# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:15:03 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: [(2S)-5,5-dimethylmorpholin-2-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)CO[C@H](CN1)CC(O)=O
#
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
 2BX  2BX  '[(2S)-5,5-dimethylmorpholin-2-yl]acetic acid'  ligand  26  12  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2BX
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
 2BX  O1   O  O      0  -0.616   2.9589  -0.8584   1.0816
 2BX  C1   C  C      0   0.410   2.9263  -0.1597   0.0489
 2BX  O2   O  OC    -1  -0.621   3.7236  -0.2177  -0.9088
 2BX  C2   C  CH2    0  -0.595   1.8196   0.9080  -0.0276
 2BX  C3   C  CH1    0   0.055   0.4627   0.4237   0.4311
 2BX  C6   C  CH2    0  -0.317  -0.5894   1.5259   0.4186
 2BX  N    N  NH1    0  -0.589  -1.9372   1.0458   0.6926
 2BX  C5   C  CT     0   0.024  -2.3039  -0.1264  -0.1118
 2BX  C8   C  CH3    0  -0.660  -3.5749  -0.7277   0.4723
 2BX  C7   C  CH3    0  -0.644  -2.5621   0.3051  -1.5547
 2BX  C4   C  CH2    0  -0.140  -1.1845  -1.1715  -0.0601
 2BX  O3   O  O2     0  -0.495   0.0613  -0.6311  -0.4304
 2BX  H2   H  HCH2   0   0.230   2.1131   1.7450   0.6168
 2BX  H3   H  HCH2   0   0.206   1.7446   1.3159  -1.0400
 2BX  H4   H  HCH1   0   0.185   0.5475   0.0350   1.4584
 2BX  H5   H  HCH2   0   0.235  -0.3371   2.2832   1.1649
 2BX  H6   H  HCH2   0   0.215  -0.5774   2.0324  -0.5526
 2BX  H7   H  HNH1   0   0.337  -1.9885   0.7871   1.6726
 2BX  H9   H  HCH3   0   0.234  -4.3885  -0.0010   0.4552
 2BX  H10  H  HCH3   0   0.229  -3.8904  -1.6019  -0.0991
 2BX  H11  H  HCH3   0   0.227  -3.4275  -1.0435   1.5081
 2BX  H12  H  HCH3   0   0.230  -1.6673   0.6909  -2.0428
 2BX  H13  H  HCH3   0   0.222  -2.9158  -0.5407  -2.1472
 2BX  H14  H  HCH3   0   0.226  -3.3255   1.0837  -1.5897
 2BX  H15  H  HCH2   0   0.190  -1.1328  -1.5883   0.9593
 2BX  H16  H  HCH2   0   0.221  -1.3943  -1.9996  -0.7434

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
 2BX  N   C6   single  1.457  0.020  1.457
 2BX  N   C5   single  1.468  0.020  1.468
 2BX  C8  C5   single  1.523  0.020  1.523
 2BX  C6  C3   single  1.524  0.020  1.524
 2BX  C5  C4   single  1.532  0.020  1.532
 2BX  C5  C7   single  1.528  0.020  1.528
 2BX  C3  C2   single  1.512  0.020  1.512
 2BX  C3  O3   single  1.420  0.020  1.420
 2BX  C4  O3   single  1.408  0.020  1.408
 2BX  O1  C1   deloc   1.247  0.020  1.247
 2BX  C2  C1   single  1.540  0.020  1.540
 2BX  C1  O2   deloc   1.248  0.020  1.248
 2BX  C2  H2   single  0.970  0.020  1.090
 2BX  C2  H3   single  0.970  0.020  1.090
 2BX  C3  H4   single  0.970  0.020  1.090
 2BX  C6  H5   single  0.970  0.020  1.090
 2BX  C6  H6   single  0.970  0.020  1.090
 2BX  N   H7   single  0.890  0.020  1.040
 2BX  C8  H9   single  0.970  0.020  1.090
 2BX  C8  H10  single  0.970  0.020  1.090
 2BX  C8  H11  single  0.970  0.020  1.090
 2BX  C7  H12  single  0.970  0.020  1.090
 2BX  C7  H13  single  0.970  0.020  1.090
 2BX  C7  H14  single  0.970  0.020  1.090
 2BX  C4  H15  single  0.970  0.020  1.090
 2BX  C4  H16  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
 2BX  C2   C1  O2   116.97  3.000
 2BX  O2   C1  O1   126.36  3.000
 2BX  C2   C1  O1   116.65  3.000
 2BX  H3   C2  H2   106.12  3.000
 2BX  H3   C2  C3   109.79  3.000
 2BX  H2   C2  C3   107.85  3.000
 2BX  H3   C2  C1   110.72  3.000
 2BX  H2   C2  C1   107.93  3.000
 2BX  C3   C2  C1   114.07  3.000
 2BX  H4   C3  O3   108.99  3.000
 2BX  H4   C3  C6   108.42  3.000
 2BX  O3   C3  C6   109.71  3.000
 2BX  H4   C3  C2   109.08  3.000
 2BX  O3   C3  C2   107.91  3.000
 2BX  C6   C3  C2   112.67  3.000
 2BX  H6   C6  H5   106.42  3.000
 2BX  H6   C6  N    109.22  3.000
 2BX  H5   C6  N    108.27  3.000
 2BX  H6   C6  C3   109.52  3.000
 2BX  H5   C6  C3   109.65  3.000
 2BX  N    C6  C3   113.51  3.000
 2BX  H7   N   C5   108.23  3.000
 2BX  H7   N   C6   108.20  3.000
 2BX  C5   N   C6   113.03  3.000
 2BX  C4   C5  C7   110.36  3.000
 2BX  C7   C5  C8   109.43  3.000
 2BX  C4   C5  C8   109.12  3.000
 2BX  C7   C5  N    109.52  3.000
 2BX  C4   C5  N    110.10  3.000
 2BX  C8   C5  N    108.28  3.000
 2BX  H11  C8  H10  107.69  3.000
 2BX  H11  C8  H9   107.93  3.000
 2BX  H10  C8  H9   108.05  3.000
 2BX  H11  C8  C5   111.41  3.000
 2BX  H10  C8  C5   110.91  3.000
 2BX  H9   C8  C5   110.69  3.000
 2BX  H14  C7  H13  107.99  3.000
 2BX  H14  C7  H12  107.91  3.000
 2BX  H13  C7  H12  107.29  3.000
 2BX  H14  C7  C5   110.49  3.000
 2BX  H13  C7  C5   110.40  3.000
 2BX  H12  C7  C5   112.59  3.000
 2BX  H16  C4  H15  107.48  3.000
 2BX  H16  C4  O3   107.22  3.000
 2BX  H15  C4  O3   110.29  3.000
 2BX  H16  C4  C5   110.81  3.000
 2BX  H15  C4  C5   108.86  3.000
 2BX  O3   C4  C5   112.08  3.000
 2BX  C4   O3  C3   112.07  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
 2BX  Var_01  C5   N   C6  C3  -48.73  30.0  1
 2BX  Var_02  C5   C4  O3  C3   60.64  30.0  1
 2BX  Var_03  O3   C4  C5  N   -53.91  30.0  1
 2BX  Var_04  H9   C8  C5  N    59.72  30.0  3
 2BX  Var_05  H12  C7  C5  N    64.79  30.0  3
 2BX  Var_06  C3   C2  C1  O1  -43.70  30.0  2

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
 2BX  chir_01  C3  C6  C2  O3  positiv

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
 2BX  plan-1  O1  0.020
 2BX  plan-1  C1  0.020
 2BX  plan-1  O2  0.020
 2BX  plan-1  C2  0.020

