# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 23:48:14 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (8S)-9-(3,5-difluorophenyl)-2-(morpholin-4-yl)-8-(trifluoromethyl)-6,7,8,9-tetrahydro-4H-pyrimido[1,2-a]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cc(F)cc(c1)N2[C@@H](CCN3C(=O)C=C(N=C23)N4CCOCC4)C(F)(F)F
#
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
 EUT  EUT  (8S)-9-(3,5-difluorophenyl)-2-(morpholin-4-yl)-8-(trifluoromethyl)-6,7,8,9-tetrahydro-4H-pyrimido[1,2-a]pyrimidin-4-one  ligand  46  29  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_EUT
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
 EUT  C1    C  CR16  0  -0.436  -1.4861   1.3177  -1.4331
 EUT  C2    C  CR16  0  -0.410  -1.0124   1.4701   0.9327
 EUT  C3    C  CR16  0  -0.555  -1.3853   3.4899  -0.3596
 EUT  C4    C  CR6   0   0.319  -1.2067   0.7164  -0.2156
 EUT  C5    C  CR6   0   0.551  -1.5736   2.6963  -1.4730
 EUT  C6    C  CR6   0   0.543  -1.1008   2.8424   0.8284
 EUT  C7    C  CR16  0  -0.608   2.5995  -2.3176  -0.2235
 EUT  C8    C  CR6   0   0.599   2.3646  -0.9749   0.0322
 EUT  C9    C  CR6   0   0.574   1.5216  -3.1770  -0.5256
 EUT  C10   C  CR6   0   0.800   0.1066  -1.2680  -0.1862
 EUT  C11   C  CH2   0  -0.523  -2.1135  -2.9433  -0.0668
 EUT  C12   C  CH2   0  -0.307  -0.9186  -3.3667  -0.8807
 EUT  C13   C  CH2   0  -0.325   3.0405   1.2886   0.6956
 EUT  C14   C  CH2   0  -0.320   4.7321  -0.4304   0.4427
 EUT  C15   C  CH2   0  -0.187   4.0064   2.2615   0.0478
 EUT  C16   C  CH2   0  -0.182   5.6312   0.6242  -0.1807
 EUT  C17   C  CH1   0  -0.268  -2.3830  -1.4621  -0.2852
 EUT  C18   C  CT    0   1.035  -3.4225  -0.9691   0.7227
 EUT  N19   N  N     0  -0.552   1.1074  -0.4807   0.0604
 EUT  N20   N  NT    0  -0.645  -1.1445  -0.7073  -0.1538
 EUT  N21   N  NT    0  -0.513   3.3409  -0.0666   0.2621
 EUT  N22   N  NR6   0  -0.595   0.2394  -2.5770  -0.4902
 EUT  O24   O  O2    0  -0.482   5.3483   1.9143   0.3069
 EUT  F25   F  F     0  -0.306  -1.8456   3.2902  -2.6403
 EUT  F26   F  F     0  -0.307  -0.9082   3.5844   1.9251
 EUT  F27   F  F     0  -0.302  -2.9392  -0.9398   1.9679
 EUT  F28   F  F     0  -0.299  -3.8802   0.2553   0.4448
 EUT  F29   F  F     0  -0.303  -4.4859  -1.7808   0.7230
 EUT  H1    H  HCR6  0   0.293  -1.6278   0.7297  -2.3305
 EUT  H2    H  HCR6  0   0.287  -0.7813   1.0019   1.8789
 EUT  H3    H  HCR6  0   0.308  -1.4547   4.5683  -0.4143
 EUT  H7    H  HCR6  0   0.261   3.5867  -2.7508  -0.2431
 EUT  H111  H  HCH2  0   0.297  -2.9794  -3.5232  -0.3796
 EUT  H112  H  HCH2  0   0.277  -1.9267  -3.1581   0.9873
 EUT  H121  H  HCH2  0   0.291  -0.6940  -4.4130  -0.7004
 EUT  H122  H  HCH2  0   0.270  -1.1039  -3.2447  -1.9508
 EUT  H17   H  HCH1  0   0.311  -2.8107  -1.3184  -1.2843
 EUT  H131  H  HCH2  0   0.234   3.1178   1.3575   1.7880
 EUT  H132  H  HCH2  0   0.281   2.0211   1.5429   0.4203
 EUT  H151  H  HCH2  0   0.208   3.8193   2.2945  -1.0347
 EUT  H152  H  HCH2  0   0.244   3.8419   3.2625   0.4490
 EUT  H141  H  HCH2  0   0.269   4.9549  -1.3819  -0.0335
 EUT  H142  H  HCH2  0   0.242   4.9562  -0.5375   1.5111
 EUT  H161  H  HCH2  0   0.246   6.6720   0.4014   0.0570
 EUT  H162  H  HCH2  0   0.209   5.5185   0.5908  -1.2737
 EUT  O23   O  O     0  -0.523   1.6039  -4.3673  -0.8182

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
 EUT  C1   C4    aromatic  1.386  0.020  1.386
 EUT  C1   C5    aromatic  1.382  0.020  1.382
 EUT  C2   C4    aromatic  1.387  0.020  1.387
 EUT  C2   C6    aromatic  1.379  0.020  1.379
 EUT  C3   C5    aromatic  1.380  0.020  1.380
 EUT  C3   C6    aromatic  1.383  0.020  1.383
 EUT  C4   N20   single    1.426  0.020  1.426
 EUT  C5   F25   single    1.338  0.020  1.338
 EUT  C6   F26   single    1.338  0.020  1.338
 EUT  C7   C8    double    1.387  0.020  1.387
 EUT  C7   C9    single    1.411  0.020  1.411
 EUT  C8   N19   single    1.351  0.020  1.351
 EUT  C8   N21   single    1.353  0.020  1.353
 EUT  C9   N22   single    1.416  0.020  1.416
 EUT  C9   O23   double    1.229  0.020  1.229
 EUT  C10  N19   double    1.297  0.020  1.297
 EUT  C10  N20   single    1.371  0.020  1.371
 EUT  C10  N22   single    1.350  0.020  1.350
 EUT  C11  C12   single    1.506  0.020  1.506
 EUT  C11  C17   single    1.521  0.020  1.521
 EUT  C12  N22   single    1.455  0.020  1.455
 EUT  C13  C15   single    1.516  0.020  1.516
 EUT  C13  N21   single    1.454  0.020  1.454
 EUT  C14  C16   single    1.520  0.020  1.520
 EUT  C14  N21   single    1.449  0.020  1.449
 EUT  C15  O24   single    1.410  0.020  1.410
 EUT  C16  O24   single    1.408  0.020  1.408
 EUT  C17  C18   single    1.529  0.020  1.529
 EUT  C17  N20   single    1.456  0.020  1.456
 EUT  C18  F27   single    1.336  0.020  1.336
 EUT  C18  F28   single    1.336  0.020  1.336
 EUT  C18  F29   single    1.338  0.020  1.338
 EUT  C1   H1    single    0.930  0.020  1.080
 EUT  C2   H2    single    0.930  0.020  1.080
 EUT  C3   H3    single    0.930  0.020  1.080
 EUT  C7   H7    single    0.930  0.020  1.080
 EUT  C11  H111  single    0.970  0.020  1.090
 EUT  C11  H112  single    0.970  0.020  1.090
 EUT  C12  H121  single    0.970  0.020  1.090
 EUT  C12  H122  single    0.970  0.020  1.090
 EUT  C17  H17   single    0.970  0.020  1.090
 EUT  C13  H131  single    0.970  0.020  1.090
 EUT  C13  H132  single    0.970  0.020  1.090
 EUT  C15  H151  single    0.970  0.020  1.090
 EUT  C15  H152  single    0.970  0.020  1.090
 EUT  C14  H141  single    0.970  0.020  1.090
 EUT  C14  H142  single    0.970  0.020  1.090
 EUT  C16  H161  single    0.970  0.020  1.090
 EUT  C16  H162  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
 EUT  H1    C1   C5    120.65  3.000
 EUT  H1    C1   C4    121.26  3.000
 EUT  C5    C1   C4    118.08  3.000
 EUT  H2    C2   C6    120.73  3.000
 EUT  H2    C2   C4    121.29  3.000
 EUT  C6    C2   C4    117.97  3.000
 EUT  H3    C3   C6    121.56  3.000
 EUT  H3    C3   C5    121.57  3.000
 EUT  C6    C3   C5    116.87  3.000
 EUT  N20   C4   C2    120.02  3.000
 EUT  N20   C4   C1    118.67  3.000
 EUT  C2    C4   C1    121.30  3.000
 EUT  F25   C5   C3    118.45  3.000
 EUT  F25   C5   C1    118.75  3.000
 EUT  C3    C5   C1    122.80  3.000
 EUT  F26   C6   C3    118.31  3.000
 EUT  F26   C6   C2    118.72  3.000
 EUT  C3    C6   C2    122.97  3.000
 EUT  H7    C7   C9    116.79  3.000
 EUT  H7    C7   C8    123.19  3.000
 EUT  C9    C7   C8    119.97  3.000
 EUT  N21   C8   N19   114.98  3.000
 EUT  N21   C8   C7    123.99  3.000
 EUT  N19   C8   C7    121.04  3.000
 EUT  O23   C9   N22   118.50  3.000
 EUT  O23   C9   C7    126.14  3.000
 EUT  N22   C9   C7    115.36  3.000
 EUT  N22   C10  N20   119.43  3.000
 EUT  N22   C10  N19   123.73  3.000
 EUT  N20   C10  N19   116.83  3.000
 EUT  H112  C11  H111  107.99  3.000
 EUT  H112  C11  C17   111.13  3.000
 EUT  H111  C11  C17   109.67  3.000
 EUT  H112  C11  C12   109.30  3.000
 EUT  H111  C11  C12   109.03  3.000
 EUT  C17   C11  C12   109.67  3.000
 EUT  H122  C12  H121  107.78  3.000
 EUT  H122  C12  N22   109.71  3.000
 EUT  H121  C12  N22   108.30  3.000
 EUT  H122  C12  C11   111.30  3.000
 EUT  H121  C12  C11   110.20  3.000
 EUT  N22   C12  C11   109.49  3.000
 EUT  H132  C13  H131  107.68  3.000
 EUT  H132  C13  N21   109.67  3.000
 EUT  H131  C13  N21   109.92  3.000
 EUT  H132  C13  C15   109.84  3.000
 EUT  H131  C13  C15   109.88  3.000
 EUT  N21   C13  C15   109.82  3.000
 EUT  H142  C14  H141  107.42  3.000
 EUT  H142  C14  N21   110.00  3.000
 EUT  H141  C14  N21   111.22  3.000
 EUT  H142  C14  C16   110.27  3.000
 EUT  H141  C14  C16   107.85  3.000
 EUT  N21   C14  C16   110.03  3.000
 EUT  H152  C15  H151  108.00  3.000
 EUT  H152  C15  O24   107.57  3.000
 EUT  H151  C15  O24   110.51  3.000
 EUT  H152  C15  C13   109.61  3.000
 EUT  H151  C15  C13   109.36  3.000
 EUT  O24   C15  C13   111.70  3.000
 EUT  H162  C16  H161  107.96  3.000
 EUT  H162  C16  O24   110.59  3.000
 EUT  H161  C16  O24   107.67  3.000
 EUT  H162  C16  C14   109.03  3.000
 EUT  H161  C16  C14   109.47  3.000
 EUT  O24   C16  C14   112.02  3.000
 EUT  H17   C17  N20   110.25  3.000
 EUT  H17   C17  C18   107.05  3.000
 EUT  N20   C17  C18   110.58  3.000
 EUT  H17   C17  C11   109.12  3.000
 EUT  N20   C17  C11   109.94  3.000
 EUT  C18   C17  C11   109.85  3.000
 EUT  F29   C18  F28   106.48  3.000
 EUT  F29   C18  F27   107.49  3.000
 EUT  F28   C18  F27   107.31  3.000
 EUT  F29   C18  C17   110.17  3.000
 EUT  F28   C18  C17   113.02  3.000
 EUT  F27   C18  C17   112.05  3.000
 EUT  C10   N19  C8    119.47  3.000
 EUT  C17   N20  C10   124.18  3.000
 EUT  C17   N20  C4    118.44  3.000
 EUT  C10   N20  C4    116.54  3.000
 EUT  C14   N21  C13   113.27  3.000
 EUT  C14   N21  C8    123.04  3.000
 EUT  C13   N21  C8    121.81  3.000
 EUT  C12   N22  C10   120.55  3.000
 EUT  C12   N22  C9    118.95  3.000
 EUT  C10   N22  C9    120.35  3.000
 EUT  C16   O24  C15   110.68  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
 EUT  CONST_01  C6    C2   C4   C1      0.00   0.0  0
 EUT  CONST_02  C6    C3   C5   C1      0.00   0.0  0
 EUT  CONST_03  C5    C1   C4   C2      0.00   0.0  0
 EUT  CONST_04  C5    C3   C6   C2      0.00   0.0  0
 EUT  CONST_05  C4    C1   C5   C3      0.00   0.0  0
 EUT  CONST_06  C4    C2   C6   C3      0.00   0.0  0
 EUT  CONST_07  N20   C4   C1   C5    180.00   0.0  0
 EUT  CONST_08  N20   C4   C2   C6    180.00   0.0  0
 EUT  CONST_11  C10   N19  C8   C7      0.00   0.0  0
 EUT  CONST_12  C13   N21  C8   C7    180.00   0.0  0
 EUT  CONST_13  C14   N21  C8   C7      0.00   0.0  0
 EUT  CONST_14  C10   N22  C9   C7      0.00   0.0  0
 EUT  CONST_15  C12   N22  C9   C7    180.00   0.0  0
 EUT  CONST_16  N20   C10  N19  C8    180.00   0.0  0
 EUT  CONST_17  N22   C10  N19  C8      0.00   0.0  0
 EUT  CONST_18  N19   C10  N22  C9      0.00   0.0  0
 EUT  CONST_19  N20   C10  N22  C9    180.00   0.0  0
 EUT  CONST_20  N21   C8   N19  C10   180.00   0.0  0
 EUT  CONST_21  N19   C10  N22  C12   180.00   0.0  0
 EUT  CONST_22  N20   C10  N22  C12     0.00   0.0  0
 EUT  CONST_23  N19   C8   N21  C13     0.00   0.0  0
 EUT  CONST_24  N19   C8   N21  C14   180.00   0.0  0
 EUT  CONST_25  N19   C10  N20  C17   180.00   0.0  0
 EUT  CONST_26  N22   C10  N20  C17     0.00   0.0  0
 EUT  CONST_27  F25   C5   C1   C4    180.00   0.0  0
 EUT  CONST_28  F26   C6   C2   C4    180.00   0.0  0
 EUT  CONST_29  F26   C6   C3   C5    180.00   0.0  0
 EUT  CONST_30  F25   C5   C3   C6    180.00   0.0  0
 EUT  CONST_31  O23   C9   N22  C10   180.00   0.0  0
 EUT  CONST_32  O23   C9   N22  C12     0.00   0.0  0
 EUT  CONST_33  H2    C2   C4   C1    180.00   0.0  0
 EUT  CONST_34  H3    C3   C5   C1    180.00   0.0  0
 EUT  CONST_35  H1    C1   C4   C2    180.00   0.0  0
 EUT  Var_01    C10   N20  C4   C1     99.24  30.0  2
 EUT  Var_02    C15   C13  N21  C8   -143.07  30.0  1
 EUT  Var_03    C16   C14  N21  C8    143.89  30.0  1
 EUT  Var_04    C11   C12  N22  C9    146.68  30.0  1
 EUT  Var_05    N22   C12  C11  C17    58.70  30.0  1
 EUT  Var_06    O24   C15  C13  N21   -55.38  30.0  1
 EUT  Var_07    O24   C16  C14  N21    54.30  30.0  1
 EUT  Var_08    H161  C16  O24  C15  -179.22  30.0  1
 EUT  Var_09    H151  C15  O24  C16   -62.61  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
 EUT  chir_01  C17  C11  C18  N20  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
 EUT  plan-1  C1   0.020
 EUT  plan-1  C2   0.020
 EUT  plan-1  C3   0.020
 EUT  plan-1  C4   0.020
 EUT  plan-1  C5   0.020
 EUT  plan-1  C6   0.020
 EUT  plan-1  N20  0.020
 EUT  plan-1  F25  0.020
 EUT  plan-1  F26  0.020
 EUT  plan-1  H1   0.020
 EUT  plan-1  H2   0.020
 EUT  plan-1  H3   0.020
 EUT  plan-2  C4   0.020
 EUT  plan-2  C7   0.020
 EUT  plan-2  C8   0.020
 EUT  plan-2  C9   0.020
 EUT  plan-2  C10  0.020
 EUT  plan-2  C12  0.020
 EUT  plan-2  C13  0.020
 EUT  plan-2  C14  0.020
 EUT  plan-2  C17  0.020
 EUT  plan-2  N19  0.020
 EUT  plan-2  N20  0.020
 EUT  plan-2  N21  0.020
 EUT  plan-2  N22  0.020
 EUT  plan-2  H7   0.020
 EUT  plan-2  O23  0.020

