# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 14:50:29 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: N-[(1R,2R,3S,4R,6S)-2,3-dihydroxy-4-(hydroxymethyl)-6-(methylsulfanyl)cyclohexyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CS[C@H]1C[C@H](CO)[C@H](O)[C@H](O)[C@H]1NC(C)=O
#
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
 Q3M  Q3M  N-[(1R,2R,3S,4R,6S)-2,3-dihydroxy-4-(hydroxymethyl)-6-(methylsulfanyl)cyclohexyl]acetamide  ligand  35  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_Q3M
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
 Q3M  C01  C  CH3   0  -0.762  -14.0419  -12.7684   5.0689
 Q3M  S02  S  S2    0  -0.046  -13.4525  -11.0690   5.2287
 Q3M  C03  C  CH1   0  -0.381  -15.0517  -10.1770   5.2015
 Q3M  C04  C  CH2   0  -0.402  -15.7920  -10.2683   6.5305
 Q3M  C05  C  CH1   0  -0.295  -15.0944   -9.4834   7.6367
 Q3M  C06  C  CH2   0  -0.138  -15.8212   -9.5806   8.9691
 Q3M  O07  O  OH1   0  -0.666  -15.7981  -10.9199   9.4091
 Q3M  C08  C  CH1   0  -0.013  -14.9010   -8.0219   7.2210
 Q3M  O09  O  OH1   0  -0.668  -16.1224   -7.3416   7.0306
 Q3M  C10  C  CH1   0   0.052  -14.1097   -7.9445   5.9124
 Q3M  O11  O  OH1   0  -0.662  -13.9227   -6.6235   5.4749
 Q3M  C12  C  CH1   0  -0.070  -14.8298   -8.7100   4.8023
 Q3M  N13  N  NH1   0  -0.626  -14.1278   -8.5724   3.5505
 Q3M  C14  C  C     0   0.519  -14.7382   -8.6235   2.3533
 Q3M  C15  C  CH3   0  -0.776  -13.8285   -8.4879   1.1574
 Q3M  O16  O  O     0  -0.501  -15.9483   -8.7581   2.2278
 Q3M  H1   H  HCH3  0   0.274  -13.1654  -13.4102   4.9976
 Q3M  H2   H  HCH3  0   0.262  -14.6259  -13.0793   5.9334
 Q3M  H3   H  HCH3  0   0.261  -14.6383  -12.8899   4.1657
 Q3M  H4   H  HCH1  0   0.288  -15.6490  -10.6498   4.4175
 Q3M  H5   H  HCH2  0   0.234  -16.8049   -9.8770   6.3862
 Q3M  H6   H  HCH2  0   0.252  -15.9094  -11.3141   6.8177
 Q3M  H7   H  HCH1  0   0.232  -14.0911   -9.9023   7.7823
 Q3M  H8   H  HCH2  0   0.200  -15.3281   -8.9161   9.6937
 Q3M  H9   H  HCH2  0   0.189  -16.8529   -9.2220   8.8562
 Q3M  H10  H  HOH1  0   0.451  -16.3436  -10.9874  10.1976
 Q3M  H11  H  HCH1  0   0.231  -14.3021   -7.5193   7.9966
 Q3M  H12  H  HOH1  0   0.455  -16.4797   -7.0932   7.8875
 Q3M  H13  H  HCH1  0   0.217  -13.1381   -8.4290   6.1028
 Q3M  H14  H  HOH1  0   0.450  -13.3990   -6.1569   6.1343
 Q3M  H15  H  HCH1  0   0.272  -15.8232   -8.2723   4.6702
 Q3M  H16  H  HNH1  0   0.397  -13.1224   -8.5154   3.5735
 Q3M  H17  H  HCH3  0   0.264  -14.1151   -7.6043   0.5869
 Q3M  H18  H  HCH3  0   0.247  -12.7745   -8.4032   1.4148
 Q3M  H19  H  HCH3  0   0.262  -13.9578   -9.3506   0.5043

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
 Q3M  C15  C14  single  1.509  0.020  1.509
 Q3M  O16  C14  double  1.224  0.020  1.224
 Q3M  C14  N13  single  1.345  0.020  1.345
 Q3M  N13  C12  single  1.442  0.020  1.442
 Q3M  C12  C03  single  1.536  0.020  1.536
 Q3M  C12  C10  single  1.529  0.020  1.529
 Q3M  C03  S02  single  1.831  0.020  1.831
 Q3M  C03  C04  single  1.524  0.020  1.524
 Q3M  S02  C01  single  1.806  0.020  1.806
 Q3M  O11  C10  single  1.404  0.020  1.404
 Q3M  C10  C08  single  1.531  0.020  1.531
 Q3M  C04  C05  single  1.525  0.020  1.525
 Q3M  C08  O09  single  1.411  0.020  1.411
 Q3M  C08  C05  single  1.532  0.020  1.532
 Q3M  C05  C06  single  1.521  0.020  1.521
 Q3M  C06  O07  single  1.410  0.020  1.410
 Q3M  C01  H1   single  0.970  0.020  1.090
 Q3M  C01  H2   single  0.970  0.020  1.090
 Q3M  C01  H3   single  0.970  0.020  1.090
 Q3M  C03  H4   single  0.970  0.020  1.090
 Q3M  C04  H5   single  0.970  0.020  1.090
 Q3M  C04  H6   single  0.970  0.020  1.090
 Q3M  C05  H7   single  0.970  0.020  1.090
 Q3M  C06  H8   single  0.970  0.020  1.090
 Q3M  C06  H9   single  0.970  0.020  1.090
 Q3M  O07  H10  single  0.850  0.020  0.980
 Q3M  C08  H11  single  0.970  0.020  1.090
 Q3M  O09  H12  single  0.850  0.020  0.980
 Q3M  C10  H13  single  0.970  0.020  1.090
 Q3M  O11  H14  single  0.850  0.020  0.980
 Q3M  C12  H15  single  0.970  0.020  1.090
 Q3M  N13  H16  single  0.860  0.020  1.020
 Q3M  C15  H17  single  0.970  0.020  1.090
 Q3M  C15  H18  single  0.970  0.020  1.090
 Q3M  C15  H19  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
 Q3M  H3   C01  H2   109.45  3.000
 Q3M  H3   C01  H1   108.71  3.000
 Q3M  H2   C01  H1   108.40  3.000
 Q3M  H3   C01  S02  110.92  3.000
 Q3M  H2   C01  S02  111.94  3.000
 Q3M  H1   C01  S02  107.33  3.000
 Q3M  C03  S02  C01   99.91  3.000
 Q3M  H4   C03  C12  107.79  3.000
 Q3M  H4   C03  C04  109.52  3.000
 Q3M  C12  C03  C04  110.73  3.000
 Q3M  H4   C03  S02  106.09  3.000
 Q3M  C04  C03  S02  112.46  3.000
 Q3M  C12  C03  S02  110.05  3.000
 Q3M  H6   C04  H5   106.12  3.000
 Q3M  H6   C04  C05  110.59  3.000
 Q3M  H5   C04  C05  109.54  3.000
 Q3M  H6   C04  C03  109.84  3.000
 Q3M  H5   C04  C03  108.24  3.000
 Q3M  C05  C04  C03  112.30  3.000
 Q3M  H7   C05  C08  106.55  3.000
 Q3M  H7   C05  C06  107.24  3.000
 Q3M  C08  C05  C06  111.05  3.000
 Q3M  H7   C05  C04  108.54  3.000
 Q3M  C06  C05  C04  112.58  3.000
 Q3M  C08  C05  C04  110.61  3.000
 Q3M  H9   C06  H8   106.95  3.000
 Q3M  H9   C06  O07  110.96  3.000
 Q3M  H8   C06  O07  111.17  3.000
 Q3M  H9   C06  C05  109.75  3.000
 Q3M  H8   C06  C05  108.92  3.000
 Q3M  O07  C06  C05  109.05  3.000
 Q3M  H10  O07  C06  108.27  3.000
 Q3M  H11  C08  C10  107.32  3.000
 Q3M  H11  C08  O09  110.23  3.000
 Q3M  C10  C08  O09  107.92  3.000
 Q3M  H11  C08  C05  108.24  3.000
 Q3M  O09  C08  C05  112.79  3.000
 Q3M  C10  C08  C05  110.21  3.000
 Q3M  H12  O09  C08  109.03  3.000
 Q3M  H13  C10  C12  108.69  3.000
 Q3M  H13  C10  O11  110.49  3.000
 Q3M  C12  C10  O11  107.92  3.000
 Q3M  H13  C10  C08  106.60  3.000
 Q3M  O11  C10  C08  112.50  3.000
 Q3M  C12  C10  C08  110.60  3.000
 Q3M  H14  O11  C10  108.36  3.000
 Q3M  H15  C12  N13  107.41  3.000
 Q3M  H15  C12  C10  108.37  3.000
 Q3M  N13  C12  C10  110.69  3.000
 Q3M  H15  C12  C03  106.40  3.000
 Q3M  C10  C12  C03  110.95  3.000
 Q3M  N13  C12  C03  112.77  3.000
 Q3M  H16  N13  C14  118.40  3.000
 Q3M  H16  N13  C12  118.13  3.000
 Q3M  C14  N13  C12  123.25  3.000
 Q3M  O16  C14  C15  121.65  3.000
 Q3M  O16  C14  N13  122.97  3.000
 Q3M  C15  C14  N13  115.38  3.000
 Q3M  H19  C15  H18  108.56  3.000
 Q3M  H19  C15  H17  107.27  3.000
 Q3M  H18  C15  H17  108.37  3.000
 Q3M  H19  C15  C14  109.42  3.000
 Q3M  H18  C15  C14  113.80  3.000
 Q3M  H17  C15  C14  109.22  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
 Q3M  CONST_01  C15  C14  N13  C12   180.00   0.0  0
 Q3M  CONST_02  O16  C14  N13  C12     0.00   0.0  0
 Q3M  CONST_03  H16  N13  C14  C15     0.00   0.0  0
 Q3M  Var_01    H1   C01  S02  C03   175.88  30.0  3
 Q3M  Var_02    H17  C15  C14  N13  -118.98  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
 Q3M  chir_01  C03  C12  S02  C04  negativ
 Q3M  chir_02  C05  C04  C08  C06  negativ
 Q3M  chir_03  C08  O09  C05  C10  negativ
 Q3M  chir_04  C10  O11  C08  C12  negativ
 Q3M  chir_05  C12  N13  C03  C10  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
 Q3M  plan-1  C12  0.020
 Q3M  plan-1  N13  0.020
 Q3M  plan-1  C14  0.020
 Q3M  plan-1  C15  0.020
 Q3M  plan-1  O16  0.020
 Q3M  plan-1  H16  0.020

