# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 23:45:02 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (3S,4R,5R,6S)-azepane-3,4,5,6-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CNC[C@H](O)[C@@H](O)[C@@H]1O
#
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
 3RK  3RK  (3S,4R,5R,6S)-azepane-3,4,5,6-tetrol  ligand  24  11  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3RK
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
 3RK  OAA   O  OH1   0  -0.684   2.8757  -0.0044  -0.1937
 3RK  OAB   O  OH1   0  -0.683  -2.8599   0.0389   0.1881
 3RK  OAC   O  OH1   0  -0.679   1.2974  -2.0704   0.3464
 3RK  OAD   O  OH1   0  -0.679  -1.3191  -2.0364  -0.3242
 3RK  CAE   C  CH2   0  -0.354   1.0903   1.5823  -0.5752
 3RK  CAF   C  CH2   0  -0.320  -1.0857   1.6063   0.6263
 3RK  NAG   N  NH1   0  -0.603  -0.0022   2.3414  -0.0017
 3RK  CAH   C  CH1   0   0.001   1.5477   0.3271   0.1778
 3RK  CAI   C  CH1   0  -0.003  -1.5219   0.3638  -0.1495
 3RK  CAJ   C  CH1   0   0.038   0.7299  -0.9070  -0.2090
 3RK  CAK   C  CH1   0   0.039  -0.7257  -0.8895   0.2373
 3RK  HOAA  H  HOH1  0   0.460   3.4768   0.6212   0.2212
 3RK  HOAC  H  HOH1  0   0.445   2.2489  -2.0129   0.2020
 3RK  HOAD  H  HOH1  0   0.445  -2.2700  -1.9535  -0.1879
 3RK  HAE   H  HCH2  0   0.219   0.8517   1.2971  -1.6074
 3RK  HAEA  H  HCH2  0   0.252   1.9392   2.2653  -0.6491
 3RK  HAF   H  HCH2  0   0.206  -0.8648   1.3019   1.6607
 3RK  HAFA  H  HCH2  0   0.239  -1.9452   2.2804   0.6888
 3RK  HNAG  H  HNH1  0   0.357   0.3680   2.9996   0.6683
 3RK  HAH   H  HCH1  0   0.220   1.4836   0.4953   1.2631
 3RK  HAI   H  HCH1  0   0.224  -1.4364   0.5467  -1.2304
 3RK  HAJ   H  HCH1  0   0.198   0.7406  -0.9594  -1.3122
 3RK  HAK   H  HCH1  0   0.199  -0.7397  -0.9445   1.3400
 3RK  HOAB  H  HOH1  0   0.461  -3.4483   0.6667  -0.2417

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
 3RK  OAA  CAH   single  1.418  0.020  1.418
 3RK  OAA  HOAA  single  0.850  0.020  0.980
 3RK  CAI  OAB   single  1.418  0.020  1.418
 3RK  OAB  HOAB  single  0.850  0.020  0.980
 3RK  OAC  CAJ   single  1.409  0.020  1.409
 3RK  OAC  HOAC  single  0.850  0.020  0.980
 3RK  CAK  OAD   single  1.408  0.020  1.408
 3RK  OAD  HOAD  single  0.850  0.020  0.980
 3RK  CAH  CAE   single  1.534  0.020  1.534
 3RK  CAE  NAG   single  1.449  0.020  1.449
 3RK  CAE  HAE   single  0.970  0.020  1.090
 3RK  CAE  HAEA  single  0.970  0.020  1.090
 3RK  NAG  CAF   single  1.452  0.020  1.452
 3RK  CAF  CAI   single  1.528  0.020  1.528
 3RK  CAF  HAF   single  0.970  0.020  1.090
 3RK  CAF  HAFA  single  0.970  0.020  1.090
 3RK  NAG  HNAG  single  0.890  0.020  1.040
 3RK  CAH  CAJ   single  1.530  0.020  1.530
 3RK  CAH  HAH   single  0.970  0.020  1.090
 3RK  CAK  CAI   single  1.534  0.020  1.534
 3RK  CAI  HAI   single  0.970  0.020  1.090
 3RK  CAJ  CAK   single  1.523  0.020  1.523
 3RK  CAJ  HAJ   single  0.970  0.020  1.090
 3RK  CAK  HAK   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
 3RK  HOAA  OAA  CAH  108.68  3.000
 3RK  HOAB  OAB  CAI  108.75  3.000
 3RK  HOAC  OAC  CAJ  106.82  3.000
 3RK  HOAD  OAD  CAK  106.81  3.000
 3RK  HAEA  CAE  HAE  105.54  3.000
 3RK  HAEA  CAE  CAH  108.26  3.000
 3RK  HAE   CAE  CAH  108.30  3.000
 3RK  HAEA  CAE  NAG  106.57  3.000
 3RK  HAE   CAE  NAG  110.16  3.000
 3RK  CAH   CAE  NAG  117.35  3.000
 3RK  HAFA  CAF  HAF  105.92  3.000
 3RK  HAFA  CAF  CAI  107.79  3.000
 3RK  HAF   CAF  CAI  108.03  3.000
 3RK  HAFA  CAF  NAG  107.40  3.000
 3RK  HAF   CAF  NAG  113.37  3.000
 3RK  CAI   CAF  NAG  113.89  3.000
 3RK  HNAG  NAG  CAF  108.46  3.000
 3RK  HNAG  NAG  CAE  109.14  3.000
 3RK  CAF   NAG  CAE  117.94  3.000
 3RK  HAH   CAH  CAJ  109.97  3.000
 3RK  HAH   CAH  CAE  109.99  3.000
 3RK  CAJ   CAH  CAE  112.12  3.000
 3RK  HAH   CAH  OAA  110.41  3.000
 3RK  CAJ   CAH  OAA  104.23  3.000
 3RK  CAE   CAH  OAA  110.00  3.000
 3RK  HAI   CAI  CAK  110.08  3.000
 3RK  HAI   CAI  CAF  109.97  3.000
 3RK  CAK   CAI  CAF  112.83  3.000
 3RK  HAI   CAI  OAB  110.22  3.000
 3RK  CAK   CAI  OAB  104.04  3.000
 3RK  CAF   CAI  OAB  109.57  3.000
 3RK  HAJ   CAJ  CAK  107.61  3.000
 3RK  HAJ   CAJ  CAH  106.59  3.000
 3RK  CAK   CAJ  CAH  115.32  3.000
 3RK  HAJ   CAJ  OAC  110.53  3.000
 3RK  CAK   CAJ  OAC  106.21  3.000
 3RK  CAH   CAJ  OAC  110.56  3.000
 3RK  HAK   CAK  CAJ  107.71  3.000
 3RK  HAK   CAK  CAI  106.61  3.000
 3RK  CAJ   CAK  CAI  115.57  3.000
 3RK  HAK   CAK  OAD  110.63  3.000
 3RK  CAJ   CAK  OAD  106.06  3.000
 3RK  CAI   CAK  OAD  110.25  3.000

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
 3RK  chir_01  CAH  OAA  CAE  CAJ  negativ
 3RK  chir_02  CAI  OAB  CAF  CAK  negativ
 3RK  chir_03  CAJ  OAC  CAK  CAH  negativ
 3RK  chir_04  CAK  OAD  CAJ  CAI  negativ

