# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 09:04:57 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 AN6  AN6  5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine  L-peptide  53  28  .  2022-07-24  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AN6
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 AN6  C'    C  C     0   0.515  -2.0878  -2.8779  -0.0389
 AN6  N'    N  NH2   0  -0.780  -4.0394  -2.1736   1.3453
 AN6  O'    O  O     0  -0.439  -1.5978  -3.5846   0.8062
 AN6  C1    C  CH3   0  -0.670  -3.7282   2.6672   2.8052
 AN6  N1    N  N     0  -0.473   3.9240  -2.5536   1.1857
 AN6  C2    C  CR16  0   0.046   4.0406  -1.2526   1.4369
 AN6  C3    C  CH2   0  -0.283  -3.4124   2.9614   1.3478
 AN6  N3    N  N     0  -0.458   3.3363  -0.2528   0.9349
 AN6  C4    C  CR56  0   0.490   2.4148  -0.6814   0.0771
 AN6  C5    C  CR56  0   0.013   2.1731  -1.9971  -0.2800
 AN6  C6    C  CR6   0   0.463   2.9903  -2.9702   0.3234
 AN6  N6    N  NH2   0  -0.815   2.8593  -4.2748   0.0791
 AN6  N7    N  N     0  -0.475   1.1460  -2.0717  -1.1861
 AN6  C8    C  CR15  0   0.119   0.7815  -0.8370  -1.3664
 AN6  N9    N  NR5   0  -0.546   1.5142   0.0603  -0.6387
 AN6  C1'   C  CH1   0   0.220   1.3099   1.4816  -0.5080
 AN6  N10   N  NT    0  -0.413  -2.6655   1.9007   0.6950
 AN6  C2'   C  CH1   0  -0.061   0.9656   2.1916  -1.8147
 AN6  O2'   O  OH1   0  -0.654   2.1310   2.4526  -2.5372
 AN6  C3'   C  CH1   0  -0.031   0.2349   3.4265  -1.2832
 AN6  O3'   O  OH1   0  -0.670   1.1488   4.3731  -0.7893
 AN6  C4'   C  CH1   0   0.005  -0.5436   2.8393  -0.1115
 AN6  O4'   O  O2    0  -0.481   0.2364   1.7306   0.3566
 AN6  C5'   C  CH2   0  -0.306  -1.9493   2.3767  -0.4731
 AN6  O5'   O  OH1   0  -0.602  -1.6732  -2.8466  -1.3011
 AN6  CA'   C  CH1   0  -0.199  -3.1895  -1.8621   0.2215
 AN6  CB'   C  CH2   0  -0.444  -2.4787  -0.5196   0.4348
 AN6  CG'   C  CH2   0  -0.270  -3.4150   0.6793   0.4719
 AN6  HN'   H  HNH2  0   0.354  -4.5091  -3.0579   1.1994
 AN6  HN'A  H  HNH2  0   0.343  -3.4802  -2.2822   2.1827
 AN6  H1    H  HCH3  0   0.224  -4.4249   1.8378   2.9285
 AN6  H1A   H  HCH3  0   0.222  -2.8159   2.4264   3.3516
 AN6  H1B   H  HCH3  0   0.229  -4.1838   3.5405   3.2728
 AN6  H3    H  HCH2  0   0.196  -4.3391   3.2082   0.8038
 AN6  H3A   H  HCH2  0   0.228  -2.7990   3.8653   1.3161
 AN6  HN6   H  HNH2  0   0.410   2.2215  -4.6072  -0.6227
 AN6  HN6A  H  HNH2  0   0.405   3.5190  -4.9283   0.4650
 AN6  H8    H  HCR5  0   0.301  -0.0151  -0.5259  -2.0243
 AN6  H1'   H  HCH1  0   0.256   2.2464   1.8804  -0.1029
 AN6  H2'   H  HCH1  0   0.251   0.2550   1.5954  -2.4001
 AN6  HO2'  H  HOH1  0   0.470   1.8969   2.6298  -3.4537
 AN6  H3'   H  HCH1  0   0.249  -0.4304   3.8644  -2.0386
 AN6  HO3'  H  HOH1  0   0.449   1.8318   4.5056  -1.4571
 AN6  H4'   H  HCH1  0   0.249  -0.6111   3.5777   0.6943
 AN6  H5'   H  HCH2  0   0.236  -1.8874   1.5855  -1.2254
 AN6  H5'A  H  HCH2  0   0.230  -2.4785   3.2081  -0.9623
 AN6  HO5'  H  HOH1  0   0.476  -0.7952  -3.2581  -1.3812
 AN6  HA'   H  HCH1  0   0.261  -3.8108  -1.7913  -0.6771
 AN6  HB'   H  HCH2  0   0.233  -1.9117  -0.5529   1.3697
 AN6  HB'A  H  HCH2  0   0.236  -1.7460  -0.3793  -0.3606
 AN6  HG'   H  HCH2  0   0.238  -4.1240   0.5412   1.2875
 AN6  HG'A  H  HCH2  0   0.199  -4.0148   0.7164  -0.4530
 AN6  H2    H  HCR6  0   0.254   4.8163  -0.9824   2.1457

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 AN6  O'   C'    double    1.206  0.020  1.206
 AN6  C'   O5'   single    1.329  0.020  1.329
 AN6  C'   CA'   single    1.521  0.020  1.521
 AN6  N'   CA'   single    1.443  0.020  1.443
 AN6  N'   HN'   single    0.890  0.020  1.040
 AN6  N'   HN'A  single    0.890  0.020  1.040
 AN6  C1   C3    single    1.520  0.020  1.520
 AN6  C1   H1    single    0.970  0.020  1.090
 AN6  C1   H1A   single    0.970  0.020  1.090
 AN6  C1   H1B   single    0.970  0.020  1.090
 AN6  C6   N1    aromatic  1.337  0.020  1.337
 AN6  N1   C2    aromatic  1.330  0.020  1.330
 AN6  N3   C2    aromatic  1.322  0.020  1.322
 AN6  C2   H2    single    0.930  0.020  1.080
 AN6  C3   N10   single    1.452  0.020  1.452
 AN6  C3   H3    single    0.970  0.020  1.090
 AN6  C3   H3A   single    0.970  0.020  1.090
 AN6  C4   N3    aromatic  1.330  0.020  1.330
 AN6  N9   C4    aromatic  1.369  0.020  1.369
 AN6  C5   C4    aromatic  1.385  0.020  1.385
 AN6  N7   C5    aromatic  1.372  0.020  1.372
 AN6  C5   C6    aromatic  1.407  0.020  1.407
 AN6  N6   C6    single    1.334  0.020  1.334
 AN6  N6   HN6   single    0.860  0.020  1.020
 AN6  N6   HN6A  single    0.860  0.020  1.020
 AN6  C8   N7    aromatic  1.300  0.020  1.300
 AN6  C8   N9    aromatic  1.368  0.020  1.368
 AN6  C8   H8    single    0.930  0.020  1.080
 AN6  N9   C1'   single    1.442  0.020  1.442
 AN6  O4'  C1'   single    1.401  0.020  1.401
 AN6  C2'  C1'   single    1.526  0.020  1.526
 AN6  C1'  H1'   single    0.970  0.020  1.090
 AN6  CG'  N10   single    1.450  0.020  1.450
 AN6  N10  C5'   single    1.450  0.020  1.450
 AN6  C3'  C2'   single    1.530  0.020  1.530
 AN6  C2'  O2'   single    1.396  0.020  1.396
 AN6  C2'  H2'   single    0.970  0.020  1.090
 AN6  O2'  HO2'  single    0.850  0.020  0.980
 AN6  C4'  C3'   single    1.524  0.020  1.524
 AN6  C3'  O3'   single    1.405  0.020  1.405
 AN6  C3'  H3'   single    0.970  0.020  1.090
 AN6  O3'  HO3'  single    0.850  0.020  0.980
 AN6  C5'  C4'   single    1.523  0.020  1.523
 AN6  O4'  C4'   single    1.434  0.020  1.434
 AN6  C4'  H4'   single    0.970  0.020  1.090
 AN6  C5'  H5'   single    0.970  0.020  1.090
 AN6  C5'  H5'A  single    0.970  0.020  1.090
 AN6  O5'  HO5'  single    0.850  0.020  0.980
 AN6  CB'  CA'   single    1.534  0.020  1.534
 AN6  CA'  HA'   single    0.970  0.020  1.090
 AN6  CG'  CB'   single    1.522  0.020  1.522
 AN6  CB'  HB'   single    0.970  0.020  1.090
 AN6  CB'  HB'A  single    0.970  0.020  1.090
 AN6  CG'  HG'   single    0.970  0.020  1.090
 AN6  CG'  HG'A  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 AN6  CA'   C'   O5'  111.90  3.000
 AN6  CA'   C'   O'   124.46  3.000
 AN6  O5'   C'   O'   123.55  3.000
 AN6  HN'A  N'   HN'  106.37  3.000
 AN6  HN'A  N'   CA'  109.99  3.000
 AN6  HN'   N'   CA'  110.47  3.000
 AN6  H1B   C1   H1A  108.15  3.000
 AN6  H1B   C1   H1   107.08  3.000
 AN6  H1A   C1   H1   108.06  3.000
 AN6  H1B   C1   C3   110.06  3.000
 AN6  H1A   C1   C3   110.45  3.000
 AN6  H1    C1   C3   112.86  3.000
 AN6  C6    N1   C2   119.18  3.000
 AN6  H2    C2   N3   116.15  3.000
 AN6  H2    C2   N1   115.44  3.000
 AN6  N3    C2   N1   128.41  3.000
 AN6  H3A   C3   H3   105.79  3.000
 AN6  H3A   C3   N10  107.60  3.000
 AN6  H3    C3   N10  111.96  3.000
 AN6  H3A   C3   C1   107.73  3.000
 AN6  H3    C3   C1   109.99  3.000
 AN6  N10   C3   C1   113.36  3.000
 AN6  C4    N3   C2   111.74  3.000
 AN6  N9    C4   C5   105.38  3.000
 AN6  C5    C4   N3   126.41  3.000
 AN6  N9    C4   N3   128.21  3.000
 AN6  N7    C5   C6   132.90  3.000
 AN6  C6    C5   C4   116.44  3.000
 AN6  N7    C5   C4   110.65  3.000
 AN6  N6    C6   C5   122.75  3.000
 AN6  N6    C6   N1   119.43  3.000
 AN6  C5    C6   N1   117.81  3.000
 AN6  HN6A  N6   HN6  118.00  3.000
 AN6  HN6A  N6   C6   120.06  3.000
 AN6  HN6   N6   C6   120.92  3.000
 AN6  C8    N7   C5   104.48  3.000
 AN6  H8    C8   N9   122.05  3.000
 AN6  H8    C8   N7   124.44  3.000
 AN6  N9    C8   N7   113.52  3.000
 AN6  C1'   N9   C8   128.23  3.000
 AN6  C1'   N9   C4   125.45  3.000
 AN6  C8    N9   C4   105.97  3.000
 AN6  H1'   C1'  O4'  111.23  3.000
 AN6  H1'   C1'  C2'  109.88  3.000
 AN6  O4'   C1'  C2'  105.83  3.000
 AN6  H1'   C1'  N9   105.74  3.000
 AN6  C2'   C1'  N9   114.38  3.000
 AN6  O4'   C1'  N9   109.87  3.000
 AN6  CG'   N10  C5'  114.06  3.000
 AN6  C5'   N10  C3   112.11  3.000
 AN6  CG'   N10  C3   114.74  3.000
 AN6  H2'   C2'  C3'  108.35  3.000
 AN6  H2'   C2'  O2'  111.49  3.000
 AN6  C3'   C2'  O2'  115.31  3.000
 AN6  H2'   C2'  C1'  110.50  3.000
 AN6  O2'   C2'  C1'  109.98  3.000
 AN6  C3'   C2'  C1'  100.70  3.000
 AN6  HO2'  O2'  C2'  108.91  3.000
 AN6  H3'   C3'  C4'  111.90  3.000
 AN6  H3'   C3'  O3'  111.55  3.000
 AN6  C4'   C3'  O3'  108.75  3.000
 AN6  H3'   C3'  C2'  111.86  3.000
 AN6  O3'   C3'  C2'  110.81  3.000
 AN6  C4'   C3'  C2'  101.54  3.000
 AN6  HO3'  O3'  C3'  108.04  3.000
 AN6  H4'   C4'  C5'  108.82  3.000
 AN6  H4'   C4'  O4'  108.34  3.000
 AN6  C5'   C4'  O4'  110.16  3.000
 AN6  H4'   C4'  C3'  109.71  3.000
 AN6  O4'   C4'  C3'  105.72  3.000
 AN6  C5'   C4'  C3'  113.94  3.000
 AN6  C4'   O4'  C1'  110.66  3.000
 AN6  H5'A  C5'  H5'  105.55  3.000
 AN6  H5'A  C5'  C4'  108.65  3.000
 AN6  H5'   C5'  C4'  109.31  3.000
 AN6  H5'A  C5'  N10  111.63  3.000
 AN6  H5'   C5'  N10  110.16  3.000
 AN6  C4'   C5'  N10  111.35  3.000
 AN6  HO5'  O5'  C'   110.48  3.000
 AN6  HA'   CA'  CB'  108.69  3.000
 AN6  HA'   CA'  N'   108.60  3.000
 AN6  CB'   CA'  N'   110.70  3.000
 AN6  HA'   CA'  C'   108.28  3.000
 AN6  CB'   CA'  C'   105.83  3.000
 AN6  N'    CA'  C'   114.57  3.000
 AN6  HB'A  CB'  HB'  106.21  3.000
 AN6  HB'A  CB'  CG'  109.26  3.000
 AN6  HB'   CB'  CG'  108.78  3.000
 AN6  HB'A  CB'  CA'  108.82  3.000
 AN6  HB'   CB'  CA'  109.41  3.000
 AN6  CG'   CB'  CA'  114.07  3.000
 AN6  HG'A  CG'  HG'  106.15  3.000
 AN6  HG'A  CG'  CB'  109.92  3.000
 AN6  HG'   CG'  CB'  108.59  3.000
 AN6  HG'A  CG'  N10  112.43  3.000
 AN6  HG'   CG'  N10  109.14  3.000
 AN6  CB'   CG'  N10  110.45  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 AN6  CONST_01  C4    C5   C6   N1      0.00   0.0  0
 AN6  CONST_02  N7    C5   C6   N1    180.00   0.0  0
 AN6  CONST_03  C4    N3   C2   N1      0.00   0.0  0
 AN6  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 AN6  CONST_05  N9    C4   N3   C2    180.00   0.0  0
 AN6  CONST_06  C5    C4   N3   C2      0.00   0.0  0
 AN6  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 AN6  CONST_08  C8    N9   C4   N3    180.00   0.0  0
 AN6  CONST_09  N7    C5   C4   N3    180.00   0.0  0
 AN6  CONST_10  C6    C5   C4   N3      0.00   0.0  0
 AN6  CONST_11  N7    C8   N9   C4      0.00   0.0  0
 AN6  CONST_12  C8    N7   C5   C4      0.00   0.0  0
 AN6  CONST_13  C8    N9   C4   C5      0.00   0.0  0
 AN6  CONST_14  N9    C8   N7   C5      0.00   0.0  0
 AN6  CONST_15  N9    C4   C5   C6    180.00   0.0  0
 AN6  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 AN6  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 AN6  CONST_18  C1'   N9   C4   N3      0.00   0.0  0
 AN6  CONST_19  C1'   N9   C4   C5    180.00   0.0  0
 AN6  CONST_20  C1'   N9   C8   N7    180.00   0.0  0
 AN6  CONST_21  N6    C6   N1   C2    180.00   0.0  0
 AN6  CONST_22  N6    C6   C5   C4    180.00   0.0  0
 AN6  CONST_23  N7    C5   C6   N6      0.00   0.0  0
 AN6  CONST_24  H2    C2   N3   C4    180.00   0.0  0
 AN6  CONST_25  H8    C8   N9   C4    180.00   0.0  0
 AN6  CONST_26  HN6   N6   C6   N1    180.00   0.0  0
 AN6  CONST_27  HN6A  N6   C6   N1      0.00   0.0  0
 AN6  Var_01    C4'   C5'  N10  C3     90.60  30.0  3
 AN6  Var_02    CB'   CG'  N10  C3   -152.77  30.0  3
 AN6  Var_03    CA'   CB'  CG'  N10   179.21  30.0  3
 AN6  Var_04    H1    C1   C3   N10   -67.03  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 AN6  chir_01  C1'  N9   O4'  C2'  positiv
 AN6  chir_02  C2'  O2'  C1'  C3'  negativ
 AN6  chir_03  C3'  O3'  C4'  C2'  positiv
 AN6  chir_04  C4'  O4'  C3'  C5'  negativ
 AN6  chir_05  CA'  N'   C'   CB'  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 AN6  plan-1  N1    0.020
 AN6  plan-1  C2    0.020
 AN6  plan-1  N3    0.020
 AN6  plan-1  C4    0.020
 AN6  plan-1  C5    0.020
 AN6  plan-1  C6    0.020
 AN6  plan-1  N6    0.020
 AN6  plan-1  N7    0.020
 AN6  plan-1  C8    0.020
 AN6  plan-1  N9    0.020
 AN6  plan-1  C1'   0.020
 AN6  plan-1  H8    0.020
 AN6  plan-1  H2    0.020
 AN6  plan-2  C6    0.020
 AN6  plan-2  N6    0.020
 AN6  plan-2  HN6   0.020
 AN6  plan-2  HN6A  0.020
 AN6  plan-3  C'    0.020
 AN6  plan-3  O'    0.020
 AN6  plan-3  O5'   0.020
 AN6  plan-3  CA'   0.020
 AN6  plan-3  HO5'  0.020

