# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 22:41:55 2022
#   Inital geometry file: a 43 line input string
#   Ligand name: 1-[(2R)-oxolan-2-yl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H]1CCCO1
#
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
 XHG  XHG  1-[(2R)-oxolan-2-yl]methanamine  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 PERFECT
;

data_comp_XHG
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
 XHG  N01   N  NH2   0  -0.797  -48.6073  -5.5246  -3.3286
 XHG  C02   C  CH2   0  -0.287  -49.3830  -5.0760  -4.4736
 XHG  C03   C  CR15  0   0.040  -49.3987  -3.5566  -4.5850
 XHG  C04   C  CH2   0  -0.497  -50.2741  -3.0726  -5.7418
 XHG  C05   C  CH2   0  -0.502  -51.6236  -2.8646  -5.0626
 XHG  C06   C  CH2   0  -0.147  -51.1969  -2.3551  -3.6944
 XHG  O07   O  O     0  -0.500  -49.9449  -2.9608  -3.4139
 XHG  H1    H  HNH2  0   0.345  -48.6770  -6.5310  -3.2512
 XHG  H012  H  HNH2  0   0.336  -47.6263  -5.3318  -3.4924
 XHG  H022  H  HCH2  0   0.192  -49.0185  -5.4703  -5.4333
 XHG  H021  H  HCH2  0   0.217  -50.4096  -5.4379  -4.3609
 XHG  H031  H  HCR5  0   0.218  -48.3651  -3.2058  -4.6979
 XHG  H042  H  HCH2  0   0.241  -49.8995  -2.1267  -6.1390
 XHG  H041  H  HCH2  0   0.244  -50.3097  -3.7843  -6.5674
 XHG  H051  H  HCH2  0   0.247  -52.2648  -2.1566  -5.5870
 XHG  H052  H  HCH2  0   0.236  -52.1680  -3.8077  -4.9800
 XHG  H061  H  HCH2  0   0.197  -51.0933  -1.2631  -3.7058
 XHG  H062  H  HCH2  0   0.217  -51.9090  -2.6106  -2.9056

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
 XHG  C02  N01   single  1.454  0.020  1.454
 XHG  C03  C02   single  1.524  0.020  1.524
 XHG  C04  C03   single  1.529  0.020  1.529
 XHG  C05  C04   single  1.525  0.020  1.525
 XHG  C06  C05   single  1.521  0.020  1.521
 XHG  O07  C06   single  1.419  0.020  1.419
 XHG  C03  O07   single  1.423  0.020  1.423
 XHG  N01  H1    single  0.890  0.020  1.040
 XHG  N01  H012  single  0.890  0.020  1.040
 XHG  C02  H022  single  0.970  0.020  1.090
 XHG  C02  H021  single  0.970  0.020  1.090
 XHG  C03  H031  single  0.970  0.020  1.090
 XHG  C04  H042  single  0.970  0.020  1.090
 XHG  C04  H041  single  0.970  0.020  1.090
 XHG  C05  H051  single  0.970  0.020  1.090
 XHG  C05  H052  single  0.970  0.020  1.090
 XHG  C06  H061  single  0.970  0.020  1.090
 XHG  C06  H062  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
 XHG  H012  N01  H1    105.57  3.000
 XHG  H012  N01  C02   109.30  3.000
 XHG  H1    N01  C02   109.29  3.000
 XHG  H021  C02  H022  106.39  3.000
 XHG  H021  C02  C03   109.13  3.000
 XHG  H022  C02  C03   107.29  3.000
 XHG  H021  C02  N01   108.51  3.000
 XHG  H022  C02  N01   113.56  3.000
 XHG  C03   C02  N01   111.77  3.000
 XHG  H031  C03  O07   108.20  3.000
 XHG  H031  C03  C04   111.11  3.000
 XHG  O07   C03  C04   105.68  3.000
 XHG  H031  C03  C02   108.46  3.000
 XHG  O07   C03  C02   111.18  3.000
 XHG  C04   C03  C02   112.14  3.000
 XHG  H041  C04  H042  107.52  3.000
 XHG  H041  C04  C05   113.41  3.000
 XHG  H042  C04  C05   110.33  3.000
 XHG  H041  C04  C03   112.63  3.000
 XHG  H042  C04  C03   110.66  3.000
 XHG  C05   C04  C03   102.29  3.000
 XHG  H052  C05  H051  107.71  3.000
 XHG  H052  C05  C06   111.16  3.000
 XHG  H051  C05  C06   112.35  3.000
 XHG  H052  C05  C04   110.92  3.000
 XHG  H051  C05  C04   113.27  3.000
 XHG  C06   C05  C04   101.42  3.000
 XHG  H062  C06  H061  107.56  3.000
 XHG  H062  C06  O07   109.42  3.000
 XHG  H061  C06  O07   110.11  3.000
 XHG  H062  C06  C05   112.83  3.000
 XHG  H061  C06  C05   110.52  3.000
 XHG  O07   C06  C05   106.40  3.000
 XHG  C06   O07  C03   110.78  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
 XHG  Var_01  C06  C05  C04  C03   35.76  30.0  1
 XHG  Var_02  C05  C06  O07  C03   13.25  30.0  1
 XHG  Var_03  O07  C06  C05  C04  -30.89  30.0  1
 XHG  Var_04  H1   N01  C02  C03  175.92  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
 XHG  chir_01  C03  C02  C04  O07  negativ

