# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 21:44:59 2022
#   Inital geometry file: a 35 line input string
#   Ligand name: (3S)-1,2,4-triazolidin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1NCNN1
#
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
 XGJ  XGJ  (3S)-1,2,4-triazolidin-3-amine  ligand  14  6  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_XGJ
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
 XGJ  N01   N  NH2   0  -0.816  -11.4159  29.5043  -15.0165
 XGJ  C02   C  CH1   0   0.166  -11.3273  30.8125  -15.6020
 XGJ  N03   N  NH1   0  -0.623  -11.0062  31.8103  -14.5787
 XGJ  C04   C  CH2   0  -0.142  -11.7070  33.0190  -15.0041
 XGJ  N05   N  NH1   0  -0.521  -12.3937  32.6173  -16.2493
 XGJ  N06   N  NH1   0  -0.466  -12.6061  31.2148  -16.1602
 XGJ  H011  H  HNH2  0   0.360  -11.5519  28.8179  -15.7483
 XGJ  H1    H  HNH2  0   0.360  -10.5317  29.2732  -14.5803
 XGJ  H021  H  HCH1  0   0.216  -10.5867  30.8930  -16.4093
 XGJ  H2    H  HNH1  0   0.346  -11.4198  31.4827  -13.7128
 XGJ  H041  H  HCH2  0   0.214  -12.3879  33.3599  -14.2160
 XGJ  H042  H  HCH2  0   0.215  -11.0200  33.8378  -15.2309
 XGJ  H051  H  HNH1  0   0.364  -13.2815  33.0851  -16.3726
 XGJ  H061  H  HNH1  0   0.328  -13.3030  31.0111  -15.4386

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
 XGJ  C02  N01   single  1.436  0.020  1.436
 XGJ  N03  C02   single  1.465  0.020  1.465
 XGJ  C04  N03   single  1.461  0.020  1.461
 XGJ  N05  C04   single  1.478  0.020  1.478
 XGJ  N06  N05   single  1.421  0.020  1.421
 XGJ  C02  N06   single  1.452  0.020  1.452
 XGJ  N01  H011  single  0.890  0.020  1.040
 XGJ  N01  H1    single  0.890  0.020  1.040
 XGJ  C02  H021  single  0.970  0.020  1.090
 XGJ  N03  H2    single  0.890  0.020  1.040
 XGJ  C04  H041  single  0.970  0.020  1.090
 XGJ  C04  H042  single  0.970  0.020  1.090
 XGJ  N05  H051  single  0.890  0.020  1.040
 XGJ  N06  H061  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
 XGJ  H1    N01  H011  105.89  3.000
 XGJ  H1    N01  C02   109.25  3.000
 XGJ  H011  N01  C02   109.34  3.000
 XGJ  H021  C02  N06   106.91  3.000
 XGJ  H021  C02  N03   108.40  3.000
 XGJ  N06   C02  N03   105.84  3.000
 XGJ  H021  C02  N01   114.08  3.000
 XGJ  N06   C02  N01   110.78  3.000
 XGJ  N03   C02  N01   110.44  3.000
 XGJ  H2    N03  C04   108.69  3.000
 XGJ  H2    N03  C02   106.68  3.000
 XGJ  C04   N03  C02   104.77  3.000
 XGJ  H042  C04  H041  107.87  3.000
 XGJ  H042  C04  N05   108.73  3.000
 XGJ  H041  C04  N05   113.70  3.000
 XGJ  H042  C04  N03   112.27  3.000
 XGJ  H041  C04  N03   110.24  3.000
 XGJ  N05   C04  N03   104.09  3.000
 XGJ  H051  N05  N06   109.45  3.000
 XGJ  H051  N05  C04   112.64  3.000
 XGJ  N06   N05  C04   106.55  3.000
 XGJ  H061  N06  N05   110.02  3.000
 XGJ  H061  N06  C02   105.87  3.000
 XGJ  N05   N06  C02    99.55  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
 XGJ  Var_01  N05  C04  N03  C02    0.38  30.0  1
 XGJ  Var_02  C04  N05  N06  C02  -41.76  30.0  1
 XGJ  Var_03  N06  N05  C04  N03   26.43  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
 XGJ  chir_01  C02  N01  N03  N06  positiv

