# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 20:32:06 2021
#   Inital geometry file: a 78 line input string
#   Ligand name: 2-[(2~{R},5~{S})-2,5-dimethylmorpholin-4-yl]-~{N}-ethyl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)CN1C[C@@H](C)OC[C@@H]1C
#
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
 S8D  S8D  2-[(2~{R},5~{S})-2,5-dimethylmorpholin-4-yl]-~{N}-ethyl-ethanamide  ligand  34  14  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_S8D
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
 S8D  N1   N  NT    0  -0.424  49.3953  5.4173  63.0074
 S8D  C4   C  CH2   0  -0.284  48.0415  5.8434  63.3161
 S8D  C5   C  CH1   0   0.034  47.5364  6.8477  62.2951
 S8D  C6   C  CH3   0  -0.689  46.1544  7.3577  62.6430
 S8D  C7   C  CH2   0  -0.158  49.7255  7.5525  61.9206
 S8D  C8   C  CH1   0  -0.084  50.2955  6.5639  62.9306
 S8D  N    N  NH1   0  -0.597  48.9051  2.5560  62.5878
 S8D  C    C  CH3   0  -0.686  49.7494  1.7423  60.4547
 S8D  O    O  O     0  -0.501  48.4643  2.6256  64.7881
 S8D  C1   C  CH2   0  -0.255  49.5443  2.9541  61.3458
 S8D  C2   C  C     0   0.480  49.0048  3.1176  63.8033
 S8D  C3   C  CH2   0  -0.409  49.8360  4.3860  63.9191
 S8D  C9   C  CH3   0  -0.703  51.7015  6.1856  62.4874
 S8D  O1   O  O2    0  -0.491  48.4141  7.9545  62.2264
 S8D  H2   H  HCH2  0   0.197  47.9718  6.2805  64.3288
 S8D  H3   H  HCH2  0   0.246  47.3724  4.9795  63.2955
 S8D  H4   H  HCH1  0   0.203  47.5065  6.3454  61.3150
 S8D  H5   H  HCH3  0   0.233  45.4407  6.5342  62.6524
 S8D  H6   H  HCH3  0   0.227  46.1427  7.8268  63.6283
 S8D  H7   H  HCH3  0   0.241  45.8087  8.0878  61.9108
 S8D  H8   H  HCH2  0   0.193  49.7676  7.0960  60.9196
 S8D  H9   H  HCH2  0   0.234  50.3433  8.4526  61.9044
 S8D  H10  H  HCH1  0   0.200  50.3588  7.0735  63.9096
 S8D  H11  H  HNH1  0   0.387  48.3065  1.7433  62.5408
 S8D  H12  H  HCH3  0   0.241  50.2269  2.0424  59.5226
 S8D  H13  H  HCH3  0   0.232  50.3849  0.9985  60.9362
 S8D  H14  H  HCH3  0   0.231  48.7999  1.2678  60.2012
 S8D  H15  H  HCH2  0   0.240  50.5062  3.4140  61.5647
 S8D  H16  H  HCH2  0   0.233  48.9481  3.7086  60.8284
 S8D  H17  H  HCH2  0   0.275  50.8741  4.1200  63.7040
 S8D  H18  H  HCH2  0   0.235  49.8009  4.7028  64.9723
 S8D  H19  H  HCH3  0   0.243  52.2486  5.6221  63.2416
 S8D  H20  H  HCH3  0   0.233  51.6748  5.5949  61.5700
 S8D  H21  H  HCH3  0   0.243  52.2799  7.0888  62.2888

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
 S8D  C   C1   single  1.518  0.020  1.518
 S8D  C1  N    single  1.452  0.020  1.452
 S8D  C5  C6   single  1.514  0.020  1.514
 S8D  C5  O1   single  1.414  0.020  1.414
 S8D  C5  C4   single  1.519  0.020  1.519
 S8D  C7  O1   single  1.405  0.020  1.405
 S8D  C7  C8   single  1.524  0.020  1.524
 S8D  N1  C4   single  1.452  0.020  1.452
 S8D  N1  C8   single  1.460  0.020  1.460
 S8D  N1  C3   single  1.445  0.020  1.445
 S8D  N   C2   single  1.343  0.020  1.343
 S8D  C9  C8   single  1.522  0.020  1.522
 S8D  C3  C2   single  1.521  0.020  1.521
 S8D  C2  O    double  1.226  0.020  1.226
 S8D  C4  H2   single  0.970  0.020  1.090
 S8D  C4  H3   single  0.970  0.020  1.090
 S8D  C5  H4   single  0.970  0.020  1.090
 S8D  C6  H5   single  0.970  0.020  1.090
 S8D  C6  H6   single  0.970  0.020  1.090
 S8D  C6  H7   single  0.970  0.020  1.090
 S8D  C7  H8   single  0.970  0.020  1.090
 S8D  C7  H9   single  0.970  0.020  1.090
 S8D  C8  H10  single  0.970  0.020  1.090
 S8D  N   H11  single  0.860  0.020  1.020
 S8D  C   H12  single  0.970  0.020  1.090
 S8D  C   H13  single  0.970  0.020  1.090
 S8D  C   H14  single  0.970  0.020  1.090
 S8D  C1  H15  single  0.970  0.020  1.090
 S8D  C1  H16  single  0.970  0.020  1.090
 S8D  C3  H17  single  0.970  0.020  1.090
 S8D  C3  H18  single  0.970  0.020  1.090
 S8D  C9  H19  single  0.970  0.020  1.090
 S8D  C9  H20  single  0.970  0.020  1.090
 S8D  C9  H21  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
 S8D  C3   N1  C8   113.93  3.000
 S8D  C3   N1  C4   111.07  3.000
 S8D  C8   N1  C4   110.83  3.000
 S8D  H3   C4  H2   106.94  3.000
 S8D  H3   C4  C5   107.85  3.000
 S8D  H2   C4  C5   109.49  3.000
 S8D  H3   C4  N1   109.55  3.000
 S8D  H2   C4  N1   111.69  3.000
 S8D  C5   C4  N1   111.17  3.000
 S8D  H4   C5  O1   109.30  3.000
 S8D  H4   C5  C6   109.47  3.000
 S8D  O1   C5  C6   108.31  3.000
 S8D  H4   C5  C4   107.79  3.000
 S8D  O1   C5  C4   110.11  3.000
 S8D  C6   C5  C4   111.84  3.000
 S8D  H7   C6  H6   108.36  3.000
 S8D  H7   C6  H5   107.71  3.000
 S8D  H6   C6  H5   108.06  3.000
 S8D  H7   C6  C5   111.15  3.000
 S8D  H6   C6  C5   111.23  3.000
 S8D  H5   C6  C5   110.21  3.000
 S8D  H9   C7  H8   107.86  3.000
 S8D  H9   C7  O1   107.18  3.000
 S8D  H8   C7  O1   110.62  3.000
 S8D  H9   C7  C8   109.45  3.000
 S8D  H8   C7  C8   108.62  3.000
 S8D  O1   C7  C8   112.98  3.000
 S8D  H10  C8  C9   108.63  3.000
 S8D  H10  C8  C7   108.02  3.000
 S8D  C9   C8  C7   108.29  3.000
 S8D  H10  C8  N1   110.53  3.000
 S8D  C9   C8  N1   112.94  3.000
 S8D  C7   C8  N1   108.29  3.000
 S8D  H11  N   C2   114.99  3.000
 S8D  H11  N   C1   116.19  3.000
 S8D  C2   N   C1   128.81  3.000
 S8D  H14  C   H13  108.24  3.000
 S8D  H14  C   H12  107.60  3.000
 S8D  H13  C   H12  108.08  3.000
 S8D  H14  C   C1   111.46  3.000
 S8D  H13  C   C1   111.35  3.000
 S8D  H12  C   C1   109.97  3.000
 S8D  H16  C1  H15  106.61  3.000
 S8D  H16  C1  C    110.32  3.000
 S8D  H15  C1  C    109.63  3.000
 S8D  H16  C1  N    110.75  3.000
 S8D  H15  C1  N    109.44  3.000
 S8D  C    C1  N    110.04  3.000
 S8D  C3   C2  O    120.95  3.000
 S8D  O    C2  N    121.77  3.000
 S8D  C3   C2  N    117.28  3.000
 S8D  H18  C3  H17  106.78  3.000
 S8D  H18  C3  C2   107.19  3.000
 S8D  H17  C3  C2   107.53  3.000
 S8D  H18  C3  N1   112.87  3.000
 S8D  H17  C3  N1   109.82  3.000
 S8D  C2   C3  N1   112.36  3.000
 S8D  H21  C9  H20  107.94  3.000
 S8D  H21  C9  H19  106.75  3.000
 S8D  H20  C9  H19  108.32  3.000
 S8D  H21  C9  C8   109.70  3.000
 S8D  H20  C9  C8   110.90  3.000
 S8D  H19  C9  C8   113.03  3.000
 S8D  C7   O1  C5   111.46  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
 S8D  CONST_01  C1   N   C2  O   180.00   0.0  0
 S8D  CONST_02  C3   C2  N   C1    0.00   0.0  0
 S8D  CONST_03  H11  N   C2  O     0.00   0.0  0
 S8D  Var_01    C8   C7  O1  C5  -58.27  30.0  1
 S8D  Var_02    C8   N1  C4  C5   56.74  30.0  1
 S8D  Var_03    C2   C3  N1  C4   63.49  30.0  3
 S8D  Var_04    N    C2  C3  N1   55.16  30.0  3
 S8D  Var_05    C2   N   C1  C   151.04  30.0  3
 S8D  Var_06    H12  C   C1  N   179.88  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
 S8D  chir_01  C5  C6  O1  C4  negativ
 S8D  chir_02  C8  N1  C9  C7  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
 S8D  plan-1  N    0.020
 S8D  plan-1  O    0.020
 S8D  plan-1  C1   0.020
 S8D  plan-1  C2   0.020
 S8D  plan-1  C3   0.020
 S8D  plan-1  H11  0.020

