# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 13:06:50 2022
#   Inital geometry file: a 127 line input string
#   Ligand name: 9-(4-cyclohexyloxyphenyl)-7-methyl-3,4-dihydropyrazino[2,1-c][1,2,4]thiadiazine 2,2-dioxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN2CC[S](=O)(=O)N=C2C(=N1)c3ccc(OC4CCCCC4)cc3
#
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
 0YK  0YK  '9-(4-cyclohexyloxyphenyl)-7-methyl-3,4-dihydropyrazino[2,1-c][1,2,4]thiadiazine 2,2-dioxide'  ligand  49  26  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0YK
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
 0YK  C4   C  CR16  0  -0.345  31.1407  -55.2614  18.6397
 0YK  C5   C  CR6   0   0.056  32.9332  -56.8457  19.0076
 0YK  C6   C  CR6   0   0.394  32.0336  -54.1909  18.7530
 0YK  C7   C  CR16  0  -0.024  34.1861  -60.8205  19.1045
 0YK  C8   C  CR6   0   0.100  33.3740  -58.2484  19.0807
 0YK  C10  C  CR66  0   0.551  34.3691  -58.6530  20.0668
 0YK  C13  C  CH2   0  -0.441  33.8558  -50.2243  17.5546
 0YK  C15  C  CH2   0  -0.466  33.0393  -51.5097  17.4371
 0YK  C17  C  C     0  -0.652  35.7621  -59.9058  22.2276
 0YK  C1   C  CR16  0  -0.247  33.8163  -55.7730  19.1083
 0YK  C2   C  CR16  0  -0.263  31.5885  -56.5614  18.7541
 0YK  C3   C  CR16  0  -0.367  33.3843  -54.4633  18.9733
 0YK  C9   C  CR6   0   0.148  33.2017  -60.4058  18.2725
 0YK  C11  C  CH2   0  -0.429  32.9746  -49.0484  17.9623
 0YK  C12  C  CH2   0  -0.444  32.2232  -49.3518  19.2540
 0YK  C14  C  CH2   0  -0.448  31.4170  -50.6439  19.1406
 0YK  C16  C  C     0  -0.330  35.8666  -60.4416  20.8177
 0YK  C18  C  CH1   0   0.039  32.3225  -51.8005  18.7493
 0YK  C19  C  CH3   0  -0.717  32.5052  -61.3291  17.3284
 0YK  N20  N  N     0  -0.370  32.8323  -59.1001  18.2672
 0YK  N21  N  N     0  -0.663  34.7763  -57.7862  20.9567
 0YK  N22  N  N     0  -0.488  34.7696  -59.9501  19.9782
 0YK  O23  O  OS    0  -0.667  35.3550  -57.5372  23.3637
 0YK  O24  O  OS    0  -0.677  37.1818  -57.7512  21.6869
 0YK  O25  O  O2    0  -0.484  31.5008  -52.9648  18.6502
 0YK  S26  S  S     0   1.324  35.8418  -58.1265  22.1257
 0YK  H1   H  HCR6  0   0.261  30.0905  -55.0611  18.4683
 0YK  H2   H  HCR6  0   0.322  34.5539  -61.8358  19.1246
 0YK  H4   H  HCH2  0   0.235  34.3549  -50.0183  16.6057
 0YK  H5   H  HCH2  0   0.226  32.2912  -51.3982  16.6453
 0YK  H6   H  HCH2  0   0.244  33.6861  -52.3419  17.1506
 0YK  H7   H  H     0   0.319  34.8194  -60.1829  22.7010
 0YK  H8   H  H     0   0.335  36.5922  -60.2629  22.8370
 0YK  H9   H  HCR6  0   0.257  34.8689  -55.9471  19.2775
 0YK  H10  H  HCR6  0   0.253  30.8773  -57.3724  18.6635
 0YK  H11  H  HCR6  0   0.278  34.1190  -53.6738  19.0458
 0YK  H12  H  HCH2  0   0.231  33.5772  -48.1449  18.0783
 0YK  H13  H  HCH2  0   0.213  32.2533  -48.8457  17.1638
 0YK  H14  H  HCH2  0   0.217  32.9388  -49.4434  20.0776
 0YK  H15  H  HCH2  0   0.236  31.5572  -48.5262  19.5126
 0YK  H16  H  HCH2  0   0.224  30.6359  -50.5244  18.3826
 0YK  H17  H  HCH2  0   0.240  30.9202  -50.8657  20.0880
 0YK  H18  H  H     0   0.314  35.8239  -61.5276  20.8323
 0YK  H19  H  H     0   0.309  36.8130  -60.1517  20.3579
 0YK  H20  H  HCH1  0   0.223  33.0626  -51.9416  19.5479
 0YK  H21  H  HCH3  0   0.253  31.4389  -61.3779  17.5531
 0YK  H22  H  HCH3  0   0.252  32.6064  -60.9818  16.2997
 0YK  H23  H  HCH3  0   0.249  32.9095  -62.3379  17.3887
 0YK  H3   H  HCH2  0   0.218  34.6473  -50.3630  18.2985

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
 0YK  C19  C9   single    1.493  0.020  1.493
 0YK  C13  C15  single    1.527  0.020  1.527
 0YK  C13  C11  single    1.525  0.020  1.525
 0YK  C15  C18  single    1.523  0.020  1.523
 0YK  N20  C9   single    1.357  0.020  1.357
 0YK  N20  C8   double    1.296  0.020  1.296
 0YK  C11  C12  single    1.525  0.020  1.525
 0YK  C9   C7   double    1.354  0.020  1.354
 0YK  C2   C5   aromatic  1.398  0.020  1.398
 0YK  C2   C4   aromatic  1.380  0.020  1.380
 0YK  C5   C8   single    1.472  0.020  1.472
 0YK  C5   C1   aromatic  1.393  0.020  1.393
 0YK  C8   C10  single    1.458  0.020  1.458
 0YK  C4   C6   aromatic  1.399  0.020  1.399
 0YK  C1   C3   aromatic  1.386  0.020  1.386
 0YK  C6   C3   aromatic  1.395  0.020  1.395
 0YK  C6   O25  single    1.341  0.020  1.341
 0YK  C18  O25  single    1.429  0.020  1.429
 0YK  C18  C14  single    1.520  0.020  1.520
 0YK  C7   N22  single    1.364  0.020  1.364
 0YK  C12  C14  single    1.527  0.020  1.527
 0YK  C10  N22  single    1.360  0.020  1.360
 0YK  C10  N21  double    1.307  0.020  1.307
 0YK  N22  C16  single    1.466  0.020  1.466
 0YK  N21  S26  single    1.618  0.020  1.618
 0YK  C16  C17  single    1.512  0.020  1.512
 0YK  O24  S26  double    1.459  0.020  1.459
 0YK  S26  C17  single    1.784  0.020  1.784
 0YK  S26  O23  double    1.455  0.020  1.455
 0YK  C4   H1   single    0.930  0.020  1.080
 0YK  C7   H2   single    0.930  0.020  1.080
 0YK  C13  H3   single    0.970  0.020  1.090
 0YK  C13  H4   single    0.970  0.020  1.090
 0YK  C15  H5   single    0.970  0.020  1.090
 0YK  C15  H6   single    0.970  0.020  1.090
 0YK  C17  H7   single    0.970  0.020  1.090
 0YK  C17  H8   single    0.970  0.020  1.090
 0YK  C1   H9   single    0.930  0.020  1.080
 0YK  C2   H10  single    0.930  0.020  1.080
 0YK  C3   H11  single    0.930  0.020  1.080
 0YK  C11  H12  single    0.970  0.020  1.090
 0YK  C11  H13  single    0.970  0.020  1.090
 0YK  C12  H14  single    0.970  0.020  1.090
 0YK  C12  H15  single    0.970  0.020  1.090
 0YK  C14  H16  single    0.970  0.020  1.090
 0YK  C14  H17  single    0.970  0.020  1.090
 0YK  C16  H18  single    0.970  0.020  1.090
 0YK  C16  H19  single    0.970  0.020  1.090
 0YK  C18  H20  single    0.970  0.020  1.090
 0YK  C19  H21  single    0.970  0.020  1.090
 0YK  C19  H22  single    0.970  0.020  1.090
 0YK  C19  H23  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
 0YK  H1   C4   C2   120.14  3.000
 0YK  H1   C4   C6   119.37  3.000
 0YK  C2   C4   C6   120.48  3.000
 0YK  C2   C5   C1   117.80  3.000
 0YK  C1   C5   C8   122.70  3.000
 0YK  C2   C5   C8   119.40  3.000
 0YK  O25  C6   C3   125.12  3.000
 0YK  O25  C6   C4   116.10  3.000
 0YK  C3   C6   C4   118.78  3.000
 0YK  H2   C7   N22  116.24  3.000
 0YK  H2   C7   C9   123.16  3.000
 0YK  N22  C7   C9   120.59  3.000
 0YK  N20  C8   C10  121.81  3.000
 0YK  C10  C8   C5   120.15  3.000
 0YK  N20  C8   C5   118.02  3.000
 0YK  N22  C10  N21  125.79  3.000
 0YK  N21  C10  C8   119.27  3.000
 0YK  N22  C10  C8   114.92  3.000
 0YK  H4   C13  H3   106.50  3.000
 0YK  H4   C13  C11  110.55  3.000
 0YK  H3   C13  C11  109.49  3.000
 0YK  H4   C13  C15  109.65  3.000
 0YK  H3   C13  C15  109.39  3.000
 0YK  C11  C13  C15  111.14  3.000
 0YK  H6   C15  H5   107.01  3.000
 0YK  H6   C15  C18  111.05  3.000
 0YK  H5   C15  C18  108.72  3.000
 0YK  H6   C15  C13  110.17  3.000
 0YK  H5   C15  C13  109.58  3.000
 0YK  C18  C15  C13  110.24  3.000
 0YK  H8   C17  H7   109.41  3.000
 0YK  H8   C17  S26  108.94  3.000
 0YK  H7   C17  S26  108.47  3.000
 0YK  H8   C17  C16  110.65  3.000
 0YK  H7   C17  C16  112.00  3.000
 0YK  S26  C17  C16  107.29  3.000
 0YK  H9   C1   C3   118.12  3.000
 0YK  H9   C1   C5   120.33  3.000
 0YK  C3   C1   C5   121.54  3.000
 0YK  H10  C2   C5   119.67  3.000
 0YK  H10  C2   C4   119.06  3.000
 0YK  C5   C2   C4   121.26  3.000
 0YK  H11  C3   C1   118.16  3.000
 0YK  H11  C3   C6   121.73  3.000
 0YK  C1   C3   C6   120.11  3.000
 0YK  N20  C9   C19  117.75  3.000
 0YK  N20  C9   C7   119.67  3.000
 0YK  C19  C9   C7   122.57  3.000
 0YK  H13  C11  H12  106.72  3.000
 0YK  H13  C11  C12  109.27  3.000
 0YK  H12  C11  C12  110.27  3.000
 0YK  H13  C11  C13  109.18  3.000
 0YK  H12  C11  C13  110.33  3.000
 0YK  C12  C11  C13  110.97  3.000
 0YK  H15  C12  H14  106.48  3.000
 0YK  H15  C12  C14  109.59  3.000
 0YK  H14  C12  C14  109.27  3.000
 0YK  H15  C12  C11  110.54  3.000
 0YK  H14  C12  C11  109.38  3.000
 0YK  C14  C12  C11  111.44  3.000
 0YK  H17  C14  H16  107.34  3.000
 0YK  H17  C14  C18  109.86  3.000
 0YK  H16  C14  C18  109.26  3.000
 0YK  H17  C14  C12  110.33  3.000
 0YK  H16  C14  C12  109.61  3.000
 0YK  C18  C14  C12  110.39  3.000
 0YK  H19  C16  H18  107.77  3.000
 0YK  H19  C16  N22  108.57  3.000
 0YK  H18  C16  N22  108.25  3.000
 0YK  H19  C16  C17  111.02  3.000
 0YK  H18  C16  C17  109.81  3.000
 0YK  N22  C16  C17  111.31  3.000
 0YK  H20  C18  O25  109.48  3.000
 0YK  H20  C18  C14  108.19  3.000
 0YK  O25  C18  C14  107.18  3.000
 0YK  H20  C18  C15  109.51  3.000
 0YK  C14  C18  C15  110.91  3.000
 0YK  O25  C18  C15  111.50  3.000
 0YK  H23  C19  H22  108.24  3.000
 0YK  H23  C19  H21  108.07  3.000
 0YK  H22  C19  H21  107.41  3.000
 0YK  H23  C19  C9   111.40  3.000
 0YK  H22  C19  C9   110.87  3.000
 0YK  H21  C19  C9   110.70  3.000
 0YK  C9   N20  C8   121.06  3.000
 0YK  S26  N21  C10  123.88  3.000
 0YK  C16  N22  C10  120.17  3.000
 0YK  C16  N22  C7   118.21  3.000
 0YK  C10  N22  C7   121.61  3.000
 0YK  C18  O25  C6   120.76  3.000
 0YK  O24  S26  O23  117.33  3.000
 0YK  O23  S26  N21  108.01  3.000
 0YK  O24  S26  N21  109.47  3.000
 0YK  O23  S26  C17  109.90  3.000
 0YK  O24  S26  C17  108.35  3.000
 0YK  N21  S26  C17  102.80  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
 0YK  CONST_01  C1   C5   C2   C4      0.00   0.0  0
 0YK  CONST_02  C1   C3   C6   C4      0.00   0.0  0
 0YK  CONST_03  C6   C4   C2   C5      0.00   0.0  0
 0YK  CONST_04  C6   C3   C1   C5      0.00   0.0  0
 0YK  CONST_05  C3   C1   C5   C2      0.00   0.0  0
 0YK  CONST_06  C3   C6   C4   C2      0.00   0.0  0
 0YK  CONST_07  C8   C5   C2   C4    180.00   0.0  0
 0YK  CONST_08  C3   C1   C5   C8    180.00   0.0  0
 0YK  CONST_09  C8   C10  N22  C7      0.00   0.0  0
 0YK  CONST_10  N21  C10  N22  C7    180.00   0.0  0
 0YK  CONST_11  C16  N22  C10  C8    180.00   0.0  0
 0YK  CONST_12  S26  N21  C10  C8    180.00   0.0  0
 0YK  CONST_13  N21  C10  N22  C16     0.00   0.0  0
 0YK  CONST_14  S26  N21  C10  N22     0.00   0.0  0
 0YK  CONST_15  O25  C6   C3   C1    180.00   0.0  0
 0YK  CONST_16  O25  C6   C4   C2    180.00   0.0  0
 0YK  CONST_17  H11  C3   C6   C4    180.00   0.0  0
 0YK  CONST_18  H1   C4   C2   C5    180.00   0.0  0
 0YK  CONST_19  H10  C2   C4   C6    180.00   0.0  0
 0YK  CONST_20  H9   C1   C3   C6    180.00   0.0  0
 0YK  Var_01    C17  C16  N22  C7   -139.25  30.0  1
 0YK  Var_02    C2   C5   C8   C10  -141.45  30.0  1
 0YK  Var_03    C17  S26  N21  C10   -20.17  30.0  1
 0YK  Var_04    C14  C12  C11  C13   -55.04  30.0  1
 0YK  Var_05    C12  C11  C13  C15    55.38  30.0  1
 0YK  Var_06    C18  C15  C13  C11   -56.75  30.0  1
 0YK  Var_07    C18  C14  C12  C11    56.02  30.0  1
 0YK  Var_08    N21  S26  C17  C16    48.29  30.0  1
 0YK  Var_09    S26  C17  C16  N22   -60.24  30.0  1
 0YK  Var_10    H21  C19  C9   C7    118.83  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
 0YK  chir_01  C18  C15  O25  C14  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
 0YK  plan-1  C4   0.020
 0YK  plan-1  C5   0.020
 0YK  plan-1  C6   0.020
 0YK  plan-1  C8   0.020
 0YK  plan-1  C1   0.020
 0YK  plan-1  C2   0.020
 0YK  plan-1  C3   0.020
 0YK  plan-1  O25  0.020
 0YK  plan-1  H1   0.020
 0YK  plan-1  H9   0.020
 0YK  plan-1  H10  0.020
 0YK  plan-1  H11  0.020
 0YK  plan-2  C5   0.020
 0YK  plan-2  C7   0.020
 0YK  plan-2  C8   0.020
 0YK  plan-2  C10  0.020
 0YK  plan-2  C9   0.020
 0YK  plan-2  C16  0.020
 0YK  plan-2  C19  0.020
 0YK  plan-2  N20  0.020
 0YK  plan-2  N21  0.020
 0YK  plan-2  N22  0.020
 0YK  plan-2  S26  0.020
 0YK  plan-2  H2   0.020

