# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 10:17:15 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: (2Z,6S)-2-imino-6-methyl-3-{3-[(4R)-2-oxo-4-phenylpyrrolidin-1-yl]benzyl}-6-(propan-2-yl)tetrahydropyrimidin-4(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@]1(C)CC(=O)N(Cc2cccc(c2)N3C[C@H](CC3=O)c4ccccc4)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
 70Y  70Y  (2Z,6S)-2-imino-6-methyl-3-{3-[(4R)-2-oxo-4-phenylpyrrolidin-1-yl]benzyl}-6-(propan-2-yl)tetrahydropyrimidin-4(1H)-one  ligand  61  31  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_70Y
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
 70Y  C25  C  CR16  0  -0.330   4.8173   1.9596  -1.7726
 70Y  C26  C  CR16  0  -0.237   5.3403   3.2352  -1.5973
 70Y  C27  C  CR16  0  -0.271   5.5061   3.7487  -0.3192
 70Y  C28  C  CR16  0  -0.238   5.1436   2.9792   0.7803
 70Y  C29  C  CR16  0  -0.319   4.6225   1.7066   0.6004
 70Y  C24  C  CR6   0   0.191   4.4535   1.1793  -0.6797
 70Y  C23  C  CH2   0  -0.254   2.4801  -0.3877  -0.3242
 70Y  C22  C  CH1   0  -0.400   3.8933  -0.2005  -0.8845
 70Y  C20  C  C     0   0.518   3.6272  -2.4007   0.0321
 70Y  C4   C  C     0   0.556  -3.4587  -0.7015  -0.3995
 70Y  C2   C  CT    0   0.075  -4.0073   1.7475  -0.5935
 70Y  C3   C  CH2   0  -0.556  -3.8528   0.4173  -1.3211
 70Y  C11  C  CH3   0  -0.675  -4.0881   2.8772  -1.6137
 70Y  C17  C  CR16  0  -0.241  -0.2782  -4.3728   0.1239
 70Y  C16  C  CR16  0  -0.309   0.9565  -3.8023  -0.1397
 70Y  C15  C  CR6   0   0.388   1.1680  -2.4542   0.1584
 70Y  C14  C  CR16  0  -0.380   0.1269  -1.7040   0.6999
 70Y  N1   N  NH1   0  -0.670  -2.7609   1.9100   0.1435
 70Y  N5   N  NT    0  -0.528  -2.6635  -0.3658   0.6657
 70Y  C6   C  C     0   0.649  -2.1972   0.9381   0.9056
 70Y  N7   N  N     0  -0.696  -1.2816   1.1038   1.7800
 70Y  C10  C  CH1   0  -0.217  -5.2262   1.7359   0.3700
 70Y  C13  C  CR6   0   0.136  -1.1157  -2.2778   0.9505
 70Y  C18  C  CR16  0  -0.319  -1.3140  -3.6215   0.6626
 70Y  N19  N  NT    0  -0.582   2.3968  -1.8246  -0.1001
 70Y  C21  C  CH2   0  -0.563   4.6665  -1.3322  -0.2104
 70Y  O30  O  O     0  -0.468   3.8466  -3.5591   0.3250
 70Y  H1   H  HCR6  0   0.252   4.6892   1.5664  -2.7743
 70Y  H2   H  HCR6  0   0.255   5.6165   3.8256  -2.4615
 70Y  H3   H  HCR6  0   0.256   5.9151   4.7407  -0.1773
 70Y  H4   H  HCR6  0   0.256   5.2686   3.3713   1.7814
 70Y  H5   H  HCH3  0   0.238  -7.3730   1.5266   0.3734
 70Y  H6   H  HCH3  0   0.224  -6.7704   2.4336  -1.0058
 70Y  H7   H  HCH3  0   0.233  -6.6135   0.6786  -0.9597
 70Y  H8   H  HCR6  0   0.251   4.3463   1.1210   1.4702
 70Y  H9   H  HCH2  0   0.252   2.3451   0.1648   0.6110
 70Y  H10  H  HCH2  0   0.273   1.7114  -0.0596  -1.0240
 70Y  H11  H  HCH1  0   0.285   3.8551  -0.4053  -1.9574
 70Y  H12  H  HCH2  0   0.294  -3.0642   0.5141  -2.0754
 70Y  H13  H  HCH2  0   0.280  -4.7589   0.1259  -1.8483
 70Y  H14  H  HCH3  0   0.245  -4.1591   3.8534  -1.1323
 70Y  H15  H  HCH3  0   0.247  -3.1991   2.8780  -2.2445
 70Y  H16  H  HCH3  0   0.247  -4.9564   2.7605  -2.2600
 70Y  H17  H  HCR6  0   0.256  -0.4382  -5.4166  -0.1136
 70Y  H18  H  HCR6  0   0.267   1.7339  -4.4013  -0.5879
 70Y  H19  H  HCR6  0   0.280   0.2702  -0.6604   0.9508
 70Y  H20  H  HCH3  0   0.223  -5.3774   3.8888   0.7122
 70Y  H21  H  HCH3  0   0.237  -6.1075   2.8924   1.9617
 70Y  H22  H  HCH3  0   0.229  -4.3612   3.0510   1.8879
 70Y  H23  H  HNH1  0   0.396  -2.4814   2.8509   0.3732
 70Y  H24  H  H     0   0.333  -1.0566   2.0860   1.8878
 70Y  H25  H  HCH2  0   0.284  -1.8986  -0.9912   2.4755
 70Y  H26  H  HCH2  0   0.276  -3.0830  -2.0768   1.7693
 70Y  H27  H  HCH1  0   0.229  -5.1094   0.8624   1.0224
 70Y  H28  H  HCR6  0   0.248  -2.2777  -4.0783   0.8490
 70Y  H29  H  HCH2  0   0.289   5.4950  -1.7136  -0.8062
 70Y  H30  H  HCH2  0   0.282   5.0755  -1.0289   0.7590
 70Y  C9   C  CH2   0  -0.399  -2.2241  -1.4465   1.5440
 70Y  O8   O  O     0  -0.449  -3.7980  -1.8527  -0.5901
 70Y  C12  C  CH3   0  -0.663  -5.2609   2.9630   1.2785
 70Y  C31  C  CH3   0  -0.667  -6.5622   1.5837  -0.3538

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
 70Y  O8   C4   double    1.215  0.020  1.215
 70Y  C4   N5   single    1.371  0.020  1.371
 70Y  C4   C3   single    1.502  0.020  1.502
 70Y  C9   N5   single    1.460  0.020  1.460
 70Y  C9   C13  single    1.507  0.020  1.507
 70Y  N5   C6   single    1.405  0.020  1.405
 70Y  C3   C2   single    1.524  0.020  1.524
 70Y  N7   C6   double    1.277  0.020  1.277
 70Y  C18  C13  aromatic  1.388  0.020  1.388
 70Y  C18  C17  aromatic  1.388  0.020  1.388
 70Y  C6   N1   single    1.358  0.020  1.358
 70Y  C13  C14  aromatic  1.391  0.020  1.391
 70Y  C17  C16  aromatic  1.385  0.020  1.385
 70Y  C11  C2   single    1.524  0.020  1.524
 70Y  N1   C2   single    1.457  0.020  1.457
 70Y  C2   C10  single    1.554  0.020  1.554
 70Y  C14  C15  aromatic  1.393  0.020  1.393
 70Y  C16  C15  aromatic  1.397  0.020  1.397
 70Y  C15  N19  single    1.405  0.020  1.405
 70Y  C10  C31  single    1.527  0.020  1.527
 70Y  C10  C12  single    1.527  0.020  1.527
 70Y  N19  C20  single    1.365  0.020  1.365
 70Y  N19  C23  single    1.457  0.020  1.457
 70Y  O30  C20  double    1.215  0.020  1.215
 70Y  C26  C25  aromatic  1.390  0.020  1.390
 70Y  C26  C27  aromatic  1.387  0.020  1.387
 70Y  C25  C24  aromatic  1.391  0.020  1.391
 70Y  C20  C21  single    1.510  0.020  1.510
 70Y  C23  C22  single    1.532  0.020  1.532
 70Y  C27  C28  aromatic  1.390  0.020  1.390
 70Y  C24  C22  single    1.503  0.020  1.503
 70Y  C24  C29  aromatic  1.395  0.020  1.395
 70Y  C22  C21  single    1.527  0.020  1.527
 70Y  C28  C29  aromatic  1.387  0.020  1.387
 70Y  C25  H1   single    0.930  0.020  1.080
 70Y  C26  H2   single    0.930  0.020  1.080
 70Y  C27  H3   single    0.930  0.020  1.080
 70Y  C28  H4   single    0.930  0.020  1.080
 70Y  C31  H5   single    0.970  0.020  1.090
 70Y  C31  H6   single    0.970  0.020  1.090
 70Y  C31  H7   single    0.970  0.020  1.090
 70Y  C29  H8   single    0.930  0.020  1.080
 70Y  C23  H9   single    0.970  0.020  1.090
 70Y  C23  H10  single    0.970  0.020  1.090
 70Y  C22  H11  single    0.970  0.020  1.090
 70Y  C3   H12  single    0.970  0.020  1.090
 70Y  C3   H13  single    0.970  0.020  1.090
 70Y  C11  H14  single    0.970  0.020  1.090
 70Y  C11  H15  single    0.970  0.020  1.090
 70Y  C11  H16  single    0.970  0.020  1.090
 70Y  C17  H17  single    0.930  0.020  1.080
 70Y  C16  H18  single    0.930  0.020  1.080
 70Y  C14  H19  single    0.930  0.020  1.080
 70Y  C12  H20  single    0.970  0.020  1.090
 70Y  C12  H21  single    0.970  0.020  1.090
 70Y  C12  H22  single    0.970  0.020  1.090
 70Y  N1   H23  single    0.890  0.020  1.040
 70Y  N7   H24  single    0.890  0.020  1.040
 70Y  C9   H25  single    0.970  0.020  1.090
 70Y  C9   H26  single    0.970  0.020  1.090
 70Y  C10  H27  single    0.970  0.020  1.090
 70Y  C18  H28  single    0.930  0.020  1.080
 70Y  C21  H29  single    0.970  0.020  1.090
 70Y  C21  H30  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
 70Y  H1   C25  C24  119.45  3.000
 70Y  H1   C25  C26  119.61  3.000
 70Y  C24  C25  C26  120.94  3.000
 70Y  H2   C26  C27  120.21  3.000
 70Y  H2   C26  C25  119.73  3.000
 70Y  C27  C26  C25  120.06  3.000
 70Y  H3   C27  C28  120.15  3.000
 70Y  H3   C27  C26  120.34  3.000
 70Y  C28  C27  C26  119.51  3.000
 70Y  H4   C28  C29  119.72  3.000
 70Y  H4   C28  C27  120.06  3.000
 70Y  C29  C28  C27  120.22  3.000
 70Y  H8   C29  C24  120.07  3.000
 70Y  H8   C29  C28  119.16  3.000
 70Y  C24  C29  C28  120.77  3.000
 70Y  C22  C24  C29  121.15  3.000
 70Y  C29  C24  C25  118.50  3.000
 70Y  C22  C24  C25  120.35  3.000
 70Y  H10  C23  H9   108.04  3.000
 70Y  H10  C23  N19  110.82  3.000
 70Y  H9   C23  N19  111.06  3.000
 70Y  H10  C23  C22  112.27  3.000
 70Y  H9   C23  C22  111.38  3.000
 70Y  N19  C23  C22  103.28  3.000
 70Y  H11  C22  C21  108.18  3.000
 70Y  H11  C22  C23  107.69  3.000
 70Y  C21  C22  C23  102.42  3.000
 70Y  H11  C22  C24  108.59  3.000
 70Y  C21  C22  C24  115.55  3.000
 70Y  C23  C22  C24  113.97  3.000
 70Y  O30  C20  C21  126.09  3.000
 70Y  C21  C20  N19  107.83  3.000
 70Y  O30  C20  N19  126.06  3.000
 70Y  O8   C4   N5   121.05  3.000
 70Y  N5   C4   C3   116.52  3.000
 70Y  O8   C4   C3   122.42  3.000
 70Y  C10  C2   N1   110.99  3.000
 70Y  C10  C2   C11  112.27  3.000
 70Y  N1   C2   C11  107.54  3.000
 70Y  C10  C2   C3   111.66  3.000
 70Y  N1   C2   C3   104.60  3.000
 70Y  C11  C2   C3   109.43  3.000
 70Y  H13  C3   H12  106.83  3.000
 70Y  H13  C3   C2   112.37  3.000
 70Y  H12  C3   C2   108.94  3.000
 70Y  H13  C3   C4   108.44  3.000
 70Y  H12  C3   C4   107.43  3.000
 70Y  C2   C3   C4   112.57  3.000
 70Y  H16  C11  H15  107.88  3.000
 70Y  H16  C11  H14  107.82  3.000
 70Y  H15  C11  H14  107.92  3.000
 70Y  H16  C11  C2   111.11  3.000
 70Y  H15  C11  C2   110.16  3.000
 70Y  H14  C11  C2   111.80  3.000
 70Y  H17  C17  C18  119.78  3.000
 70Y  H17  C17  C16  119.15  3.000
 70Y  C18  C17  C16  121.06  3.000
 70Y  H18  C16  C15  121.03  3.000
 70Y  H18  C16  C17  119.51  3.000
 70Y  C15  C16  C17  119.45  3.000
 70Y  N19  C15  C14  118.95  3.000
 70Y  N19  C15  C16  121.72  3.000
 70Y  C14  C15  C16  119.32  3.000
 70Y  H19  C14  C13  118.28  3.000
 70Y  H19  C14  C15  120.68  3.000
 70Y  C13  C14  C15  121.03  3.000
 70Y  H23  N1   C6   115.16  3.000
 70Y  H23  N1   C2   117.16  3.000
 70Y  C6   N1   C2   124.01  3.000
 70Y  C9   N5   C6   118.95  3.000
 70Y  C6   N5   C4   123.52  3.000
 70Y  C9   N5   C4   117.43  3.000
 70Y  N7   C6   N5   118.37  3.000
 70Y  N7   C6   N1   126.11  3.000
 70Y  N5   C6   N1   115.50  3.000
 70Y  H24  N7   C6   110.97  3.000
 70Y  H27  C10  C12  106.77  3.000
 70Y  H27  C10  C2   106.94  3.000
 70Y  C12  C10  C2   112.38  3.000
 70Y  H27  C10  C31  107.21  3.000
 70Y  C12  C10  C31  110.01  3.000
 70Y  C2   C10  C31  113.15  3.000
 70Y  C18  C13  C9   120.69  3.000
 70Y  C18  C13  C14  119.29  3.000
 70Y  C9   C13  C14  120.01  3.000
 70Y  H28  C18  C13  119.98  3.000
 70Y  H28  C18  C17  120.17  3.000
 70Y  C13  C18  C17  119.84  3.000
 70Y  C15  N19  C20  125.56  3.000
 70Y  C20  N19  C23  112.31  3.000
 70Y  C15  N19  C23  121.37  3.000
 70Y  H30  C21  H29  107.28  3.000
 70Y  H30  C21  C20  108.11  3.000
 70Y  H29  C21  C20  111.32  3.000
 70Y  H30  C21  C22  111.99  3.000
 70Y  H29  C21  C22  113.77  3.000
 70Y  C20  C21  C22  104.28  3.000
 70Y  H26  C9   H25  107.55  3.000
 70Y  H26  C9   C13  110.01  3.000
 70Y  H25  C9   C13  110.39  3.000
 70Y  H26  C9   N5   108.39  3.000
 70Y  H25  C9   N5   107.20  3.000
 70Y  C13  C9   N5   113.12  3.000
 70Y  H22  C12  H21  107.21  3.000
 70Y  H22  C12  H20  108.03  3.000
 70Y  H21  C12  H20  107.29  3.000
 70Y  H22  C12  C10  112.25  3.000
 70Y  H21  C12  C10  109.78  3.000
 70Y  H20  C12  C10  112.04  3.000
 70Y  H7   C31  H6   107.79  3.000
 70Y  H7   C31  H5   106.98  3.000
 70Y  H6   C31  H5   107.30  3.000
 70Y  H7   C31  C10  112.79  3.000
 70Y  H6   C31  C10  111.87  3.000
 70Y  H5   C31  C10  109.85  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
 70Y  CONST_01  C28  C27  C26  C25     0.00   0.0  0
 70Y  CONST_02  C28  C29  C24  C25     0.00   0.0  0
 70Y  CONST_03  C29  C24  C25  C26     0.00   0.0  0
 70Y  CONST_04  C29  C28  C27  C26     0.00   0.0  0
 70Y  CONST_05  C24  C25  C26  C27     0.00   0.0  0
 70Y  CONST_06  C24  C29  C28  C27     0.00   0.0  0
 70Y  CONST_07  C14  C13  C18  C17     0.00   0.0  0
 70Y  CONST_08  C14  C15  C16  C17     0.00   0.0  0
 70Y  CONST_09  C13  C18  C17  C16     0.00   0.0  0
 70Y  CONST_10  C13  C14  C15  C16     0.00   0.0  0
 70Y  CONST_11  C18  C13  C14  C15     0.00   0.0  0
 70Y  CONST_12  C18  C17  C16  C15     0.00   0.0  0
 70Y  CONST_13  C22  C24  C25  C26   180.00   0.0  0
 70Y  CONST_14  C22  C24  C29  C28   180.00   0.0  0
 70Y  CONST_15  N19  C15  C16  C17   180.00   0.0  0
 70Y  CONST_16  N19  C15  C14  C13   180.00   0.0  0
 70Y  CONST_17  C21  C20  N19  C23     0.00   0.0  0
 70Y  CONST_18  N1   C6   N5   C4      0.00   0.0  0
 70Y  CONST_20  C6   N5   C4   C3      0.00   0.0  0
 70Y  CONST_21  C21  C20  N19  C15   180.00   0.0  0
 70Y  CONST_22  C9   C13  C18  C17   180.00   0.0  0
 70Y  CONST_23  C9   C13  C14  C15   180.00   0.0  0
 70Y  CONST_24  O30  C20  N19  C23   180.00   0.0  0
 70Y  CONST_25  N7   C6   N5   C4    180.00   0.0  0
 70Y  CONST_27  C9   N5   C4   C3    180.00   0.0  0
 70Y  CONST_28  O30  C20  N19  C15     0.00   0.0  0
 70Y  CONST_29  C9   N5   C6   N1    180.00   0.0  0
 70Y  CONST_30  O8   C4   N5   C6    180.00   0.0  0
 70Y  CONST_31  H3   C27  C26  C25   180.00   0.0  0
 70Y  CONST_32  H8   C29  C24  C25   180.00   0.0  0
 70Y  CONST_33  H4   C28  C27  C26   180.00   0.0  0
 70Y  CONST_34  H1   C25  C26  C27   180.00   0.0  0
 70Y  CONST_35  H2   C26  C27  C28   180.00   0.0  0
 70Y  CONST_36  H28  C18  C17  C16   180.00   0.0  0
 70Y  CONST_37  H19  C14  C15  C16   180.00   0.0  0
 70Y  CONST_38  H17  C17  C16  C15   180.00   0.0  0
 70Y  CONST_39  H18  C16  C15  C14   180.00   0.0  0
 70Y  CONST_40  H23  N1   C6   N5    180.00   0.0  0
 70Y  CONST_41  C9   N5   C6   N7      0.00   0.0  0
 70Y  CONST_42  C9   N5   C4   O8      0.00   0.0  0
 70Y  CONST_43  H24  N7   C6   N1      0.00   0.0  0
 70Y  Var_01    C14  C15  N19  C23   -24.36  30.0  2
 70Y  Var_02    C15  N19  C23  C22  -166.98  30.0  1
 70Y  Var_03    N19  C20  C21  C22   -15.89  30.0  1
 70Y  Var_04    C13  C9   N5   C4     76.16  30.0  2
 70Y  Var_05    N5   C9   C13  C14    64.64  30.0  2
 70Y  Var_06    H12  C3   C4   N5     87.46  30.0  1
 70Y  Var_07    H5   C31  C10  C2    176.87  30.0  3
 70Y  Var_08    H20  C12  C10  C2     63.14  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
 70Y  chir_01  C22  C23  C24  C21  negativ
 70Y  chir_02  C2   C3   N1   C10  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
 70Y  plan-1  C25  0.020
 70Y  plan-1  C26  0.020
 70Y  plan-1  C27  0.020
 70Y  plan-1  C28  0.020
 70Y  plan-1  C29  0.020
 70Y  plan-1  C24  0.020
 70Y  plan-1  C22  0.020
 70Y  plan-1  H1   0.020
 70Y  plan-1  H2   0.020
 70Y  plan-1  H3   0.020
 70Y  plan-1  H4   0.020
 70Y  plan-1  H8   0.020
 70Y  plan-2  C4   0.020
 70Y  plan-2  C2   0.020
 70Y  plan-2  C3   0.020
 70Y  plan-2  N1   0.020
 70Y  plan-2  N5   0.020
 70Y  plan-2  C6   0.020
 70Y  plan-2  N7   0.020
 70Y  plan-2  H23  0.020
 70Y  plan-2  H24  0.020
 70Y  plan-2  C9   0.020
 70Y  plan-2  O8   0.020
 70Y  plan-3  C17  0.020
 70Y  plan-3  C16  0.020
 70Y  plan-3  C15  0.020
 70Y  plan-3  C14  0.020
 70Y  plan-3  C13  0.020
 70Y  plan-3  C18  0.020
 70Y  plan-3  N19  0.020
 70Y  plan-3  H17  0.020
 70Y  plan-3  H18  0.020
 70Y  plan-3  H19  0.020
 70Y  plan-3  H28  0.020
 70Y  plan-3  C9   0.020
 70Y  plan-4  C23  0.020
 70Y  plan-4  C20  0.020
 70Y  plan-4  C15  0.020
 70Y  plan-4  N19  0.020
 70Y  plan-4  C21  0.020
 70Y  plan-4  O30  0.020

