# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 17:10:08 2021
#   Inital geometry file: a 75 line input string
#   Ligand name: (2R,4R)-1-cyclohexylhexahydropyrimidine-2,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CCN(C2CCCCC2)[C@H](O)N1
#
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
 X1Y  X1Y  (2R,4R)-1-cyclohexylhexahydropyrimidine-2,4-diol  ligand  34  14  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_X1Y
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
 X1Y  N1   N  NT    0  -0.467  -22.7062  3.0512  28.6103
 X1Y  C4   C  CH1   0  -0.050  -23.7294  2.5272  29.5084
 X1Y  C5   C  CH2   0  -0.462  -23.1436  1.9257  30.7851
 X1Y  C6   C  CH2   0  -0.430  -24.2194  1.1952  31.5856
 X1Y  C7   C  CH2   0  -0.430  -25.3899  2.1148  31.9151
 X1Y  C8   C  CH2   0  -0.429  -25.9616  2.7512  30.6534
 X1Y  C10  C  CH1   0   0.297  -21.6441  3.8568  29.1461
 X1Y  C1   C  CH1   0   0.157  -20.9077  4.3595  26.8409
 X1Y  C2   C  CH2   0  -0.450  -22.0718  3.5299  26.3195
 X1Y  C3   C  CH2   0  -0.300  -23.2073  3.5115  27.3282
 X1Y  C9   C  CH2   0  -0.450  -24.8790  3.4819  29.8628
 X1Y  N2   N  NH1   0  -0.653  -20.5640  4.0466  28.2122
 X1Y  O1   O  OH1   0  -0.671  -21.2530  5.7164  26.7132
 X1Y  O2   O  OH1   0  -0.665  -22.0372  5.1572  29.5551
 X1Y  H2   H  HCH1  0   0.217  -24.1883  1.6946  28.9556
 X1Y  H3   H  HCH2  0   0.236  -22.3279  1.2416  30.5362
 X1Y  H4   H  HCH2  0   0.212  -22.7163  2.7096  31.4208
 X1Y  H5   H  HCH2  0   0.213  -24.5787  0.3353  31.0104
 X1Y  H6   H  HCH2  0   0.230  -23.7841  0.7928  32.5032
 X1Y  H7   H  HCH2  0   0.210  -25.0475  2.9050  32.5922
 X1Y  H8   H  HCH2  0   0.228  -26.1663  1.5627  32.4500
 X1Y  H9   H  HCH2  0   0.230  -26.7705  3.4407  30.9050
 X1Y  H10  H  HCH2  0   0.213  -26.4042  1.9745  30.0201
 X1Y  H11  H  HCH1  0   0.226  -21.2186  3.3167  29.9976
 X1Y  H12  H  HCH1  0   0.210  -20.0085  4.1318  26.2521
 X1Y  H13  H  HCH2  0   0.232  -22.4144  3.9137  25.3558
 X1Y  H14  H  HCH2  0   0.224  -21.7193  2.5092  26.1514
 X1Y  H15  H  HCH2  0   0.207  -23.6798  4.5016  27.3798
 X1Y  H16  H  HCH2  0   0.233  -23.9814  2.8158  26.9946
 X1Y  H17  H  HCH2  0   0.193  -24.5161  4.3249  30.4627
 X1Y  H18  H  HCH2  0   0.240  -25.3081  3.9148  28.9562
 X1Y  H19  H  HNH1  0   0.364  -19.9444  3.2496  28.2418
 X1Y  H21  H  HOH1  0   0.440  -20.6918  6.2113  27.3191
 X1Y  H22  H  HOH1  0   0.441  -22.7025  5.0718  30.2447

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
 X1Y  C2   C1   single  1.522  0.020  1.522
 X1Y  C2   C3   single  1.519  0.020  1.519
 X1Y  C1   O1   single  1.406  0.020  1.406
 X1Y  C1   N2   single  1.448  0.020  1.448
 X1Y  C3   N1   single  1.451  0.020  1.451
 X1Y  N2   C10  single  1.440  0.020  1.440
 X1Y  N1   C10  single  1.437  0.020  1.437
 X1Y  N1   C4   single  1.459  0.020  1.459
 X1Y  C10  O2   single  1.419  0.020  1.419
 X1Y  C9   C4   single  1.536  0.020  1.536
 X1Y  C9   C8   single  1.527  0.020  1.527
 X1Y  C4   C5   single  1.528  0.020  1.528
 X1Y  C8   C7   single  1.524  0.020  1.524
 X1Y  C5   C6   single  1.527  0.020  1.527
 X1Y  C7   C6   single  1.525  0.020  1.525
 X1Y  C4   H2   single  0.970  0.020  1.090
 X1Y  C5   H3   single  0.970  0.020  1.090
 X1Y  C5   H4   single  0.970  0.020  1.090
 X1Y  C6   H5   single  0.970  0.020  1.090
 X1Y  C6   H6   single  0.970  0.020  1.090
 X1Y  C7   H7   single  0.970  0.020  1.090
 X1Y  C7   H8   single  0.970  0.020  1.090
 X1Y  C8   H9   single  0.970  0.020  1.090
 X1Y  C8   H10  single  0.970  0.020  1.090
 X1Y  C10  H11  single  0.970  0.020  1.090
 X1Y  C1   H12  single  0.970  0.020  1.090
 X1Y  C2   H13  single  0.970  0.020  1.090
 X1Y  C2   H14  single  0.970  0.020  1.090
 X1Y  C3   H15  single  0.970  0.020  1.090
 X1Y  C3   H16  single  0.970  0.020  1.090
 X1Y  C9   H17  single  0.970  0.020  1.090
 X1Y  C9   H18  single  0.970  0.020  1.090
 X1Y  N2   H19  single  0.890  0.020  1.040
 X1Y  O1   H21  single  0.850  0.020  0.980
 X1Y  O2   H22  single  0.850  0.020  0.980

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
 X1Y  C3   N1   C10  114.01  3.000
 X1Y  C10  N1   C4   119.36  3.000
 X1Y  C3   N1   C4   114.56  3.000
 X1Y  H2   C4   C9   105.92  3.000
 X1Y  H2   C4   C5   106.38  3.000
 X1Y  C9   C4   C5   109.81  3.000
 X1Y  H2   C4   N1   104.78  3.000
 X1Y  C5   C4   N1   112.76  3.000
 X1Y  C9   C4   N1   116.35  3.000
 X1Y  H4   C5   H3   106.78  3.000
 X1Y  H4   C5   C6   108.23  3.000
 X1Y  H3   C5   C6   110.22  3.000
 X1Y  H4   C5   C4   110.64  3.000
 X1Y  H3   C5   C4   110.00  3.000
 X1Y  C6   C5   C4   110.87  3.000
 X1Y  H6   C6   H5   106.42  3.000
 X1Y  H6   C6   C7   110.28  3.000
 X1Y  H5   C6   C7   109.59  3.000
 X1Y  H6   C6   C5   109.62  3.000
 X1Y  H5   C6   C5   109.35  3.000
 X1Y  C7   C6   C5   111.45  3.000
 X1Y  H8   C7   H7   106.50  3.000
 X1Y  H8   C7   C8   110.47  3.000
 X1Y  H7   C7   C8   109.12  3.000
 X1Y  H8   C7   C6   110.28  3.000
 X1Y  H7   C7   C6   109.20  3.000
 X1Y  C8   C7   C6   111.15  3.000
 X1Y  H10  C8   H9   106.35  3.000
 X1Y  H10  C8   C9   109.05  3.000
 X1Y  H9   C8   C9   110.01  3.000
 X1Y  H10  C8   C7   109.51  3.000
 X1Y  H9   C8   C7   110.53  3.000
 X1Y  C9   C8   C7   111.25  3.000
 X1Y  H11  C10  O2   109.62  3.000
 X1Y  H11  C10  N2   106.14  3.000
 X1Y  O2   C10  N2   105.90  3.000
 X1Y  H11  C10  N1   107.51  3.000
 X1Y  O2   C10  N1   114.62  3.000
 X1Y  N2   C10  N1   112.73  3.000
 X1Y  H12  C1   O1   110.63  3.000
 X1Y  H12  C1   N2   105.57  3.000
 X1Y  O1   C1   N2   110.67  3.000
 X1Y  H12  C1   C2   109.24  3.000
 X1Y  N2   C1   C2   112.85  3.000
 X1Y  O1   C1   C2   107.89  3.000
 X1Y  H14  C2   H13  107.07  3.000
 X1Y  H14  C2   C3   109.39  3.000
 X1Y  H13  C2   C3   110.83  3.000
 X1Y  H14  C2   C1   108.37  3.000
 X1Y  H13  C2   C1   110.52  3.000
 X1Y  C3   C2   C1   110.54  3.000
 X1Y  H16  C3   H15  106.47  3.000
 X1Y  H16  C3   C2   109.54  3.000
 X1Y  H15  C3   C2   109.99  3.000
 X1Y  H16  C3   N1   108.19  3.000
 X1Y  H15  C3   N1   113.14  3.000
 X1Y  C2   C3   N1   109.41  3.000
 X1Y  H18  C9   H17  106.22  3.000
 X1Y  H18  C9   C8   109.93  3.000
 X1Y  H17  C9   C8   108.62  3.000
 X1Y  H18  C9   C4   110.42  3.000
 X1Y  H17  C9   C4   110.88  3.000
 X1Y  C8   C9   C4   110.65  3.000
 X1Y  H19  N2   C1   110.11  3.000
 X1Y  H19  N2   C10  109.70  3.000
 X1Y  C1   N2   C10  117.68  3.000
 X1Y  H21  O1   C1   107.20  3.000
 X1Y  H22  O2   C10  108.47  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
 X1Y  Var_01  C1  C2  C3  N1   -54.69  30.0  1
 X1Y  Var_02  C2  C3  N1  C4  -158.73  30.0  1
 X1Y  Var_03  C7  C8  C9  C4    56.83  30.0  1
 X1Y  Var_04  C7  C6  C5  C4   -56.39  30.0  1
 X1Y  Var_05  C8  C7  C6  C5    54.72  30.0  1
 X1Y  Var_06  C9  C8  C7  C6   -55.01  30.0  1

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
 X1Y  chir_01  C4   N1  C9  C5  positiv
 X1Y  chir_02  C10  O2  N2  N1  positiv
 X1Y  chir_03  C1   O1  N2  C2  negativ

