# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 02:05:41 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-(difluoromethoxy)-1-[(2R,6S)-2,6-dimethylmorpholin-4-yl]ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CN(C[C@H](C)O1)C(=O)COC(F)F
#
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
 LO6  LO6  "2-(difluoromethoxy)-1-[(2R,6S)-2,6-dimethylmorpholin-4-yl]ethan-1-one"
  ligand  30  15  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LO6
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
 LO6  N1   N  NT    0  -0.452  32.7632  33.0302  92.7711
 LO6  C4   C  CH2   0  -0.385  33.1056  33.7990  91.5918
 LO6  C5   C  CH1   0   0.067  34.4572  33.3277  91.0547
 LO6  C6   C  CH3   0  -0.680  35.6147  33.8722  91.8700
 LO6  C7   C  C     0   0.509  32.5362  33.6375  93.9499
 LO6  C8   C  CH2   0  -0.308  32.3076  32.7248  95.1470
 LO6  C2   C  CH1   0  -0.000  33.3246  31.2269  91.2187
 LO6  C3   C  CH2   0  -0.264  32.6982  31.5849  92.5663
 LO6  O1   O  O2    0  -0.495  34.5495  31.9076  91.0691
 LO6  O2   O  O     0  -0.477  32.5264  34.8498  94.0991
 LO6  O3   O  O2    0  -0.470  33.5866  32.2047  95.5001
 LO6  C9   C  CH1   0   0.659  33.6199  31.4859  96.6415
 LO6  F1   F  F     0  -0.342  33.0500  30.2648  96.4575
 LO6  F2   F  F     0  -0.316  34.9162  31.2674  96.9185
 LO6  H1   H  HCH2  0   0.282  33.1571  34.8552  91.8431
 LO6  H2   H  HCH2  0   0.271  32.3212  33.6872  90.8389
 LO6  H3   H  HCH1  0   0.219  34.5447  33.6857  90.0201
 LO6  H4   H  HCH3  0   0.227  35.6542  34.9591  91.7964
 LO6  H5   H  HCH3  0   0.227  35.5166  33.6026  92.9232
 LO6  H6   H  HCH3  0   0.239  36.5653  33.4797  91.5073
 LO6  H7   H  HCH2  0   0.278  31.8983  33.3257  95.9633
 LO6  H8   H  HCH2  0   0.265  31.5975  31.9236  94.9238
 LO6  H12  H  HCH1  0   0.223  32.6296  31.4946  90.4106
 LO6  H13  H  HCH2  0   0.251  31.6628  31.2313  92.5867
 LO6  H14  H  HCH2  0   0.251  33.2470  31.0645  93.3520
 LO6  H15  H  HCH1  0   0.190  33.1280  31.9661  97.4932
 LO6  C1   C  CH3   0  -0.677  33.5910  29.7388  91.1326
 LO6  H9   H  HCH3  0   0.235  32.6634  29.1817  91.2658
 LO6  H10  H  HCH3  0   0.244  34.0017  29.4741  90.1586
 LO6  H11  H  HCH3  0   0.230  34.2927  29.4188  91.9041

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
 LO6  C5  O1   single  1.423  0.020  1.423
 LO6  C5  C6   single  1.517  0.020  1.517
 LO6  C5  C4   single  1.529  0.020  1.529
 LO6  O1  C2   single  1.409  0.020  1.409
 LO6  C1  C2   single  1.514  0.020  1.514
 LO6  C2  C3   single  1.529  0.020  1.529
 LO6  C4  N1   single  1.449  0.020  1.449
 LO6  C3  N1   single  1.461  0.020  1.461
 LO6  N1  C7   single  1.345  0.020  1.345
 LO6  C7  O2   double  1.222  0.020  1.222
 LO6  C7  C8   single  1.523  0.020  1.523
 LO6  C8  O3   single  1.425  0.020  1.425
 LO6  O3  C9   single  1.349  0.020  1.349
 LO6  F1  C9   single  1.360  0.020  1.360
 LO6  C9  F2   single  1.343  0.020  1.343
 LO6  C4  H1   single  0.970  0.020  1.090
 LO6  C4  H2   single  0.970  0.020  1.090
 LO6  C5  H3   single  0.970  0.020  1.090
 LO6  C6  H4   single  0.970  0.020  1.090
 LO6  C6  H5   single  0.970  0.020  1.090
 LO6  C6  H6   single  0.970  0.020  1.090
 LO6  C8  H7   single  0.970  0.020  1.090
 LO6  C8  H8   single  0.970  0.020  1.090
 LO6  C1  H9   single  0.970  0.020  1.090
 LO6  C1  H10  single  0.970  0.020  1.090
 LO6  C1  H11  single  0.970  0.020  1.090
 LO6  C2  H12  single  0.970  0.020  1.090
 LO6  C3  H13  single  0.970  0.020  1.090
 LO6  C3  H14  single  0.970  0.020  1.090
 LO6  C9  H15  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
 LO6  C3   N1  C7   124.18  3.000
 LO6  C7   N1  C4   120.90  3.000
 LO6  C3   N1  C4   114.92  3.000
 LO6  H2   C4  H1   107.02  3.000
 LO6  H2   C4  C5   111.16  3.000
 LO6  H1   C4  C5   109.82  3.000
 LO6  H2   C4  N1   109.68  3.000
 LO6  H1   C4  N1   109.79  3.000
 LO6  C5   C4  N1   109.35  3.000
 LO6  H3   C5  O1   109.25  3.000
 LO6  H3   C5  C6   109.18  3.000
 LO6  O1   C5  C6   107.65  3.000
 LO6  H3   C5  C4   107.51  3.000
 LO6  C6   C5  C4   112.03  3.000
 LO6  O1   C5  C4   111.19  3.000
 LO6  H6   C6  H5   108.08  3.000
 LO6  H6   C6  H4   107.75  3.000
 LO6  H5   C6  H4   108.33  3.000
 LO6  H6   C6  C5   110.93  3.000
 LO6  H5   C6  C5   111.19  3.000
 LO6  H4   C6  C5   110.44  3.000
 LO6  O2   C7  C8   119.85  3.000
 LO6  C8   C7  N1   116.34  3.000
 LO6  O2   C7  N1   123.81  3.000
 LO6  H8   C8  H7   108.18  3.000
 LO6  H8   C8  O3   111.47  3.000
 LO6  H7   C8  O3   110.59  3.000
 LO6  H8   C8  C7   112.09  3.000
 LO6  H7   C8  C7   108.28  3.000
 LO6  O3   C8  C7   106.19  3.000
 LO6  H12  C2  O1   110.73  3.000
 LO6  H12  C2  C3   109.39  3.000
 LO6  O1   C2  C3   109.67  3.000
 LO6  H12  C2  C1   107.99  3.000
 LO6  C3   C2  C1   110.63  3.000
 LO6  O1   C2  C1   108.41  3.000
 LO6  H14  C3  H13  107.96  3.000
 LO6  H14  C3  C2   108.49  3.000
 LO6  H13  C3  C2   109.18  3.000
 LO6  H14  C3  N1   110.40  3.000
 LO6  H13  C3  N1   111.05  3.000
 LO6  C2   C3  N1   109.69  3.000
 LO6  C2   O1  C5   115.26  3.000
 LO6  C9   O3  C8   115.22  3.000
 LO6  H15  C9  F2   110.15  3.000
 LO6  H15  C9  F1   108.10  3.000
 LO6  F2   C9  F1   106.63  3.000
 LO6  H15  C9  O3   114.42  3.000
 LO6  F2   C9  O3   106.55  3.000
 LO6  F1   C9  O3   110.70  3.000
 LO6  H11  C1  H10  108.57  3.000
 LO6  H11  C1  H9   108.12  3.000
 LO6  H10  C1  H9   107.80  3.000
 LO6  H11  C1  C2   111.18  3.000
 LO6  H10  C1  C2   110.84  3.000
 LO6  H9   C1  C2   110.22  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
 LO6  CONST_01  O2   C7  N1  C4     0.00   0.0  0
 LO6  CONST_02  C8   C7  N1  C4   180.00   0.0  0
 LO6  CONST_03  C3   N1  C7  C8     0.00   0.0  0
 LO6  CONST_04  O2   C7  N1  C3   180.00   0.0  0
 LO6  Var_01    C2   C3  N1  C4    12.96  30.0  1
 LO6  Var_02    C3   N1  C4  C5   -57.92  30.0  1
 LO6  Var_03    C7   N1  C4  C5   121.75  30.0  1
 LO6  Var_04    C2   C3  N1  C7  -166.71  30.0  1
 LO6  Var_05    H13  C3  N1  C4  -107.82  30.0  1
 LO6  Var_06    H14  C3  N1  C4   132.47  30.0  1
 LO6  Var_07    H1   C4  N1  C3  -178.47  30.0  1
 LO6  Var_08    H2   C4  N1  C3    64.20  30.0  1
 LO6  Var_09    H1   C4  N1  C7     1.21  30.0  1
 LO6  Var_10    H2   C4  N1  C7  -116.12  30.0  1
 LO6  Var_11    H13  C3  N1  C7    72.52  30.0  1
 LO6  Var_12    H14  C3  N1  C7   -47.20  30.0  1
 LO6  Var_13    O3   C8  C7  N1    75.00  30.0  3
 LO6  Var_14    H7   C8  C7  N1  -166.21  30.0  3
 LO6  Var_15    H8   C8  C7  N1   -46.95  30.0  3
 LO6  Var_16    C9   O3  C8  C7   172.79  30.0  3
 LO6  Var_17    F1   C9  O3  C8    74.04  30.0  3
 LO6  Var_18    F2   C9  O3  C8  -170.39  30.0  3
 LO6  Var_19    O3   C8  C7  O2  -103.92  30.0  3
 LO6  Var_20    H15  C9  O3  C8   -48.40  30.0  3
 LO6  Var_21    H7   C8  C7  O2    14.88  30.0  3
 LO6  Var_22    H8   C8  C7  O2   134.13  30.0  3
 LO6  Var_23    H7   C8  O3  C9    55.52  30.0  1
 LO6  Var_24    H8   C8  O3  C9   -64.87  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
 LO6  chir_01  C5  O1  C6  C4  positiv
 LO6  chir_02  C2  O1  C1  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
 LO6  plan-1  N1  0.020
 LO6  plan-1  C4  0.020
 LO6  plan-1  C7  0.020
 LO6  plan-1  C8  0.020
 LO6  plan-1  C3  0.020
 LO6  plan-1  O2  0.020

