# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar  7 20:08:07 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: (2S)-5-(morpholin-4-ylmethyl)-1,2,3,6-tetrahydropyridine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CC=C(CN1)CN2CCOCC2
#
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
 04X  04X  '(2S)-5-(morpholin-4-ylmethyl)-1,2,3,6-tetrahydropyridine-2-carboxylic acid'  L-peptide  33  16  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_04X
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
 04X  C2   C  CH2    0  -0.185  -59.6187  -51.2711  6.3199
 04X  C    C  C      0   0.413  -65.4531  -51.9769  5.1329
 04X  N1   N  NT     0  -0.423  -60.4745  -53.4573  5.6832
 04X  C1   C  CH2    0  -0.303  -60.5685  -52.0332  5.4170
 04X  O1   O  O2     0  -0.481  -58.2869  -51.7097  6.1651
 04X  CA   C  CR16   0  -0.268  -65.5360  -53.4300  5.6793
 04X  N    N  NR16   0  -0.577  -65.2366  -54.4346  4.6652
 04X  O    O  O      0  -0.607  -65.4433  -51.0767  5.9972
 04X  C4   C  CH2    0  -0.300  -59.1026  -53.8941  5.5044
 04X  CB   C  C      0  -0.451  -64.6656  -53.6262  6.9211
 04X  CG   C  CR16   0  -0.273  -63.2236  -53.7655  6.5359
 04X  CD   C  CR6    0   0.046  -62.8406  -54.1039  5.3069
 04X  CE   C  C      0  -0.348  -63.8511  -54.4058  4.2325
 04X  C0   C  CH2    0  -0.304  -61.4026  -54.2216  4.8786
 04X  C3   C  CH2    0  -0.186  -58.1832  -53.0946  6.4085
 04X  H4   H  HCH2   0   0.232  -59.6414  -50.2075  6.0775
 04X  H5   H  HCH2   0   0.197  -59.9423  -51.3862  7.3646
 04X  H15  H  HCH2   0   0.244  -61.5872  -51.6885  5.6048
 04X  H16  H  HCH2   0   0.197  -60.3376  -51.8076  4.3608
 04X  H18  H  HCR6   0   0.230  -66.5844  -53.5785  5.9687
 04X  H32  H  HCH2   0   0.239  -59.0195  -54.9527  5.7640
 04X  H33  H  HCH2   0   0.193  -58.7701  -53.7894  4.4568
 04X  H39  H  H      0   0.223  -64.7936  -52.7928  7.6120
 04X  H40  H  H      0   0.216  -64.9933  -54.5195  7.4677
 04X  H41  H  HCR6   0   0.216  -62.4694  -53.5595  7.2890
 04X  H44  H  H      0   0.228  -63.6136  -55.3739  3.7781
 04X  H45  H  H      0   0.223  -63.7311  -53.6712  3.4287
 04X  H55  H  HCH2   0   0.199  -61.3246  -53.9507  3.8091
 04X  H56  H  HCH2   0   0.244  -61.1101  -55.2769  4.9281
 04X  H63  H  HCH2   0   0.232  -57.1443  -53.3804  6.2349
 04X  H64  H  HCH2   0   0.197  -58.4246  -53.3196  7.4574
 04X  OXT  O  OC    -1  -0.597  -65.4513  -51.8168  3.8982
 04X  H2   H  HNR6   0   0.334  -65.4261  -55.3452  5.0663

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
 04X  C2  C1   single  1.516  0.020  1.516
 04X  C2  O1   single  1.411  0.020  1.411
 04X  C   CA   single  1.525  0.021  1.525
 04X  C   O    deloc   1.231  0.020  1.231
 04X  N1  C1   single  1.452  0.020  1.452
 04X  N1  C0   single  1.447  0.020  1.447
 04X  N1  C4   single  1.451  0.020  1.451
 04X  O1  C3   single  1.410  0.020  1.410
 04X  CA  N    single  1.458  0.019  1.458
 04X  CA  CB   single  1.521  0.033  1.521
 04X  N   CE   single  1.452  0.020  1.452
 04X  C4  C3   single  1.517  0.020  1.517
 04X  CB  CG   single  1.499  0.020  1.499
 04X  CG  CD   double  1.331  0.020  1.331
 04X  CD  CE   single  1.506  0.020  1.506
 04X  CD  C0   single  1.505  0.020  1.505
 04X  C2  H4   single  0.970  0.020  1.090
 04X  C2  H5   single  0.970  0.020  1.090
 04X  C1  H15  single  0.970  0.020  1.090
 04X  C1  H16  single  0.970  0.020  1.090
 04X  CA  H18  single  0.970  0.020  1.090
 04X  C4  H32  single  0.970  0.020  1.090
 04X  C4  H33  single  0.970  0.020  1.090
 04X  CB  H39  single  0.970  0.020  1.090
 04X  CB  H40  single  0.970  0.020  1.090
 04X  CG  H41  single  0.930  0.020  1.080
 04X  CE  H44  single  0.970  0.020  1.090
 04X  CE  H45  single  0.970  0.020  1.090
 04X  C0  H55  single  0.970  0.020  1.090
 04X  C0  H56  single  0.970  0.020  1.090
 04X  C3  H63  single  0.970  0.020  1.090
 04X  C3  H64  single  0.970  0.020  1.090
 04X  C   OXT  deloc   1.245  0.020  1.245
 04X  N   H2   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
 04X  H5   C2  H4   107.88  3.000
 04X  H5   C2  O1   110.46  3.000
 04X  H4   C2  O1   107.36  3.000
 04X  H5   C2  C1   109.20  3.000
 04X  H4   C2  C1   110.16  3.000
 04X  O1   C2  C1   111.71  3.000
 04X  OXT  C   O    126.45  3.000
 04X  OXT  C   CA   120.80  1.700
 04X  O    C   CA   120.80  1.700
 04X  C0   N1  C4   112.28  3.000
 04X  C4   N1  C1   109.51  3.000
 04X  C0   N1  C1   112.01  3.000
 04X  H16  C1  H15  107.17  3.000
 04X  H16  C1  N1   111.23  3.000
 04X  H15  C1  N1   109.79  3.000
 04X  H16  C1  C2   109.63  3.000
 04X  H15  C1  C2   108.87  3.000
 04X  N1   C1  C2   110.08  3.000
 04X  C3   O1  C2   110.85  3.000
 04X  H18  CA  CB   108.19  3.000
 04X  H18  CA  N    106.63  3.000
 04X  CB   CA  N    110.40  1.500
 04X  H18  CA  C    105.67  3.000
 04X  CB   CA  C    110.50  1.500
 04X  N    CA  C    111.00  2.800
 04X  H2   N   CE   108.32  3.000
 04X  H2   N   CA   107.79  3.000
 04X  CE   N   CA   112.92  3.000
 04X  H33  C4  H32  107.11  3.000
 04X  H33  C4  C3   109.45  3.000
 04X  H32  C4  C3   108.83  3.000
 04X  H33  C4  N1   111.91  3.000
 04X  H32  C4  N1   109.52  3.000
 04X  C3   C4  N1   109.94  3.000
 04X  H40  CB  H39  105.77  3.000
 04X  H40  CB  CG   109.85  3.000
 04X  H39  CB  CG   110.29  3.000
 04X  H40  CB  CA   109.82  3.000
 04X  H39  CB  CA   110.47  3.000
 04X  CG   CB  CA   110.53  3.000
 04X  H41  CG  CD   119.27  3.000
 04X  H41  CG  CB   118.19  3.000
 04X  CD   CG  CB   122.52  3.000
 04X  C0   CD  CE   115.00  3.000
 04X  C0   CD  CG   123.89  3.000
 04X  CE   CD  CG   121.12  3.000
 04X  H45  CE  H44  105.33  3.000
 04X  H45  CE  CD   108.40  3.000
 04X  H44  CE  CD   109.13  3.000
 04X  H45  CE  N    109.67  3.000
 04X  H44  CE  N    108.24  3.000
 04X  CD   CE  N    115.59  3.000
 04X  H56  C0  H55  105.11  3.000
 04X  H56  C0  CD   108.51  3.000
 04X  H55  C0  CD   108.87  3.000
 04X  H56  C0  N1   108.19  3.000
 04X  H55  C0  N1   111.29  3.000
 04X  CD   C0  N1   114.42  3.000
 04X  H64  C3  H63  107.89  3.000
 04X  H64  C3  C4   109.12  3.000
 04X  H63  C3  C4   110.12  3.000
 04X  H64  C3  O1   110.46  3.000
 04X  H63  C3  O1   107.45  3.000
 04X  C4   C3  O1   111.72  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
 04X  Var_01  C4  N1  C1  C2  -56.98  30.0  1
 04X  Var_02  C4  C3  O1  C2   56.86  30.0  1
 04X  Var_03  O1  C2  C1  N1   57.18  30.0  1
 04X  Var_04  O1  C3  C4  N1  -57.43  30.0  1
 04X  Var_05  CD  CE  N   CA   36.86  30.0  1
 04X  Var_06  CD  CG  CB  CA  -19.98  30.0  1
 04X  Var_07  CG  CD  CE  N    -6.02  30.0  1
 04X  Var_08  CE  CD  CG  CB   -1.71  30.0  1
 04X  Var_09  CD  C0  N1  C1  -73.39  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
 04X  chir_01  CA  C  N  CB  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
 04X  plan-1  C    0.020
 04X  plan-1  CA   0.020
 04X  plan-1  O    0.020
 04X  plan-1  OXT  0.020

