# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 09:47:58 2021
#   Inital geometry file: a 50 line input string
#   Ligand name: (8~{a}~{S})-1,5,6,7,8,8~{a}-hexahydro-[1,3]oxazolo[3,4-a]pyrazin-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1OC[C@@H]2CNCCN12
#
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
 L3Q  L3Q  (8~{a}~{S})-1,5,6,7,8,8~{a}-hexahydro-[1,3]oxazolo[3,4-a]pyrazin-3-one  ligand  20  10  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_L3Q
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
 L3Q  C4   C  CH2   0  -0.318  -16.2918   -8.9560  105.3400
 L3Q  C5   C  CH2   0  -0.316  -14.8078   -9.2651  105.1543
 L3Q  N1   N  NR5   0  -0.481  -14.6432  -10.6578  104.7988
 L3Q  N    N  NH1   0  -0.584  -16.9805   -9.9079  106.1968
 L3Q  C    C  CR5   0   0.693  -14.4271  -11.0962  103.5415
 L3Q  O    O  O     0  -0.498  -14.0464  -10.4681  102.5813
 L3Q  C1   C  CH2   0  -0.186  -15.0575  -12.9089  104.7627
 L3Q  C2   C  CR15  0  -0.144  -15.3244  -11.6573  105.5981
 L3Q  C3   C  CH2   0  -0.306  -16.7965  -11.2776  105.7529
 L3Q  O1   O  O     0  -0.473  -14.6858  -12.4136  103.4729
 L3Q  H1   H  HCH2  0   0.249  -16.4080   -7.9535  105.7548
 L3Q  H2   H  HCH2  0   0.231  -16.7838   -8.9568  104.3621
 L3Q  H3   H  HCH2  0   0.249  -14.2635   -9.0755  106.0835
 L3Q  H4   H  HCH2  0   0.263  -14.3652   -8.6417  104.3786
 L3Q  H5   H  HNH1  0   0.348  -16.6553   -9.8090  107.1516
 L3Q  H7   H  HCH2  0   0.257  -15.9358  -13.5457  104.6589
 L3Q  H8   H  HCH2  0   0.258  -14.2367  -13.5028  105.1665
 L3Q  H9   H  HCR5  0   0.274  -14.8592  -11.7341  106.5848
 L3Q  H10  H  HCH2  0   0.229  -17.3064  -11.4017  104.7902
 L3Q  H11  H  HCH2  0   0.255  -17.2796  -11.9554  106.4594

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
 L3Q  O   C    double  1.209  0.020  1.209
 L3Q  O1  C    single  1.344  0.020  1.344
 L3Q  O1  C1   single  1.431  0.020  1.431
 L3Q  C   N1   single  1.349  0.020  1.349
 L3Q  C1  C2   single  1.528  0.020  1.528
 L3Q  N1  C5   single  1.447  0.020  1.447
 L3Q  N1  C2   single  1.450  0.020  1.450
 L3Q  C5  C4   single  1.527  0.020  1.527
 L3Q  C4  N    single  1.454  0.020  1.454
 L3Q  C2  C3   single  1.528  0.020  1.528
 L3Q  C3  N    single  1.452  0.020  1.452
 L3Q  C4  H1   single  0.970  0.020  1.090
 L3Q  C4  H2   single  0.970  0.020  1.090
 L3Q  C5  H3   single  0.970  0.020  1.090
 L3Q  C5  H4   single  0.970  0.020  1.090
 L3Q  N   H5   single  0.890  0.020  1.040
 L3Q  C1  H7   single  0.970  0.020  1.090
 L3Q  C1  H8   single  0.970  0.020  1.090
 L3Q  C2  H9   single  0.970  0.020  1.090
 L3Q  C3  H10  single  0.970  0.020  1.090
 L3Q  C3  H11  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
 L3Q  H2   C4  H1   107.00  3.000
 L3Q  H2   C4  N    108.24  3.000
 L3Q  H1   C4  N    109.08  3.000
 L3Q  H2   C4  C5   109.15  3.000
 L3Q  H1   C4  C5   109.62  3.000
 L3Q  N    C4  C5   113.54  3.000
 L3Q  H4   C5  H3   107.67  3.000
 L3Q  H4   C5  N1   109.26  3.000
 L3Q  H3   C5  N1   108.61  3.000
 L3Q  H4   C5  C4   111.45  3.000
 L3Q  H3   C5  C4   110.20  3.000
 L3Q  N1   C5  C4   109.59  3.000
 L3Q  C2   N1  C    111.42  3.000
 L3Q  C2   N1  C5   118.34  3.000
 L3Q  C    N1  C5   124.06  3.000
 L3Q  H5   N   C3   109.85  3.000
 L3Q  H5   N   C4   109.83  3.000
 L3Q  C3   N   C4   112.18  3.000
 L3Q  O1   C   O    121.96  3.000
 L3Q  O1   C   N1   109.58  3.000
 L3Q  O    C   N1   128.46  3.000
 L3Q  H8   C1  H7   108.87  3.000
 L3Q  H8   C1  O1   109.08  3.000
 L3Q  H7   C1  O1   109.02  3.000
 L3Q  H8   C1  C2   112.03  3.000
 L3Q  H7   C1  C2   112.94  3.000
 L3Q  O1   C1  C2   104.76  3.000
 L3Q  H9   C2  C3   109.63  3.000
 L3Q  H9   C2  C1   111.18  3.000
 L3Q  C3   C2  C1   115.29  3.000
 L3Q  H9   C2  N1   110.24  3.000
 L3Q  C3   C2  N1   109.71  3.000
 L3Q  C1   C2  N1   100.43  3.000
 L3Q  H11  C3  H10  106.99  3.000
 L3Q  H11  C3  C2   109.73  3.000
 L3Q  H10  C3  C2   109.33  3.000
 L3Q  H11  C3  N    109.38  3.000
 L3Q  H10  C3  N    108.44  3.000
 L3Q  C2   C3  N    112.80  3.000
 L3Q  C1   O1  C    110.08  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
 L3Q  Var_01  C   N1  C5  C4   100.86  30.0  1
 L3Q  Var_02  C2  C3  N   C4    54.18  30.0  1
 L3Q  Var_03  O1  C   N1  C5  -162.97  30.0  1
 L3Q  Var_04  C3  N   C4  C5   -53.74  30.0  1
 L3Q  Var_05  N   C4  C5  N1    49.11  30.0  1
 L3Q  Var_06  C2  C1  O1  C     13.21  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
 L3Q  chir_01  C2  C1  N1  C3  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 L3Q  plan-1  C5  0.020
 L3Q  plan-1  N1  0.020
 L3Q  plan-1  C   0.020
 L3Q  plan-1  C2  0.020
 L3Q  plan-2  N1  0.020
 L3Q  plan-2  C   0.020
 L3Q  plan-2  O   0.020
 L3Q  plan-2  O1  0.020

