# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 14:34:46 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (1R,2R,3R,7S,7aR)-3-(aminomethyl)hexahydro-1H-pyrrolizine-1,2,7-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H]1[C@@H](O)[C@H](O)[C@H]2[C@@H](O)CCN12
#
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
 X09  X09  (1R,2R,3R,7S,7aR)-3-(aminomethyl)hexahydro-1H-pyrrolizine-1,2,7-triol  ligand  29  13  .  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_X09
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
 X09  OAC   O  OH1   0  -0.671  -1.2792   2.5061   0.6169
 X09  CAI   C  CR15  0   0.016  -0.7518   1.5012  -0.2121
 X09  CAJ   C  CR15  0   0.004   0.7713   1.3835  -0.1839
 X09  OAD   O  OH1   0  -0.676   1.4617   2.3072  -0.9914
 X09  CAL   C  CR15  0  -0.080   0.9964  -0.0356  -0.6884
 X09  CAH   C  CH1   0   0.019   2.1140  -0.8711  -0.0621
 X09  OAB   O  OH1   0  -0.671   2.3035  -0.4791   1.2796
 X09  CAF   C  CH2   0  -0.512   1.5142  -2.2720  -0.1567
 X09  CAG   C  CH2   0  -0.240   0.0506  -2.0407   0.2058
 X09  NAM   N  NR5   0  -0.455  -0.2553  -0.7593  -0.4099
 X09  CAK   C  CR15  0  -0.075  -1.1954   0.1191   0.2582
 X09  CAE   C  CH2   0  -0.261  -2.6485  -0.1732  -0.0722
 X09  NAA   N  NH2   0  -0.791  -3.0715  -1.4628   0.4527
 X09  HAC   H  HOH1  0   0.454  -1.2514   3.3425   0.1444
 X09  HAI   H  HCR5  0   0.206  -1.0737   1.6410  -1.2557
 X09  HAJ   H  HCR5  0   0.216   1.0856   1.4707   0.8636
 X09  HAK   H  HCR5  0   0.193  -1.0747   0.0721   1.3578
 X09  HAD   H  HOH1  0   0.451   1.4656   3.1582  -0.5439
 X09  HAL   H  HCR5  0   0.229   1.1792   0.0045  -1.7710
 X09  HAH   H  HCH1  0   0.219   3.0449  -0.7794  -0.6348
 X09  HAB   H  HOH1  0   0.451   2.9133  -1.1013   1.6883
 X09  HAF1  H  HCH2  0   0.235   1.6000  -2.6356  -1.1840
 X09  HAF2  H  HCH2  0   0.247   2.0114  -2.9985   0.4892
 X09  HAG1  H  HCH2  0   0.221  -0.5980  -2.8357  -0.1641
 X09  HAG2  H  HCH2  0   0.189  -0.0777  -2.0052   1.2968
 X09  HAE1  H  HCH2  0   0.193  -3.2568   0.6666   0.2929
 X09  HAE2  H  HCH2  0   0.205  -2.7532  -0.1904  -1.1607
 X09  HAA1  H  HNH2  0   0.335  -3.0238  -1.4424   1.4644
 X09  HAA2  H  HNH2  0   0.347  -4.0490  -1.6066   0.2324

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
 X09  OAC  CAI   single  1.405  0.020  1.405
 X09  CAI  CAJ   single  1.528  0.020  1.528
 X09  CAI  CAK   single  1.526  0.020  1.526
 X09  CAJ  OAD   single  1.408  0.020  1.408
 X09  CAJ  CAL   single  1.523  0.020  1.523
 X09  CAL  CAH   single  1.530  0.020  1.530
 X09  CAL  NAM   single  1.472  0.020  1.472
 X09  CAH  OAB   single  1.411  0.020  1.411
 X09  CAH  CAF   single  1.527  0.020  1.527
 X09  CAF  CAG   single  1.525  0.020  1.525
 X09  CAG  NAM   single  1.454  0.020  1.454
 X09  NAM  CAK   single  1.450  0.020  1.450
 X09  CAK  CAE   single  1.519  0.020  1.519
 X09  CAE  NAA   single  1.455  0.020  1.455
 X09  OAC  HAC   single  0.850  0.020  0.980
 X09  CAI  HAI   single  0.970  0.020  1.090
 X09  CAJ  HAJ   single  0.970  0.020  1.090
 X09  CAK  HAK   single  0.970  0.020  1.090
 X09  OAD  HAD   single  0.850  0.020  0.980
 X09  CAL  HAL   single  0.970  0.020  1.090
 X09  CAH  HAH   single  0.970  0.020  1.090
 X09  OAB  HAB   single  0.850  0.020  0.980
 X09  CAF  HAF1  single  0.970  0.020  1.090
 X09  CAF  HAF2  single  0.970  0.020  1.090
 X09  CAG  HAG1  single  0.970  0.020  1.090
 X09  CAG  HAG2  single  0.970  0.020  1.090
 X09  CAE  HAE1  single  0.970  0.020  1.090
 X09  CAE  HAE2  single  0.970  0.020  1.090
 X09  NAA  HAA1  single  0.890  0.020  1.040
 X09  NAA  HAA2  single  0.890  0.020  1.040

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
 X09  HAC   OAC  CAI   108.75  3.000
 X09  HAI   CAI  CAK   108.79  3.000
 X09  HAI   CAI  CAJ   108.58  3.000
 X09  CAK   CAI  CAJ   102.38  3.000
 X09  HAI   CAI  OAC   111.01  3.000
 X09  CAK   CAI  OAC   110.90  3.000
 X09  CAJ   CAI  OAC   114.73  3.000
 X09  HAJ   CAJ  CAL   110.37  3.000
 X09  HAJ   CAJ  OAD   110.79  3.000
 X09  CAL   CAJ  OAD   110.42  3.000
 X09  HAJ   CAJ  CAI   107.28  3.000
 X09  CAL   CAJ  CAI   102.30  3.000
 X09  OAD   CAJ  CAI   115.33  3.000
 X09  HAD   OAD  CAJ   108.41  3.000
 X09  HAL   CAL  NAM   110.23  3.000
 X09  HAL   CAL  CAH   107.57  3.000
 X09  NAM   CAL  CAH   105.98  3.000
 X09  HAL   CAL  CAJ   108.48  3.000
 X09  NAM   CAL  CAJ   105.65  3.000
 X09  CAH   CAL  CAJ   118.77  3.000
 X09  HAH   CAH  CAF   112.20  3.000
 X09  HAH   CAH  OAB   111.07  3.000
 X09  CAF   CAH  OAB   111.51  3.000
 X09  HAH   CAH  CAL   111.14  3.000
 X09  CAF   CAH  CAL   100.88  3.000
 X09  OAB   CAH  CAL   109.63  3.000
 X09  HAB   OAB  CAH   108.03  3.000
 X09  HAF2  CAF  HAF1  107.39  3.000
 X09  HAF2  CAF  CAG   113.40  3.000
 X09  HAF1  CAF  CAG   110.43  3.000
 X09  HAF2  CAF  CAH   113.26  3.000
 X09  HAF1  CAF  CAH   109.43  3.000
 X09  CAG   CAF  CAH   102.89  3.000
 X09  HAG2  CAG  HAG1  106.91  3.000
 X09  HAG2  CAG  NAM   111.55  3.000
 X09  HAG1  CAG  NAM   111.94  3.000
 X09  HAG2  CAG  CAF   110.65  3.000
 X09  HAG1  CAG  CAF   112.30  3.000
 X09  NAM   CAG  CAF   103.58  3.000
 X09  CAK   NAM  CAG   118.37  3.000
 X09  CAK   NAM  CAL   109.91  3.000
 X09  CAG   NAM  CAL   109.53  3.000
 X09  HAK   CAK  CAE   108.19  3.000
 X09  HAK   CAK  NAM   111.18  3.000
 X09  CAE   CAK  NAM   113.80  3.000
 X09  HAK   CAK  CAI   108.23  3.000
 X09  CAE   CAK  CAI   112.68  3.000
 X09  NAM   CAK  CAI   102.61  3.000
 X09  HAE2  CAE  HAE1  106.82  3.000
 X09  HAE2  CAE  NAA   108.50  3.000
 X09  HAE1  CAE  NAA   113.35  3.000
 X09  HAE2  CAE  CAK   108.13  3.000
 X09  HAE1  CAE  CAK   108.07  3.000
 X09  NAA   CAE  CAK   111.74  3.000
 X09  HAA2  NAA  HAA1  105.40  3.000
 X09  HAA2  NAA  CAE   109.15  3.000
 X09  HAA1  NAA  CAE   109.19  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
 X09  Var_01  CAF   CAG  NAM  CAL  -19.31  30.0  1
 X09  Var_02  NAM   CAG  CAF  CAH   37.47  30.0  1
 X09  Var_03  HAA1  NAA  CAE  CAK   63.76  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
 X09  chir_01  CAI  OAC  CAJ  CAK  negativ
 X09  chir_02  CAJ  OAD  CAI  CAL  negativ
 X09  chir_03  CAL  NAM  CAH  CAJ  positiv
 X09  chir_04  CAH  OAB  CAL  CAF  positiv
 X09  chir_05  CAK  NAM  CAE  CAI  positiv

