# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 22:18:01 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 2-[cyclohexyl(methylsulfonyl)amino]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)N(CC(N)=O)C1CCCCC1
#
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
 AYJ  AYJ  2-[cyclohexyl(methylsulfonyl)amino]ethanamide  ligand  33  15  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AYJ
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
 AYJ  N1   N  N     0  -0.591   0.3898   0.0024   0.4084
 AYJ  C4   C  CH1   0  -0.086  -0.9526   0.4964   0.0818
 AYJ  C5   C  CH2   0  -0.417  -1.7053  -0.4308  -0.8669
 AYJ  C6   C  CH2   0  -0.438  -3.0795   0.1384  -1.2084
 AYJ  C7   C  CH2   0  -0.432  -3.8949   0.4269   0.0472
 AYJ  C8   C  CH2   0  -0.438  -3.1333   1.3475   0.9938
 AYJ  C1   C  CH3   0  -0.782   1.7895   2.2737   0.8028
 AYJ  S1   S  S     0   1.345   1.6974   0.7959  -0.1832
 AYJ  O1   O  OS    0  -0.670   2.8693  -0.0164   0.1200
 AYJ  O2   O  OS    0  -0.667   1.4619   1.2132  -1.5591
 AYJ  C2   C  CH2   0  -0.434   0.5818  -1.2766   1.0398
 AYJ  C3   C  C     0   0.520   1.0414  -2.3781   0.0894
 AYJ  O3   O  O     0  -0.475   1.0881  -2.2277  -1.1182
 AYJ  N2   N  NH2   0  -0.803   1.3606  -3.5205   0.7133
 AYJ  C9   C  CH2   0  -0.420  -1.7601   0.7826   1.3465
 AYJ  H1   H  HCH1  0   0.248  -0.8200   1.4518  -0.4359
 AYJ  H2   H  HCH2  0   0.244  -1.1134  -0.5825  -1.7695
 AYJ  H3   H  HCH2  0   0.215  -1.8315  -1.4129  -0.3978
 AYJ  H4   H  HCH2  0   0.215  -2.9599   1.0628  -1.7842
 AYJ  H5   H  HCH2  0   0.234  -3.6138  -0.5600  -1.8565
 AYJ  H6   H  HCH2  0   0.231  -4.8539   0.8763  -0.2211
 AYJ  H7   H  HCH2  0   0.213  -4.1243  -0.5151   0.5568
 AYJ  H8   H  HCH2  0   0.216  -3.0078   2.3276   0.5206
 AYJ  H9   H  HCH2  0   0.235  -3.7064   1.5169   1.9078
 AYJ  H10  H  HCH3  0   0.298   2.6366   2.8619   0.4537
 AYJ  H11  H  HCH3  0   0.285   0.8757   2.8534   0.6909
 AYJ  H12  H  HCH3  0   0.288   1.9305   1.9962   1.8444
 AYJ  H13  H  HCH2  0   0.294   1.2703  -1.2087   1.8854
 AYJ  H14  H  HCH2  0   0.302  -0.3742  -1.5837   1.4680
 AYJ  H15  H  HNH2  0   0.408   1.3402  -3.6056   1.7153
 AYJ  H16  H  HNH2  0   0.403   1.6675  -4.3225   0.1882
 AYJ  H17  H  HCH2  0   0.221  -1.8854  -0.1354   1.9300
 AYJ  H18  H  HCH2  0   0.240  -1.2122   1.4846   1.9803

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
 AYJ  O2  S1   double  1.457  0.020  1.457
 AYJ  S1  O1   double  1.458  0.020  1.458
 AYJ  S1  N1   single  1.640  0.020  1.640
 AYJ  S1  C1   single  1.779  0.020  1.779
 AYJ  C2  C3   single  1.526  0.020  1.526
 AYJ  C2  N1   single  1.439  0.020  1.439
 AYJ  N2  C3   single  1.340  0.020  1.340
 AYJ  C3  O3   double  1.218  0.020  1.218
 AYJ  N1  C4   single  1.467  0.020  1.467
 AYJ  C4  C5   single  1.525  0.020  1.525
 AYJ  C4  C9   single  1.528  0.020  1.528
 AYJ  C5  C6   single  1.526  0.020  1.526
 AYJ  C9  C8   single  1.526  0.020  1.526
 AYJ  C6  C7   single  1.525  0.020  1.525
 AYJ  C8  C7   single  1.524  0.020  1.524
 AYJ  C4  H1   single  0.970  0.020  1.090
 AYJ  C5  H2   single  0.970  0.020  1.090
 AYJ  C5  H3   single  0.970  0.020  1.090
 AYJ  C6  H4   single  0.970  0.020  1.090
 AYJ  C6  H5   single  0.970  0.020  1.090
 AYJ  C7  H6   single  0.970  0.020  1.090
 AYJ  C7  H7   single  0.970  0.020  1.090
 AYJ  C8  H8   single  0.970  0.020  1.090
 AYJ  C8  H9   single  0.970  0.020  1.090
 AYJ  C1  H10  single  0.970  0.020  1.090
 AYJ  C1  H11  single  0.970  0.020  1.090
 AYJ  C1  H12  single  0.970  0.020  1.090
 AYJ  C2  H13  single  0.970  0.020  1.090
 AYJ  C2  H14  single  0.970  0.020  1.090
 AYJ  N2  H15  single  0.860  0.020  1.020
 AYJ  N2  H16  single  0.860  0.020  1.020
 AYJ  C9  H17  single  0.970  0.020  1.090
 AYJ  C9  H18  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
 AYJ  C2   N1  S1   118.81  3.000
 AYJ  C2   N1  C4   121.26  3.000
 AYJ  S1   N1  C4   119.10  3.000
 AYJ  H1   C4  C9   106.98  3.000
 AYJ  H1   C4  C5   107.23  3.000
 AYJ  C9   C4  C5   111.59  3.000
 AYJ  H1   C4  N1   106.76  3.000
 AYJ  C9   C4  N1   111.25  3.000
 AYJ  C5   C4  N1   112.66  3.000
 AYJ  H3   C5  H2   106.99  3.000
 AYJ  H3   C5  C6   109.05  3.000
 AYJ  H2   C5  C6   110.83  3.000
 AYJ  H3   C5  C4   109.60  3.000
 AYJ  H2   C5  C4   109.37  3.000
 AYJ  C6   C5  C4   110.91  3.000
 AYJ  H5   C6  H4   106.32  3.000
 AYJ  H5   C6  C7   110.37  3.000
 AYJ  H4   C6  C7   109.36  3.000
 AYJ  H5   C6  C5   109.56  3.000
 AYJ  H4   C6  C5   109.51  3.000
 AYJ  C7   C6  C5   111.59  3.000
 AYJ  H7   C7  H6   106.51  3.000
 AYJ  H7   C7  C8   109.58  3.000
 AYJ  H6   C7  C8   110.04  3.000
 AYJ  H7   C7  C6   109.41  3.000
 AYJ  H6   C7  C6   110.19  3.000
 AYJ  C8   C7  C6   111.01  3.000
 AYJ  H9   C8  H8   106.44  3.000
 AYJ  H9   C8  C9   109.64  3.000
 AYJ  H8   C8  C9   109.14  3.000
 AYJ  H9   C8  C7   110.56  3.000
 AYJ  H8   C8  C7   109.23  3.000
 AYJ  C9   C8  C7   111.68  3.000
 AYJ  H12  C1  H11  110.09  3.000
 AYJ  H12  C1  H10  110.13  3.000
 AYJ  H11  C1  H10  109.43  3.000
 AYJ  H12  C1  S1   109.01  3.000
 AYJ  H11  C1  S1   110.01  3.000
 AYJ  H10  C1  S1   108.14  3.000
 AYJ  O2   S1  O1   119.07  3.000
 AYJ  O1   S1  C1   107.82  3.000
 AYJ  O2   S1  C1   107.09  3.000
 AYJ  C1   S1  N1   104.08  3.000
 AYJ  O1   S1  N1   107.24  3.000
 AYJ  O2   S1  N1   110.51  3.000
 AYJ  H14  C2  H13  105.41  3.000
 AYJ  H14  C2  C3   107.76  3.000
 AYJ  H13  C2  C3   109.70  3.000
 AYJ  H14  C2  N1   107.77  3.000
 AYJ  H13  C2  N1   111.62  3.000
 AYJ  C3   C2  N1   114.11  3.000
 AYJ  N2   C3  O3   123.91  3.000
 AYJ  O3   C3  C2   122.69  3.000
 AYJ  N2   C3  C2   113.40  3.000
 AYJ  H16  N2  H15  117.29  3.000
 AYJ  H16  N2  C3   120.59  3.000
 AYJ  H15  N2  C3   122.08  3.000
 AYJ  H18  C9  H17  106.67  3.000
 AYJ  H18  C9  C8   110.32  3.000
 AYJ  H17  C9  C8   109.30  3.000
 AYJ  H18  C9  C4   109.59  3.000
 AYJ  H17  C9  C4   110.16  3.000
 AYJ  C8   C9  C4   110.71  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
 AYJ  CONST_01  H15  N2  C3  C2     0.00   0.0  0
 AYJ  CONST_02  H16  N2  C3  C2   180.00   0.0  0
 AYJ  Var_01    C7   C6  C5  C4   -55.29  30.0  1
 AYJ  Var_02    C7   C8  C9  C4    55.38  30.0  1
 AYJ  Var_03    C8   C7  C6  C5    55.19  30.0  1
 AYJ  Var_04    C9   C8  C7  C6   -55.33  30.0  1
 AYJ  Var_05    O2   S1  N1  C4   -40.22  30.0  2
 AYJ  Var_06    C3   C2  N1  C4   102.43  30.0  3
 AYJ  Var_07    N2   C3  C2  N1   172.90  30.0  3
 AYJ  Var_08    H10  C1  S1  N1  -179.29  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
 AYJ  chir_01  C4  N1  C5  C9  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
 AYJ  plan-1  C2   0.020
 AYJ  plan-1  C3   0.020
 AYJ  plan-1  O3   0.020
 AYJ  plan-1  N2   0.020
 AYJ  plan-1  H15  0.020
 AYJ  plan-1  H16  0.020

