# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 05:37:47 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: (2R,4R)-1-phenylhexahydropyrimidine-2,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CCN([C@H](O)N1)c2ccccc2
#
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
 XWS  XWS  (2R,4R)-1-phenylhexahydropyrimidine-2,4-diol  ligand  28  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 PERFECT
;

data_comp_XWS
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
 XWS  N1   N  NT    0  -0.556  -22.5860  3.0072  28.9705
 XWS  C4   C  CH2   0  -0.518  -20.7560  4.5988  29.0506
 XWS  C5   C  CR6   0   0.385  -23.6832  2.7993  29.7928
 XWS  C6   C  CR16  0  -0.341  -23.5295  2.1063  31.0046
 XWS  C7   C  CR16  0  -0.241  -24.6046  1.8903  31.8510
 XWS  C8   C  CR16  0  -0.292  -25.8762  2.3387  31.5203
 XWS  C10  C  CR16  0  -0.343  -24.9756  3.2399  29.4646
 XWS  C1   C  CH2   0  -0.305  -21.2738  3.2622  29.5538
 XWS  C2   C  CH1   0   0.358  -22.7906  3.4883  27.6249
 XWS  C3   C  CH1   0   0.199  -20.5549  4.5485  27.5403
 XWS  C9   C  CR16  0  -0.245  -26.0444  3.0109  30.3182
 XWS  N2   N  NH1   0  -0.665  -21.5044  3.6191  26.9865
 XWS  O1   O  OH1   0  -0.663  -23.5230  2.5334  26.9156
 XWS  O2   O  OH1   0  -0.665  -19.2846  4.0429  27.1869
 XWS  H1   H  HCH2  0   0.258  -19.8190  4.8654  29.5431
 XWS  H2   H  HCH2  0   0.240  -21.4806  5.3763  29.3067
 XWS  H3   H  HCR6  0   0.260  -22.5623  1.7096  31.2839
 XWS  H4   H  HCR6  0   0.247  -24.4425  1.3512  32.7762
 XWS  H5   H  HCR6  0   0.243  -26.7151  2.1651  32.1808
 XWS  H6   H  HCR6  0   0.253  -25.1681  3.7834  28.5513
 XWS  H7   H  HCH2  0   0.230  -20.5650  2.4612  29.3241
 XWS  H8   H  HCH2  0   0.254  -21.3674  3.3004  30.6371
 XWS  H9   H  HCH1  0   0.191  -23.3556  4.4394  27.6300
 XWS  H10  H  HCH1  0   0.202  -20.6700  5.5617  27.1243
 XWS  H11  H  HCR6  0   0.248  -27.0242  3.3743  30.0337
 XWS  H12  H  HNH1  0   0.365  -21.6445  3.7817  25.9974
 XWS  H14  H  HOH1  0   0.458  -24.2063  2.9736  26.4010
 XWS  H15  H  HOH1  0   0.443  -18.6312  4.7233  27.3803

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
 XWS  O1   C2   single    1.397  0.020  1.397
 XWS  N2   C3   single    1.439  0.020  1.439
 XWS  N2   C2   single    1.442  0.020  1.442
 XWS  O2   C3   single    1.412  0.020  1.412
 XWS  C3   C4   single    1.525  0.020  1.525
 XWS  C2   N1   single    1.444  0.020  1.444
 XWS  C4   C1   single    1.519  0.020  1.519
 XWS  N1   C1   single    1.458  0.020  1.458
 XWS  N1   C5   single    1.387  0.020  1.387
 XWS  C10  C5   aromatic  1.404  0.020  1.404
 XWS  C10  C9   aromatic  1.387  0.020  1.387
 XWS  C5   C6   aromatic  1.404  0.020  1.404
 XWS  C9   C8   aromatic  1.387  0.020  1.387
 XWS  C6   C7   aromatic  1.385  0.020  1.385
 XWS  C8   C7   aromatic  1.388  0.020  1.388
 XWS  C4   H1   single    0.970  0.020  1.090
 XWS  C4   H2   single    0.970  0.020  1.090
 XWS  C6   H3   single    0.930  0.020  1.080
 XWS  C7   H4   single    0.930  0.020  1.080
 XWS  C8   H5   single    0.930  0.020  1.080
 XWS  C10  H6   single    0.930  0.020  1.080
 XWS  C1   H7   single    0.970  0.020  1.090
 XWS  C1   H8   single    0.970  0.020  1.090
 XWS  C2   H9   single    0.970  0.020  1.090
 XWS  C3   H10  single    0.970  0.020  1.090
 XWS  C9   H11  single    0.930  0.020  1.080
 XWS  N2   H12  single    0.890  0.020  1.040
 XWS  O1   H14  single    0.850  0.020  0.980
 XWS  O2   H15  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
 XWS  C2   N1   C1   116.24  3.000
 XWS  C1   N1   C5   120.06  3.000
 XWS  C2   N1   C5   119.37  3.000
 XWS  H2   C4   H1   106.83  3.000
 XWS  H2   C4   C3   110.06  3.000
 XWS  H1   C4   C3   109.99  3.000
 XWS  H2   C4   C1   108.80  3.000
 XWS  H1   C4   C1   110.98  3.000
 XWS  C3   C4   C1   110.13  3.000
 XWS  C10  C5   C6   117.21  3.000
 XWS  C6   C5   N1   119.93  3.000
 XWS  C10  C5   N1   122.85  3.000
 XWS  H3   C6   C7   118.62  3.000
 XWS  H3   C6   C5   120.09  3.000
 XWS  C7   C6   C5   121.28  3.000
 XWS  H4   C7   C8   120.10  3.000
 XWS  H4   C7   C6   118.91  3.000
 XWS  C8   C7   C6   120.99  3.000
 XWS  H5   C8   C9   120.85  3.000
 XWS  H5   C8   C7   120.86  3.000
 XWS  C9   C8   C7   118.29  3.000
 XWS  H6   C10  C9   117.78  3.000
 XWS  H6   C10  C5   121.30  3.000
 XWS  C9   C10  C5   120.91  3.000
 XWS  H8   C1   H7   106.88  3.000
 XWS  H8   C1   C4   109.16  3.000
 XWS  H7   C1   C4   110.72  3.000
 XWS  H8   C1   N1   109.08  3.000
 XWS  H7   C1   N1   111.78  3.000
 XWS  C4   C1   N1   109.15  3.000
 XWS  H9   C2   O1   108.80  3.000
 XWS  H9   C2   N2   112.31  3.000
 XWS  O1   C2   N2   107.76  3.000
 XWS  H9   C2   N1   110.77  3.000
 XWS  N2   C2   N1   108.45  3.000
 XWS  O1   C2   N1   108.66  3.000
 XWS  H10  C3   O2   109.20  3.000
 XWS  H10  C3   N2   112.32  3.000
 XWS  O2   C3   N2   105.42  3.000
 XWS  H10  C3   C4   109.27  3.000
 XWS  O2   C3   C4   112.24  3.000
 XWS  N2   C3   C4   108.38  3.000
 XWS  H11  C9   C10  118.70  3.000
 XWS  H11  C9   C8   119.99  3.000
 XWS  C10  C9   C8   121.31  3.000
 XWS  H12  N2   C3   111.32  3.000
 XWS  H12  N2   C2   108.89  3.000
 XWS  C3   N2   C2   118.47  3.000
 XWS  H14  O1   C2   109.34  3.000
 XWS  H15  O2   C3   107.89  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
 XWS  CONST_01  C8   C9   C10  C5    0.00   0.0  0
 XWS  CONST_02  C8   C7   C6   C5    0.00   0.0  0
 XWS  CONST_03  C9   C10  C5   C6    0.00   0.0  0
 XWS  CONST_04  C9   C8   C7   C6    0.00   0.0  0
 XWS  CONST_05  C10  C5   C6   C7    0.00   0.0  0
 XWS  CONST_06  C10  C9   C8   C7    0.00   0.0  0
 XWS  CONST_07  C9   C10  C5   N1  180.00   0.0  0
 XWS  CONST_08  C7   C6   C5   N1  180.00   0.0  0
 XWS  CONST_09  H6   C10  C5   N1    0.00   0.0  0
 XWS  CONST_10  H3   C6   C5   N1    0.00   0.0  0
 XWS  CONST_11  H11  C9   C10  C5  180.00   0.0  0
 XWS  CONST_12  H4   C7   C6   C5  180.00   0.0  0
 XWS  CONST_13  H5   C8   C7   C6  180.00   0.0  0
 XWS  Var_01    C3   C4   C1   N1  -63.47  30.0  1
 XWS  Var_02    C2   N1   C1   C4   34.47  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
 XWS  chir_01  C2  O1  N2  N1  positiv
 XWS  chir_02  C3  O2  N2  C4  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
 XWS  plan-1  N1   0.020
 XWS  plan-1  C5   0.020
 XWS  plan-1  C6   0.020
 XWS  plan-1  C7   0.020
 XWS  plan-1  C8   0.020
 XWS  plan-1  C10  0.020
 XWS  plan-1  C9   0.020
 XWS  plan-1  H3   0.020
 XWS  plan-1  H4   0.020
 XWS  plan-1  H5   0.020
 XWS  plan-1  H6   0.020
 XWS  plan-1  H11  0.020

