# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 23:22:45 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 2-(2,4-dioxo-1,3-diazaspiro[4.4]nonan-3-yl)-N-(4-sulfamoylphenyl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[S](=O)(=O)c1ccc(NC(=O)CN2C(=O)NC3(CCCC3)C2=O)cc1
#
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
 M8J  M8J  2-(2,4-dioxo-1,3-diazaspiro[4.4]nonan-3-yl)-N-(4-sulfamoylphenyl)acetamide  ligand  43  25  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_M8J
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
 M8J  C14  C  CR16  0  -0.302  -2.1972  -0.4281   0.2452
 M8J  C22  C  CR16  0  -0.340  -2.9164   1.7468  -0.5124
 M8J  C15  C  CR16  0  -0.226  -3.5233  -0.8273   0.3054
 M8J  C21  C  CR16  0  -0.198  -4.2325   1.3449  -0.4577
 M8J  C13  C  CR6   0   0.401  -1.8821   0.8688  -0.1624
 M8J  C16  C  CR6   0  -0.231  -4.5347   0.0525  -0.0406
 M8J  C2   C  CR5   0   0.582   3.6956   0.2419  -0.9283
 M8J  C24  C  CR5   0   0.706   3.5060   0.6755   1.3108
 M8J  C11  C  C     0   0.551   0.5931   0.7307  -0.0370
 M8J  C5   C  CH2   0  -0.463   6.2734  -2.3980  -0.0254
 M8J  C6   C  CH2   0  -0.462   7.1544  -1.1347  -0.1735
 M8J  C4   C  CH2   0  -0.413   4.8675  -1.9841  -0.4799
 M8J  C7   C  CH2   0  -0.410   6.2213  -0.0309  -0.6919
 M8J  C3   C  C     0  -0.040   4.8301  -0.4749  -0.2264
 M8J  C10  C  CH2   0  -0.463   1.7973   1.6500  -0.2015
 M8J  N8   N  NR15  0  -0.677   4.5617  -0.1375   1.1553
 M8J  N9   N  NR5   0  -0.542   3.0112   0.9342   0.0261
 M8J  N19  N  NC2   0  -0.886  -6.8448   0.5651   1.1234
 M8J  N12  N  NH1   0  -0.749  -0.5873   1.3702  -0.2384
 M8J  O25  O  O     0  -0.481   3.0326   1.1325   2.3277
 M8J  O23  O  O     0  -0.438   0.7172  -0.4411   0.2441
 M8J  S17  S  S     0   1.360  -6.2180  -0.4699  -0.0009
 M8J  H1   H  HCR6  0   0.295  -1.4289  -1.1308   0.5201
 M8J  H2   H  HCR6  0   0.288  -2.6827   2.7548  -0.8316
 M8J  H3   H  HCR6  0   0.286  -3.7517  -1.8331   0.6293
 M8J  H4   H  HCR6  0   0.289  -5.0133   2.0426  -0.7300
 M8J  H5   H  HCH2  0   0.247   6.6465  -3.2336  -0.6169
 M8J  H6   H  HCH2  0   0.241   6.2563  -2.7346   1.0122
 M8J  H7   H  HCH2  0   0.242   7.5862  -0.8528   0.7879
 M8J  H8   H  HCH2  0   0.247   7.9880  -1.2920  -0.8568
 M8J  H9   H  HCH2  0   0.250   4.7449  -2.1546  -1.5512
 M8J  H10  H  HCH2  0   0.260   4.0654  -2.5119   0.0365
 M8J  H11  H  HCH2  0   0.260   6.4769   0.9663  -0.3334
 M8J  H12  H  HCH2  0   0.250   6.2291  -0.0061  -1.7835
 M8J  H13  H  HCH2  0   0.321   1.8104   2.0760  -1.2062
 M8J  H14  H  HCH2  0   0.321   1.7273   2.4841   0.4989
 M8J  H15  H  HNR5  0   0.415   5.1276  -0.4309   1.9355
 M8J  H16  H  HNC2  0   0.419  -7.8589   0.5974   1.0734
 M8J  H17  H  HNC2  0   0.415  -6.5469   0.3463   2.0685
 M8J  H18  H  HNH1  0   0.429  -0.5238   2.3480  -0.4847
 M8J  O1   O  O     0  -0.432   3.4422   0.2202  -2.1090
 M8J  O18  O  OS    0  -0.669  -6.8716  -0.1278  -1.2567
 M8J  O20  O  OS    0  -0.654  -6.2446  -1.8629   0.4267

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
 M8J  C4   C5   single    1.534  0.020  1.534
 M8J  C4   C3   single    1.531  0.020  1.531
 M8J  C5   C6   single    1.547  0.020  1.547
 M8J  O1   C2   double    1.208  0.020  1.208
 M8J  C6   C7   single    1.535  0.020  1.535
 M8J  C3   C2   single    1.514  0.020  1.514
 M8J  C3   C7   single    1.533  0.020  1.533
 M8J  C3   N8   single    1.447  0.020  1.447
 M8J  C2   N9   single    1.363  0.020  1.363
 M8J  N8   C24  single    1.342  0.020  1.342
 M8J  N9   C24  single    1.401  0.020  1.401
 M8J  N9   C10  single    1.428  0.020  1.428
 M8J  C24  O25  double    1.211  0.020  1.211
 M8J  C10  C11  single    1.524  0.020  1.524
 M8J  O23  C11  double    1.211  0.020  1.211
 M8J  C11  N12  single    1.358  0.020  1.358
 M8J  N12  C13  single    1.391  0.020  1.391
 M8J  C13  C14  aromatic  1.395  0.020  1.395
 M8J  C13  C22  aromatic  1.401  0.020  1.401
 M8J  C14  C15  aromatic  1.386  0.020  1.386
 M8J  C22  C21  aromatic  1.377  0.020  1.377
 M8J  C15  C16  aromatic  1.384  0.020  1.384
 M8J  C21  C16  aromatic  1.391  0.020  1.391
 M8J  C16  S17  single    1.763  0.020  1.763
 M8J  N19  S17  single    1.652  0.020  1.652
 M8J  O20  S17  double    1.457  0.020  1.457
 M8J  S17  O18  double    1.456  0.020  1.456
 M8J  C14  H1   single    0.930  0.020  1.080
 M8J  C22  H2   single    0.930  0.020  1.080
 M8J  C15  H3   single    0.930  0.020  1.080
 M8J  C21  H4   single    0.930  0.020  1.080
 M8J  C5   H5   single    0.970  0.020  1.090
 M8J  C5   H6   single    0.970  0.020  1.090
 M8J  C6   H7   single    0.970  0.020  1.090
 M8J  C6   H8   single    0.970  0.020  1.090
 M8J  C4   H9   single    0.970  0.020  1.090
 M8J  C4   H10  single    0.970  0.020  1.090
 M8J  C7   H11  single    0.970  0.020  1.090
 M8J  C7   H12  single    0.970  0.020  1.090
 M8J  C10  H13  single    0.970  0.020  1.090
 M8J  C10  H14  single    0.970  0.020  1.090
 M8J  N8   H15  single    0.860  0.020  1.020
 M8J  N19  H16  single    0.890  0.020  1.040
 M8J  N19  H17  single    0.890  0.020  1.040
 M8J  N12  H18  single    0.860  0.020  1.020

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
 M8J  H1   C14  C13  121.33  3.000
 M8J  H1   C14  C15  118.92  3.000
 M8J  C13  C14  C15  119.75  3.000
 M8J  H2   C22  C13  119.84  3.000
 M8J  H2   C22  C21  119.32  3.000
 M8J  C13  C22  C21  120.84  3.000
 M8J  H3   C15  C16  120.78  3.000
 M8J  H3   C15  C14  118.88  3.000
 M8J  C16  C15  C14  120.34  3.000
 M8J  H4   C21  C16  121.18  3.000
 M8J  H4   C21  C22  119.44  3.000
 M8J  C16  C21  C22  119.38  3.000
 M8J  N12  C13  C22  116.60  3.000
 M8J  C22  C13  C14  119.25  3.000
 M8J  N12  C13  C14  124.15  3.000
 M8J  S17  C16  C21  119.30  3.000
 M8J  S17  C16  C15  120.24  3.000
 M8J  C21  C16  C15  120.43  3.000
 M8J  O1   C2   N9   126.03  3.000
 M8J  N9   C2   C3   106.97  3.000
 M8J  O1   C2   C3   126.99  3.000
 M8J  O25  C24  N9   124.21  3.000
 M8J  O25  C24  N8   129.32  3.000
 M8J  N9   C24  N8   106.47  3.000
 M8J  O23  C11  N12  125.39  3.000
 M8J  N12  C11  C10  112.76  3.000
 M8J  O23  C11  C10  121.85  3.000
 M8J  H6   C5   H5   106.56  3.000
 M8J  H6   C5   C4   110.52  3.000
 M8J  H5   C5   C4   111.09  3.000
 M8J  H6   C5   C6   110.60  3.000
 M8J  H5   C5   C6   112.29  3.000
 M8J  C4   C5   C6   105.85  3.000
 M8J  H8   C6   H7   106.69  3.000
 M8J  H8   C6   C7   110.92  3.000
 M8J  H7   C6   C7   110.63  3.000
 M8J  H8   C6   C5   112.20  3.000
 M8J  H7   C6   C5   110.61  3.000
 M8J  C7   C6   C5   105.86  3.000
 M8J  H10  C4   H9   107.85  3.000
 M8J  H10  C4   C3   112.38  3.000
 M8J  H9   C4   C3   108.29  3.000
 M8J  H10  C4   C5   113.78  3.000
 M8J  H9   C4   C5   110.57  3.000
 M8J  C3   C4   C5   103.85  3.000
 M8J  H12  C7   H11  107.84  3.000
 M8J  H12  C7   C3   108.46  3.000
 M8J  H11  C7   C3   112.21  3.000
 M8J  H12  C7   C6   110.45  3.000
 M8J  H11  C7   C6   113.84  3.000
 M8J  C3   C7   C6   103.93  3.000
 M8J  N8   C3   C7   112.99  3.000
 M8J  N8   C3   C4   113.11  3.000
 M8J  C7   C3   C4   102.30  3.000
 M8J  N8   C3   C2   101.14  3.000
 M8J  C7   C3   C2   113.71  3.000
 M8J  C4   C3   C2   114.09  3.000
 M8J  H14  C10  H13  107.05  3.000
 M8J  H14  C10  N9   109.60  3.000
 M8J  H13  C10  N9   109.41  3.000
 M8J  H14  C10  C11  109.95  3.000
 M8J  H13  C10  C11  110.14  3.000
 M8J  N9   C10  C11  110.63  3.000
 M8J  H15  N8   C3   124.56  3.000
 M8J  H15  N8   C24  121.92  3.000
 M8J  C3   N8   C24  113.44  3.000
 M8J  C10  N9   C24  122.63  3.000
 M8J  C10  N9   C2   124.74  3.000
 M8J  C24  N9   C2   111.78  3.000
 M8J  H17  N19  H16  110.23  3.000
 M8J  H17  N19  S17  112.80  3.000
 M8J  H16  N19  S17  111.42  3.000
 M8J  H18  N12  C11  115.94  3.000
 M8J  H18  N12  C13  114.89  3.000
 M8J  C11  N12  C13  129.17  3.000
 M8J  O20  S17  O18  117.99  3.000
 M8J  O18  S17  N19  105.63  3.000
 M8J  O20  S17  N19  113.10  3.000
 M8J  O18  S17  C16  109.85  3.000
 M8J  O20  S17  C16  107.89  3.000
 M8J  N19  S17  C16  101.06  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
 M8J  CONST_01  C21  C22  C13  C14     0.00   0.0  0
 M8J  CONST_02  C21  C16  C15  C14     0.00   0.0  0
 M8J  CONST_03  C15  C14  C13  C22     0.00   0.0  0
 M8J  CONST_04  C15  C16  C21  C22     0.00   0.0  0
 M8J  CONST_05  C16  C15  C14  C13     0.00   0.0  0
 M8J  CONST_06  C16  C21  C22  C13     0.00   0.0  0
 M8J  CONST_07  C24  N8   C3   C2      0.00   0.0  0
 M8J  CONST_08  N8   C24  N9   C2      0.00   0.0  0
 M8J  CONST_09  C3   C2   N9   C24     0.00   0.0  0
 M8J  CONST_10  N9   C24  N8   C3      0.00   0.0  0
 M8J  CONST_11  N9   C2   C3   N8      0.00   0.0  0
 M8J  CONST_12  S17  C16  C15  C14   180.00   0.0  0
 M8J  CONST_13  S17  C16  C21  C22   180.00   0.0  0
 M8J  CONST_14  N12  C13  C14  C15   180.00   0.0  0
 M8J  CONST_15  N12  C13  C22  C21   180.00   0.0  0
 M8J  CONST_16  O25  C24  N9   C2    180.00   0.0  0
 M8J  CONST_17  O1   C2   N9   C24   180.00   0.0  0
 M8J  CONST_18  C10  N9   C2   C3    180.00   0.0  0
 M8J  CONST_19  O25  C24  N8   C3    180.00   0.0  0
 M8J  CONST_20  N8   C24  N9   C10   180.00   0.0  0
 M8J  CONST_21  H2   C22  C13  C14   180.00   0.0  0
 M8J  CONST_22  H1   C14  C13  C22   180.00   0.0  0
 M8J  CONST_23  H4   C21  C16  C15   180.00   0.0  0
 M8J  CONST_24  H3   C15  C16  C21   180.00   0.0  0
 M8J  CONST_25  H15  N8   C3   C2    180.00   0.0  0
 M8J  CONST_26  C11  N12  C13  C14     0.00   0.0  0
 M8J  CONST_27  C11  N12  C13  C22   180.00   0.0  0
 M8J  CONST_28  O1   C2   N9   C10     0.00   0.0  0
 M8J  CONST_29  O25  C24  N9   C10     0.00   0.0  0
 M8J  CONST_30  H18  N12  C13  C14   180.00   0.0  0
 M8J  CONST_31  C10  C11  N12  C13   180.00   0.0  0
 M8J  CONST_32  O23  C11  N12  C13     0.00   0.0  0
 M8J  Var_01    C5   C4   C3   C2    164.38  30.0  3
 M8J  Var_02    C6   C7   C3   C2   -164.20  30.0  3
 M8J  Var_03    C4   C3   N8   C24  -124.65  30.0  1
 M8J  Var_04    C3   C7   C6   C5     24.70  30.0  1
 M8J  Var_05    C3   C4   C5   C6    -25.85  30.0  1
 M8J  Var_06    C7   C6   C5   C4      0.69  30.0  1
 M8J  Var_07    N9   C2   C3   C4    125.72  30.0  1
 M8J  Var_08    N19  S17  C16  C15   118.81  30.0  2
 M8J  Var_09    C11  C10  N9   C2     87.40  30.0  3
 M8J  Var_10    O23  C11  C10  N9     -0.29  30.0  3
 M8J  Var_11    H16  N19  S17  C16   162.76  30.0  3

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
 M8J  plan-1  C13  0.020
 M8J  plan-1  C11  0.020
 M8J  plan-1  C10  0.020
 M8J  plan-1  N12  0.020
 M8J  plan-1  O23  0.020
 M8J  plan-1  H18  0.020
 M8J  plan-2  C14  0.020
 M8J  plan-2  C22  0.020
 M8J  plan-2  C15  0.020
 M8J  plan-2  C21  0.020
 M8J  plan-2  C13  0.020
 M8J  plan-2  C16  0.020
 M8J  plan-2  N12  0.020
 M8J  plan-2  S17  0.020
 M8J  plan-2  H1   0.020
 M8J  plan-2  H2   0.020
 M8J  plan-2  H3   0.020
 M8J  plan-2  H4   0.020
 M8J  plan-3  C2   0.020
 M8J  plan-3  C24  0.020
 M8J  plan-3  C3   0.020
 M8J  plan-3  C10  0.020
 M8J  plan-3  N8   0.020
 M8J  plan-3  N9   0.020
 M8J  plan-3  O25  0.020
 M8J  plan-3  H15  0.020
 M8J  plan-3  O1   0.020

