# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 22:17:23 2022
#   Inital geometry file: a 37 line input string
#   Ligand name: (3S)-pyrazolidin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CCNN1
#
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
 XHJ  XHJ  '(3S)-pyrazolidin-3-amine '  ligand  15  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_XHJ
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
 XHJ  N01   N  NH2   0  -0.815  -30.7412  24.7052  -6.6480
 XHJ  C02   C  CH1   0   0.073  -31.0579  23.2970  -6.6540
 XHJ  C03   C  CH2   0  -0.511  -32.3230  22.9732  -7.4847
 XHJ  C04   C  CH2   0  -0.286  -33.1324  22.0659  -6.5500
 XHJ  N05   N  NH1   0  -0.500  -32.1345  21.6852  -5.5480
 XHJ  N06   N  NH1   0  -0.467  -31.3730  22.8575  -5.2959
 XHJ  H012  H  HNH2  0   0.350  -29.7997  24.8495  -6.3050
 XHJ  H011  H  HNH2  0   0.354  -30.7521  25.0614  -7.5942
 XHJ  H021  H  HCH1  0   0.214  -30.2308  22.6687  -7.0093
 XHJ  H031  H  HCH2  0   0.237  -32.8717  23.8850  -7.7267
 XHJ  H032  H  HCH2  0   0.241  -32.0664  22.4801  -8.4222
 XHJ  H041  H  HCH2  0   0.206  -33.9744  22.6199  -6.1152
 XHJ  H042  H  HCH2  0   0.229  -33.5349  21.1830  -7.0476
 XHJ  H051  H  HNH1  0   0.356  -32.5502  21.3708  -4.6810
 XHJ  H061  H  HNH1  0   0.319  -31.9829  23.5853  -4.9123

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
 XHJ  C02  N01   single  1.443  0.020  1.443
 XHJ  C03  C02   single  1.548  0.020  1.548
 XHJ  C04  C03   single  1.534  0.020  1.534
 XHJ  N05  C04   single  1.465  0.020  1.465
 XHJ  N06  N05   single  1.420  0.020  1.420
 XHJ  C02  N06   single  1.462  0.020  1.462
 XHJ  N01  H012  single  0.890  0.020  1.040
 XHJ  N01  H011  single  0.890  0.020  1.040
 XHJ  C02  H021  single  0.970  0.020  1.090
 XHJ  C03  H031  single  0.970  0.020  1.090
 XHJ  C03  H032  single  0.970  0.020  1.090
 XHJ  C04  H041  single  0.970  0.020  1.090
 XHJ  C04  H042  single  0.970  0.020  1.090
 XHJ  N05  H051  single  0.890  0.020  1.040
 XHJ  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
 XHJ  H011  N01  H012  106.07  3.000
 XHJ  H011  N01  C02   109.72  3.000
 XHJ  H012  N01  C02   110.16  3.000
 XHJ  H021  C02  N06   106.92  3.000
 XHJ  H021  C02  C03   108.81  3.000
 XHJ  N06   C02  C03   105.04  3.000
 XHJ  H021  C02  N01   113.23  3.000
 XHJ  N06   C02  N01   109.68  3.000
 XHJ  C03   C02  N01   112.69  3.000
 XHJ  H032  C03  H031  107.80  3.000
 XHJ  H032  C03  C04   112.38  3.000
 XHJ  H031  C03  C04   111.35  3.000
 XHJ  H032  C03  C02   111.34  3.000
 XHJ  H031  C03  C02   110.80  3.000
 XHJ  C04   C03  C02   103.18  3.000
 XHJ  H042  C04  H041  107.83  3.000
 XHJ  H042  C04  N05   110.68  3.000
 XHJ  H041  C04  N05   112.51  3.000
 XHJ  H042  C04  C03   113.31  3.000
 XHJ  H041  C04  C03   110.35  3.000
 XHJ  N05   C04  C03   102.19  3.000
 XHJ  H051  N05  N06   108.95  3.000
 XHJ  H051  N05  C04   112.78  3.000
 XHJ  N06   N05  C04   105.79  3.000
 XHJ  H061  N06  N05   109.49  3.000
 XHJ  H061  N06  C02   105.23  3.000
 XHJ  N05   N06  C02   101.47  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
 XHJ  Var_01  N05  C04  C03  C02  -15.30  30.0  1
 XHJ  Var_02  C04  N05  N06  C02  -48.81  30.0  1
 XHJ  Var_03  N06  N05  C04  C03   40.00  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
 XHJ  chir_01  C02  N01  C03  N06  positiv

