# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 22:44:39 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: trans-3-[(2,6-dimethylpyrimidin-4-yl)(methyl)amino]cyclobutan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN([C@@H]1C[C@@H](O)C1)c2cc(C)nc(C)n2
#
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
 NUJ  NUJ  trans-3-[(2,6-dimethylpyrimidin-4-yl)(methyl)amino]cyclobutan-1-ol  ligand  32  15  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NUJ
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
 NUJ  N1   N  NT    0  -0.487   0.6316   0.5790   0.0502
 NUJ  N3   N  N     0  -0.496  -1.0577  -0.9983  -0.0602
 NUJ  C4   C  C     0   0.059   3.7797  -0.0143   0.0192
 NUJ  C5   C  C     0  -0.491   2.7482  -0.3767   1.1104
 NUJ  C6   C  CR6   0   0.579  -0.6869   0.2830   0.0194
 NUJ  C7   C  CR16  0  -0.459  -1.6748   1.2913   0.0657
 NUJ  C8   C  CR6   0   0.266  -2.9906   0.8926   0.0227
 NUJ  C10  C  CR6   0   0.340  -2.3527  -1.2773  -0.0955
 NUJ  C1   C  CH3   0  -0.564   1.0369   1.9669   0.1101
 NUJ  C11  C  CH3   0  -0.728  -2.7142  -2.7292  -0.1736
 NUJ  C2   C  C     0  -0.135   1.6424  -0.4558   0.0283
 NUJ  C3   C  C     0  -0.483   2.7390  -0.3410  -1.0610
 NUJ  C9   C  CH3   0  -0.721  -4.1054   1.8885   0.0682
 NUJ  N2   N  N     0  -0.474  -3.3436  -0.3995  -0.0601
 NUJ  O1   O  OH1   0  -0.673   4.9506  -0.7768  -0.0728
 NUJ  H1   H  H     0   0.203   4.0160   1.0572   0.0395
 NUJ  H2   H  H     0   0.249   2.9415  -1.3560   1.5507
 NUJ  H3   H  H     0   0.249   2.6059   0.3443   1.9166
 NUJ  H4   H  HCR6  0   0.271  -1.4321   2.3410   0.1334
 NUJ  H5   H  HCH3  0   0.251   0.6942   2.4541   1.0255
 NUJ  H6   H  HCH3  0   0.265   2.1196   2.0411   0.0911
 NUJ  H7   H  HCH3  0   0.252   0.6606   2.5347  -0.7427
 NUJ  H8   H  HCH3  0   0.252  -2.4336  -3.2397   0.7494
 NUJ  H9   H  HCH3  0   0.242  -3.7822  -2.8606  -0.3287
 NUJ  H10  H  HCH3  0   0.249  -2.1741  -3.2177  -0.9846
 NUJ  H11  H  H     0   0.282   1.1197  -1.4056   0.0121
 NUJ  H12  H  H     0   0.254   2.5906   0.4025  -1.8448
 NUJ  H13  H  H     0   0.250   2.9282  -1.3078  -1.5299
 NUJ  H14  H  HCH3  0   0.252  -4.7525   1.7771  -0.8025
 NUJ  H15  H  HCH3  0   0.253  -4.7257   1.7252   0.9509
 NUJ  H16  H  HCH3  0   0.244  -3.7358   2.9115   0.0957
 NUJ  H17  H  HOH1  0   0.450   5.5561  -0.4873   0.6167

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
 NUJ  O1   C4   single    1.400  0.020  1.400
 NUJ  C4   C3   single    1.535  0.020  1.535
 NUJ  C4   C5   single    1.545  0.020  1.545
 NUJ  C3   C2   single    1.550  0.020  1.550
 NUJ  C5   C2   single    1.549  0.020  1.549
 NUJ  C1   N1   single    1.447  0.020  1.447
 NUJ  C2   N1   single    1.447  0.020  1.447
 NUJ  C9   C8   single    1.496  0.020  1.496
 NUJ  C7   C8   aromatic  1.376  0.020  1.376
 NUJ  C7   C6   aromatic  1.412  0.020  1.412
 NUJ  N1   C6   single    1.352  0.020  1.352
 NUJ  C8   N2   aromatic  1.342  0.020  1.342
 NUJ  C6   N3   aromatic  1.336  0.020  1.336
 NUJ  N2   C10  aromatic  1.324  0.020  1.324
 NUJ  N3   C10  aromatic  1.325  0.020  1.325
 NUJ  C10  C11  single    1.498  0.020  1.498
 NUJ  C4   H1   single    0.970  0.020  1.090
 NUJ  C5   H2   single    0.970  0.020  1.090
 NUJ  C5   H3   single    0.970  0.020  1.090
 NUJ  C7   H4   single    0.930  0.020  1.080
 NUJ  C1   H5   single    0.970  0.020  1.090
 NUJ  C1   H6   single    0.970  0.020  1.090
 NUJ  C1   H7   single    0.970  0.020  1.090
 NUJ  C11  H8   single    0.970  0.020  1.090
 NUJ  C11  H9   single    0.970  0.020  1.090
 NUJ  C11  H10  single    0.970  0.020  1.090
 NUJ  C2   H11  single    0.970  0.020  1.090
 NUJ  C3   H12  single    0.970  0.020  1.090
 NUJ  C3   H13  single    0.970  0.020  1.090
 NUJ  C9   H14  single    0.970  0.020  1.090
 NUJ  C9   H15  single    0.970  0.020  1.090
 NUJ  C9   H16  single    0.970  0.020  1.090
 NUJ  O1   H17  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
 NUJ  C2   N1   C1   119.40  3.000
 NUJ  C2   N1   C6   121.64  3.000
 NUJ  C1   N1   C6   118.96  3.000
 NUJ  C10  N3   C6   118.33  3.000
 NUJ  H1   C4   O1   110.66  3.000
 NUJ  H1   C4   C3   111.52  3.000
 NUJ  O1   C4   C3   113.88  3.000
 NUJ  H1   C4   C5   111.09  3.000
 NUJ  C3   C4   C5    89.68  3.000
 NUJ  O1   C4   C5   118.49  3.000
 NUJ  H3   C5   H2   108.55  3.000
 NUJ  H3   C5   C2   117.18  3.000
 NUJ  H2   C5   C2   111.26  3.000
 NUJ  H3   C5   C4   117.00  3.000
 NUJ  H2   C5   C4   112.17  3.000
 NUJ  C2   C5   C4    89.72  3.000
 NUJ  C7   C6   N3   119.50  3.000
 NUJ  N3   C6   N1   118.82  3.000
 NUJ  C7   C6   N1   121.68  3.000
 NUJ  H4   C7   C8   119.93  3.000
 NUJ  H4   C7   C6   122.61  3.000
 NUJ  C8   C7   C6   117.46  3.000
 NUJ  N2   C8   C9   116.55  3.000
 NUJ  N2   C8   C7   122.19  3.000
 NUJ  C9   C8   C7   121.27  3.000
 NUJ  N2   C10  C11  117.59  3.000
 NUJ  C11  C10  N3   116.18  3.000
 NUJ  N2   C10  N3   126.23  3.000
 NUJ  H7   C1   H6   107.14  3.000
 NUJ  H7   C1   H5   108.34  3.000
 NUJ  H6   C1   H5   107.29  3.000
 NUJ  H7   C1   N1   111.72  3.000
 NUJ  H6   C1   N1   110.13  3.000
 NUJ  H5   C1   N1   112.00  3.000
 NUJ  H10  C11  H9   109.05  3.000
 NUJ  H10  C11  H8   106.99  3.000
 NUJ  H9   C11  H8   108.46  3.000
 NUJ  H10  C11  C10  110.71  3.000
 NUJ  H9   C11  C10  111.20  3.000
 NUJ  H8   C11  C10  110.31  3.000
 NUJ  H11  C2   C3   113.30  3.000
 NUJ  H11  C2   C5   113.53  3.000
 NUJ  C3   C2   C5    88.98  3.000
 NUJ  H11  C2   N1   106.86  3.000
 NUJ  C5   C2   N1   116.85  3.000
 NUJ  C3   C2   N1   116.87  3.000
 NUJ  H13  C3   H12  108.59  3.000
 NUJ  H13  C3   C2   111.05  3.000
 NUJ  H12  C3   C2   117.35  3.000
 NUJ  H13  C3   C4   111.92  3.000
 NUJ  H12  C3   C4   116.93  3.000
 NUJ  C2   C3   C4    90.05  3.000
 NUJ  H16  C9   H15  108.26  3.000
 NUJ  H16  C9   H14  108.53  3.000
 NUJ  H15  C9   H14  107.05  3.000
 NUJ  H16  C9   C8   111.94  3.000
 NUJ  H15  C9   C8   110.41  3.000
 NUJ  H14  C9   C8   110.49  3.000
 NUJ  C10  N2   C8   116.29  3.000
 NUJ  H17  O1   C4   108.38  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
 NUJ  CONST_01  C8   C7   C6   N3     0.00   0.0  0
 NUJ  CONST_02  C8   N2   C10  N3     0.00   0.0  0
 NUJ  CONST_03  N2   C8   C7   C6     0.00   0.0  0
 NUJ  CONST_04  N2   C10  N3   C6     0.00   0.0  0
 NUJ  CONST_05  C10  N2   C8   C7     0.00   0.0  0
 NUJ  CONST_06  C10  N3   C6   C7     0.00   0.0  0
 NUJ  CONST_07  C8   C7   C6   N1   180.00   0.0  0
 NUJ  CONST_08  C10  N3   C6   N1   180.00   0.0  0
 NUJ  CONST_09  C9   C8   C7   C6   180.00   0.0  0
 NUJ  CONST_10  C11  C10  N3   C6   180.00   0.0  0
 NUJ  CONST_11  C11  C10  N2   C8   180.00   0.0  0
 NUJ  CONST_12  C9   C8   N2   C10  180.00   0.0  0
 NUJ  CONST_13  C2   N1   C6   N3     0.00   0.0  0
 NUJ  CONST_14  C2   N1   C6   C7   180.00   0.0  0
 NUJ  CONST_15  H4   C7   C6   N3   180.00   0.0  0
 NUJ  CONST_16  C1   N1   C6   N3   180.00   0.0  0
 NUJ  CONST_17  C1   N1   C6   C7     0.00   0.0  0
 NUJ  Var_01    H8   C11  C10  N3    67.03  30.0  2
 NUJ  Var_02    H14  C9   C8   C7   123.38  30.0  2
 NUJ  Var_03    H5   C1   N1   C6    62.81  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
 NUJ  chir_01  C4  O1  C3  C5  negativ
 NUJ  chir_02  C2  N1  C5  C3  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
 NUJ  plan-1  N1   0.020
 NUJ  plan-1  N3   0.020
 NUJ  plan-1  C6   0.020
 NUJ  plan-1  C7   0.020
 NUJ  plan-1  C8   0.020
 NUJ  plan-1  C10  0.020
 NUJ  plan-1  C11  0.020
 NUJ  plan-1  C9   0.020
 NUJ  plan-1  N2   0.020
 NUJ  plan-1  H4   0.020
 NUJ  plan-2  N1   0.020
 NUJ  plan-2  C6   0.020
 NUJ  plan-2  C1   0.020
 NUJ  plan-2  C2   0.020

