# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 08:03:09 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: (2R)-2-(methoxymethyl)-4-(pyridin-2-yl)morpholine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC[C@H]1CN(CCO1)c2ccccn2
#
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
 O2J  O2J  (2R)-2-(methoxymethyl)-4-(pyridin-2-yl)morpholine  ligand  31  15  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O2J
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
 O2J  N1   N  NT    0  -0.519  -0.5762   0.4065   0.2841
 O2J  C4   C  CH2   0  -0.293   0.4929  -0.5769   0.2868
 O2J  C5   C  CH2   0  -0.318  -0.2405   1.6310   0.9825
 O2J  C6   C  CH2   0  -0.185   1.0929   2.1585   0.4879
 O2J  C7   C  CR6   0   0.542  -1.8776  -0.0245   0.1942
 O2J  C8   C  CR16  0  -0.412  -2.9709   0.7865   0.5614
 O2J  C10  C  CR16  0  -0.366  -4.4423  -0.9818  -0.1282
 O2J  C1   C  CH3   0  -0.398   5.1813  -1.2926  -0.5538
 O2J  O1   O  O2    0  -0.485   4.0919  -0.4085  -0.6228
 O2J  C2   C  CH2   0  -0.139   2.9327  -0.9428  -0.0435
 O2J  C3   C  CH1   0  -0.010   1.7994   0.0501  -0.1753
 O2J  O2   O  O2    0  -0.486   2.1120   1.1939   0.5889
 O2J  C9   C  CR16  0  -0.149  -4.2479   0.2951   0.3890
 O2J  C11  C  CR16  0  -0.061  -3.3081  -1.7064  -0.4410
 O2J  N2   N  N     0  -0.477  -2.0710  -1.2537  -0.2849
 O2J  H1   H  HCH2  0   0.223   0.6185  -1.0026   1.2938
 O2J  H2   H  HCH2  0   0.269   0.2292  -1.3923  -0.3812
 O2J  H3   H  HCH2  0   0.260  -0.9834   2.4021   0.7866
 O2J  H4   H  HCH2  0   0.231  -0.2060   1.4708   2.0687
 O2J  H5   H  HCH2  0   0.208   0.9842   2.4956  -0.5524
 O2J  H6   H  HCH2  0   0.247   1.3914   3.0182   1.0891
 O2J  H7   H  HCR6  0   0.268  -2.8391   1.7740   0.9770
 O2J  H8   H  HCR6  0   0.258  -5.4286  -1.3982  -0.2737
 O2J  H9   H  HCH3  0   0.235   6.0307  -0.8205  -1.0459
 O2J  H10  H  HCH3  0   0.205   5.4635  -1.5195   0.4812
 O2J  H11  H  HCH3  0   0.204   4.9716  -2.2425  -1.0605
 O2J  H12  H  HCH2  0   0.207   2.6386  -1.8781  -0.5415
 O2J  H13  H  HCH2  0   0.204   3.0947  -1.1839   1.0178
 O2J  H14  H  HCH1  0   0.216   1.6883   0.3310  -1.2350
 O2J  H15  H  HCR6  0   0.267  -5.0948   0.9100   0.6663
 O2J  H16  H  HCR6  0   0.254  -3.3955  -2.7122  -0.8393

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
 O2J  C1   O1   single    1.405  0.020  1.405
 O2J  O1   C2   single    1.402  0.020  1.402
 O2J  C2   C3   single    1.512  0.020  1.512
 O2J  C3   C4   single    1.521  0.020  1.521
 O2J  C3   O2   single    1.411  0.020  1.411
 O2J  C4   N1   single    1.453  0.020  1.453
 O2J  O2   C6   single    1.407  0.020  1.407
 O2J  N2   C11  aromatic  1.327  0.020  1.327
 O2J  N2   C7   aromatic  1.333  0.020  1.333
 O2J  N1   C7   single    1.374  0.020  1.374
 O2J  N1   C5   single    1.449  0.020  1.449
 O2J  C6   C5   single    1.517  0.020  1.517
 O2J  C11  C10  aromatic  1.382  0.020  1.382
 O2J  C7   C8   aromatic  1.410  0.020  1.410
 O2J  C10  C9   aromatic  1.391  0.020  1.391
 O2J  C8   C9   aromatic  1.379  0.020  1.379
 O2J  C4   H1   single    0.970  0.020  1.090
 O2J  C4   H2   single    0.970  0.020  1.090
 O2J  C5   H3   single    0.970  0.020  1.090
 O2J  C5   H4   single    0.970  0.020  1.090
 O2J  C6   H5   single    0.970  0.020  1.090
 O2J  C6   H6   single    0.970  0.020  1.090
 O2J  C8   H7   single    0.930  0.020  1.080
 O2J  C10  H8   single    0.930  0.020  1.080
 O2J  C1   H9   single    0.970  0.020  1.090
 O2J  C1   H10  single    0.970  0.020  1.090
 O2J  C1   H11  single    0.970  0.020  1.090
 O2J  C2   H12  single    0.970  0.020  1.090
 O2J  C2   H13  single    0.970  0.020  1.090
 O2J  C3   H14  single    0.970  0.020  1.090
 O2J  C9   H15  single    0.930  0.020  1.080
 O2J  C11  H16  single    0.930  0.020  1.080

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
 O2J  C7   N1   C5   121.06  3.000
 O2J  C5   N1   C4   113.62  3.000
 O2J  C7   N1   C4   119.01  3.000
 O2J  H2   C4   H1   107.46  3.000
 O2J  H2   C4   C3   109.33  3.000
 O2J  H1   C4   C3   109.84  3.000
 O2J  H2   C4   N1   109.16  3.000
 O2J  H1   C4   N1   110.34  3.000
 O2J  C3   C4   N1   110.64  3.000
 O2J  H4   C5   H3   107.62  3.000
 O2J  H4   C5   C6   110.21  3.000
 O2J  H3   C5   C6   107.15  3.000
 O2J  H4   C5   N1   111.14  3.000
 O2J  H3   C5   N1   110.72  3.000
 O2J  C6   C5   N1   109.90  3.000
 O2J  H6   C6   H5   107.89  3.000
 O2J  H6   C6   O2   107.62  3.000
 O2J  H5   C6   O2   110.48  3.000
 O2J  H6   C6   C5   109.57  3.000
 O2J  H5   C6   C5   109.17  3.000
 O2J  O2   C6   C5   112.02  3.000
 O2J  N2   C7   C8   120.76  3.000
 O2J  C8   C7   N1   122.49  3.000
 O2J  N2   C7   N1   116.75  3.000
 O2J  H7   C8   C9   119.15  3.000
 O2J  H7   C8   C7   122.12  3.000
 O2J  C9   C8   C7   118.72  3.000
 O2J  H8   C10  C11  121.12  3.000
 O2J  H8   C10  C9   122.09  3.000
 O2J  C11  C10  C9   116.79  3.000
 O2J  H11  C1   H10  107.82  3.000
 O2J  H11  C1   H9   108.41  3.000
 O2J  H10  C1   H9   108.39  3.000
 O2J  H11  C1   O1   111.97  3.000
 O2J  H10  C1   O1   112.10  3.000
 O2J  H9   C1   O1   108.04  3.000
 O2J  C2   O1   C1   112.41  3.000
 O2J  H13  C2   H12  106.85  3.000
 O2J  H13  C2   C3   109.77  3.000
 O2J  H12  C2   C3   108.57  3.000
 O2J  H13  C2   O1   111.13  3.000
 O2J  H12  C2   O1   110.98  3.000
 O2J  C3   C2   O1   109.48  3.000
 O2J  H14  C3   O2   109.67  3.000
 O2J  H14  C3   C2   109.07  3.000
 O2J  O2   C3   C2   108.60  3.000
 O2J  H14  C3   C4   108.10  3.000
 O2J  O2   C3   C4   111.10  3.000
 O2J  C2   C3   C4   110.28  3.000
 O2J  C3   O2   C6   110.89  3.000
 O2J  H15  C9   C10  120.48  3.000
 O2J  H15  C9   C8   119.34  3.000
 O2J  C10  C9   C8   120.18  3.000
 O2J  H16  C11  N2   115.76  3.000
 O2J  H16  C11  C10  120.19  3.000
 O2J  N2   C11  C10  124.05  3.000
 O2J  C11  N2   C7   119.48  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
 O2J  CONST_01  C10  C11  N2   C7     0.00   0.0  0
 O2J  CONST_02  C10  C9   C8   C7     0.00   0.0  0
 O2J  CONST_03  C11  N2   C7   C8     0.00   0.0  0
 O2J  CONST_04  C11  C10  C9   C8     0.00   0.0  0
 O2J  CONST_05  N2   C11  C10  C9     0.00   0.0  0
 O2J  CONST_06  N2   C7   C8   C9     0.00   0.0  0
 O2J  CONST_07  C11  N2   C7   N1   180.00   0.0  0
 O2J  CONST_08  C9   C8   C7   N1   180.00   0.0  0
 O2J  CONST_09  H7   C8   C7   N1     0.00   0.0  0
 O2J  CONST_10  H16  C11  N2   C7   180.00   0.0  0
 O2J  CONST_11  H15  C9   C8   C7   180.00   0.0  0
 O2J  CONST_12  H8   C10  C9   C8   180.00   0.0  0
 O2J  Var_01    O2   C6   C5   N1   -54.63  30.0  1
 O2J  Var_02    N2   C7   N1   C4   -19.76  30.0  2
 O2J  Var_03    C6   C5   N1   C4    50.56  30.0  1
 O2J  Var_04    C3   C4   N1   C5   -50.78  30.0  1
 O2J  Var_05    C3   C2   O1   C1  -179.02  30.0  3
 O2J  Var_06    H9   C1   O1   C2   178.45  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
 O2J  chir_01  C3  C2  C4  O2  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
 O2J  plan-1  N1   0.020
 O2J  plan-1  C7   0.020
 O2J  plan-1  C8   0.020
 O2J  plan-1  C10  0.020
 O2J  plan-1  C9   0.020
 O2J  plan-1  C11  0.020
 O2J  plan-1  N2   0.020
 O2J  plan-1  H7   0.020
 O2J  plan-1  H8   0.020
 O2J  plan-1  H15  0.020
 O2J  plan-1  H16  0.020

