# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 16:15:07 2022
#   Inital geometry file: a 65 line input string
#   Ligand name: (1S,6S,7R,8R,8aR)-6-aminooctahydroindolizine-1,7,8-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CN2CC[C@H](O)[C@@H]2[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
 X05  X05  (1S,6S,7R,8R,8aR)-6-aminooctahydroindolizine-1,7,8-triol  ligand  29  13  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X05
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
 X05  OAD   O  OH1   0  -0.680   0.1350   2.3418   0.6628
 X05  CAK   C  CH1   0   0.057   0.3079   1.1262  -0.0255
 X05  CAL   C  CH1   0  -0.093  -0.7727   0.1661   0.4361
 X05  CAI   C  CH1   0   0.055  -2.2180   0.5168   0.1040
 X05  OAB   O  OH1   0  -0.676  -2.2747   1.0228  -1.2106
 X05  CAE   C  CH2   0  -0.519  -2.9126  -0.8509   0.2477
 X05  CAF   C  CH2   0  -0.263  -1.7846  -1.8943   0.1579
 X05  NAM   N  NT    0  -0.444  -0.6104  -1.1235  -0.2045
 X05  CAG   C  CH2   0  -0.281   0.6547  -1.7515   0.0765
 X05  CAH   C  CH1   0  -0.103   1.7943  -0.8612  -0.4074
 X05  NAA   N  NH2   0  -0.812   3.0690  -1.4700  -0.0603
 X05  CAJ   C  CH1   0   0.020   1.6728   0.5059   0.2611
 X05  OAC   O  OH1   0  -0.682   2.6571   1.4131  -0.2002
 X05  HAD   H  HOH1  0   0.446   0.8658   2.9206   0.4210
 X05  HAK   H  HCH1  0   0.201   0.2171   1.2695  -1.1116
 X05  HAL   H  HCH1  0   0.207  -0.6991   0.0759   1.5391
 X05  HAJ   H  HCH1  0   0.203   1.7660   0.3608   1.3482
 X05  HAI   H  HCH1  0   0.215  -2.6228   1.2425   0.8179
 X05  HAB   H  HOH1  0   0.449  -3.1990   1.1667  -1.4342
 X05  HAE1  H  HCH2  0   0.242  -3.4234  -0.9191   1.2082
 X05  HAE2  H  HCH2  0   0.247  -3.6712  -0.9859  -0.5249
 X05  HAF1  H  HCH2  0   0.198  -1.6565  -2.3900   1.1329
 X05  HAF2  H  HCH2  0   0.231  -1.9763  -2.6776  -0.5785
 X05  HAG1  H  HCH2  0   0.189   0.7886  -1.9543   1.1554
 X05  HAG2  H  HCH2  0   0.239   0.6988  -2.7167  -0.4365
 X05  HAH   H  HCH1  0   0.203   1.6674  -0.7214  -1.4928
 X05  HAA1  H  HNH2  0   0.348   3.1352  -2.3792  -0.5018
 X05  HAA2  H  HNH2  0   0.344   3.8230  -0.9278  -0.4634
 X05  HAC   H  HOH1  0   0.458   3.4376   1.3348   0.3550

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
 X05  OAD  CAK   single  1.408  0.020  1.408
 X05  CAK  CAL   single  1.517  0.020  1.517
 X05  CAK  CAJ   single  1.526  0.020  1.526
 X05  CAL  CAI   single  1.524  0.020  1.524
 X05  CAL  NAM   single  1.449  0.020  1.449
 X05  CAI  OAB   single  1.410  0.020  1.410
 X05  CAI  CAE   single  1.541  0.020  1.541
 X05  CAE  CAF   single  1.539  0.020  1.539
 X05  CAF  NAM   single  1.451  0.020  1.451
 X05  NAM  CAG   single  1.440  0.020  1.440
 X05  CAG  CAH   single  1.525  0.020  1.525
 X05  CAH  NAA   single  1.455  0.020  1.455
 X05  CAH  CAJ   single  1.527  0.020  1.527
 X05  CAJ  OAC   single  1.416  0.020  1.416
 X05  OAD  HAD   single  0.850  0.020  0.980
 X05  CAK  HAK   single  0.970  0.020  1.090
 X05  CAL  HAL   single  0.970  0.020  1.090
 X05  CAJ  HAJ   single  0.970  0.020  1.090
 X05  CAI  HAI   single  0.970  0.020  1.090
 X05  OAB  HAB   single  0.850  0.020  0.980
 X05  CAE  HAE1  single  0.970  0.020  1.090
 X05  CAE  HAE2  single  0.970  0.020  1.090
 X05  CAF  HAF1  single  0.970  0.020  1.090
 X05  CAF  HAF2  single  0.970  0.020  1.090
 X05  CAG  HAG1  single  0.970  0.020  1.090
 X05  CAG  HAG2  single  0.970  0.020  1.090
 X05  CAH  HAH   single  0.970  0.020  1.090
 X05  NAA  HAA1  single  0.890  0.020  1.040
 X05  NAA  HAA2  single  0.890  0.020  1.040
 X05  OAC  HAC   single  0.850  0.020  0.980

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
 X05  HAD   OAD  CAK   107.64  3.000
 X05  HAK   CAK  CAJ   108.20  3.000
 X05  HAK   CAK  CAL   108.92  3.000
 X05  CAJ   CAK  CAL   108.81  3.000
 X05  HAK   CAK  OAD   111.13  3.000
 X05  CAJ   CAK  OAD   111.65  3.000
 X05  CAL   CAK  OAD   108.07  3.000
 X05  HAL   CAL  NAM   111.09  3.000
 X05  HAL   CAL  CAI   107.36  3.000
 X05  NAM   CAL  CAI   102.40  3.000
 X05  HAL   CAL  CAK   107.86  3.000
 X05  NAM   CAL  CAK   110.42  3.000
 X05  CAI   CAL  CAK   117.61  3.000
 X05  HAI   CAI  CAE   111.14  3.000
 X05  HAI   CAI  OAB   110.80  3.000
 X05  CAE   CAI  OAB   112.80  3.000
 X05  HAI   CAI  CAL   111.15  3.000
 X05  CAE   CAI  CAL   101.71  3.000
 X05  OAB   CAI  CAL   108.90  3.000
 X05  HAB   OAB  CAI   108.01  3.000
 X05  HAE2  CAE  HAE1  106.88  3.000
 X05  HAE2  CAE  CAF   112.60  3.000
 X05  HAE1  CAE  CAF   110.63  3.000
 X05  HAE2  CAE  CAI   110.93  3.000
 X05  HAE1  CAE  CAI   110.43  3.000
 X05  CAF   CAE  CAI   105.42  3.000
 X05  HAF2  CAF  HAF1  107.13  3.000
 X05  HAF2  CAF  NAM   110.78  3.000
 X05  HAF1  CAF  NAM   111.48  3.000
 X05  HAF2  CAF  CAE   113.39  3.000
 X05  HAF1  CAF  CAE   109.80  3.000
 X05  NAM   CAF  CAE   104.33  3.000
 X05  CAG   NAM  CAF   115.51  3.000
 X05  CAG   NAM  CAL   113.59  3.000
 X05  CAF   NAM  CAL   105.77  3.000
 X05  HAG2  CAG  HAG1  106.90  3.000
 X05  HAG2  CAG  CAH   109.65  3.000
 X05  HAG1  CAG  CAH   109.04  3.000
 X05  HAG2  CAG  NAM   109.18  3.000
 X05  HAG1  CAG  NAM   112.13  3.000
 X05  CAH   CAG  NAM   109.88  3.000
 X05  HAH   CAH  CAJ   107.98  3.000
 X05  HAH   CAH  NAA   112.90  3.000
 X05  CAJ   CAH  NAA   109.88  3.000
 X05  HAH   CAH  CAG   107.50  3.000
 X05  CAJ   CAH  CAG   108.93  3.000
 X05  NAA   CAH  CAG   109.56  3.000
 X05  HAA2  NAA  HAA1  104.99  3.000
 X05  HAA2  NAA  CAH   109.48  3.000
 X05  HAA1  NAA  CAH   109.20  3.000
 X05  HAJ   CAJ  OAC   110.33  3.000
 X05  HAJ   CAJ  CAH   107.92  3.000
 X05  OAC   CAJ  CAH   112.07  3.000
 X05  HAJ   CAJ  CAK   108.35  3.000
 X05  OAC   CAJ  CAK   107.46  3.000
 X05  CAH   CAJ  CAK   110.66  3.000
 X05  HAC   OAC  CAJ   108.92  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
 X05  Var_01  CAE  CAF  NAM  CAL   33.39  30.0  1
 X05  Var_02  CAH  CAG  NAM  CAL  -59.94  30.0  1
 X05  Var_03  NAM  CAF  CAE  CAI   -7.59  30.0  1

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
 X05  chir_01  CAK  OAD  CAL  CAJ  positiv
 X05  chir_02  CAL  NAM  CAK  CAI  negativ
 X05  chir_03  CAI  OAB  CAL  CAE  positiv
 X05  chir_04  CAH  NAA  CAG  CAJ  negativ
 X05  chir_05  CAJ  OAC  CAH  CAK  positiv

