# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 01:56:22 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (2R)-2-[(R)-(2-ethoxyphenoxy)(phenyl)methyl]morpholine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1ccccc1O[C@@H]([C@H]2CNCCO2)c3ccccc3
#
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
 41X  41X  (2R)-2-[(R)-(2-ethoxyphenoxy)(phenyl)methyl]morpholine  ligand  46  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_41X
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
 41X  C12  C  CH3   0  -0.679  -3.4888   2.9633   1.6605
 41X  C11  C  CH2   0  -0.188  -3.8402   1.6529   0.9968
 41X  O2   O  O2    0  -0.459  -2.6327   1.0400   0.5723
 41X  C10  C  CR6   0   0.299  -2.6976  -0.1463  -0.0581
 41X  C9   C  CR16  0  -0.389  -3.8645  -0.8442  -0.3306
 41X  C8   C  CR16  0  -0.266  -3.8167  -2.0658  -1.0017
 41X  C7   C  CR16  0  -0.274  -2.6041  -2.5900  -1.4001
 41X  C6   C  CR16  0  -0.352  -1.4227  -1.9000  -1.1277
 41X  C5   C  CR6   0   0.316  -1.4589  -0.6852  -0.4641
 41X  O1   O  O2    0  -0.483  -0.3828   0.0679  -0.1540
 41X  C4   C  CH1   0  -0.075   0.8729  -0.2481  -0.7141
 41X  C13  C  CR6   0   0.092   1.5453  -1.4010  -0.0059
 41X  C18  C  CR16  0  -0.289   1.2925  -1.6840   1.3320
 41X  C17  C  CR16  0  -0.243   1.9532  -2.7298   1.9626
 41X  C16  C  CR16  0  -0.266   2.8794  -3.4971   1.2679
 41X  C15  C  CR16  0  -0.243   3.1390  -3.2154  -0.0668
 41X  C14  C  CR16  0  -0.297   2.4708  -2.1751  -0.6984
 41X  C    C  CH1   0   0.052   1.7273   1.0143  -0.6536
 41X  O    O  O2    0  -0.488   1.9640   1.3297   0.6979
 41X  C3   C  CH2   0  -0.187   2.8026   2.4586   0.8471
 41X  C2   C  CH2   0  -0.334   2.2150   3.6720   0.1456
 41X  N    N  NH1   0  -0.589   1.9076   3.4106  -1.2529
 41X  C1   C  CH2   0  -0.324   1.1057   2.2035  -1.3852
 41X  H1   H  HCH3  0   0.234  -2.8541   2.8101   2.5332
 41X  H2   H  HCH3  0   0.234  -2.9751   3.6325   0.9702
 41X  H3   H  HCH3  0   0.236  -4.4010   3.4582   1.9924
 41X  H4   H  HCH2  0   0.222  -4.3728   0.9994   1.6960
 41X  H5   H  HCH2  0   0.221  -4.5016   1.8256   0.1407
 41X  H6   H  HCR6  0   0.280  -4.8259  -0.4500  -0.0312
 41X  H7   H  HCR6  0   0.253  -4.7386  -2.5947  -1.2041
 41X  H8   H  HCR6  0   0.252  -2.5568  -3.5375  -1.9203
 41X  H9   H  HCR6  0   0.279  -0.4812  -2.3348  -1.4348
 41X  H10  H  HCH1  0   0.257   0.7605  -0.4976  -1.7787
 41X  H11  H  HCR6  0   0.250   0.5745  -1.0965   1.8885
 41X  H12  H  HCR6  0   0.255   1.7448  -2.9441   3.0030
 41X  H13  H  HCR6  0   0.255   3.3920  -4.3116   1.7631
 41X  H14  H  HCR6  0   0.255   3.8553  -3.8086  -0.6203
 41X  H15  H  HCR6  0   0.251   2.6701  -1.9663  -1.7434
 41X  H16  H  HCH1  0   0.218   2.6783   0.7686  -1.1573
 41X  H17  H  HCH2  0   0.233   2.9126   2.6368   1.9187
 41X  H18  H  HCH2  0   0.197   3.8022   2.2464   0.4390
 41X  H19  H  HCH2  0   0.226   1.2934   3.9759   0.6524
 41X  H20  H  HCH2  0   0.240   2.9106   4.5109   0.2135
 41X  H21  H  HNH1  0   0.343   2.7742   3.2916  -1.7654
 41X  H23  H  HCH2  0   0.240   0.9898   1.9652  -2.4451
 41X  H24  H  HCH2  0   0.235   0.1095   2.4057  -0.9826

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
 41X  C7   C8   aromatic  1.380  0.020  1.380
 41X  C7   C6   aromatic  1.395  0.020  1.395
 41X  C8   C9   aromatic  1.395  0.020  1.395
 41X  C6   C5   aromatic  1.385  0.020  1.385
 41X  C9   C10  aromatic  1.387  0.020  1.387
 41X  C5   C10  aromatic  1.411  0.020  1.411
 41X  C5   O1   single    1.350  0.020  1.350
 41X  C17  C18  aromatic  1.388  0.020  1.388
 41X  C17  C16  aromatic  1.389  0.020  1.389
 41X  C10  O2   single    1.345  0.020  1.345
 41X  C18  C13  aromatic  1.391  0.020  1.391
 41X  C16  C15  aromatic  1.389  0.020  1.389
 41X  O1   C4   single    1.411  0.020  1.411
 41X  C13  C4   single    1.511  0.020  1.511
 41X  C13  C14  aromatic  1.391  0.020  1.391
 41X  C15  C14  aromatic  1.388  0.020  1.388
 41X  O2   C11  single    1.419  0.020  1.419
 41X  C4   C    single    1.526  0.020  1.526
 41X  C1   C    single    1.528  0.020  1.528
 41X  C1   N    single    1.455  0.020  1.455
 41X  C11  C12  single    1.510  0.020  1.510
 41X  C    O    single    1.408  0.020  1.408
 41X  N    C2   single    1.456  0.020  1.456
 41X  O    C3   single    1.414  0.020  1.414
 41X  C2   C3   single    1.520  0.020  1.520
 41X  C12  H1   single    0.970  0.020  1.090
 41X  C12  H2   single    0.970  0.020  1.090
 41X  C12  H3   single    0.970  0.020  1.090
 41X  C11  H4   single    0.970  0.020  1.090
 41X  C11  H5   single    0.970  0.020  1.090
 41X  C9   H6   single    0.930  0.020  1.080
 41X  C8   H7   single    0.930  0.020  1.080
 41X  C7   H8   single    0.930  0.020  1.080
 41X  C6   H9   single    0.930  0.020  1.080
 41X  C4   H10  single    0.970  0.020  1.090
 41X  C18  H11  single    0.930  0.020  1.080
 41X  C17  H12  single    0.930  0.020  1.080
 41X  C16  H13  single    0.930  0.020  1.080
 41X  C15  H14  single    0.930  0.020  1.080
 41X  C14  H15  single    0.930  0.020  1.080
 41X  C    H16  single    0.970  0.020  1.090
 41X  C3   H17  single    0.970  0.020  1.090
 41X  C3   H18  single    0.970  0.020  1.090
 41X  C2   H19  single    0.970  0.020  1.090
 41X  C2   H20  single    0.970  0.020  1.090
 41X  N    H21  single    0.890  0.020  1.040
 41X  C1   H23  single    0.970  0.020  1.090
 41X  C1   H24  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
 41X  H3   C12  H2   107.97  3.000
 41X  H3   C12  H1   107.91  3.000
 41X  H2   C12  H1   108.60  3.000
 41X  H3   C12  C11  109.46  3.000
 41X  H2   C12  C11  111.34  3.000
 41X  H1   C12  C11  111.43  3.000
 41X  H5   C11  H4   107.41  3.000
 41X  H5   C11  O2   110.37  3.000
 41X  H4   C11  O2   110.31  3.000
 41X  H5   C11  C12  110.31  3.000
 41X  H4   C11  C12  110.50  3.000
 41X  O2   C11  C12  107.95  3.000
 41X  C10  O2   C11  118.70  3.000
 41X  C5   C10  C9   119.35  3.000
 41X  C5   C10  O2   115.44  3.000
 41X  C9   C10  O2   125.21  3.000
 41X  H6   C9   C8   118.88  3.000
 41X  H6   C9   C10  120.68  3.000
 41X  C8   C9   C10  120.43  3.000
 41X  H7   C8   C7   120.60  3.000
 41X  H7   C8   C9   119.28  3.000
 41X  C7   C8   C9   120.12  3.000
 41X  H8   C7   C6   119.34  3.000
 41X  H8   C7   C8   120.66  3.000
 41X  C6   C7   C8   120.00  3.000
 41X  H9   C6   C5   120.77  3.000
 41X  H9   C6   C7   118.88  3.000
 41X  C5   C6   C7   120.35  3.000
 41X  O1   C5   C6   125.37  3.000
 41X  O1   C5   C10  114.89  3.000
 41X  C6   C5   C10  119.74  3.000
 41X  C4   O1   C5   119.57  3.000
 41X  H10  C4   C    106.48  3.000
 41X  H10  C4   C13  109.04  3.000
 41X  C    C4   C13  111.32  3.000
 41X  H10  C4   O1   110.14  3.000
 41X  C    C4   O1   107.30  3.000
 41X  C13  C4   O1   112.39  3.000
 41X  C14  C13  C18  119.11  3.000
 41X  C14  C13  C4   119.17  3.000
 41X  C18  C13  C4   121.69  3.000
 41X  H11  C18  C17  119.42  3.000
 41X  H11  C18  C13  120.33  3.000
 41X  C17  C18  C13  120.25  3.000
 41X  H12  C17  C16  119.98  3.000
 41X  H12  C17  C18  119.61  3.000
 41X  C16  C17  C18  120.42  3.000
 41X  H13  C16  C15  120.26  3.000
 41X  H13  C16  C17  120.18  3.000
 41X  C15  C16  C17  119.56  3.000
 41X  H14  C15  C14  119.77  3.000
 41X  H14  C15  C16  120.27  3.000
 41X  C14  C15  C16  119.96  3.000
 41X  H15  C14  C15  119.63  3.000
 41X  H15  C14  C13  119.66  3.000
 41X  C15  C14  C13  120.71  3.000
 41X  H16  C    C1   107.76  3.000
 41X  H16  C    O    110.07  3.000
 41X  C1   C    O    110.71  3.000
 41X  H16  C    C4   106.27  3.000
 41X  O    C    C4   108.52  3.000
 41X  C1   C    C4   113.40  3.000
 41X  C3   O    C    112.32  3.000
 41X  H18  C3   H17  107.70  3.000
 41X  H18  C3   C2   109.51  3.000
 41X  H17  C3   C2   111.21  3.000
 41X  H18  C3   O    110.22  3.000
 41X  H17  C3   O    107.08  3.000
 41X  C2   C3   O    111.06  3.000
 41X  H20  C2   H19  107.11  3.000
 41X  H20  C2   N    109.41  3.000
 41X  H19  C2   N    108.47  3.000
 41X  H20  C2   C3   109.78  3.000
 41X  H19  C2   C3   109.47  3.000
 41X  N    C2   C3   112.44  3.000
 41X  H21  N    C1   109.13  3.000
 41X  H21  N    C2   109.04  3.000
 41X  C1   N    C2   110.65  3.000
 41X  H24  C1   H23  107.51  3.000
 41X  H24  C1   N    108.37  3.000
 41X  H23  C1   N    109.13  3.000
 41X  H24  C1   C    109.77  3.000
 41X  H23  C1   C    109.74  3.000
 41X  N    C1   C    112.20  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
 41X  CONST_01  C7   C8   C9   C10    0.00   0.0  0
 41X  CONST_02  C7   C6   C5   C10    0.00   0.0  0
 41X  CONST_03  C6   C7   C8   C9     0.00   0.0  0
 41X  CONST_04  C6   C5   C10  C9     0.00   0.0  0
 41X  CONST_05  C5   C6   C7   C8     0.00   0.0  0
 41X  CONST_06  C5   C10  C9   C8     0.00   0.0  0
 41X  CONST_07  C16  C17  C18  C13    0.00   0.0  0
 41X  CONST_08  C16  C15  C14  C13    0.00   0.0  0
 41X  CONST_09  C15  C16  C17  C18    0.00   0.0  0
 41X  CONST_10  C15  C14  C13  C18    0.00   0.0  0
 41X  CONST_11  C14  C13  C18  C17    0.00   0.0  0
 41X  CONST_12  C14  C15  C16  C17    0.00   0.0  0
 41X  CONST_13  C8   C9   C10  O2   180.00   0.0  0
 41X  CONST_14  C6   C5   C10  O2   180.00   0.0  0
 41X  CONST_15  O1   C5   C10  C9   180.00   0.0  0
 41X  CONST_16  O1   C5   C6   C7   180.00   0.0  0
 41X  CONST_17  C17  C18  C13  C4   180.00   0.0  0
 41X  CONST_18  C15  C14  C13  C4   180.00   0.0  0
 41X  CONST_19  H7   C8   C9   C10  180.00   0.0  0
 41X  CONST_20  H9   C6   C5   C10  180.00   0.0  0
 41X  CONST_21  H8   C7   C8   C9   180.00   0.0  0
 41X  CONST_22  H6   C9   C8   C7   180.00   0.0  0
 41X  CONST_23  H12  C17  C18  C13  180.00   0.0  0
 41X  CONST_24  H14  C15  C14  C13  180.00   0.0  0
 41X  CONST_25  H13  C16  C17  C18  180.00   0.0  0
 41X  CONST_26  H15  C14  C13  C18  180.00   0.0  0
 41X  CONST_27  H11  C18  C17  C16  180.00   0.0  0
 41X  Var_01    C2   N    C1   C    -51.50  30.0  1
 41X  Var_02    C2   C3   O    C     57.34  30.0  1
 41X  Var_03    N    C2   C3   O    -53.98  30.0  1
 41X  Var_04    C1   N    C2   C3    51.20  30.0  1
 41X  Var_05    C9   C10  O2   C11   -0.38  30.0  1
 41X  Var_06    H4   C11  O2   C10   59.54  30.0  3
 41X  Var_07    H1   C12  C11  O2   -61.00  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
 41X  chir_01  C4  O1  C13  C   positiv
 41X  chir_02  C   O   C4   C1  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
 41X  plan-1  O2   0.020
 41X  plan-1  C10  0.020
 41X  plan-1  C9   0.020
 41X  plan-1  C8   0.020
 41X  plan-1  C7   0.020
 41X  plan-1  C6   0.020
 41X  plan-1  C5   0.020
 41X  plan-1  O1   0.020
 41X  plan-1  H6   0.020
 41X  plan-1  H7   0.020
 41X  plan-1  H8   0.020
 41X  plan-1  H9   0.020
 41X  plan-2  C4   0.020
 41X  plan-2  C13  0.020
 41X  plan-2  C18  0.020
 41X  plan-2  C17  0.020
 41X  plan-2  C16  0.020
 41X  plan-2  C15  0.020
 41X  plan-2  C14  0.020
 41X  plan-2  H11  0.020
 41X  plan-2  H12  0.020
 41X  plan-2  H13  0.020
 41X  plan-2  H14  0.020
 41X  plan-2  H15  0.020

