# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 22:37:08 2022
#   Inital geometry file: a 41 line input string
#   Ligand name: [(3R)-pyrazolidin-3-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[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
 XH4  XH4  '[(3R)-pyrazolidin-3-yl]methanol'  ligand  17  7  .  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_XH4
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
 XH4  O01   O  OH1   0  -0.665  -28.2547  17.8320  -18.5784
 XH4  C02   C  CH2   0  -0.166  -28.4087  17.5313  -17.2110
 XH4  C03   C  CH1   0  -0.107  -27.3458  18.2877  -16.4411
 XH4  C04   C  CH2   0  -0.488  -25.8902  17.8840  -16.7839
 XH4  C05   C  CH2   0  -0.289  -25.2436  17.7194  -15.4021
 XH4  N06   N  NH1   0  -0.493  -26.1905  18.4147  -14.5297
 XH4  N07   N  NH1   0  -0.472  -27.4853  18.0621  -15.0046
 XH4  H011  H  HOH1  0   0.454  -28.9170  17.3393  -19.0707
 XH4  H021  H  HCH2  0   0.207  -29.4009  17.8208  -16.8407
 XH4  H022  H  HCH2  0   0.190  -28.2944  16.4543  -17.0190
 XH4  H031  H  HCH1  0   0.237  -27.4774  19.3589  -16.6216
 XH4  H042  H  HCH2  0   0.236  -25.8495  16.9537  -17.3525
 XH4  H041  H  HCH2  0   0.239  -25.3958  18.6512  -17.3792
 XH4  H052  H  HCH2  0   0.205  -25.1452  16.6549  -15.1511
 XH4  H051  H  HCH2  0   0.230  -24.2535  18.1712  -15.3328
 XH4  H061  H  HNH1  0   0.355  -26.1114  18.1253  -13.5631
 XH4  H071  H  HNH1  0   0.327  -27.6180  17.0554  -14.8739

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
 XH4  C02  O01   single  1.409  0.020  1.409
 XH4  C03  C02   single  1.515  0.020  1.515
 XH4  C04  C03   single  1.549  0.020  1.549
 XH4  C05  C04   single  1.534  0.020  1.534
 XH4  N06  C05   single  1.463  0.020  1.463
 XH4  N07  N06   single  1.424  0.020  1.424
 XH4  C03  N07   single  1.461  0.020  1.461
 XH4  O01  H011  single  0.850  0.020  0.980
 XH4  C02  H021  single  0.970  0.020  1.090
 XH4  C02  H022  single  0.970  0.020  1.090
 XH4  C03  H031  single  0.970  0.020  1.090
 XH4  C04  H042  single  0.970  0.020  1.090
 XH4  C04  H041  single  0.970  0.020  1.090
 XH4  C05  H052  single  0.970  0.020  1.090
 XH4  C05  H051  single  0.970  0.020  1.090
 XH4  N06  H061  single  0.890  0.020  1.040
 XH4  N07  H071  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
 XH4  H011  O01  C02   108.21  3.000
 XH4  H022  C02  H021  107.05  3.000
 XH4  H022  C02  C03   109.10  3.000
 XH4  H021  C02  C03   109.33  3.000
 XH4  H022  C02  O01   111.53  3.000
 XH4  H021  C02  O01   111.71  3.000
 XH4  C03   C02  O01   108.07  3.000
 XH4  H031  C03  N07   107.57  3.000
 XH4  H031  C03  C04   109.37  3.000
 XH4  N07   C03  C04   105.49  3.000
 XH4  H031  C03  C02   108.70  3.000
 XH4  N07   C03  C02   110.84  3.000
 XH4  C04   C03  C02   114.63  3.000
 XH4  H041  C04  H042  107.38  3.000
 XH4  H041  C04  C05   112.11  3.000
 XH4  H042  C04  C05   111.23  3.000
 XH4  H041  C04  C03   111.33  3.000
 XH4  H042  C04  C03   111.88  3.000
 XH4  C05   C04  C03   102.98  3.000
 XH4  H051  C05  H052  107.80  3.000
 XH4  H051  C05  N06   110.66  3.000
 XH4  H052  C05  N06   112.48  3.000
 XH4  H051  C05  C04   113.29  3.000
 XH4  H052  C05  C04   110.34  3.000
 XH4  N06   C05  C04   102.31  3.000
 XH4  H061  N06  N07   108.59  3.000
 XH4  H061  N06  C05   112.52  3.000
 XH4  N07   N06  C05   105.78  3.000
 XH4  H071  N07  N06   108.59  3.000
 XH4  H071  N07  C03   106.84  3.000
 XH4  N06   N07  C03   101.71  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
 XH4  Var_01  N06  C05  C04  C03  -16.71  30.0  1
 XH4  Var_02  C05  N06  N07  C03  -48.05  30.0  1
 XH4  Var_03  N07  N06  C05  C04   40.48  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
 XH4  chir_01  C03  C02  C04  N07  positiv

