# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 12:37:54 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (3S)-6-cyclohexyl-3-{3-[(dimethylamino)methyl]-1,2,4-oxadiazol-5-yl}-N-hydroxyhexanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)Cc1noc(n1)[C@@H](CCCC2CCCCC2)CC(=O)NO
#
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
 E8M  E8M  (3S)-6-cyclohexyl-3-{3-[(dimethylamino)methyl]-1,2,4-oxadiazol-5-yl}-N-hydroxyhexanamide  ligand  54  24  .  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_E8M
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
 E8M  C10  C  CH2   0  -0.353  -4.4858   2.2748  -0.1027
 E8M  C13  C  CR5   0   0.283  -3.3207   1.5462   0.4727
 E8M  C20  C  CH2   0  -0.416   0.8875   0.5096   0.7879
 E8M  C26  C  CH2   0  -0.403   3.3862   0.8412   0.6408
 E8M  N05  N  NT    0  -0.403  -5.1907   1.4574  -1.0654
 E8M  C06  C  CH3   0  -0.520  -6.1806   2.2338  -1.7797
 E8M  N14  N  N     0  -0.151  -3.1421   1.4166   1.7497
 E8M  O15  O  O     0  -0.336  -1.9838   0.6890   1.8455
 E8M  C16  C  CR5   0   0.564  -1.5847   0.4230   0.6100
 E8M  N17  N  N     0  -0.444  -2.3569   0.9458  -0.2825
 E8M  C18  C  CH1   0  -0.383  -0.3302  -0.3501   0.4047
 E8M  C29  C  CH1   0  -0.223   4.7445   0.3399   0.1531
 E8M  C31  C  CH2   0  -0.414   5.8745   1.1570   0.7817
 E8M  C34  C  CH2   0  -0.431   7.2528   0.6980   0.3174
 E8M  C37  C  CH2   0  -0.429   7.3576   0.7249  -1.2034
 E8M  C40  C  CH2   0  -0.428   6.2451  -0.1000  -1.8409
 E8M  C43  C  CH2   0  -0.421   4.8663   0.3562  -1.3712
 E8M  C46  C  CH2   0  -0.592  -0.3431  -1.6735   1.1770
 E8M  C49  C  C     0   0.555  -1.5279  -2.5408   0.8151
 E8M  O50  O  O     0  -0.462  -2.6605  -2.1016   0.7134
 E8M  N51  N  NH1   0  -0.379  -1.2157  -3.8393   0.6662
 E8M  O53  O  OH1   0  -0.542  -2.1581  -4.7234   0.2392
 E8M  H1   H  HCH2  0   0.226  -5.1233   2.6228   0.7256
 E8M  H2   H  HCH2  0   0.269  -4.1139   3.1686  -0.6118
 E8M  H3   H  HCH2  0   0.249   0.7382   1.5260   0.4128
 E8M  H4   H  HCH2  0   0.235   0.9469   0.5866   1.8777
 E8M  H5   H  HCH2  0   0.208   3.2325   1.8666   0.2841
 E8M  H6   H  HCH2  0   0.217   3.4092   0.9028   1.7346
 E8M  H7   H  HCH3  0   0.196  -6.5208   0.5046   0.3118
 E8M  H8   H  HCH3  0   0.238  -6.2628  -0.3208  -1.2330
 E8M  H9   H  HCH3  0   0.244  -5.0019  -0.3487  -0.0117
 E8M  H11  H  HCH3  0   0.236  -5.7049   3.0751  -2.2864
 E8M  H12  H  HCH3  0   0.237  -6.6554   1.6136  -2.5406
 E8M  H13  H  HCH3  0   0.196  -6.9752   2.6355  -1.1324
 E8M  H14  H  HCH1  0   0.290  -0.2827  -0.5602  -0.6672
 E8M  H15  H  HCH2  0   0.222   2.3765  -1.0499   0.5693
 E8M  H16  H  HCH2  0   0.226   2.1223  -0.0712  -0.8602
 E8M  H17  H  HCH1  0   0.201   4.8612  -0.7013   0.4871
 E8M  H18  H  HCH2  0   0.203   5.7391   2.2136   0.5192
 E8M  H19  H  HCH2  0   0.221   5.8050   1.1004   1.8723
 E8M  H20  H  HCH2  0   0.223   8.0280   1.3263   0.7634
 E8M  H21  H  HCH2  0   0.206   7.4368  -0.3208   0.6761
 E8M  H22  H  HCH2  0   0.206   7.2831   1.7616  -1.5503
 E8M  H23  H  HCH2  0   0.224   8.3354   0.3584  -1.5255
 E8M  H24  H  HCH2  0   0.223   6.3067  -0.0432  -2.9308
 E8M  H25  H  HCH2  0   0.206   6.3823  -1.1550  -1.5785
 E8M  H26  H  HCH2  0   0.227   4.0999  -0.2791  -1.8224
 E8M  H27  H  HCH2  0   0.202   4.6746   1.3746  -1.7324
 E8M  H28  H  HCH2  0   0.280   0.5960  -2.1994   1.0019
 E8M  H29  H  HCH2  0   0.287  -0.3863  -1.4772   2.2523
 E8M  H30  H  HNH1  0   0.418  -0.2620  -4.1598   0.5814
 E8M  H31  H  HOH1  0   0.479  -2.4995  -5.1568   1.0323
 E8M  C23  C  CH2   0  -0.437   2.2012  -0.0247   0.2293
 E8M  C01  C  CH3   0  -0.532  -5.7730   0.2768  -0.4636

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
 E8M  O50  C49  double    1.219  0.020  1.219
 E8M  C49  C46  single    1.512  0.020  1.512
 E8M  C49  N51  single    1.344  0.020  1.344
 E8M  C46  C18  single    1.532  0.020  1.532
 E8M  O15  N14  aromatic  1.371  0.020  1.371
 E8M  O15  C16  aromatic  1.325  0.020  1.325
 E8M  O53  N51  single    1.361  0.020  1.361
 E8M  C43  C40  single    1.526  0.020  1.526
 E8M  C43  C29  single    1.529  0.020  1.529
 E8M  N14  C13  aromatic  1.296  0.020  1.296
 E8M  C40  C37  single    1.525  0.020  1.525
 E8M  C20  C18  single    1.539  0.020  1.539
 E8M  C20  C23  single    1.524  0.020  1.524
 E8M  C16  C18  single    1.488  0.020  1.488
 E8M  C16  N17  aromatic  1.291  0.020  1.291
 E8M  C13  N17  aromatic  1.364  0.020  1.364
 E8M  C13  C10  single    1.490  0.020  1.490
 E8M  C23  C26  single    1.524  0.020  1.524
 E8M  C37  C34  single    1.525  0.020  1.525
 E8M  C26  C29  single    1.528  0.020  1.528
 E8M  C29  C31  single    1.530  0.020  1.530
 E8M  C10  N05  single    1.446  0.020  1.446
 E8M  C31  C34  single    1.525  0.020  1.525
 E8M  N05  C06  single    1.447  0.020  1.447
 E8M  N05  C01  single    1.447  0.020  1.447
 E8M  C10  H1   single    0.970  0.020  1.090
 E8M  C10  H2   single    0.970  0.020  1.090
 E8M  C20  H3   single    0.970  0.020  1.090
 E8M  C20  H4   single    0.970  0.020  1.090
 E8M  C26  H5   single    0.970  0.020  1.090
 E8M  C26  H6   single    0.970  0.020  1.090
 E8M  C01  H7   single    0.970  0.020  1.090
 E8M  C01  H8   single    0.970  0.020  1.090
 E8M  C01  H9   single    0.970  0.020  1.090
 E8M  C06  H11  single    0.970  0.020  1.090
 E8M  C06  H12  single    0.970  0.020  1.090
 E8M  C06  H13  single    0.970  0.020  1.090
 E8M  C18  H14  single    0.970  0.020  1.090
 E8M  C23  H15  single    0.970  0.020  1.090
 E8M  C23  H16  single    0.970  0.020  1.090
 E8M  C29  H17  single    0.970  0.020  1.090
 E8M  C31  H18  single    0.970  0.020  1.090
 E8M  C31  H19  single    0.970  0.020  1.090
 E8M  C34  H20  single    0.970  0.020  1.090
 E8M  C34  H21  single    0.970  0.020  1.090
 E8M  C37  H22  single    0.970  0.020  1.090
 E8M  C37  H23  single    0.970  0.020  1.090
 E8M  C40  H24  single    0.970  0.020  1.090
 E8M  C40  H25  single    0.970  0.020  1.090
 E8M  C43  H26  single    0.970  0.020  1.090
 E8M  C43  H27  single    0.970  0.020  1.090
 E8M  C46  H28  single    0.970  0.020  1.090
 E8M  C46  H29  single    0.970  0.020  1.090
 E8M  N51  H30  single    0.860  0.020  1.020
 E8M  O53  H31  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
 E8M  H2   C10  H1   106.77  3.000
 E8M  H2   C10  N05  108.52  3.000
 E8M  H1   C10  N05  113.39  3.000
 E8M  H2   C10  C13  108.27  3.000
 E8M  H1   C10  C13  108.46  3.000
 E8M  N05  C10  C13  111.22  3.000
 E8M  N17  C13  N14  113.84  3.000
 E8M  N17  C13  C10  123.65  3.000
 E8M  N14  C13  C10  122.50  3.000
 E8M  H4   C20  H3   106.48  3.000
 E8M  H4   C20  C23  110.05  3.000
 E8M  H3   C20  C23  108.52  3.000
 E8M  H4   C20  C18  109.29  3.000
 E8M  H3   C20  C18  109.01  3.000
 E8M  C23  C20  C18  113.26  3.000
 E8M  H6   C26  H5   105.97  3.000
 E8M  H6   C26  C29  108.57  3.000
 E8M  H5   C26  C29  109.13  3.000
 E8M  H6   C26  C23  108.53  3.000
 E8M  H5   C26  C23  109.53  3.000
 E8M  C29  C26  C23  114.75  3.000
 E8M  C06  N05  C01  111.58  3.000
 E8M  C01  N05  C10  112.35  3.000
 E8M  C06  N05  C10  111.03  3.000
 E8M  H13  C06  H12  107.67  3.000
 E8M  H13  C06  H11  107.84  3.000
 E8M  H12  C06  H11  107.72  3.000
 E8M  H13  C06  N05  113.54  3.000
 E8M  H12  C06  N05  109.71  3.000
 E8M  H11  C06  N05  110.17  3.000
 E8M  O15  N14  C13  103.79  3.000
 E8M  C16  O15  N14  107.20  3.000
 E8M  C18  C16  N17  128.27  3.000
 E8M  N17  C16  O15  112.53  3.000
 E8M  C18  C16  O15  119.13  3.000
 E8M  C16  N17  C13  102.60  3.000
 E8M  H14  C18  C46  109.18  3.000
 E8M  H14  C18  C16  105.77  3.000
 E8M  C46  C18  C16  111.85  3.000
 E8M  H14  C18  C20  108.49  3.000
 E8M  C16  C18  C20  110.03  3.000
 E8M  C46  C18  C20  111.32  3.000
 E8M  H17  C29  C43  107.72  3.000
 E8M  H17  C29  C31  107.61  3.000
 E8M  C43  C29  C31  110.19  3.000
 E8M  H17  C29  C26  107.94  3.000
 E8M  C31  C29  C26  110.51  3.000
 E8M  C43  C29  C26  112.67  3.000
 E8M  H19  C31  H18  106.29  3.000
 E8M  H19  C31  C34  110.20  3.000
 E8M  H18  C31  C34  109.18  3.000
 E8M  H19  C31  C29  109.57  3.000
 E8M  H18  C31  C29  108.96  3.000
 E8M  C34  C31  C29  112.44  3.000
 E8M  H21  C34  H20  106.37  3.000
 E8M  H21  C34  C37  109.35  3.000
 E8M  H20  C34  C37  110.37  3.000
 E8M  H21  C34  C31  109.39  3.000
 E8M  H20  C34  C31  110.11  3.000
 E8M  C37  C34  C31  111.13  3.000
 E8M  H23  C37  H22  106.55  3.000
 E8M  H23  C37  C40  110.38  3.000
 E8M  H22  C37  C40  109.26  3.000
 E8M  H23  C37  C34  110.47  3.000
 E8M  H22  C37  C34  109.13  3.000
 E8M  C40  C37  C34  110.94  3.000
 E8M  H25  C40  H24  106.36  3.000
 E8M  H25  C40  C43  109.09  3.000
 E8M  H24  C40  C43  110.01  3.000
 E8M  H25  C40  C37  109.23  3.000
 E8M  H24  C40  C37  110.35  3.000
 E8M  C43  C40  C37  111.64  3.000
 E8M  H27  C43  H26  106.33  3.000
 E8M  H27  C43  C40  109.50  3.000
 E8M  H26  C43  C40  109.43  3.000
 E8M  H27  C43  C29  108.91  3.000
 E8M  H26  C43  C29  110.45  3.000
 E8M  C40  C43  C29  112.05  3.000
 E8M  H29  C46  H28  106.16  3.000
 E8M  H29  C46  C49  107.90  3.000
 E8M  H28  C46  C49  111.08  3.000
 E8M  H29  C46  C18  109.92  3.000
 E8M  H28  C46  C18  109.17  3.000
 E8M  C49  C46  C18  112.41  3.000
 E8M  N51  C49  O50  123.70  3.000
 E8M  N51  C49  C46  113.50  3.000
 E8M  O50  C49  C46  122.77  3.000
 E8M  H30  N51  O53  114.93  3.000
 E8M  H30  N51  C49  122.38  3.000
 E8M  O53  N51  C49  120.11  3.000
 E8M  H31  O53  N51  106.17  3.000
 E8M  H16  C23  H15  106.34  3.000
 E8M  H16  C23  C26  110.45  3.000
 E8M  H15  C23  C26  108.89  3.000
 E8M  H16  C23  C20  108.54  3.000
 E8M  H15  C23  C20  110.65  3.000
 E8M  C26  C23  C20  111.84  3.000
 E8M  H9   C01  H8   107.19  3.000
 E8M  H9   C01  H7   107.87  3.000
 E8M  H8   C01  H7   107.77  3.000
 E8M  H9   C01  N05  110.83  3.000
 E8M  H8   C01  N05  109.54  3.000
 E8M  H7   C01  N05  113.41  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
 E8M  CONST_01  C16  O15  N14  C13     0.00   0.0  0
 E8M  CONST_02  O15  C16  N17  C13     0.00   0.0  0
 E8M  CONST_03  N17  C16  O15  N14     0.00   0.0  0
 E8M  CONST_04  C16  N17  C13  N14     0.00   0.0  0
 E8M  CONST_05  N17  C13  N14  O15     0.00   0.0  0
 E8M  CONST_06  O15  N14  C13  C10   180.00   0.0  0
 E8M  CONST_07  C16  N17  C13  C10   180.00   0.0  0
 E8M  CONST_08  C18  C16  N17  C13   180.00   0.0  0
 E8M  CONST_09  C18  C16  O15  N14   180.00   0.0  0
 E8M  CONST_10  O53  N51  C49  C46   180.00   0.0  0
 E8M  CONST_11  O53  N51  C49  O50     0.00   0.0  0
 E8M  CONST_12  H30  N51  C49  C46     0.00   0.0  0
 E8M  Var_01    C37  C40  C43  C29   -55.22  30.0  1
 E8M  Var_02    C37  C34  C31  C29    55.58  30.0  1
 E8M  Var_03    C40  C37  C34  C31   -55.12  30.0  1
 E8M  Var_04    C43  C40  C37  C34    55.19  30.0  1
 E8M  Var_05    N14  C13  C10  N05  -126.90  30.0  1
 E8M  Var_06    C06  N05  C10  C13  -170.59  30.0  3
 E8M  Var_07    C29  C26  C23  C20   178.13  30.0  3
 E8M  Var_08    C18  C20  C23  C26  -179.36  30.0  1
 E8M  Var_09    O50  C49  C46  C18   -44.79  30.0  1
 E8M  Var_10    H11  C06  N05  C10    58.11  30.0  3
 E8M  Var_11    H7   C01  N05  C10    61.44  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
 E8M  chir_01  C18  C46  C20  C16  positiv
 E8M  chir_02  C29  C43  C26  C31  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
 E8M  plan-1  C10  0.020
 E8M  plan-1  C13  0.020
 E8M  plan-1  N14  0.020
 E8M  plan-1  O15  0.020
 E8M  plan-1  C16  0.020
 E8M  plan-1  N17  0.020
 E8M  plan-1  C18  0.020
 E8M  plan-2  C46  0.020
 E8M  plan-2  C49  0.020
 E8M  plan-2  O50  0.020
 E8M  plan-2  N51  0.020
 E8M  plan-2  O53  0.020
 E8M  plan-2  H30  0.020

