# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 18:09:06 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: cis-4-methyl-N-[(1S)-3-(methylsulfanyl)-1-(pyridin-4-ylcarbamoyl)propyl]cyclohexanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@H](NC(=O)[C@@H]1CC[C@H](C)CC1)C(=O)Nc2ccncc2
#
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
 CM9  CM9  cis-4-methyl-N-[(1S)-3-(methylsulfanyl)-1-(pyridin-4-ylcarbamoyl)propyl]cyclohexanecarboxamide  ligand  51  24  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CM9
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
 CM9  O1    O  O     0  -0.479  -18.7289  -0.0519  68.2417
 CM9  C8    C  C     0   0.559  -18.5365  -0.6180  69.3067
 CM9  C9    C  CH1   0  -0.379  -19.6643  -1.1159  70.1807
 CM9  C10   C  CH2   0  -0.422  -20.1082   0.0164  71.1351
 CM9  C11   C  CH2   0  -0.431  -20.8578  -0.5349  72.3550
 CM9  C12   C  CH1   0  -0.235  -21.6322  -1.8028  72.0116
 CM9  C13   C  CH3   0  -0.661  -22.5463  -2.2438  73.1460
 CM9  C14   C  CH2   0  -0.413  -20.6471  -2.9186  71.6231
 CM9  C15   C  CH2   0  -0.468  -19.3620  -2.3812  70.9803
 CM9  N3    N  NH1   0  -0.671  -17.2798  -0.7963  69.7792
 CM9  C7    C  CH1   0  -0.173  -16.1340  -0.2569  69.0893
 CM9  C16   C  CH2   0  -0.462  -14.8859  -0.3647  69.9728
 CM9  C17   C  CH2   0  -0.577  -14.9343   0.5962  71.1527
 CM9  S     S  S2    0  -0.023  -13.4858   0.4706  72.2332
 CM9  C18   C  CH3   0  -0.772  -13.8377  -1.0885  73.0778
 CM9  C6    C  C     0   0.536  -15.8614  -0.9466  67.7523
 CM9  O2    O  O     0  -0.446  -15.3347  -0.3447  66.8395
 CM9  N2    N  NH1   0  -0.733  -16.1842  -2.2662  67.7232
 CM9  C5    C  CR6   0   0.471  -15.9910  -3.1919  66.7090
 CM9  C1    C  CR16  0  -0.376  -15.4292  -2.9117  65.4634
 CM9  C2    C  CR16  0  -0.068  -15.2990  -3.9524  64.5566
 CM9  N1    N  N     0  -0.417  -15.6726  -5.2057  64.7808
 CM9  C3    C  CR16  0  -0.062  -16.2097  -5.4605  65.9703
 CM9  C4    C  CR16  0  -0.419  -16.3888  -4.5082  66.9538
 CM9  H9    H  HCH1  0   0.268  -20.4882  -1.3343  69.4952
 CM9  H3    H  HNH1  0   0.409  -17.1383  -1.2588  70.6634
 CM9  H101  H  HCH2  0   0.232  -19.2372   0.5844  71.4729
 CM9  H102  H  HCH2  0   0.242  -20.7409   0.7148  70.5844
 CM9  H151  H  HCH2  0   0.247  -18.9109  -3.1501  70.3487
 CM9  H152  H  HCH2  0   0.226  -18.6334  -2.1598  71.7679
 CM9  H111  H  HCH2  0   0.219  -20.1488  -0.7598  73.1590
 CM9  H112  H  HCH2  0   0.235  -21.5289   0.2321  72.7489
 CM9  H12   H  HCH1  0   0.222  -22.2648  -1.5839  71.1425
 CM9  H131  H  HCH3  0   0.214  -21.9803  -2.3898  74.0690
 CM9  H132  H  HCH3  0   0.225  -23.3218  -1.5019  73.3440
 CM9  H133  H  HCH3  0   0.226  -23.0419  -3.1876  72.9111
 CM9  H141  H  HCH2  0   0.223  -20.3790  -3.4939  72.5137
 CM9  H142  H  HCH2  0   0.231  -21.1415  -3.6159  70.9425
 CM9  H7    H  HCH1  0   0.291  -16.3069   0.7961  68.8496
 CM9  H161  H  HCH2  0   0.256  -14.7690  -1.3980  70.3120
 CM9  H162  H  HCH2  0   0.277  -14.0074  -0.1332  69.3693
 CM9  H171  H  HCH2  0   0.290  -14.9485   1.6255  70.7895
 CM9  H172  H  HCH2  0   0.265  -15.8302   0.4627  71.7630
 CM9  H181  H  HCH3  0   0.261  -13.8205  -1.9369  72.3958
 CM9  H182  H  HCH3  0   0.279  -13.0612  -1.2348  73.8264
 CM9  H183  H  HCH3  0   0.263  -14.8029  -1.0477  73.5810
 CM9  H2    H  HNH1  0   0.410  -16.6134  -2.6311  68.5617
 CM9  H1    H  HCR6  0   0.291  -15.0990  -1.9252  65.1868
 CM9  H4    H  HCR6  0   0.281  -16.8320  -4.7910  67.9006
 CM9  HA    H  HCR6  0   0.266  -14.8601  -3.7449  63.5866
 CM9  HB    H  HCR6  0   0.268  -16.5173  -6.4831  66.1583

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
 CM9  O1   C8    double    1.221  0.020  1.221
 CM9  C8   C9    single    1.511  0.020  1.511
 CM9  C8   N3    single    1.354  0.020  1.354
 CM9  C9   C10   single    1.546  0.020  1.546
 CM9  C9   C15   single    1.527  0.020  1.527
 CM9  C10  C11   single    1.534  0.020  1.534
 CM9  C11  C12   single    1.525  0.020  1.525
 CM9  C12  C13   single    1.522  0.020  1.522
 CM9  C12  C14   single    1.538  0.020  1.538
 CM9  C14  C15   single    1.534  0.020  1.534
 CM9  N3   C7    single    1.442  0.020  1.442
 CM9  C7   C16   single    1.533  0.020  1.533
 CM9  C7   C6    single    1.529  0.020  1.529
 CM9  C16  C17   single    1.522  0.020  1.522
 CM9  C17  S     single    1.811  0.020  1.811
 CM9  S    C18   single    1.808  0.020  1.808
 CM9  C6   O2    double    1.214  0.020  1.214
 CM9  C6   N2    single    1.359  0.020  1.359
 CM9  N2   C5    single    1.387  0.020  1.387
 CM9  C5   C1    aromatic  1.395  0.020  1.395
 CM9  C5   C4    aromatic  1.397  0.020  1.397
 CM9  C1   C2    aromatic  1.386  0.020  1.386
 CM9  C2   N1    aromatic  1.327  0.020  1.327
 CM9  N1   C3    aromatic  1.330  0.020  1.330
 CM9  C3   C4    aromatic  1.381  0.020  1.381
 CM9  C9   H9    single    0.970  0.020  1.090
 CM9  N3   H3    single    0.860  0.020  1.020
 CM9  C10  H101  single    0.970  0.020  1.090
 CM9  C10  H102  single    0.970  0.020  1.090
 CM9  C15  H151  single    0.970  0.020  1.090
 CM9  C15  H152  single    0.970  0.020  1.090
 CM9  C11  H111  single    0.970  0.020  1.090
 CM9  C11  H112  single    0.970  0.020  1.090
 CM9  C12  H12   single    0.970  0.020  1.090
 CM9  C13  H131  single    0.970  0.020  1.090
 CM9  C13  H132  single    0.970  0.020  1.090
 CM9  C13  H133  single    0.970  0.020  1.090
 CM9  C14  H141  single    0.970  0.020  1.090
 CM9  C14  H142  single    0.970  0.020  1.090
 CM9  C7   H7    single    0.970  0.020  1.090
 CM9  C16  H161  single    0.970  0.020  1.090
 CM9  C16  H162  single    0.970  0.020  1.090
 CM9  C17  H171  single    0.970  0.020  1.090
 CM9  C17  H172  single    0.970  0.020  1.090
 CM9  C18  H181  single    0.970  0.020  1.090
 CM9  C18  H182  single    0.970  0.020  1.090
 CM9  C18  H183  single    0.970  0.020  1.090
 CM9  N2   H2    single    0.860  0.020  1.020
 CM9  C1   H1    single    0.930  0.020  1.080
 CM9  C4   H4    single    0.930  0.020  1.080
 CM9  C2   HA    single    0.930  0.020  1.080
 CM9  C3   HB    single    0.930  0.020  1.080

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
 CM9  N3    C8   C9    116.58  3.000
 CM9  N3    C8   O1    120.75  3.000
 CM9  C9    C8   O1    122.65  3.000
 CM9  H9    C9   C15   108.17  3.000
 CM9  H9    C9   C10   108.48  3.000
 CM9  C15   C9   C10   109.90  3.000
 CM9  H9    C9   C8    105.40  3.000
 CM9  C15   C9   C8    115.35  3.000
 CM9  C10   C9   C8    109.27  3.000
 CM9  H102  C10  H101  106.58  3.000
 CM9  H102  C10  C11   110.36  3.000
 CM9  H101  C10  C11   109.28  3.000
 CM9  H102  C10  C9    108.88  3.000
 CM9  H101  C10  C9    110.03  3.000
 CM9  C11   C10  C9    111.59  3.000
 CM9  H112  C11  H111  106.09  3.000
 CM9  H112  C11  C12   110.66  3.000
 CM9  H111  C11  C12   108.86  3.000
 CM9  H112  C11  C10   109.54  3.000
 CM9  H111  C11  C10   109.95  3.000
 CM9  C12   C11  C10   111.58  3.000
 CM9  H12   C12  C14   108.29  3.000
 CM9  H12   C12  C13   107.57  3.000
 CM9  C14   C12  C13   111.26  3.000
 CM9  H12   C12  C11   107.78  3.000
 CM9  C14   C12  C11   109.56  3.000
 CM9  C13   C12  C11   112.22  3.000
 CM9  H133  C13  H132  107.71  3.000
 CM9  H133  C13  H131  107.55  3.000
 CM9  H132  C13  H131  107.81  3.000
 CM9  H133  C13  C12   111.27  3.000
 CM9  H132  C13  C12   111.41  3.000
 CM9  H131  C13  C12   110.92  3.000
 CM9  H142  C14  H141  106.41  3.000
 CM9  H142  C14  C15   109.97  3.000
 CM9  H141  C14  C15   108.67  3.000
 CM9  H142  C14  C12   109.30  3.000
 CM9  H141  C14  C12   109.44  3.000
 CM9  C15   C14  C12   112.84  3.000
 CM9  H152  C15  H151  106.45  3.000
 CM9  H152  C15  C14   109.07  3.000
 CM9  H151  C15  C14   109.98  3.000
 CM9  H152  C15  C9    109.91  3.000
 CM9  H151  C15  C9    111.23  3.000
 CM9  C14   C15  C9    110.11  3.000
 CM9  H3    N3   C7    118.67  3.000
 CM9  H3    N3   C8    119.79  3.000
 CM9  C7    N3   C8    121.41  3.000
 CM9  H7    C7   C6    105.71  3.000
 CM9  H7    C7   C16   108.83  3.000
 CM9  C6    C7   C16   109.09  3.000
 CM9  H7    C7   N3    109.84  3.000
 CM9  C6    C7   N3    113.03  3.000
 CM9  C16   C7   N3    110.17  3.000
 CM9  H162  C16  H161  106.62  3.000
 CM9  H162  C16  C17   108.69  3.000
 CM9  H161  C16  C17   111.06  3.000
 CM9  H162  C16  C7    108.78  3.000
 CM9  H161  C16  C7    109.40  3.000
 CM9  C17   C16  C7    112.11  3.000
 CM9  H172  C17  H171  106.89  3.000
 CM9  H172  C17  S     108.31  3.000
 CM9  H171  C17  S     105.92  3.000
 CM9  H172  C17  C16   112.46  3.000
 CM9  H171  C17  C16   109.74  3.000
 CM9  S     C17  C16   113.15  3.000
 CM9  C18   S    C17   100.54  3.000
 CM9  H183  C18  H182  108.62  3.000
 CM9  H183  C18  H181  109.43  3.000
 CM9  H182  C18  H181  108.35  3.000
 CM9  H183  C18  S     110.86  3.000
 CM9  H182  C18  S     107.36  3.000
 CM9  H181  C18  S     112.11  3.000
 CM9  N2    C6   O2    124.65  3.000
 CM9  N2    C6   C7    114.49  3.000
 CM9  O2    C6   C7    120.76  3.000
 CM9  H2    N2   C5    115.16  3.000
 CM9  H2    N2   C6    115.72  3.000
 CM9  C5    N2   C6    129.11  3.000
 CM9  C4    C5   C1    117.42  3.000
 CM9  C4    C5   N2    117.46  3.000
 CM9  C1    C5   N2    125.12  3.000
 CM9  H1    C1   C2    119.41  3.000
 CM9  H1    C1   C5    122.48  3.000
 CM9  C2    C1   C5    118.11  3.000
 CM9  HA    C2   N1    116.47  3.000
 CM9  HA    C2   C1    118.64  3.000
 CM9  N1    C2   C1    124.89  3.000
 CM9  C3    N1   C2    116.48  3.000
 CM9  HB    C3   C4    119.35  3.000
 CM9  HB    C3   N1    116.77  3.000
 CM9  C4    C3   N1    123.88  3.000
 CM9  H4    C4   C3    119.72  3.000
 CM9  H4    C4   C5    121.06  3.000
 CM9  C3    C4   C5    119.22  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
 CM9  CONST_01  N1    C2   C1   C5     0.00   0.0  0
 CM9  CONST_02  N1    C3   C4   C5     0.00   0.0  0
 CM9  CONST_03  C3    C4   C5   C1     0.00   0.0  0
 CM9  CONST_04  C3    N1   C2   C1     0.00   0.0  0
 CM9  CONST_05  C4    C5   C1   C2     0.00   0.0  0
 CM9  CONST_06  C4    C3   N1   C2     0.00   0.0  0
 CM9  CONST_07  C2    C1   C5   N2   180.00   0.0  0
 CM9  CONST_08  C3    C4   C5   N2   180.00   0.0  0
 CM9  CONST_09  HA    C2   C1   C5   180.00   0.0  0
 CM9  CONST_10  HB    C3   C4   C5   180.00   0.0  0
 CM9  CONST_11  H4    C4   C5   C1   180.00   0.0  0
 CM9  CONST_12  H1    C1   C2   N1   180.00   0.0  0
 CM9  CONST_13  C1    C5   N2   C6     0.00   0.0  0
 CM9  CONST_14  C4    C5   N2   C6   180.00   0.0  0
 CM9  CONST_15  H2    N2   C5   C1   180.00   0.0  0
 CM9  CONST_16  C7    N3   C8   C9   180.00   0.0  0
 CM9  CONST_17  C5    N2   C6   C7   180.00   0.0  0
 CM9  CONST_18  C5    N2   C6   O2     0.00   0.0  0
 CM9  CONST_19  H3    N3   C8   C9     0.00   0.0  0
 CM9  CONST_20  C7    N3   C8   O1     0.00   0.0  0
 CM9  Var_01    C12   C11  C10  C9   -31.46  30.0  1
 CM9  Var_02    C12   C14  C15  C9   -32.60  30.0  1
 CM9  Var_03    S     C17  C16  C7   178.94  30.0  3
 CM9  Var_04    H181  C18  S    C17   65.63  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
 CM9  chir_01  C9   C8   C10  C15  positiv
 CM9  chir_02  C12  C14  C13  C11  negativ
 CM9  chir_03  C7   N3   C6   C16  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
 CM9  plan-1  N2  0.020
 CM9  plan-1  C5  0.020
 CM9  plan-1  C1  0.020
 CM9  plan-1  C2  0.020
 CM9  plan-1  N1  0.020
 CM9  plan-1  C3  0.020
 CM9  plan-1  C4  0.020
 CM9  plan-1  H1  0.020
 CM9  plan-1  H4  0.020
 CM9  plan-1  HA  0.020
 CM9  plan-1  HB  0.020
 CM9  plan-2  C7  0.020
 CM9  plan-2  C6  0.020
 CM9  plan-2  O2  0.020
 CM9  plan-2  N2  0.020
 CM9  plan-2  C5  0.020
 CM9  plan-2  H2  0.020
 CM9  plan-3  O1  0.020
 CM9  plan-3  C8  0.020
 CM9  plan-3  C9  0.020
 CM9  plan-3  N3  0.020
 CM9  plan-3  C7  0.020
 CM9  plan-3  H3  0.020

