
'GLN': [
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)[C@@]<7>([H]<8>)([H]<9>)C<10>(=O<11>)N<12>([H]<13>)[H]<14>)C<15>=O<16>',
{
0: ('N' , 'N' , -0.4157, 1.8240),
1: ('H' , 'H' , 0.2719, 0.6000),
2: ('CA' , 'CT' , -0.0031, 1.9080),
3: ('HA' , 'H1' , 0.0850, 1.3870),
4: ('CB' , 'CT' , -0.0036, 1.9080),
5: ('HB3' , 'HC' , 0.0171, 1.4870),
6: ('HB2' , 'HC' , 0.0171, 1.4870),
7: ('CG' , 'CT' , -0.0645, 1.9080),
8: ('HG3' , 'HC' , 0.0352, 1.4870),
9: ('HG2' , 'HC' , 0.0352, 1.4870),
10: ('CD' , 'C' , 0.6951, 1.9080),
11: ('OE1' , 'O' , -0.6086, 1.6612),
12: ('NE2' , 'N' , -0.9407, 1.8240),
13: ('HE22', 'H' , 0.4251, 0.6000),
14: ('HE21', 'H' , 0.4251, 0.6000),
15: ('C' , 'C' , 0.5973, 1.9080),
16: ('O' , 'O' , -0.5679, 1.6612),
},
),
(
'C<0>(=O<1>)[C@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)[C@@]<7>([H]<8>)([H]<9>)C<10>(=O<11>)N<12>([H]<13>)[H]<14>)[N@+]<15>([H]<16>)([H]<17>)[H]<18>',
{
0: ('C' , 'C' , 0.6123, 1.9080),
1: ('O' , 'O' , -0.5713, 1.6612),
2: ('CA' , 'CT' , 0.0536, 1.9080),
3: ('HA' , 'HP' , 0.1015, 1.1000),
4: ('CB' , 'CT' , 0.0651, 1.9080),
5: ('HB3' , 'HC' , 0.0050, 1.4870),
6: ('HB2' , 'HC' , 0.0050, 1.4870),
7: ('CG' , 'CT' , -0.0903, 1.9080),
8: ('HG3' , 'HC' , 0.0331, 1.4870),
9: ('HG2' , 'HC' , 0.0331, 1.4870),
10: ('CD' , 'C' , 0.7354, 1.9080),
11: ('OE1' , 'O' , -0.6133, 1.6612),
12: ('NE2' , 'N' , -1.0031, 1.8240),
13: ('HE22', 'H' , 0.4429, 0.6000),
14: ('HE21', 'H' , 0.4429, 0.6000),
15: ('N' , 'N3' , 0.1493, 1.8240),
16: ('H3' , 'H' , 0.1996, 0.6000),
17: ('H2' , 'H' , 0.1996, 0.6000),
18: ('H1' , 'H' , 0.1996, 0.6000),
},
),
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)[C@@]<7>([H]<8>)([H]<9>)C<10>(=O<11>)N<12>([H]<13>)[H]<14>)C<15>([O-]<16>)=O<17>',
{
0: ('N' , 'N' , -0.3821, 1.8240),
1: ('H' , 'H' , 0.2681, 0.6000),
2: ('CA' , 'CT' , -0.2248, 1.9080),
3: ('HA' , 'H1' , 0.1232, 1.3870),
4: ('CB' , 'CT' , -0.0664, 1.9080),
5: ('HB3' , 'HC' , 0.0452, 1.4870),
6: ('HB2' , 'HC' , 0.0452, 1.4870),
7: ('CG' , 'CT' , -0.0210, 1.9080),
8: ('HG3' , 'HC' , 0.0203, 1.4870),
9: ('HG2' , 'HC' , 0.0203, 1.4870),
10: ('CD' , 'C' , 0.7093, 1.9080),
11: ('OE1' , 'O' , -0.6098, 1.6612),
12: ('NE2' , 'N' , -0.9574, 1.8240),
13: ('HE22', 'H' , 0.4304, 0.6000),
14: ('HE21', 'H' , 0.4304, 0.6000),
15: ('C' , 'C' , 0.7775, 1.9080),
16: ('OXT' , 'O2' , -0.8042, 1.6612),
17: ('O' , 'O2' , -0.8042, 1.6612),
},
),
],
'GLU': [
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)[C@@]<7>([H]<8>)([H]<9>)C<10>([O-]<11>)=O<12>)C<13>=O<14>',
{
0: ('N' , 'N' , -0.5163, 1.8240),
1: ('H' , 'H' , 0.2936, 0.6000),
2: ('CA' , 'CT' , 0.0397, 1.9080),
3: ('HA' , 'H1' , 0.1105, 1.3870),
4: ('CB' , 'CT' , 0.0560, 1.9080),
5: ('HB3' , 'HC' , -0.0173, 1.4870),
6: ('HB2' , 'HC' , -0.0173, 1.4870),
7: ('CG' , 'CT' , 0.0136, 1.9080),
8: ('HG3' , 'HC' , -0.0425, 1.4870),
9: ('HG2' , 'HC' , -0.0425, 1.4870),
10: ('CD' , 'C' , 0.8054, 1.9080),
11: ('OE2' , 'O2' , -0.8188, 1.6612),
12: ('OE1' , 'O2' , -0.8188, 1.6612),
13: ('C' , 'C' , 0.5366, 1.9080),
14: ('O' , 'O' , -0.5819, 1.6612),
},
),
(
'C<0>(=O<1>)[C@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)[C@@]<7>([H]<8>)([H]<9>)C<10>([O-]<11>)=O<12>)[N@+]<13>([H]<14>)([H]<15>)[H]<16>',
{
0: ('C' , 'C' , 0.5621, 1.9080),
1: ('O' , 'O' , -0.5889, 1.6612),
2: ('CA' , 'CT' , 0.0588, 1.9080),
3: ('HA' , 'HP' , 0.1202, 1.1000),
4: ('CB' , 'CT' , 0.0909, 1.9080),
5: ('HB3' , 'HC' , -0.0232, 1.4870),
6: ('HB2' , 'HC' , -0.0232, 1.4870),
7: ('CG' , 'CT' , -0.0236, 1.9080),
8: ('HG3' , 'HC' , -0.0315, 1.4870),
9: ('HG2' , 'HC' , -0.0315, 1.4870),
10: ('CD' , 'C' , 0.8087, 1.9080),
11: ('OE2' , 'O2' , -0.8189, 1.6612),
12: ('OE1' , 'O2' , -0.8189, 1.6612),
13: ('N' , 'N3' , 0.0017, 1.8240),
14: ('H3' , 'H' , 0.2391, 0.6000),
15: ('H2' , 'H' , 0.2391, 0.6000),
16: ('H1' , 'H' , 0.2391, 0.6000),
},
),
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)[C@@]<7>([H]<8>)([H]<9>)C<10>([O-]<11>)=O<12>)C<13>([O-]<14>)=O<15>',
{
0: ('N' , 'N' , -0.5192, 1.8240),
1: ('H' , 'H' , 0.3055, 0.6000),
2: ('CA' , 'CT' , -0.2059, 1.9080),
3: ('HA' , 'H1' , 0.1399, 1.3870),
4: ('CB' , 'CT' , 0.0071, 1.9080),
5: ('HB3' , 'HC' , -0.0078, 1.4870),
6: ('HB2' , 'HC' , -0.0078, 1.4870),
7: ('CG' , 'CT' , 0.0675, 1.9080),
8: ('HG3' , 'HC' , -0.0548, 1.4870),
9: ('HG2' , 'HC' , -0.0548, 1.4870),
10: ('CD' , 'C' , 0.8183, 1.9080),
11: ('OE2' , 'O2' , -0.8220, 1.6612),
12: ('OE1' , 'O2' , -0.8220, 1.6612),
13: ('C' , 'C' , 0.7420, 1.9080),
14: ('OXT' , 'O2' , -0.7930, 1.6612),
15: ('O' , 'O2' , -0.7930, 1.6612),
},
),
],
'GLY': [
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([H]<4>)C<5>=O<6>',
{
0: ('N' , 'N' , -0.4157, 1.8240),
1: ('H' , 'H' , 0.2719, 0.6000),
2: ('CA' , 'CT' , -0.0252, 1.9080),
3: ('HA' , 'H1' , 0.0698, 1.3870),
4: ('HA3' , 'H1' , 0.0698, 1.3870),
5: ('C' , 'C' , 0.5973, 1.9080),
6: ('O' , 'O' , -0.5679, 1.6612),
},
),
(
'C<0>(=O<1>)[C@]<2>([H]<3>)([H]<4>)[N@+]<5>([H]<6>)([H]<7>)[H]<8>',
{
0: ('C' , 'C' , 0.6163, 1.9080),
1: ('O' , 'O' , -0.5722, 1.6612),
2: ('CA' , 'CT' , -0.0100, 1.9080),
3: ('HA' , 'H1' , 0.0895, 1.1000),
4: ('HA3' , 'H1' , 0.0895, 1.1000),
5: ('N' , 'N' , 0.2943, 1.8240),
6: ('H2' , 'H' , 0.1642, 0.6000),
7: ('H1' , 'H' , 0.1642, 0.6000),
8: ('H3' , 'H' , 0.1642, 0.6000),
},
),
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([H]<4>)C<5>([O-]<6>)=O<7>',
{
0: ('N' , 'N' , -0.3821, 1.8240),
1: ('H' , 'H' , 0.2681, 0.6000),
2: ('CA' , 'CT' , -0.2493, 1.9080),
3: ('HA' , 'H1' , 0.1056, 1.3870),
4: ('HA3' , 'H1' , 0.1056, 1.3870),
5: ('C' , 'C' , 0.7231, 1.9080),
6: ('OXT' , 'O2' , -0.7855, 1.6612),
7: ('O' , 'O' , -0.7855, 1.6612),
},
),
],
'HIS': [
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)C<7>=1N<8>=C<9>([H]<10>)N<11>([H]<12>)C<13>=1[H]<14>)C<15>=O<16>',
{
0: ('N' , 'N' , -0.4157, 1.8240),
1: ('H' , 'H' , 0.2719, 0.6000),
2: ('CA' , 'CT' , -0.0581, 1.9080),
3: ('HA' , 'H1' , 0.1360, 1.3870),
4: ('CB' , 'CT' , -0.0074, 1.9080),
5: ('HB3' , 'HC' , 0.0367, 1.4870),
6: ('HB2' , 'HC' , 0.0367, 1.4870),
7: ('CG' , 'CC' , 0.1868, 1.9080),
8: ('ND1' , 'NB' , -0.5432, 1.8240),
9: ('CE1' , 'CR' , 0.1635, 1.9080),
10: ('HE1' , 'H5' , 0.1435, 1.3590),
11: ('NE2' , 'NA' , -0.2795, 1.8240),
12: ('HE2' , 'H' , 0.3339, 0.6000),
13: ('CD2' , 'CW' , -0.2207, 1.9080),
14: ('HD2' , 'H4' , 0.1862, 1.4090),
15: ('C' , 'C' , 0.5973, 1.9080),
16: ('O' , 'O' , -0.5679, 1.6612),
},
),
(
'C<0>(=O<1>)[C@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)C<7>=1N<8>=C<9>([H]<10>)N<11>([H]<12>)C<13>=1[H]<14>)[N@+]<15>([H]<16>)([H]<17>)[H]<18>',
{
0: ('C' , 'C' , 0.6123, 1.9080),
1: ('O' , 'O' , -0.5713, 1.6612),
2: ('CA' , 'CT' , 0.0236, 1.9080),
3: ('HA' , 'HP' , 0.1380, 1.1000),
4: ('CB' , 'CT' , 0.0489, 1.9080),
5: ('HB3' , 'HC' , 0.0223, 1.4870),
6: ('HB2' , 'HC' , 0.0223, 1.4870),
7: ('CG' , 'CC' , 0.1740, 1.9080),
8: ('ND1' , 'NB' , -0.5579, 1.8240),
9: ('CE1' , 'CR' , 0.1804, 1.9080),
10: ('HE1' , 'H5' , 0.1397, 1.3590),
11: ('NE2' , 'NA' , -0.2781, 1.8240),
12: ('HE2' , 'H' , 0.3324, 0.6000),
13: ('CD2' , 'CW' , -0.2349, 1.9080),
14: ('HD2' , 'H4' , 0.1963, 1.4090),
15: ('N' , 'N3' , 0.1472, 1.8240),
16: ('H3' , 'H' , 0.2016, 0.6000),
17: ('H2' , 'H' , 0.2016, 0.6000),
18: ('H1' , 'H' , 0.2016, 0.6000),
},
),
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)C<7>=1N<8>=C<9>([H]<10>)N<11>([H]<12>)C<13>=1[H]<14>)C<15>([O-]<16>)=O<17>',
{
0: ('N' , 'N' , -0.3821, 1.8240),
1: ('H' , 'H' , 0.2681, 0.6000),
2: ('CA' , 'CT' , -0.2699, 1.9080),
3: ('HA' , 'H1' , 0.1650, 1.3870),
4: ('CB' , 'CT' , -0.1068, 1.9080),
5: ('HB3' , 'HC' , 0.0620, 1.4870),
6: ('HB2' , 'HC' , 0.0620, 1.4870),
7: ('CG' , 'CC' , 0.2724, 1.9080),
8: ('ND1' , 'NB' , -0.5517, 1.8240),
9: ('CE1' , 'CR' , 0.1558, 1.9080),
10: ('HE1' , 'H5' , 0.1448, 1.3590),
11: ('NE2' , 'NA' , -0.2670, 1.8240),
12: ('HE2' , 'H' , 0.3319, 0.6000),
13: ('CD2' , 'CW' , -0.2588, 1.9080),
14: ('HD2' , 'H4' , 0.1957, 1.4090),
15: ('C' , 'C' , 0.7916, 1.9080),
16: ('OXT' , 'O2' , -0.8065, 1.6612),
17: ('O' , 'O2' , -0.8065, 1.6612),
},
),
],
'HIP': [
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)C<7>=1[N+]<8>([H]<9>)=C<10>([H]<11>)N<12>([H]<13>)C<14>=1[H]<15>)C<16>=O<17>',
{
0: ('N' , 'N' , -0.3479, 1.8240),
1: ('H' , 'H' , 0.2747, 0.6000),
2: ('CA' , 'CT' , -0.1354, 1.9080),
3: ('HA' , 'H1' , 0.1212, 1.3870),
4: ('CB' , 'CT' , -0.0414, 1.9080),
5: ('HB3' , 'HC' , 0.0810, 1.4870),
6: ('HB2' , 'HC' , 0.0810, 1.4870),
7: ('CG' , 'CC' , -0.0012, 1.9080),
8: ('ND1' , 'NA' , -0.1513, 1.8240),
9: ('HD1' , 'H' , 0.3866, 0.6000),
10: ('CE1' , 'CR' , -0.0170, 1.9080),
11: ('HE1' , 'H5' , 0.2681, 1.3590),
12: ('NE2' , 'NA' , -0.1718, 1.8240),
13: ('HE2' , 'H' , 0.3911, 0.6000),
14: ('CD2' , 'CW' , -0.1141, 1.9080),
15: ('HD2' , 'H4' , 0.2317, 1.4090),
16: ('C' , 'C' , 0.7341, 1.9080),
17: ('O' , 'O' , -0.5894, 1.6612),
},
),
(
'C<0>(=O<1>)[C@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)C<7>=1[N+]<8>([H]<9>)=C<10>([H]<11>)N<12>([H]<13>)C<14>=1[H]<15>)[N@+]<16>([H]<17>)([H]<18>)[H]<19>',
{
0: ('C' , 'C' , 0.7214, 1.9080),
1: ('O' , 'O' , -0.6013, 1.6612),
2: ('CA' , 'CT' , 0.0581, 1.9080),
3: ('HA' , 'HP' , 0.1047, 1.1000),
4: ('CB' , 'CT' , 0.0484, 1.9080),
5: ('HB3' , 'HC' , 0.0531, 1.4870),
6: ('HB2' , 'HC' , 0.0531, 1.4870),
7: ('CG' , 'CC' , -0.0236, 1.9080),
8: ('ND1' , 'NA' , -0.1510, 1.8240),
9: ('HD1' , 'H' , 0.3821, 0.6000),
10: ('CE1' , 'CR' , -0.0011, 1.9080),
11: ('HE1' , 'H5' , 0.2645, 1.3590),
12: ('NE2' , 'NA' , -0.1739, 1.8240),
13: ('HE2' , 'H' , 0.3921, 0.6000),
14: ('CD2' , 'CW' , -0.1433, 1.9080),
15: ('HD2' , 'H4' , 0.2495, 1.4090),
16: ('N' , 'N3' , 0.2560, 1.8240),
17: ('H3' , 'H' , 0.1704, 0.6000),
18: ('H2' , 'H' , 0.1704, 0.6000),
19: ('H1' , 'H' , 0.1704, 0.6000),
},
),
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)C<7>=1[N+]<8>([H]<9>)=C<10>([H]<11>)N<12>([H]<13>)C<14>=1[H]<15>)C<16>([O-]<17>)=O<18>',
{
0: ('N' , 'N' , -0.3481, 1.8240),
1: ('H' , 'H' , 0.2764, 0.6000),
2: ('CA' , 'CT' , -0.1445, 1.9080),
3: ('HA' , 'H1' , 0.1115, 1.3870),
4: ('CB' , 'CT' , -0.0800, 1.9080),
5: ('HB3' , 'HC' , 0.0868, 1.4870),
6: ('HB2' , 'HC' , 0.0868, 1.4870),
7: ('CG' , 'CC' , 0.0298, 1.9080),
8: ('ND1' , 'NA' , -0.1501, 1.8240),
9: ('HD1' , 'H' , 0.3883, 0.6000),
10: ('CE1' , 'CR' , -0.0251, 1.9080),
11: ('HE1' , 'H5' , 0.2694, 1.3590),
12: ('NE2' , 'NA' , -0.1683, 1.8240),
13: ('HE2' , 'H' , 0.3913, 0.6000),
14: ('CD2' , 'CW' , -0.1256, 1.9080),
15: ('HD2' , 'H4' , 0.2336, 1.4090),
16: ('C' , 'C' , 0.8032, 1.9080),
17: ('OXT' , 'O2' , -0.8177, 1.6612),
18: ('O' , 'O2' , -0.8177, 1.6612),
},
),
],
'HID': [
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)C<7>=1N<8>([H]<9>)C<10>([H]<11>)=N<12>C<13>=1[H]<14>)C<15>=O<16>',
{
0: ('N' , 'N' , -0.4157, 1.8240),
1: ('H' , 'H' , 0.2719, 0.6000),
2: ('CA' , 'CT' , 0.0188, 1.9080),
3: ('HA' , 'H1' , 0.0881, 1.3870),
4: ('CB' , 'CT' , -0.0462, 1.9080),
5: ('HB3' , 'HC' , 0.0402, 1.4870),
6: ('HB2' , 'HC' , 0.0402, 1.4870),
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16: ('OXT' , 'O2' , -0.8016, 1.6612),
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14: ('HD13', 'HC' , 0.0980, 1.4870),
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16: ('HD11', 'HC' , 0.0980, 1.4870),
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18: ('H3' , 'H' , 0.2148, 0.6000),
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12: ('HD21', 'HC' , 0.1038, 1.4870),
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14: ('HD13', 'HC' , 0.1038, 1.4870),
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16: ('HD11', 'HC' , 0.1038, 1.4870),
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9: ('HG2' , 'HC' , 0.0121, 1.4870),
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11: ('HD3' , 'HC' , 0.0633, 1.4870),
12: ('HD2' , 'HC' , 0.0633, 1.4870),
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16: ('NZ' , 'N3' , -0.3764, 1.8240),
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2: ('CA' , 'CT' , -0.2903, 1.9080),
3: ('HA' , 'H1' , 0.1438, 1.3870),
4: ('CB' , 'CT' , -0.0538, 1.9080),
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9: ('HG2' , 'HC' , 0.0134, 1.4870),
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14: ('HE3' , 'HP' , 0.1121, 1.1000),
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0: ('N' , 'N' , -0.3821, 1.8240),
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11: ('HE2' , 'HA' , 0.1461, 1.4590),
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16: ('CD1' , 'CA' , -0.1300, 1.9080),
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11: ('HA' , 'H1' , 0.0641, 1.3870),
12: ('C' , 'C' , 0.5896, 1.9080),
13: ('O' , 'O' , -0.5748, 1.6612),
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0: ('C' , 'C' , 0.5260, 1.9080),
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4: ('CB' , 'CT' , -0.1150, 1.9080),
5: ('HB3' , 'HC' , 0.1000, 1.4870),
6: ('HB2' , 'HC' , 0.1000, 1.4870),
7: ('CG' , 'CT' , -0.1210, 1.9080),
8: ('HG3' , 'HC' , 0.1000, 1.4870),
9: ('HG2' , 'HC' , 0.1000, 1.4870),
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11: ('HD3' , 'H1' , 0.1000, 1.1000),
12: ('HD2' , 'H1' , 0.1000, 1.1000),
13: ('N' , 'N3' , -0.2020, 1.8240),
14: ('H3' , 'H' , 0.3120, 0.6000),
15: ('H2' , 'H' , 0.3120, 0.6000),
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0: ('N' , 'N' , -0.2802, 1.8240),
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9: ('HB2' , 'HC' , 0.0381, 1.4870),
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11: ('HA' , 'H1' , 0.0776, 1.3870),
12: ('C' , 'C' , 0.6631, 1.9080),
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0: ('N' , 'N' , -0.4157, 1.8240),
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4: ('CB' , 'CT' , 0.2117, 1.9080),
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9: ('C' , 'C' , 0.5973, 1.9080),
10: ('O' , 'O' , -0.5679, 1.6612),
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6: ('HB2' , 'H1' , 0.0273, 1.3870),
7: ('OG' , 'OH' , -0.6714, 1.7210),
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9: ('N' , 'N3' , 0.1849, 1.8240),
10: ('H3' , 'H' , 0.1898, 0.6000),
11: ('H2' , 'H' , 0.1898, 0.6000),
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0: ('N' , 'N' , -0.3821, 1.8240),
1: ('H' , 'H' , 0.2681, 0.6000),
2: ('CA' , 'CT' , -0.2722, 1.9080),
3: ('HA' , 'H1' , 0.1304, 1.3870),
4: ('CB' , 'CT' , 0.1123, 1.9080),
5: ('HB3' , 'H1' , 0.0813, 1.3870),
6: ('HB2' , 'H1' , 0.0813, 1.3870),
7: ('OG' , 'OH' , -0.6514, 1.7210),
8: ('HG' , 'HO' , 0.4474, 0.0000),
9: ('C' , 'C' , 0.8113, 1.9080),
10: ('OXT' , 'O2' , -0.8132, 1.6612),
11: ('O' , 'O2' , -0.8132, 1.6612),
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{
0: ('N' , 'N' , -0.4157, 1.8240),
1: ('H' , 'H' , 0.2719, 0.6000),
2: ('CA' , 'CT' , -0.0389, 1.9080),
3: ('HA' , 'H1' , 0.1007, 1.3870),
4: ('CB' , 'CT' , 0.3654, 1.9080),
5: ('HB' , 'H1' , 0.0043, 1.3870),
6: ('OG1' , 'OH' , -0.6761, 1.7210),
7: ('HG1' , 'HO' , 0.4102, 0.0000),
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11: ('HG21', 'HC' , 0.0642, 1.4870),
12: ('C' , 'C' , 0.5973, 1.9080),
13: ('O' , 'O' , -0.5679, 1.6612),
},
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{
0: ('C' , 'C' , 0.6163, 1.9080),
1: ('O' , 'O' , -0.5722, 1.6612),
2: ('CA' , 'CT' , 0.0034, 1.9080),
3: ('HA' , 'HP' , 0.1087, 1.1000),
4: ('CB' , 'CT' , 0.4514, 1.9080),
5: ('HB' , 'H1' , -0.0323, 1.3870),
6: ('OG1' , 'OH' , -0.6764, 1.7210),
7: ('HG1' , 'HO' , 0.4070, 0.0000),
8: ('CG2' , 'CT' , -0.2554, 1.9080),
9: ('HG23', 'HC' , 0.0627, 1.4870),
10: ('HG22', 'HC' , 0.0627, 1.4870),
11: ('HG21', 'HC' , 0.0627, 1.4870),
12: ('N' , 'N3' , 0.1812, 1.8240),
13: ('H3' , 'H' , 0.1934, 0.6000),
14: ('H2' , 'H' , 0.1934, 0.6000),
15: ('H1' , 'H' , 0.1934, 0.6000),
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{
0: ('N' , 'N' , -0.3821, 1.8240),
1: ('H' , 'H' , 0.2681, 0.6000),
2: ('CA' , 'CT' , -0.2420, 1.9080),
3: ('HA' , 'H1' , 0.1207, 1.3870),
4: ('CB' , 'CT' , 0.3025, 1.9080),
5: ('HB' , 'H1' , 0.0078, 1.3870),
6: ('OG1' , 'OH' , -0.6496, 1.7210),
7: ('HG1' , 'HO' , 0.4119, 0.0000),
8: ('CG2' , 'CT' , -0.1853, 1.9080),
9: ('HG23', 'HC' , 0.0586, 1.4870),
10: ('HG22', 'HC' , 0.0586, 1.4870),
11: ('HG21', 'HC' , 0.0586, 1.4870),
12: ('C' , 'C' , 0.7810, 1.9080),
13: ('OXT' , 'O2' , -0.8044, 1.6612),
14: ('O' , 'O2' , -0.8044, 1.6612),
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),
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{
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1: ('H' , 'H' , 0.2719, 0.6000),
2: ('CA' , 'CT' , -0.0275, 1.9080),
3: ('HA' , 'H1' , 0.1123, 1.3870),
4: ('CB' , 'CT' , -0.0050, 1.9080),
5: ('HB3' , 'HC' , 0.0339, 1.4870),
6: ('HB2' , 'HC' , 0.0339, 1.4870),
7: ('CG' , 'C*' , -0.1415, 1.9080),
8: ('CD1' , 'CW' , -0.1638, 1.9080),
9: ('HD1' , 'H4' , 0.2062, 1.4090),
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11: ('HE1' , 'H' , 0.3412, 0.6000),
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13: ('CZ2' , 'CA' , -0.2601, 1.9080),
14: ('HZ2' , 'HA' , 0.1572, 1.4590),
15: ('CH2' , 'CA' , -0.1134, 1.9080),
16: ('HH2' , 'HA' , 0.1417, 1.4590),
17: ('CZ3' , 'CA' , -0.1972, 1.9080),
18: ('HZ3' , 'HA' , 0.1447, 1.4590),
19: ('CE3' , 'CA' , -0.2387, 1.9080),
20: ('HE3' , 'HA' , 0.1700, 1.4590),
21: ('CD2' , 'CB' , 0.1243, 1.9080),
22: ('C' , 'C' , 0.5973, 1.9080),
23: ('O' , 'O' , -0.5679, 1.6612),
},
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{
0: ('C' , 'C' , 0.6123, 1.9080),
1: ('O' , 'O' , -0.5713, 1.6612),
2: ('CA' , 'CT' , 0.0421, 1.9080),
3: ('HA' , 'HP' , 0.1162, 1.1000),
4: ('CB' , 'CT' , 0.0543, 1.9080),
5: ('HB3' , 'HC' , 0.0222, 1.4870),
6: ('HB2' , 'HC' , 0.0222, 1.4870),
7: ('CG' , 'C*' , -0.1654, 1.9080),
8: ('CD1' , 'CW' , -0.1788, 1.9080),
9: ('HD1' , 'H4' , 0.2195, 1.4090),
10: ('NE1' , 'NA' , -0.3444, 1.8240),
11: ('HE1' , 'H' , 0.3412, 0.6000),
12: ('CE2' , 'CN' , 0.1575, 1.9080),
13: ('CZ2' , 'CA' , -0.2710, 1.9080),
14: ('HZ2' , 'HA' , 0.1589, 1.4590),
15: ('CH2' , 'CA' , -0.1080, 1.9080),
16: ('HH2' , 'HA' , 0.1411, 1.4590),
17: ('CZ3' , 'CA' , -0.2034, 1.9080),
18: ('HZ3' , 'HA' , 0.1458, 1.4590),
19: ('CE3' , 'CA' , -0.2265, 1.9080),
20: ('HE3' , 'HA' , 0.1646, 1.4590),
21: ('CD2' , 'CB' , 0.1132, 1.9080),
22: ('N' , 'N3' , 0.1913, 1.8240),
23: ('H3' , 'H' , 0.1888, 0.6000),
24: ('H2' , 'H' , 0.1888, 0.6000),
25: ('H1' , 'H' , 0.1888, 0.6000),
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{
0: ('N' , 'N' , -0.3821, 1.8240),
1: ('H' , 'H' , 0.2681, 0.6000),
2: ('CA' , 'CT' , -0.2084, 1.9080),
3: ('HA' , 'H1' , 0.1272, 1.3870),
4: ('CB' , 'CT' , -0.0742, 1.9080),
5: ('HB3' , 'HC' , 0.0497, 1.4870),
6: ('HB2' , 'HC' , 0.0497, 1.4870),
7: ('CG' , 'C*' , -0.0796, 1.9080),
8: ('CD1' , 'CW' , -0.1808, 1.9080),
9: ('HD1' , 'H4' , 0.2043, 1.4090),
10: ('NE1' , 'NA' , -0.3316, 1.8240),
11: ('HE1' , 'H' , 0.3413, 0.6000),
12: ('CE2' , 'CN' , 0.1222, 1.9080),
13: ('CZ2' , 'CA' , -0.2594, 1.9080),
14: ('HZ2' , 'HA' , 0.1567, 1.4590),
15: ('CH2' , 'CA' , -0.1020, 1.9080),
16: ('HH2' , 'HA' , 0.1401, 1.4590),
17: ('CZ3' , 'CA' , -0.2287, 1.9080),
18: ('HZ3' , 'HA' , 0.1507, 1.4590),
19: ('CE3' , 'CA' , -0.1837, 1.9080),
20: ('HE3' , 'HA' , 0.1491, 1.4590),
21: ('CD2' , 'CB' , 0.1078, 1.9080),
22: ('C' , 'C' , 0.7658, 1.9080),
23: ('OXT' , 'O2' , -0.8011, 1.6612),
24: ('O' , 'O2' , -0.8011, 1.6612),
},
),
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{
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2: ('CA' , 'CT' , -0.0014, 1.9080),
3: ('HA' , 'H1' , 0.0876, 1.3870),
4: ('CB' , 'CT' , -0.0152, 1.9080),
5: ('HB3' , 'HC' , 0.0295, 1.4870),
6: ('HB2' , 'HC' , 0.0295, 1.4870),
7: ('CG' , 'CA' , -0.0011, 1.9080),
8: ('CD2' , 'CA' , -0.1906, 1.9080),
9: ('HD2' , 'HA' , 0.1699, 1.4590),
10: ('CE2' , 'CA' , -0.2341, 1.9080),
11: ('HE2' , 'HA' , 0.1656, 1.4590),
12: ('CZ' , 'CA' , 0.3226, 1.9080),
13: ('OH' , 'OH' , -0.5579, 1.7210),
14: ('HH' , 'HO' , 0.3992, 0.0000),
15: ('CE1' , 'CA' , -0.2341, 1.9080),
16: ('HE1' , 'HA' , 0.1656, 1.4590),
17: ('CD1' , 'CA' , -0.1906, 1.9080),
18: ('HD1' , 'HA' , 0.1699, 1.4590),
19: ('C' , 'C' , 0.5973, 1.9080),
20: ('O' , 'O' , -0.5679, 1.6612),
},
),
(
'C<0>(=O<1>)[C@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)C<7>=1C<8>([H]<9>)=C<10>([H]<11>)C<12>(O<13>[H]<14>)=C<15>([H]<16>)C<17>=1[H]<18>)[N@+]<19>([H]<20>)([H]<21>)[H]<22>',
{
0: ('C' , 'C' , 0.6123, 1.9080),
1: ('O' , 'O' , -0.5713, 1.6612),
2: ('CA' , 'CT' , 0.0570, 1.9080),
3: ('HA' , 'H1' , 0.0983, 1.1000),
4: ('CB' , 'CT' , 0.0659, 1.9080),
5: ('HB3' , 'HC' , 0.0102, 1.4870),
6: ('HB2' , 'HC' , 0.0102, 1.4870),
7: ('CG' , 'CA' , -0.0205, 1.9080),
8: ('CD2' , 'CA' , -0.2002, 1.9080),
9: ('HD2' , 'HA' , 0.1720, 1.4590),
10: ('CE2' , 'CA' , -0.2239, 1.9080),
11: ('HE2' , 'HA' , 0.1650, 1.4590),
12: ('CZ' , 'CA' , 0.3139, 1.9080),
13: ('OH' , 'OH' , -0.5578, 1.7210),
14: ('HH' , 'HO' , 0.4001, 0.0000),
15: ('CE1' , 'CA' , -0.2239, 1.9080),
16: ('HE1' , 'HA' , 0.1650, 1.4590),
17: ('CD1' , 'CA' , -0.2002, 1.9080),
18: ('HD1' , 'HA' , 0.1720, 1.4590),
19: ('N' , 'N' , 0.1940, 1.8240),
20: ('H3' , 'H' , 0.1873, 0.6000),
21: ('H2' , 'H' , 0.1873, 0.6000),
22: ('H1' , 'H' , 0.1873, 0.6000),
},
),
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@@]<4>([H]<5>)([H]<6>)C<7>=1C<8>([H]<9>)=C<10>([H]<11>)C<12>(O<13>[H]<14>)=C<15>([H]<16>)C<17>=1[H]<18>)C<19>([O-]<20>)=O<21>',
{
0: ('N' , 'N' , -0.3821, 1.8240),
1: ('H' , 'H' , 0.2681, 0.6000),
2: ('CA' , 'CT' , -0.2015, 1.9080),
3: ('HA' , 'H1' , 0.1092, 1.3870),
4: ('CB' , 'CT' , -0.0752, 1.9080),
5: ('HB3' , 'HC' , 0.0490, 1.4870),
6: ('HB2' , 'HC' , 0.0490, 1.4870),
7: ('CG' , 'CA' , 0.0243, 1.9080),
8: ('CD2' , 'CA' , -0.1922, 1.9080),
9: ('HD2' , 'HA' , 0.1780, 1.4590),
10: ('CE2' , 'CA' , -0.2458, 1.9080),
11: ('HE2' , 'HA' , 0.1673, 1.4590),
12: ('CZ' , 'CA' , 0.3395, 1.9080),
13: ('OH' , 'OH' , -0.5643, 1.7210),
14: ('HH' , 'HO' , 0.4017, 0.0000),
15: ('CE1' , 'CA' , -0.2458, 1.9080),
16: ('HE1' , 'HA' , 0.1673, 1.4590),
17: ('CD1' , 'CA' , -0.1922, 1.9080),
18: ('HD1' , 'HA' , 0.1780, 1.4590),
19: ('C' , 'C' , 0.7817, 1.9080),
20: ('OXT' , 'O2' , -0.8070, 1.6612),
21: ('O' , 'O' , -0.8070, 1.6612),
},
),
],
'VAL': [
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@]<4>([H]<5>)([C@]<6>([H]<7>)([H]<8>)[H]<9>)[C@]<10>([H]<11>)([H]<12>)[H]<13>)C<14>=O<15>',
{
0: ('N' , 'N' , -0.4157, 1.8240),
1: ('H' , 'H' , 0.2719, 0.6000),
2: ('CA' , 'CT' , -0.0875, 1.9080),
3: ('HA' , 'H1' , 0.0969, 1.3870),
4: ('CB' , 'CT' , 0.2985, 1.9080),
5: ('HB' , 'HC' , -0.0297, 1.4870),
6: ('CG2' , 'CT' , -0.3192, 1.9080),
7: ('HG23', 'HC' , 0.0791, 1.4870),
8: ('HG22', 'HC' , 0.0791, 1.4870),
9: ('HG21', 'HC' , 0.0791, 1.4870),
10: ('CG1' , 'CT' , -0.3192, 1.9080),
11: ('HG13', 'HC' , 0.0791, 1.4870),
12: ('HG12', 'HC' , 0.0791, 1.4870),
13: ('HG11', 'HC' , 0.0791, 1.4870),
14: ('C' , 'C' , 0.5973, 1.9080),
15: ('O' , 'O' , -0.5679, 1.6612),
},
),
(
'C<0>(=O<1>)[C@]<2>([H]<3>)([C@]<4>([H]<5>)([C@]<6>([H]<7>)([H]<8>)[H]<9>)[C@]<10>([H]<11>)([H]<12>)[H]<13>)[N@+]<14>([H]<15>)([H]<16>)[H]<17>',
{
0: ('C' , 'C' , 0.6163, 1.9080),
1: ('O' , 'O' , -0.5722, 1.6612),
2: ('CA' , 'CT' , -0.0054, 1.9080),
3: ('HA' , 'HP' , 0.1093, 1.1000),
4: ('CB' , 'CT' , 0.3196, 1.9080),
5: ('HB' , 'HC' , -0.0221, 1.4870),
6: ('CG2' , 'CT' , -0.3129, 1.9080),
7: ('HG23', 'HC' , 0.0735, 1.4870),
8: ('HG22', 'HC' , 0.0735, 1.4870),
9: ('HG21', 'HC' , 0.0735, 1.4870),
10: ('CG1' , 'CT' , -0.3129, 1.9080),
11: ('HG13', 'HC' , 0.0735, 1.4870),
12: ('HG12', 'HC' , 0.0735, 1.4870),
13: ('HG11', 'HC' , 0.0735, 1.4870),
14: ('N' , 'N3' , 0.0577, 1.8240),
15: ('H3' , 'H' , 0.2272, 0.6000),
16: ('H2' , 'H' , 0.2272, 0.6000),
17: ('H1' , 'H' , 0.2272, 0.6000),
},
),
(
'N<0>([H]<1>)[C@@]<2>([H]<3>)([C@]<4>([H]<5>)([C@]<6>([H]<7>)([H]<8>)[H]<9>)[C@]<10>([H]<11>)([H]<12>)[H]<13>)C<14>([O-]<15>)=O<16>',
{
0: ('N' , 'N' , -0.3821, 1.8240),
1: ('H' , 'H' , 0.2681, 0.6000),
2: ('CA' , 'CT' , -0.3438, 1.9080),
3: ('HA' , 'H1' , 0.1438, 1.3870),
4: ('CB' , 'CT' , 0.1940, 1.9080),
5: ('HB' , 'HC' , 0.0308, 1.4870),
6: ('CG2' , 'CT' , -0.3064, 1.9080),
7: ('HG23', 'HC' , 0.0836, 1.4870),
8: ('HG22', 'HC' , 0.0836, 1.4870),
9: ('HG21', 'HC' , 0.0836, 1.4870),
10: ('CG1' , 'CT' , -0.3064, 1.9080),
11: ('HG13', 'HC' , 0.0836, 1.4870),
12: ('HG12', 'HC' , 0.0836, 1.4870),
13: ('HG11', 'HC' , 0.0836, 1.4870),
14: ('C' , 'C' , 0.8350, 1.9080),
15: ('OXT' , 'O2' , -0.8173, 1.6612),
16: ('O' , 'O2' , -0.8173, 1.6612),
},
),
],
'WAT': [
(
'O<0>([H]<1>)[H]<2>',
{
0: ('O' , 'OW' , -0.8340, 1.6612),
1: ('H1' , 'HW' , 0.4170, 0.0000),
2: ('H2' , 'HW' , 0.4170, 0.0000),
},
),
],
'HOH': [
(
'O<0>([H]<1>)[H]<2>',
{
0: ('O' , 'OW' , -0.8340, 1.6612),
1: ('H1' , 'HW' , 0.4170, 0.0000),
2: ('H2' , 'HW' , 0.4170, 0.0000),
},
),
],
'TIP': [
(
'O<0>([H]<1>)[H]<2>',
{
0: ('O' , 'OW' , -0.8340, 1.6612),
1: ('H1' , 'HW' , 0.4170, 0.0000),
2: ('H2' , 'HW' , 0.4170, 0.0000),
},
),
],
}
# also want commong residues like PTyr, PSer,
# missing neutrals GLUH/GLUN,GLH, ASPH/ASH/ASPN, LYSN, ARGN
for alias in (
( 'HIE', 'HIS'), # default HIS is HISE
( 'HISE', 'HIS'),
( 'HISD', 'HID'),
( 'HISP', 'HIP'),
( 'GLUM', 'GLU'), # default -1
( 'ASPM', 'ASP'), # default -1
( 'LYSP', 'LYS'), # default +1
( 'ARGP', 'ARG'), # default +1
):
amber99_dict[alias[0]] = amber99_dict[alias[1]]