# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 21:42:55 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: N-[(1S,2S)-1-[(3R,6R)-6-(cyclohexylmethoxy)morpholin-3-yl]-3-(3,5-difluorophenyl)-1-hydroxypropan-2-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H](Cc1cc(F)cc(F)c1)[C@H](O)[C@H]2CO[C@H](CN2)OCC3CCCCC3
#
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
 DK7  DK7  N-[(1S,2S)-1-[(3R,6R)-6-(cyclohexylmethoxy)morpholin-3-yl]-3-(3,5-difluorophenyl)-1-hydroxypropan-2-yl]acetamide  ligand  62  30  .  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_DK7
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
 DK7  C6   C  CR6   0   0.558   6.2645  -0.5548   0.6651
 DK7  C1   C  CR6   0   0.182   4.0721   0.3411   0.9911
 DK7  C5   C  CR16  0  -0.576   6.7371   0.6396   0.1542
 DK7  C3   C  CR6   0   0.559   5.8295   1.6778   0.0767
 DK7  C2   C  CR16  0  -0.488   4.5141   1.5569   0.4791
 DK7  F4   F  F     0  -0.312   6.2501   2.8540  -0.4108
 DK7  F7   F  F     0  -0.311   7.1179  -1.5846   0.7594
 DK7  C8   C  CR16  0  -0.482   4.9612  -0.7275   1.0847
 DK7  C9   C  CH2   0  -0.522   2.6445   0.1719   1.4212
 DK7  C10  C  CH1   0  -0.102   1.8186  -0.6196   0.3911
 DK7  C12  C  CH1   0   0.055   0.3322  -0.6873   0.7994
 DK7  O14  O  OH1   0  -0.660   0.2319  -1.3063   2.0644
 DK7  C15  C  CH1   0  -0.168  -0.5501  -1.3812  -0.2550
 DK7  N17  N  NH1   0  -0.570  -0.8734  -0.4506  -1.3281
 DK7  C18  C  CH2   0  -0.349  -1.7761  -1.0424  -2.2956
 DK7  C19  C  CH1   0   0.281  -3.0253  -1.6193  -1.6487
 DK7  O21  O  O2    0  -0.504  -3.7810  -0.5483  -1.1740
 DK7  C22  C  CH2   0  -0.117  -5.0532  -0.8796  -0.6550
 DK7  C23  C  CH1   0  -0.283  -5.7143   0.3725  -0.1075
 DK7  C24  C  CH2   0  -0.423  -7.1400   0.0512   0.3427
 DK7  C25  C  CH2   0  -0.431  -7.8420   1.2794   0.9121
 DK7  C26  C  CH2   0  -0.429  -7.0435   1.8946   2.0570
 DK7  C27  C  CH2   0  -0.431  -5.6189   2.2180   1.6187
 DK7  C28  C  CH2   0  -0.414  -4.9196   0.9897   1.0446
 DK7  O29  O  O2    0  -0.506  -2.6711  -2.5141  -0.6262
 DK7  C30  C  CH2   0  -0.158  -1.8173  -1.9672   0.3700
 DK7  N31  N  NH1   0  -0.620   2.0338  -0.1688  -0.9647
 DK7  C32  C  C     0   0.551   1.6717   1.0355  -1.4386
 DK7  C33  C  CH3   0  -0.778   1.7761   1.1843  -2.9347
 DK7  O34  O  O     0  -0.509   1.2820   1.9481  -0.7216
 DK7  H1   H  HCR6  0   0.299   7.7647   0.7561  -0.1639
 DK7  H2   H  HCR6  0   0.272   3.8368   2.3961   0.3924
 DK7  H3   H  HCR6  0   0.274   4.6408  -1.6829   1.4821
 DK7  H4   H  HCH2  0   0.261   2.6148  -0.3661   2.3692
 DK7  H5   H  HCH2  0   0.260   2.1912   1.1479   1.5926
 DK7  H6   H  HCH1  0   0.262   2.1880  -1.6510   0.3970
 DK7  H7   H  HCH1  0   0.235  -0.0502   0.3274   0.9492
 DK7  H8   H  HOH1  0   0.448   0.6219  -2.1865   2.0152
 DK7  H9   H  HCH1  0   0.230   0.0156  -2.2108  -0.7045
 DK7  H10  H  HNH1  0   0.338  -1.2988   0.3827  -0.9364
 DK7  H12  H  HCH2  0   0.244  -2.0452  -0.2963  -3.0455
 DK7  H13  H  HCH2  0   0.232  -1.2543  -1.8480  -2.8206
 DK7  H14  H  HCH1  0   0.213  -3.6045  -2.2183  -2.3656
 DK7  H15  H  HCH2  0   0.209  -5.6777  -1.3199  -1.4461
 DK7  H16  H  HCH2  0   0.199  -4.9716  -1.6260   0.1451
 DK7  H17  H  HCH1  0   0.214  -5.7774   1.1108  -0.9188
 DK7  H18  H  HCH2  0   0.226  -7.7149  -0.3559  -0.4943
 DK7  H19  H  HCH2  0   0.208  -7.1068  -0.7331   1.1085
 DK7  H20  H  HCH2  0   0.209  -7.9650   2.0244   0.1178
 DK7  H21  H  HCH2  0   0.226  -8.8472   1.0144   1.2486
 DK7  H22  H  HCH2  0   0.225  -7.5424   2.7948   2.4243
 DK7  H23  H  HCH2  0   0.207  -7.0129   1.1903   2.8961
 DK7  H24  H  HCH2  0   0.208  -5.6454   3.0067   0.8585
 DK7  H25  H  HCH2  0   0.225  -5.0435   2.6167   2.4579
 DK7  H26  H  HCH2  0   0.202  -4.8028   0.2364   1.8345
 DK7  H27  H  HCH2  0   0.230  -3.9127   1.2517   0.7135
 DK7  H28  H  HCH2  0   0.228  -1.5889  -2.7932   1.0427
 DK7  H29  H  HCH2  0   0.206  -2.3441  -1.2016   0.9548
 DK7  H30  H  HNH1  0   0.396   2.2603  -0.8789  -1.6399
 DK7  H31  H  HCH3  0   0.267   0.7982   0.9660  -3.3671
 DK7  H32  H  HCH3  0   0.254   2.0426   2.2061  -3.1961
 DK7  H33  H  HCH3  0   0.247   2.4995   0.5047  -3.3829

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
 DK7  F4   C3   single    1.341  0.020  1.341
 DK7  C5   C3   aromatic  1.381  0.020  1.381
 DK7  C5   C6   aromatic  1.382  0.020  1.382
 DK7  C3   C2   aromatic  1.381  0.020  1.381
 DK7  F7   C6   single    1.341  0.020  1.341
 DK7  C6   C8   aromatic  1.380  0.020  1.380
 DK7  C2   C1   aromatic  1.391  0.020  1.391
 DK7  C8   C1   aromatic  1.393  0.020  1.393
 DK7  O34  C32  double    1.224  0.020  1.224
 DK7  C1   C9   single    1.501  0.020  1.501
 DK7  C33  C32  single    1.507  0.020  1.507
 DK7  C32  N31  single    1.344  0.020  1.344
 DK7  C9   C10  single    1.539  0.020  1.539
 DK7  N31  C10  single    1.445  0.020  1.445
 DK7  C10  C12  single    1.543  0.020  1.543
 DK7  C26  C27  single    1.525  0.020  1.525
 DK7  C26  C25  single    1.525  0.020  1.525
 DK7  C30  O29  single    1.421  0.020  1.421
 DK7  C30  C15  single    1.530  0.020  1.530
 DK7  C27  C28  single    1.526  0.020  1.526
 DK7  C28  C23  single    1.530  0.020  1.530
 DK7  C25  C24  single    1.525  0.020  1.525
 DK7  C24  C23  single    1.529  0.020  1.529
 DK7  O29  C19  single    1.404  0.020  1.404
 DK7  C12  O14  single    1.412  0.020  1.412
 DK7  C12  C15  single    1.540  0.020  1.540
 DK7  C22  C23  single    1.518  0.020  1.518
 DK7  C22  O21  single    1.413  0.020  1.413
 DK7  C15  N17  single    1.457  0.020  1.457
 DK7  C19  O21  single    1.394  0.020  1.394
 DK7  C19  C18  single    1.520  0.020  1.520
 DK7  N17  C18  single    1.450  0.020  1.450
 DK7  C5   H1   single    0.930  0.020  1.080
 DK7  C2   H2   single    0.930  0.020  1.080
 DK7  C8   H3   single    0.930  0.020  1.080
 DK7  C9   H4   single    0.970  0.020  1.090
 DK7  C9   H5   single    0.970  0.020  1.090
 DK7  C10  H6   single    0.970  0.020  1.090
 DK7  C12  H7   single    0.970  0.020  1.090
 DK7  O14  H8   single    0.850  0.020  0.980
 DK7  C15  H9   single    0.970  0.020  1.090
 DK7  N17  H10  single    0.890  0.020  1.040
 DK7  C18  H12  single    0.970  0.020  1.090
 DK7  C18  H13  single    0.970  0.020  1.090
 DK7  C19  H14  single    0.970  0.020  1.090
 DK7  C22  H15  single    0.970  0.020  1.090
 DK7  C22  H16  single    0.970  0.020  1.090
 DK7  C23  H17  single    0.970  0.020  1.090
 DK7  C24  H18  single    0.970  0.020  1.090
 DK7  C24  H19  single    0.970  0.020  1.090
 DK7  C25  H20  single    0.970  0.020  1.090
 DK7  C25  H21  single    0.970  0.020  1.090
 DK7  C26  H22  single    0.970  0.020  1.090
 DK7  C26  H23  single    0.970  0.020  1.090
 DK7  C27  H24  single    0.970  0.020  1.090
 DK7  C27  H25  single    0.970  0.020  1.090
 DK7  C28  H26  single    0.970  0.020  1.090
 DK7  C28  H27  single    0.970  0.020  1.090
 DK7  C30  H28  single    0.970  0.020  1.090
 DK7  C30  H29  single    0.970  0.020  1.090
 DK7  N31  H30  single    0.860  0.020  1.020
 DK7  C33  H31  single    0.970  0.020  1.090
 DK7  C33  H32  single    0.970  0.020  1.090
 DK7  C33  H33  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
 DK7  C8   C6   F7   118.92  3.000
 DK7  C8   C6   C5   122.92  3.000
 DK7  F7   C6   C5   118.16  3.000
 DK7  C9   C1   C8   120.09  3.000
 DK7  C9   C1   C2   120.41  3.000
 DK7  C8   C1   C2   119.49  3.000
 DK7  H1   C5   C3   121.78  3.000
 DK7  H1   C5   C6   121.76  3.000
 DK7  C3   C5   C6   116.46  3.000
 DK7  F4   C3   C2   118.79  3.000
 DK7  C2   C3   C5   122.94  3.000
 DK7  F4   C3   C5   118.27  3.000
 DK7  H2   C2   C3   120.33  3.000
 DK7  H2   C2   C1   120.56  3.000
 DK7  C3   C2   C1   119.10  3.000
 DK7  H3   C8   C1   120.82  3.000
 DK7  H3   C8   C6   120.09  3.000
 DK7  C1   C8   C6   119.09  3.000
 DK7  H5   C9   H4   107.09  3.000
 DK7  H5   C9   C10  110.03  3.000
 DK7  H4   C9   C10  108.27  3.000
 DK7  H5   C9   C1   109.87  3.000
 DK7  H4   C9   C1   109.31  3.000
 DK7  C10  C9   C1   112.12  3.000
 DK7  H6   C10  N31  104.39  3.000
 DK7  H6   C10  C12  106.38  3.000
 DK7  N31  C10  C12  113.92  3.000
 DK7  H6   C10  C9   107.43  3.000
 DK7  C12  C10  C9   111.24  3.000
 DK7  N31  C10  C9   112.81  3.000
 DK7  H7   C12  C15  108.14  3.000
 DK7  H7   C12  O14  105.01  3.000
 DK7  C15  C12  O14  112.03  3.000
 DK7  H7   C12  C10  109.39  3.000
 DK7  C15  C12  C10  112.99  3.000
 DK7  O14  C12  C10  108.95  3.000
 DK7  H8   O14  C12  109.01  3.000
 DK7  H9   C15  C30  107.70  3.000
 DK7  H9   C15  N17  107.15  3.000
 DK7  C30  C15  N17  111.21  3.000
 DK7  H9   C15  C12  108.96  3.000
 DK7  N17  C15  C12  110.10  3.000
 DK7  C30  C15  C12  111.56  3.000
 DK7  H10  N17  C18  109.39  3.000
 DK7  H10  N17  C15  109.48  3.000
 DK7  C18  N17  C15  111.66  3.000
 DK7  H13  C18  H12  106.93  3.000
 DK7  H13  C18  C19  108.46  3.000
 DK7  H12  C18  C19  110.44  3.000
 DK7  H13  C18  N17  108.89  3.000
 DK7  H12  C18  N17  109.46  3.000
 DK7  C19  C18  N17  112.49  3.000
 DK7  H14  C19  O29  105.10  3.000
 DK7  H14  C19  O21  110.80  3.000
 DK7  O29  C19  O21  112.23  3.000
 DK7  H14  C19  C18  111.23  3.000
 DK7  O21  C19  C18  107.38  3.000
 DK7  O29  C19  C18  110.14  3.000
 DK7  C22  O21  C19  115.65  3.000
 DK7  H16  C22  H15  107.12  3.000
 DK7  H16  C22  C23  109.30  3.000
 DK7  H15  C22  C23  110.02  3.000
 DK7  H16  C22  O21  111.11  3.000
 DK7  H15  C22  O21  109.93  3.000
 DK7  C23  C22  O21  109.33  3.000
 DK7  H17  C23  C28  108.36  3.000
 DK7  H17  C23  C24  107.75  3.000
 DK7  C28  C23  C24  110.33  3.000
 DK7  H17  C23  C22  108.23  3.000
 DK7  C24  C23  C22  109.81  3.000
 DK7  C28  C23  C22  112.22  3.000
 DK7  H19  C24  H18  106.50  3.000
 DK7  H19  C24  C25  109.22  3.000
 DK7  H18  C24  C25  110.10  3.000
 DK7  H19  C24  C23  109.12  3.000
 DK7  H18  C24  C23  110.05  3.000
 DK7  C25  C24  C23  111.71  3.000
 DK7  H21  C25  H20  106.55  3.000
 DK7  H21  C25  C26  110.38  3.000
 DK7  H20  C25  C26  109.18  3.000
 DK7  H21  C25  C24  110.06  3.000
 DK7  H20  C25  C24  109.18  3.000
 DK7  C26  C25  C24  111.35  3.000
 DK7  H23  C26  H22  106.54  3.000
 DK7  H23  C26  C27  109.28  3.000
 DK7  H22  C26  C27  110.38  3.000
 DK7  H23  C26  C25  109.28  3.000
 DK7  H22  C26  C25  110.21  3.000
 DK7  C27  C26  C25  111.03  3.000
 DK7  H25  C27  H24  106.43  3.000
 DK7  H25  C27  C28  109.96  3.000
 DK7  H24  C27  C28  109.24  3.000
 DK7  H25  C27  C26  110.40  3.000
 DK7  H24  C27  C26  109.23  3.000
 DK7  C28  C27  C26  111.44  3.000
 DK7  H27  C28  H26  106.54  3.000
 DK7  H27  C28  C27  110.10  3.000
 DK7  H26  C28  C27  109.30  3.000
 DK7  H27  C28  C23  110.33  3.000
 DK7  H26  C28  C23  108.69  3.000
 DK7  C27  C28  C23  111.73  3.000
 DK7  C30  O29  C19  114.62  3.000
 DK7  H29  C30  H28  107.48  3.000
 DK7  H29  C30  O29  110.69  3.000
 DK7  H28  C30  O29  105.48  3.000
 DK7  H29  C30  C15  110.36  3.000
 DK7  H28  C30  C15  111.66  3.000
 DK7  O29  C30  C15  111.02  3.000
 DK7  H30  N31  C32  117.17  3.000
 DK7  H30  N31  C10  116.31  3.000
 DK7  C32  N31  C10  124.77  3.000
 DK7  O34  C32  C33  121.99  3.000
 DK7  C33  C32  N31  114.82  3.000
 DK7  O34  C32  N31  123.18  3.000
 DK7  H33  C33  H32  108.93  3.000
 DK7  H33  C33  H31  107.90  3.000
 DK7  H32  C33  H31  108.19  3.000
 DK7  H33  C33  C32  113.14  3.000
 DK7  H32  C33  C32  110.39  3.000
 DK7  H31  C33  C32  108.15  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
 DK7  CONST_01  C2   C3   C5   C6      0.00   0.0  0
 DK7  CONST_02  C2   C1   C8   C6      0.00   0.0  0
 DK7  CONST_03  C5   C3   C2   C1      0.00   0.0  0
 DK7  CONST_04  C5   C6   C8   C1      0.00   0.0  0
 DK7  CONST_05  C8   C6   C5   C3      0.00   0.0  0
 DK7  CONST_06  C8   C1   C2   C3      0.00   0.0  0
 DK7  CONST_07  F4   C3   C5   C6    180.00   0.0  0
 DK7  CONST_08  C9   C1   C8   C6    180.00   0.0  0
 DK7  CONST_09  F4   C3   C2   C1    180.00   0.0  0
 DK7  CONST_10  F7   C6   C8   C1    180.00   0.0  0
 DK7  CONST_11  F7   C6   C5   C3    180.00   0.0  0
 DK7  CONST_12  C9   C1   C2   C3    180.00   0.0  0
 DK7  CONST_13  H2   C2   C3   C5    180.00   0.0  0
 DK7  CONST_14  H3   C8   C6   C5    180.00   0.0  0
 DK7  CONST_15  H1   C5   C3   C2    180.00   0.0  0
 DK7  CONST_16  O34  C32  N31  C10     0.00   0.0  0
 DK7  CONST_17  C33  C32  N31  C10   180.00   0.0  0
 DK7  CONST_18  H30  N31  C32  C33     0.00   0.0  0
 DK7  Var_01    C19  C18  N17  C15    53.18  30.0  1
 DK7  Var_02    C26  C27  C28  C23    55.51  30.0  1
 DK7  Var_03    C26  C25  C24  C23   -55.79  30.0  1
 DK7  Var_04    C27  C26  C25  C24    55.12  30.0  1
 DK7  Var_05    C28  C27  C26  C25   -55.00  30.0  1
 DK7  Var_06    H28  C30  O29  C19  -176.49  30.0  1
 DK7  Var_07    C10  C9   C1   C2    103.23  30.0  2
 DK7  Var_08    C23  C22  O21  C19   176.70  30.0  2
 DK7  Var_09    H31  C33  C32  N31    94.73  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
 DK7  chir_01  C10  C9   N31  C12  positiv
 DK7  chir_02  C12  O14  C10  C15  negativ
 DK7  chir_03  C15  N17  C12  C30  negativ
 DK7  chir_04  C19  O29  O21  C18  negativ
 DK7  chir_05  C23  C28  C24  C22  positiv

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
 DK7  plan-1  C6   0.020
 DK7  plan-1  C1   0.020
 DK7  plan-1  C5   0.020
 DK7  plan-1  C3   0.020
 DK7  plan-1  C2   0.020
 DK7  plan-1  F4   0.020
 DK7  plan-1  F7   0.020
 DK7  plan-1  C8   0.020
 DK7  plan-1  C9   0.020
 DK7  plan-1  H1   0.020
 DK7  plan-1  H2   0.020
 DK7  plan-1  H3   0.020
 DK7  plan-2  C10  0.020
 DK7  plan-2  N31  0.020
 DK7  plan-2  C32  0.020
 DK7  plan-2  C33  0.020
 DK7  plan-2  O34  0.020
 DK7  plan-2  H30  0.020

