# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 09:29:18 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: N-benzyl-3-{[(2Z,4S)-2-imino-4-methyl-6-oxo-4-(propan-2-yl)tetrahydropyrimidin-1(2H)-yl]methyl}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@]1(C)CC(=O)N(Cc2cccc(c2)C(=O)NCc3ccccc3)C(=N)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
 70X  70X  N-benzyl-3-{[(2Z,4S)-2-imino-4-methyl-6-oxo-4-(propan-2-yl)tetrahydropyrimidin-1(2H)-yl]methyl}benzamide  ligand  57  29  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_70X
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
 70X  C27  C  CR16  0  -0.267  -8.3244  -0.2628   1.3442
 70X  C28  C  CR16  0  -0.239  -7.8224   0.8929   1.9245
 70X  C29  C  CR16  0  -0.309  -6.6194   1.4296   1.4805
 70X  C26  C  CR16  0  -0.240  -7.6189  -0.8782   0.3160
 70X  C25  C  CR16  0  -0.286  -6.4211  -0.3383  -0.1276
 70X  C24  C  CR6   0   0.075  -5.9098   0.8232   0.4504
 70X  C23  C  CH2   0  -0.322  -4.6197   1.4199  -0.0459
 70X  C14  C  CR6   0   0.141   0.7363  -1.4267  -1.0468
 70X  C15  C  CR16  0  -0.324  -0.2157  -0.4158  -1.1245
 70X  C16  C  CR6   0  -0.017  -1.5371  -0.6503  -0.7573
 70X  C17  C  CR16  0  -0.303  -1.9171  -1.9227  -0.3333
 70X  C18  C  CR16  0  -0.232  -0.9772  -2.9394  -0.2716
 70X  C19  C  CR16  0  -0.294   0.3432  -2.6902  -0.6178
 70X  C20  C  C     0   0.534  -2.5176   0.4701  -0.8879
 70X  N1   N  NH1   0  -0.667   3.9064   1.7592  -0.0566
 70X  C2   C  CT    0   0.070   4.8366   1.1312   0.8728
 70X  C3   C  CH2   0  -0.554   3.9888   0.1072   1.6181
 70X  C4   C  C     0   0.555   3.2793  -0.8229   0.6771
 70X  N5   N  NT    0  -0.527   2.8712  -0.2851  -0.5165
 70X  C6   C  C     0   0.646   3.0693   1.0624  -0.8678
 70X  N7   N  N     0  -0.695   2.4456   1.5231  -1.8819
 70X  C10  C  CH1   0  -0.216   6.0094   0.4600   0.1048
 70X  C11  C  CH3   0  -0.674   5.3201   2.1981   1.8457
 70X  C12  C  CH3   0  -0.664   6.7809   1.4520  -0.7628
 70X  C13  C  CH3   0  -0.665   6.9821  -0.2960   1.0075
 70X  O21  O  O     0  -0.490  -2.3705   1.3508  -1.7247
 70X  N22  N  NH1   0  -0.646  -3.5588   0.4364  -0.0380
 70X  H1   H  HCR6  0   0.257  -9.2593  -0.6845   1.6901
 70X  H2   H  HCR6  0   0.257  -8.3640   1.3776   2.7265
 70X  H3   H  HCR6  0   0.254  -6.2310   2.3291   1.9435
 70X  H4   H  HCR6  0   0.257  -8.0044  -1.7797  -0.1427
 70X  H5   H  HCR6  0   0.253  -5.8774  -0.8242  -0.9295
 70X  H6   H  HCH2  0   0.266  -4.7437   1.7802  -1.0682
 70X  H7   H  HCH2  0   0.257  -4.3510   2.2889   0.5620
 70X  H8   H  HCR6  0   0.262   0.0848   0.5649  -1.4729
 70X  H9   H  HCR6  0   0.257  -2.9468  -2.1402  -0.0782
 70X  H10  H  HCR6  0   0.262  -1.2768  -3.9299   0.0439
 70X  H11  H  HCR6  0   0.256   1.0733  -3.4871  -0.5612
 70X  H12  H  HCH2  0   0.280   4.5689  -0.4862   2.3221
 70X  H13  H  HCH2  0   0.295   3.2272   0.6351   2.2027
 70X  H14  H  H     0   0.334   2.7053   2.4863  -2.0601
 70X  H16  H  HCH2  0   0.278   2.7127  -2.0995  -1.5221
 70X  H17  H  HCH2  0   0.285   2.1961  -0.6817  -2.4212
 70X  H18  H  HCH1  0   0.230   5.5578  -0.2724  -0.5744
 70X  H19  H  HCH3  0   0.247   4.4733   2.6741   2.3405
 70X  H20  H  HCH3  0   0.246   5.9555   1.7597   2.6142
 70X  H21  H  HCH3  0   0.247   5.8972   2.9739   1.3408
 70X  H22  H  HCH3  0   0.224   7.3692   2.1465  -0.1607
 70X  H23  H  HCH3  0   0.238   7.4783   0.9160  -1.4081
 70X  H24  H  HCH3  0   0.227   6.1275   2.0356  -1.4116
 70X  H25  H  HCH3  0   0.232   6.4960  -1.0499   1.6270
 70X  H26  H  HCH3  0   0.238   7.7214  -0.8148   0.3959
 70X  H27  H  HCH3  0   0.224   7.5288   0.3786   1.6680
 70X  H28  H  HNH1  0   0.406  -3.5329  -0.1998   0.7427
 70X  H29  H  HNH1  0   0.396   4.1091   2.7014  -0.3515
 70X  C9   C  CH2   0  -0.402   2.1645  -1.1614  -1.4470
 70X  O8   O  O     0  -0.449   3.0552  -1.9860   0.9494

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
 70X  O8   C4   double    1.215  0.020  1.215
 70X  C4   N5   single    1.371  0.020  1.371
 70X  C4   C3   single    1.501  0.020  1.501
 70X  C9   N5   single    1.460  0.020  1.460
 70X  C9   C14  single    1.507  0.020  1.507
 70X  C19  C14  aromatic  1.391  0.020  1.391
 70X  C19  C18  aromatic  1.388  0.020  1.388
 70X  N5   C6   single    1.407  0.020  1.407
 70X  C3   C2   single    1.524  0.020  1.524
 70X  N7   C6   double    1.277  0.020  1.277
 70X  C14  C15  aromatic  1.391  0.020  1.391
 70X  C18  C17  aromatic  1.386  0.020  1.386
 70X  C6   N1   single    1.358  0.020  1.358
 70X  N1   C2   single    1.457  0.020  1.457
 70X  C11  C2   single    1.523  0.020  1.523
 70X  C2   C10  single    1.554  0.020  1.554
 70X  C15  C16  aromatic  1.391  0.020  1.391
 70X  C17  C16  aromatic  1.394  0.020  1.394
 70X  C16  C20  single    1.495  0.020  1.495
 70X  C10  C13  single    1.527  0.020  1.527
 70X  C10  C12  single    1.527  0.020  1.527
 70X  C20  O21  double    1.224  0.020  1.224
 70X  C20  N22  single    1.344  0.020  1.344
 70X  N22  C23  single    1.447  0.020  1.447
 70X  C23  C24  single    1.506  0.020  1.506
 70X  C24  C29  aromatic  1.390  0.020  1.390
 70X  C24  C25  aromatic  1.394  0.020  1.394
 70X  C29  C28  aromatic  1.390  0.020  1.390
 70X  C28  C27  aromatic  1.387  0.020  1.387
 70X  C25  C26  aromatic  1.387  0.020  1.387
 70X  C26  C27  aromatic  1.391  0.020  1.391
 70X  C27  H1   single    0.930  0.020  1.080
 70X  C28  H2   single    0.930  0.020  1.080
 70X  C29  H3   single    0.930  0.020  1.080
 70X  C26  H4   single    0.930  0.020  1.080
 70X  C25  H5   single    0.930  0.020  1.080
 70X  C23  H6   single    0.970  0.020  1.090
 70X  C23  H7   single    0.970  0.020  1.090
 70X  C15  H8   single    0.930  0.020  1.080
 70X  C17  H9   single    0.930  0.020  1.080
 70X  C18  H10  single    0.930  0.020  1.080
 70X  C19  H11  single    0.930  0.020  1.080
 70X  C3   H12  single    0.970  0.020  1.090
 70X  C3   H13  single    0.970  0.020  1.090
 70X  N7   H14  single    0.890  0.020  1.040
 70X  C9   H16  single    0.970  0.020  1.090
 70X  C9   H17  single    0.970  0.020  1.090
 70X  C10  H18  single    0.970  0.020  1.090
 70X  C11  H19  single    0.970  0.020  1.090
 70X  C11  H20  single    0.970  0.020  1.090
 70X  C11  H21  single    0.970  0.020  1.090
 70X  C12  H22  single    0.970  0.020  1.090
 70X  C12  H23  single    0.970  0.020  1.090
 70X  C12  H24  single    0.970  0.020  1.090
 70X  C13  H25  single    0.970  0.020  1.090
 70X  C13  H26  single    0.970  0.020  1.090
 70X  C13  H27  single    0.970  0.020  1.090
 70X  N22  H28  single    0.860  0.020  1.020
 70X  N1   H29  single    0.890  0.020  1.040

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
 70X  H1   C27  C26  120.14  3.000
 70X  H1   C27  C28  120.23  3.000
 70X  C26  C27  C28  119.63  3.000
 70X  H2   C28  C29  119.79  3.000
 70X  H2   C28  C27  120.13  3.000
 70X  C29  C28  C27  120.08  3.000
 70X  H3   C29  C24  119.72  3.000
 70X  H3   C29  C28  119.61  3.000
 70X  C24  C29  C28  120.66  3.000
 70X  H4   C26  C25  119.76  3.000
 70X  H4   C26  C27  120.08  3.000
 70X  C25  C26  C27  120.16  3.000
 70X  H5   C25  C24  119.75  3.000
 70X  H5   C25  C26  119.69  3.000
 70X  C24  C25  C26  120.56  3.000
 70X  C23  C24  C25  120.51  3.000
 70X  C25  C24  C29  118.90  3.000
 70X  C23  C24  C29  120.58  3.000
 70X  H7   C23  H6   106.63  3.000
 70X  H7   C23  N22  110.91  3.000
 70X  H6   C23  N22  108.24  3.000
 70X  H7   C23  C24  110.00  3.000
 70X  H6   C23  C24  110.02  3.000
 70X  N22  C23  C24  110.92  3.000
 70X  C9   C14  C19  120.64  3.000
 70X  C19  C14  C15  118.95  3.000
 70X  C9   C14  C15  120.40  3.000
 70X  H8   C15  C16  120.06  3.000
 70X  H8   C15  C14  119.09  3.000
 70X  C16  C15  C14  120.85  3.000
 70X  C20  C16  C17  122.14  3.000
 70X  C20  C16  C15  118.27  3.000
 70X  C17  C16  C15  119.54  3.000
 70X  H9   C17  C18  119.14  3.000
 70X  H9   C17  C16  120.95  3.000
 70X  C18  C17  C16  119.89  3.000
 70X  H10  C18  C19  120.05  3.000
 70X  H10  C18  C17  119.79  3.000
 70X  C19  C18  C17  120.16  3.000
 70X  H11  C19  C18  119.78  3.000
 70X  H11  C19  C14  119.63  3.000
 70X  C18  C19  C14  120.59  3.000
 70X  N22  C20  O21  122.91  3.000
 70X  N22  C20  C16  115.72  3.000
 70X  O21  C20  C16  121.36  3.000
 70X  H29  N1   C6   115.39  3.000
 70X  H29  N1   C2   117.47  3.000
 70X  C6   N1   C2   123.59  3.000
 70X  C11  C2   C10  112.25  3.000
 70X  C10  C2   C3   111.80  3.000
 70X  C11  C2   C3   109.57  3.000
 70X  C10  C2   N1   110.65  3.000
 70X  C11  C2   N1   107.95  3.000
 70X  C3   C2   N1   104.26  3.000
 70X  H13  C3   H12  106.74  3.000
 70X  H13  C3   C4   107.73  3.000
 70X  H12  C3   C4   108.63  3.000
 70X  H13  C3   C2   108.90  3.000
 70X  H12  C3   C2   112.71  3.000
 70X  C4   C3   C2   111.88  3.000
 70X  O8   C4   N5   121.03  3.000
 70X  N5   C4   C3   116.30  3.000
 70X  O8   C4   C3   122.66  3.000
 70X  C9   N5   C6   118.94  3.000
 70X  C6   N5   C4   123.45  3.000
 70X  C9   N5   C4   117.59  3.000
 70X  N7   C6   N5   118.38  3.000
 70X  N7   C6   N1   126.20  3.000
 70X  N5   C6   N1   115.41  3.000
 70X  H14  N7   C6   110.94  3.000
 70X  H18  C10  C13  107.33  3.000
 70X  H18  C10  C12  106.87  3.000
 70X  C13  C10  C12  109.61  3.000
 70X  H18  C10  C2   106.48  3.000
 70X  C12  C10  C2   112.43  3.000
 70X  C13  C10  C2   113.72  3.000
 70X  H21  C11  H20  107.71  3.000
 70X  H21  C11  H19  108.09  3.000
 70X  H20  C11  H19  107.98  3.000
 70X  H21  C11  C2   111.75  3.000
 70X  H20  C11  C2   110.73  3.000
 70X  H19  C11  C2   110.44  3.000
 70X  H24  C12  H23  107.11  3.000
 70X  H24  C12  H22  108.10  3.000
 70X  H23  C12  H22  107.13  3.000
 70X  H24  C12  C10  112.53  3.000
 70X  H23  C12  C10  109.87  3.000
 70X  H22  C12  C10  111.85  3.000
 70X  H27  C13  H26  107.09  3.000
 70X  H27  C13  H25  107.87  3.000
 70X  H26  C13  H25  106.98  3.000
 70X  H27  C13  C10  111.77  3.000
 70X  H26  C13  C10  109.62  3.000
 70X  H25  C13  C10  113.22  3.000
 70X  H28  N22  C20  119.07  3.000
 70X  H28  N22  C23  116.90  3.000
 70X  C20  N22  C23  123.19  3.000
 70X  H17  C9   H16  107.69  3.000
 70X  H17  C9   N5   107.00  3.000
 70X  H16  C9   N5   108.50  3.000
 70X  H17  C9   C14  110.08  3.000
 70X  H16  C9   C14  110.10  3.000
 70X  N5   C9   C14  113.27  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
 70X  CONST_01  C24  C29  C28  C27     0.00   0.0  0
 70X  CONST_02  C24  C25  C26  C27     0.00   0.0  0
 70X  CONST_03  C25  C24  C29  C28     0.00   0.0  0
 70X  CONST_04  C25  C26  C27  C28     0.00   0.0  0
 70X  CONST_05  C26  C25  C24  C29     0.00   0.0  0
 70X  CONST_06  C26  C27  C28  C29     0.00   0.0  0
 70X  CONST_07  C17  C18  C19  C14     0.00   0.0  0
 70X  CONST_08  C17  C16  C15  C14     0.00   0.0  0
 70X  CONST_09  C18  C19  C14  C15     0.00   0.0  0
 70X  CONST_10  C18  C17  C16  C15     0.00   0.0  0
 70X  CONST_11  C19  C14  C15  C16     0.00   0.0  0
 70X  CONST_12  C19  C18  C17  C16     0.00   0.0  0
 70X  CONST_13  C4   N5   C6   N1      0.00   0.0  0
 70X  CONST_15  C6   N5   C4   C3      0.00   0.0  0
 70X  CONST_16  C23  C24  C29  C28   180.00   0.0  0
 70X  CONST_17  C23  C24  C25  C26   180.00   0.0  0
 70X  CONST_18  C20  C16  C15  C14   180.00   0.0  0
 70X  CONST_19  C9   C14  C15  C16   180.00   0.0  0
 70X  CONST_20  C9   C14  C19  C18   180.00   0.0  0
 70X  CONST_21  C20  C16  C17  C18   180.00   0.0  0
 70X  CONST_22  C9   N5   C6   N1    180.00   0.0  0
 70X  CONST_24  C9   N5   C4   C3    180.00   0.0  0
 70X  CONST_25  N7   C6   N5   C4    180.00   0.0  0
 70X  CONST_26  O8   C4   N5   C6    180.00   0.0  0
 70X  CONST_27  H3   C29  C28  C27   180.00   0.0  0
 70X  CONST_28  H5   C25  C26  C27   180.00   0.0  0
 70X  CONST_29  H4   C26  C27  C28   180.00   0.0  0
 70X  CONST_30  H1   C27  C28  C29   180.00   0.0  0
 70X  CONST_31  H2   C28  C27  C26   180.00   0.0  0
 70X  CONST_32  H10  C18  C19  C14   180.00   0.0  0
 70X  CONST_33  H11  C19  C14  C15   180.00   0.0  0
 70X  CONST_34  H9   C17  C16  C15   180.00   0.0  0
 70X  CONST_35  H8   C15  C16  C17   180.00   0.0  0
 70X  CONST_36  H29  N1   C6   N5    180.00   0.0  0
 70X  CONST_37  C9   N5   C6   N7      0.00   0.0  0
 70X  CONST_38  C9   N5   C4   O8      0.00   0.0  0
 70X  CONST_39  H14  N7   C6   N1      0.00   0.0  0
 70X  CONST_40  C16  C20  N22  C23   180.00   0.0  0
 70X  CONST_41  H28  N22  C20  C16     0.00   0.0  0
 70X  CONST_42  O21  C20  N22  C23     0.00   0.0  0
 70X  Var_01    C4   N5   C9   C14    75.70  30.0  3
 70X  Var_02    N5   C9   C14  C15    70.13  30.0  2
 70X  Var_03    H12  C3   C4   N5   -159.18  30.0  1
 70X  Var_04    N22  C23  C24  C29   127.11  30.0  2
 70X  Var_05    O21  C20  C16  C15    28.27  30.0  2
 70X  Var_06    C20  N22  C23  C24   151.42  30.0  1
 70X  Var_07    H25  C13  C10  C2     55.44  30.0  3
 70X  Var_08    H22  C12  C10  C2     70.76  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
 70X  chir_01  C2  N1  C3  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
 70X  plan-1  C27  0.020
 70X  plan-1  C28  0.020
 70X  plan-1  C29  0.020
 70X  plan-1  C26  0.020
 70X  plan-1  C25  0.020
 70X  plan-1  C24  0.020
 70X  plan-1  C23  0.020
 70X  plan-1  H1   0.020
 70X  plan-1  H2   0.020
 70X  plan-1  H3   0.020
 70X  plan-1  H4   0.020
 70X  plan-1  H5   0.020
 70X  plan-2  C14  0.020
 70X  plan-2  C15  0.020
 70X  plan-2  C16  0.020
 70X  plan-2  C17  0.020
 70X  plan-2  C18  0.020
 70X  plan-2  C19  0.020
 70X  plan-2  C20  0.020
 70X  plan-2  H8   0.020
 70X  plan-2  H9   0.020
 70X  plan-2  H10  0.020
 70X  plan-2  H11  0.020
 70X  plan-2  C9   0.020
 70X  plan-3  C23  0.020
 70X  plan-3  C16  0.020
 70X  plan-3  C20  0.020
 70X  plan-3  O21  0.020
 70X  plan-3  N22  0.020
 70X  plan-3  H28  0.020
 70X  plan-4  N1   0.020
 70X  plan-4  C2   0.020
 70X  plan-4  C3   0.020
 70X  plan-4  C4   0.020
 70X  plan-4  N5   0.020
 70X  plan-4  C6   0.020
 70X  plan-4  N7   0.020
 70X  plan-4  H14  0.020
 70X  plan-4  H29  0.020
 70X  plan-4  C9   0.020
 70X  plan-4  O8   0.020

