# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 22:37:58 2022
#   Inital geometry file: a 43 line input string
#   Ligand name: (4S)-1-methylimidazolidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CN[C@H](N)C1
#
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
 XGY  XGY  (4S)-1-methylimidazolidin-4-amine  ligand  18  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_XGY
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
 XGY  C01   C  CH3   0  -0.518  -17.5957  22.3252   -7.5613
 XGY  N02   N  NT    0  -0.426  -16.6457  22.9315   -8.4586
 XGY  C03   C  CH2   0  -0.114  -16.1925  24.2468   -8.0441
 XGY  N04   N  NH1   0  -0.629  -14.9729  24.4867   -8.7955
 XGY  C05   C  CH1   0   0.049  -14.5475  23.2144   -9.3823
 XGY  N06   N  NH2   0  -0.792  -14.7445  23.2278  -10.8191
 XGY  C07   C  CH2   0  -0.317  -15.4039  22.2032   -8.6135
 XGY  H013  H  HCH3  0   0.235  -17.8905  21.3441   -7.9352
 XGY  H011  H  HCH3  0   0.191  -17.2029  22.1931   -6.5410
 XGY  H012  H  HCH3  0   0.232  -18.4959  22.9384   -7.4960
 XGY  H031  H  HCH2  0   0.227  -16.9486  25.0117   -8.2377
 XGY  H032  H  HCH2  0   0.177  -15.9822  24.2630   -6.9588
 XGY  H041  H  HNH1  0   0.347  -15.1164  25.1616   -9.5338
 XGY  H051  H  HCH1  0   0.220  -13.4835  23.0320   -9.2055
 XGY  H3    H  HNH2  0   0.345  -14.2768  22.4332  -11.2379
 XGY  H061  H  HNH2  0   0.337  -15.7321  23.1236  -11.0267
 XGY  H071  H  HCH2  0   0.240  -15.5401  21.2698   -9.1631
 XGY  H072  H  HCH2  0   0.196  -14.9402  21.9580   -7.6411

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
 XGY  N02  C01   single  1.441  0.020  1.441
 XGY  C03  N02   single  1.452  0.020  1.452
 XGY  N04  C03   single  1.452  0.020  1.452
 XGY  C05  N04   single  1.464  0.020  1.464
 XGY  N06  C05   single  1.450  0.020  1.450
 XGY  C07  C05   single  1.532  0.020  1.532
 XGY  N02  C07   single  1.448  0.020  1.448
 XGY  C01  H013  single  0.970  0.020  1.090
 XGY  C01  H011  single  0.970  0.020  1.090
 XGY  C01  H012  single  0.970  0.020  1.090
 XGY  C03  H031  single  0.970  0.020  1.090
 XGY  C03  H032  single  0.970  0.020  1.090
 XGY  N04  H041  single  0.890  0.020  1.040
 XGY  C05  H051  single  0.970  0.020  1.090
 XGY  N06  H3    single  0.890  0.020  1.040
 XGY  N06  H061  single  0.890  0.020  1.040
 XGY  C07  H071  single  0.970  0.020  1.090
 XGY  C07  H072  single  0.970  0.020  1.090

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
 XGY  H012  C01  H011  107.83  3.000
 XGY  H012  C01  H013  107.65  3.000
 XGY  H011  C01  H013  107.83  3.000
 XGY  H012  C01  N02   110.17  3.000
 XGY  H011  C01  N02   113.10  3.000
 XGY  H013  C01  N02   110.08  3.000
 XGY  C07   N02  C03   102.62  3.000
 XGY  C07   N02  C01   114.87  3.000
 XGY  C03   N02  C01   114.17  3.000
 XGY  H032  C03  H031  107.17  3.000
 XGY  H032  C03  N04   110.23  3.000
 XGY  H031  C03  N04   111.95  3.000
 XGY  H032  C03  N02   110.67  3.000
 XGY  H031  C03  N02   111.57  3.000
 XGY  N04   C03  N02   105.31  3.000
 XGY  H041  N04  C05   109.19  3.000
 XGY  H041  N04  C03   111.65  3.000
 XGY  C05   N04  C03   107.93  3.000
 XGY  H051  C05  C07   110.64  3.000
 XGY  H051  C05  N06   107.09  3.000
 XGY  C07   C05  N06   115.30  3.000
 XGY  H051  C05  N04   111.27  3.000
 XGY  C07   C05  N04   102.12  3.000
 XGY  N06   C05  N04   110.46  3.000
 XGY  H061  N06  H3    106.52  3.000
 XGY  H061  N06  C05   109.51  3.000
 XGY  H3    N06  C05   109.86  3.000
 XGY  H072  C07  H071  107.80  3.000
 XGY  H072  C07  C05   110.71  3.000
 XGY  H071  C07  C05   112.42  3.000
 XGY  H072  C07  N02   112.18  3.000
 XGY  H071  C07  N02   112.14  3.000
 XGY  C05   C07  N02   101.60  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
 XGY  Var_01  C05   N04  C03  N02  -13.50  30.0  1
 XGY  Var_02  C05   C07  N02  C03  -45.23  30.0  1
 XGY  Var_03  C07   N02  C03  N04   37.15  30.0  1
 XGY  Var_04  H013  C01  N02  C03  179.97  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
 XGY  chir_01  C05  N04  N06  C07  positiv

