# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 20:42:17 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: N-{(1S,2S)-3-(3,5-difluorophenyl)-1-[(3R,5S,6R)-6-(2,2-dimethylpropoxy)-5-methylmorpholin-3-yl]-1-hydroxypropan-2-yl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1N[C@H](CO[C@H]1OCC(C)(C)C)[C@@H](O)[C@H](Cc2cc(F)cc(F)c2)NC(C)=O
#
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
 DKJ  DKJ  N-{(1S,2S)-3-(3,5-difluorophenyl)-1-[(3R,5S,6R)-6-(2,2-dimethylpropoxy)-5-methylmorpholin-3-yl]-1-hydroxypropan-2-yl}acetamide  ligand  61  29  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DKJ
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
 DKJ  O1   O  O     0  -0.495  -2.2083   2.8262  -0.7961
 DKJ  C7   C  C     0   0.525  -2.2195   2.3023   0.3094
 DKJ  O2   O  O2    0  -0.504   2.5991   0.5901   1.6145
 DKJ  C6   C  CR6   0   0.560  -4.9721  -2.1618   0.3930
 DKJ  C1   C  CR16  0  -0.493  -4.6973   0.3116  -0.7740
 DKJ  N1   N  NH1   0  -0.593   2.1956   1.6788  -0.9650
 DKJ  C5   C  CR6   0   0.562  -5.8593  -0.0480  -0.1194
 DKJ  C4   C  CR6   0   0.179  -3.6473  -0.5995  -0.8399
 DKJ  C3   C  CR16  0  -0.574  -6.0331  -1.2801   0.4795
 DKJ  C2   C  CR16  0  -0.477  -3.7906  -1.8535  -0.2502
 DKJ  C8   C  CH2   0  -0.177   1.5373   0.0934   0.8133
 DKJ  C9   C  CH1   0  -0.133   1.0807   1.1406  -0.1985
 DKJ  C10  C  CH1   0  -0.166   3.2909   2.1336  -0.1156
 DKJ  C11  C  CH1   0   0.313   3.7064   1.0519   0.8824
 DKJ  C12  C  CH3   0  -0.773  -2.7972   2.9968   1.5174
 DKJ  C13  C  CH3   0  -0.672   2.9449   3.4348   0.5966
 DKJ  C14  C  CH3   0  -0.638   6.7810  -1.0836  -0.8063
 DKJ  C15  C  CH3   0  -0.638   4.8183  -2.6375  -0.9152
 DKJ  C16  C  CH3   0  -0.645   6.5085  -2.8763   0.9085
 DKJ  C17  C  CH2   0  -0.524  -2.3556  -0.2247  -1.5055
 DKJ  C19  C  CH1   0   0.019   0.0122   0.6384  -1.1732
 DKJ  C20  C  CH1   0  -0.115  -1.2700   0.1453  -0.4765
 DKJ  C21  C  CT    0  -0.145   5.7667  -1.8807   0.0157
 DKJ  N2   N  NH1   0  -0.638  -1.7466   1.0631   0.5387
 DKJ  O3   O  OH1   0  -0.660   0.5110  -0.3589  -2.0423
 DKJ  O4   O  O2    0  -0.497   4.3179   0.0325   0.1626
 DKJ  F1   F  F     0  -0.310  -6.8657   0.8351  -0.0598
 DKJ  F2   F  F     0  -0.310  -5.1046  -3.3698   0.9584
 DKJ  H1   H  HCR6  0   0.275  -4.6124   1.2910  -1.2273
 DKJ  H33  H  HNH1  0   0.342   2.5448   0.9588  -1.5875
 DKJ  H3   H  HCR6  0   0.301  -6.9520  -1.5427   0.9869
 DKJ  H2   H  HCR6  0   0.276  -2.9924  -2.5839  -0.2946
 DKJ  H5   H  HCH2  0   0.198   1.8446  -0.8334   0.3102
 DKJ  H4   H  HCH2  0   0.231   0.7360  -0.1612   1.5098
 DKJ  H6   H  HCH1  0   0.242   0.6390   1.9690   0.3613
 DKJ  H7   H  HCH1  0   0.246   4.1464   2.3265  -0.7688
 DKJ  H8   H  HCH1  0   0.210   4.3928   1.4593   1.6389
 DKJ  H10  H  HCH3  0   0.266  -3.8853   2.9156   1.4872
 DKJ  H9   H  HCH3  0   0.253  -2.4564   2.5760   2.4616
 DKJ  H11  H  HCH3  0   0.264  -2.5467   4.0554   1.4919
 DKJ  H12  H  HCH3  0   0.226   2.1617   3.3091   1.3441
 DKJ  H13  H  HCH3  0   0.233   3.8217   3.8347   1.1069
 DKJ  H14  H  HCH3  0   0.236   2.6092   4.1793  -0.1249
 DKJ  H17  H  HCH3  0   0.221   7.3994  -1.7559  -1.4043
 DKJ  H15  H  HCH3  0   0.230   6.2941  -0.3869  -1.4889
 DKJ  H16  H  HCH3  0   0.217   7.4485  -0.5092  -0.1600
 DKJ  H20  H  HCH3  0   0.222   5.3743  -3.3122  -1.5700
 DKJ  H19  H  HCH3  0   0.218   4.1068  -3.2413  -0.3464
 DKJ  H18  H  HCH3  0   0.229   4.2470  -1.9565  -1.5467
 DKJ  H23  H  HCH3  0   0.224   7.1978  -2.3682   1.5873
 DKJ  H21  H  HCH3  0   0.224   5.8157  -3.4648   1.5141
 DKJ  H22  H  HCH3  0   0.230   7.0935  -3.5736   0.3058
 DKJ  H25  H  HCH2  0   0.267  -1.9894  -1.0652  -2.0955
 DKJ  H24  H  HCH2  0   0.264  -2.5145   0.6051  -2.1947
 DKJ  H26  H  HCH2  0   0.206   4.2551  -1.5430   1.5150
 DKJ  H27  H  HCH2  0   0.202   5.6555  -0.4720   1.6498
 DKJ  H28  H  HCH1  0   0.249  -0.2396   1.4808  -1.8209
 DKJ  H29  H  HCH1  0   0.272  -1.0218  -0.7684   0.0731
 DKJ  H31  H  HNH1  0   0.405  -1.8222   0.7016   1.4744
 DKJ  H32  H  HOH1  0   0.445   0.6319  -1.1807  -1.5549
 DKJ  C18  C  CH2   0  -0.102   4.9734  -0.9516   0.9316

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
 DKJ  F1   C5   single    1.340  0.020  1.340
 DKJ  C3   C5   aromatic  1.381  0.020  1.381
 DKJ  C3   C6   aromatic  1.382  0.020  1.382
 DKJ  C5   C1   aromatic  1.381  0.020  1.381
 DKJ  F2   C6   single    1.340  0.020  1.340
 DKJ  C6   C2   aromatic  1.380  0.020  1.380
 DKJ  C1   C4   aromatic  1.392  0.020  1.392
 DKJ  C2   C4   aromatic  1.393  0.020  1.393
 DKJ  C4   C17  single    1.501  0.020  1.501
 DKJ  C17  C20  single    1.541  0.020  1.541
 DKJ  O1   C7   double    1.223  0.020  1.223
 DKJ  C20  N2   single    1.449  0.020  1.449
 DKJ  C20  C19  single    1.540  0.020  1.540
 DKJ  C7   C12  single    1.508  0.020  1.508
 DKJ  C7   N2   single    1.346  0.020  1.346
 DKJ  C16  C21  single    1.529  0.020  1.529
 DKJ  O3   C19  single    1.414  0.020  1.414
 DKJ  C14  C21  single    1.530  0.020  1.530
 DKJ  C19  C9   single    1.531  0.020  1.531
 DKJ  C21  C15  single    1.529  0.020  1.529
 DKJ  C21  C18  single    1.527  0.020  1.527
 DKJ  C8   C9   single    1.526  0.020  1.526
 DKJ  C8   O2   single    1.420  0.020  1.420
 DKJ  C9   N1   single    1.456  0.020  1.456
 DKJ  C18  O4   single    1.410  0.020  1.410
 DKJ  O2   C11  single    1.405  0.020  1.405
 DKJ  O4   C11  single    1.390  0.020  1.390
 DKJ  N1   C10  single    1.459  0.020  1.459
 DKJ  C11  C10  single    1.529  0.020  1.529
 DKJ  C10  C13  single    1.523  0.020  1.523
 DKJ  C1   H1   single    0.930  0.020  1.080
 DKJ  N1   H33  single    0.890  0.020  1.040
 DKJ  C3   H3   single    0.930  0.020  1.080
 DKJ  C2   H2   single    0.930  0.020  1.080
 DKJ  C8   H5   single    0.970  0.020  1.090
 DKJ  C8   H4   single    0.970  0.020  1.090
 DKJ  C9   H6   single    0.970  0.020  1.090
 DKJ  C10  H7   single    0.970  0.020  1.090
 DKJ  C11  H8   single    0.970  0.020  1.090
 DKJ  C12  H10  single    0.970  0.020  1.090
 DKJ  C12  H9   single    0.970  0.020  1.090
 DKJ  C12  H11  single    0.970  0.020  1.090
 DKJ  C13  H12  single    0.970  0.020  1.090
 DKJ  C13  H13  single    0.970  0.020  1.090
 DKJ  C13  H14  single    0.970  0.020  1.090
 DKJ  C14  H17  single    0.970  0.020  1.090
 DKJ  C14  H15  single    0.970  0.020  1.090
 DKJ  C14  H16  single    0.970  0.020  1.090
 DKJ  C15  H20  single    0.970  0.020  1.090
 DKJ  C15  H19  single    0.970  0.020  1.090
 DKJ  C15  H18  single    0.970  0.020  1.090
 DKJ  C16  H23  single    0.970  0.020  1.090
 DKJ  C16  H21  single    0.970  0.020  1.090
 DKJ  C16  H22  single    0.970  0.020  1.090
 DKJ  C17  H25  single    0.970  0.020  1.090
 DKJ  C17  H24  single    0.970  0.020  1.090
 DKJ  C18  H26  single    0.970  0.020  1.090
 DKJ  C18  H27  single    0.970  0.020  1.090
 DKJ  C19  H28  single    0.970  0.020  1.090
 DKJ  C20  H29  single    0.970  0.020  1.090
 DKJ  N2   H31  single    0.860  0.020  1.020
 DKJ  O3   H32  single    0.850  0.020  0.980

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
 DKJ  N2   C7   C12  114.96  3.000
 DKJ  N2   C7   O1   123.02  3.000
 DKJ  C12  C7   O1   122.00  3.000
 DKJ  C11  O2   C8   114.22  3.000
 DKJ  F2   C6   C2   118.85  3.000
 DKJ  C2   C6   C3   122.94  3.000
 DKJ  F2   C6   C3   118.21  3.000
 DKJ  H1   C1   C4   120.88  3.000
 DKJ  H1   C1   C5   120.00  3.000
 DKJ  C4   C1   C5   119.12  3.000
 DKJ  H33  N1   C10  108.68  3.000
 DKJ  H33  N1   C9   108.93  3.000
 DKJ  C10  N1   C9   112.56  3.000
 DKJ  F1   C5   C3   118.30  3.000
 DKJ  C3   C5   C1   122.94  3.000
 DKJ  F1   C5   C1   118.76  3.000
 DKJ  C17  C4   C2   120.07  3.000
 DKJ  C17  C4   C1   120.46  3.000
 DKJ  C2   C4   C1   119.45  3.000
 DKJ  H3   C3   C5   121.79  3.000
 DKJ  H3   C3   C6   121.76  3.000
 DKJ  C5   C3   C6   116.45  3.000
 DKJ  H2   C2   C4   120.93  3.000
 DKJ  H2   C2   C6   119.97  3.000
 DKJ  C4   C2   C6   119.10  3.000
 DKJ  H4   C8   H5   107.50  3.000
 DKJ  H4   C8   C9   111.31  3.000
 DKJ  H5   C8   C9   111.04  3.000
 DKJ  H4   C8   O2   105.69  3.000
 DKJ  H5   C8   O2   110.15  3.000
 DKJ  C9   C8   O2   110.97  3.000
 DKJ  H6   C9   C19  107.02  3.000
 DKJ  H6   C9   C8   107.54  3.000
 DKJ  C19  C9   C8   113.95  3.000
 DKJ  H6   C9   N1   107.39  3.000
 DKJ  C8   C9   N1   111.93  3.000
 DKJ  C19  C9   N1   108.69  3.000
 DKJ  H7   C10  C13  107.83  3.000
 DKJ  H7   C10  C11  107.58  3.000
 DKJ  C13  C10  C11  111.15  3.000
 DKJ  H7   C10  N1   107.14  3.000
 DKJ  C13  C10  N1   111.59  3.000
 DKJ  C11  C10  N1   111.31  3.000
 DKJ  H8   C11  O4   110.69  3.000
 DKJ  H8   C11  C10  110.88  3.000
 DKJ  O4   C11  C10  107.48  3.000
 DKJ  H8   C11  O2   104.78  3.000
 DKJ  C10  C11  O2   111.00  3.000
 DKJ  O4   C11  O2   112.05  3.000
 DKJ  H11  C12  H9   108.93  3.000
 DKJ  H11  C12  H10  107.53  3.000
 DKJ  H9   C12  H10  107.90  3.000
 DKJ  H11  C12  C7   109.94  3.000
 DKJ  H9   C12  C7   113.38  3.000
 DKJ  H10  C12  C7   108.99  3.000
 DKJ  H14  C13  H13  107.88  3.000
 DKJ  H14  C13  H12  108.15  3.000
 DKJ  H13  C13  H12  107.41  3.000
 DKJ  H14  C13  C10  110.12  3.000
 DKJ  H13  C13  C10  110.45  3.000
 DKJ  H12  C13  C10  112.67  3.000
 DKJ  H16  C14  H15  107.90  3.000
 DKJ  H16  C14  H17  107.57  3.000
 DKJ  H15  C14  H17  107.67  3.000
 DKJ  H16  C14  C21  111.18  3.000
 DKJ  H15  C14  C21  111.92  3.000
 DKJ  H17  C14  C21  110.43  3.000
 DKJ  H18  C15  H19  107.79  3.000
 DKJ  H18  C15  H20  107.77  3.000
 DKJ  H19  C15  H20  107.59  3.000
 DKJ  H18  C15  C21  111.61  3.000
 DKJ  H19  C15  C21  111.12  3.000
 DKJ  H20  C15  C21  110.79  3.000
 DKJ  H22  C16  H21  107.57  3.000
 DKJ  H22  C16  H23  107.58  3.000
 DKJ  H21  C16  H23  107.83  3.000
 DKJ  H22  C16  C21  110.70  3.000
 DKJ  H21  C16  C21  111.52  3.000
 DKJ  H23  C16  C21  111.46  3.000
 DKJ  H24  C17  H25  107.07  3.000
 DKJ  H24  C17  C20  110.00  3.000
 DKJ  H25  C17  C20  108.05  3.000
 DKJ  H24  C17  C4   110.18  3.000
 DKJ  H25  C17  C4   109.67  3.000
 DKJ  C20  C17  C4   111.73  3.000
 DKJ  H28  C19  O3   105.13  3.000
 DKJ  H28  C19  C20  108.86  3.000
 DKJ  O3   C19  C20  110.24  3.000
 DKJ  H28  C19  C9   106.59  3.000
 DKJ  O3   C19  C9   112.12  3.000
 DKJ  C20  C19  C9   113.45  3.000
 DKJ  H29  C20  N2   104.56  3.000
 DKJ  H29  C20  C19  107.79  3.000
 DKJ  N2   C20  C19  112.82  3.000
 DKJ  H29  C20  C17  107.13  3.000
 DKJ  C19  C20  C17  111.18  3.000
 DKJ  N2   C20  C17  112.84  3.000
 DKJ  C18  C21  C16  107.33  3.000
 DKJ  C18  C21  C15  110.12  3.000
 DKJ  C16  C21  C15  109.51  3.000
 DKJ  C18  C21  C14  110.48  3.000
 DKJ  C15  C21  C14  110.00  3.000
 DKJ  C16  C21  C14  109.35  3.000
 DKJ  H31  N2   C20  116.66  3.000
 DKJ  H31  N2   C7   117.58  3.000
 DKJ  C20  N2   C7   125.40  3.000
 DKJ  H32  O3   C19  109.58  3.000
 DKJ  C18  O4   C11  115.72  3.000
 DKJ  H27  C18  H26  107.06  3.000
 DKJ  H27  C18  O4   109.86  3.000
 DKJ  H26  C18  O4   111.18  3.000
 DKJ  H27  C18  C21  109.55  3.000
 DKJ  H26  C18  C21  109.32  3.000
 DKJ  O4   C18  C21  109.81  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
 DKJ  CONST_01  C1   C5   C3   C6      0.00   0.0  0
 DKJ  CONST_02  C1   C4   C2   C6      0.00   0.0  0
 DKJ  CONST_03  C2   C6   C3   C5      0.00   0.0  0
 DKJ  CONST_04  C2   C4   C1   C5      0.00   0.0  0
 DKJ  CONST_05  C3   C5   C1   C4      0.00   0.0  0
 DKJ  CONST_06  C3   C6   C2   C4      0.00   0.0  0
 DKJ  CONST_07  F1   C5   C3   C6    180.00   0.0  0
 DKJ  CONST_08  C17  C4   C2   C6    180.00   0.0  0
 DKJ  CONST_09  F2   C6   C3   C5    180.00   0.0  0
 DKJ  CONST_10  C17  C4   C1   C5    180.00   0.0  0
 DKJ  CONST_11  F1   C5   C1   C4    180.00   0.0  0
 DKJ  CONST_12  F2   C6   C2   C4    180.00   0.0  0
 DKJ  CONST_13  H3   C3   C5   C1    180.00   0.0  0
 DKJ  CONST_14  H2   C2   C4   C1    180.00   0.0  0
 DKJ  CONST_15  H1   C1   C5   C3    180.00   0.0  0
 DKJ  CONST_16  C20  N2   C7   O1      0.00   0.0  0
 DKJ  CONST_17  C20  N2   C7   C12   180.00   0.0  0
 DKJ  CONST_18  H31  N2   C7   O1    180.00   0.0  0
 DKJ  Var_01    H5   C8   O2   C11    67.84  30.0  1
 DKJ  Var_02    C20  C17  C4   C1    101.17  30.0  2
 DKJ  Var_03    C21  C18  O4   C11  -171.63  30.0  1
 DKJ  Var_04    O4   C18  C21  C14    58.01  30.0  3
 DKJ  Var_05    H10  C12  C7   O1     78.74  30.0  3
 DKJ  Var_06    H23  C16  C21  C14    59.32  30.0  3
 DKJ  Var_07    H20  C15  C21  C14    58.48  30.0  3
 DKJ  Var_08    H17  C14  C21  C15   -62.52  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
 DKJ  chir_01  C9   C19  C8   N1   negativ
 DKJ  chir_02  C10  N1   C11  C13  positiv
 DKJ  chir_03  C11  O2   O4   C10  negativ
 DKJ  chir_04  C19  O3   C9   C20  positiv
 DKJ  chir_05  C20  N2   C17  C19  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
 DKJ  plan-1  C6   0.020
 DKJ  plan-1  C1   0.020
 DKJ  plan-1  C5   0.020
 DKJ  plan-1  C4   0.020
 DKJ  plan-1  C3   0.020
 DKJ  plan-1  C2   0.020
 DKJ  plan-1  C17  0.020
 DKJ  plan-1  F1   0.020
 DKJ  plan-1  F2   0.020
 DKJ  plan-1  H1   0.020
 DKJ  plan-1  H3   0.020
 DKJ  plan-1  H2   0.020
 DKJ  plan-2  O1   0.020
 DKJ  plan-2  C7   0.020
 DKJ  plan-2  C12  0.020
 DKJ  plan-2  C20  0.020
 DKJ  plan-2  N2   0.020
 DKJ  plan-2  H31  0.020

