# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 23:02:11 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (8S)-9-[(2R)-2-hydroxy-2-phenylethyl]-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: O[C@@H](CN1[C@@H](CCN2C(=O)C=C(N=C12)N3CCOCC3)C(F)(F)F)c4ccccc4
#
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
 JXM  JXM  (8S)-9-[(2R)-2-hydroxy-2-phenylethyl]-2-(morpholin-4-yl)-8-(trifluoromethyl)-6,7,8,9-tetrahydro-4H-pyrimido[1,2-a]pyrimidin-4-one  ligand  53  30  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JXM
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
 JXM  C1    C  CR16  0  -0.268  -2.2377  -5.0532  -0.1385
 JXM  C2    C  CR16  0  -0.239  -3.3002  -4.1614  -0.0761
 JXM  C3    C  CR16  0  -0.236  -0.9562  -4.6154   0.1697
 JXM  C4    C  CR16  0  -0.302  -3.0785  -2.8414   0.2919
 JXM  C5    C  CR16  0  -0.318  -0.7380  -3.2944   0.5365
 JXM  C6    C  CR6   0   0.115  -1.7976  -2.3934   0.5999
 JXM  C7    C  CR16  0  -0.606   3.0415   1.8820   0.2613
 JXM  C8    C  CR6   0   0.608   2.5181   0.6574  -0.1081
 JXM  C9    C  CR6   0   0.581   2.1688   2.9543   0.5451
 JXM  C10   C  CR6   0   0.835   0.3604   1.4705  -0.0305
 JXM  C11   C  CH2   0  -0.525  -1.4199   3.5986  -0.0886
 JXM  C12   C  CH2   0  -0.289  -0.1353   3.7753   0.6709
 JXM  C13   C  CH2   0  -0.328   2.7659  -1.5688  -1.1106
 JXM  C14   C  CH2   0  -0.320   4.7140  -0.4326  -0.2149
 JXM  C15   C  CH2   0  -0.191   3.3437  -2.8712  -0.5936
 JXM  C16   C  CH2   0  -0.183   5.2090  -1.7921   0.2522
 JXM  C17   C  CH1   0  -0.266  -1.9788   2.2075   0.1681
 JXM  C18   C  CH2   0  -0.399  -1.3481  -0.1807  -0.3845
 JXM  C19   C  CH1   0  -0.034  -1.5709  -0.9353   0.9353
 JXM  C20   C  CT    0   1.030  -3.2856   2.0420  -0.6115
 JXM  N21   N  N     0  -0.616   1.1862   0.4802  -0.2432
 JXM  N22   N  NT    0  -0.511   3.2693  -0.4503  -0.3286
 JXM  N23   N  NR6   0  -0.602   0.7886   2.6957   0.3551
 JXM  N24   N  NT    0  -0.542  -0.9741   1.2195  -0.2086
 JXM  O26   O  O2    0  -0.480   4.7522  -2.8383  -0.5720
 JXM  O27   O  OH1   0  -0.663  -0.5273  -0.7307   1.8521
 JXM  F28   F  F     0  -0.302  -3.0832   1.9158  -1.9258
 JXM  F29   F  F     0  -0.306  -4.0097   0.9867  -0.2122
 JXM  F30   F  F     0  -0.300  -4.0687   3.1094  -0.4293
 JXM  H1    H  HCR6  0   0.257  -2.4080  -6.0840  -0.4206
 JXM  H2    H  HCR6  0   0.258  -4.3036  -4.4944  -0.3078
 JXM  H3    H  HCR6  0   0.256  -0.1236  -5.3056   0.1280
 JXM  H4    H  HCR6  0   0.247  -3.9139  -2.1520   0.3440
 JXM  H5    H  HCR6  0   0.235   0.2691  -2.9800   0.7848
 JXM  H19   H  HCH1  0   0.253  -2.4751  -0.5541   1.4210
 JXM  H7    H  HCR6  0   0.265   4.0987   2.0711   0.3604
 JXM  H111  H  HCH2  0   0.295  -2.1191   4.3593   0.2505
 JXM  H112  H  HCH2  0   0.278  -1.2474   3.7477  -1.1568
 JXM  H121  H  HCH2  0   0.286   0.3283   4.7182   0.3964
 JXM  H122  H  HCH2  0   0.267  -0.3176   3.7960   1.7477
 JXM  H17   H  HCH1  0   0.309  -2.2398   2.1129   1.2301
 JXM  H132  H  HCH2  0   0.271   1.6816  -1.6044  -1.0560
 JXM  H151  H  HCH2  0   0.205   2.9497  -3.0761   0.4127
 JXM  H152  H  HCH2  0   0.247   3.0424  -3.6900  -1.2485
 JXM  H141  H  HCH2  0   0.266   5.0294   0.3009   0.5244
 JXM  H142  H  HCH2  0   0.240   5.1764  -0.1625  -1.1723
 JXM  H161  H  HCH2  0   0.247   6.2993  -1.8072   0.2330
 JXM  H162  H  HCH2  0   0.210   4.8849  -1.9522   1.2900
 JXM  H181  H  HCH2  0   0.305  -0.5599  -0.6643  -0.9550
 JXM  H182  H  HCH2  0   0.285  -2.2352  -0.2666  -1.0040
 JXM  H27   H  HOH1  0   0.456   0.3111  -0.7111   1.3739
 JXM  O25   O  O     0  -0.520   2.5032   4.0717   0.9278
 JXM  H131  H  HCH2  0   0.240   3.0363  -1.4359  -2.1657

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
 JXM  C1   C2    aromatic  1.389  0.020  1.389
 JXM  C1   C3    aromatic  1.389  0.020  1.389
 JXM  C2   C4    aromatic  1.388  0.020  1.388
 JXM  C3   C5    aromatic  1.388  0.020  1.388
 JXM  C4   C6    aromatic  1.392  0.020  1.392
 JXM  C5   C6    aromatic  1.392  0.020  1.392
 JXM  C6   C19   single    1.513  0.020  1.513
 JXM  C7   C8    double    1.382  0.020  1.382
 JXM  C7   C9    single    1.411  0.020  1.411
 JXM  C8   N21   single    1.350  0.020  1.350
 JXM  C8   N22   single    1.356  0.020  1.356
 JXM  C9   N23   single    1.417  0.020  1.417
 JXM  C9   O25   double    1.228  0.020  1.228
 JXM  C10  N21   double    1.307  0.020  1.307
 JXM  C10  N23   single    1.354  0.020  1.354
 JXM  C10  N24   single    1.370  0.020  1.370
 JXM  C11  C12   single    1.503  0.020  1.503
 JXM  C11  C17   single    1.521  0.020  1.521
 JXM  C12  N23   single    1.456  0.020  1.456
 JXM  C13  C15   single    1.516  0.020  1.516
 JXM  C13  N22   single    1.455  0.020  1.455
 JXM  C14  C16   single    1.520  0.020  1.520
 JXM  C14  N22   single    1.449  0.020  1.449
 JXM  C15  O26   single    1.409  0.020  1.409
 JXM  C16  O26   single    1.408  0.020  1.408
 JXM  C17  C20   single    1.531  0.020  1.531
 JXM  C17  N24   single    1.459  0.020  1.459
 JXM  C18  C19   single    1.537  0.020  1.537
 JXM  C18  N24   single    1.460  0.020  1.460
 JXM  C19  O27   single    1.404  0.020  1.404
 JXM  C20  F28   single    1.336  0.020  1.336
 JXM  C20  F29   single    1.341  0.020  1.341
 JXM  C20  F30   single    1.336  0.020  1.336
 JXM  C1   H1    single    0.930  0.020  1.080
 JXM  C2   H2    single    0.930  0.020  1.080
 JXM  C3   H3    single    0.930  0.020  1.080
 JXM  C4   H4    single    0.930  0.020  1.080
 JXM  C5   H5    single    0.930  0.020  1.080
 JXM  C19  H19   single    0.970  0.020  1.090
 JXM  C7   H7    single    0.930  0.020  1.080
 JXM  C11  H111  single    0.970  0.020  1.090
 JXM  C11  H112  single    0.970  0.020  1.090
 JXM  C12  H121  single    0.970  0.020  1.090
 JXM  C12  H122  single    0.970  0.020  1.090
 JXM  C17  H17   single    0.970  0.020  1.090
 JXM  C13  H131  single    0.970  0.020  1.090
 JXM  C13  H132  single    0.970  0.020  1.090
 JXM  C15  H151  single    0.970  0.020  1.090
 JXM  C15  H152  single    0.970  0.020  1.090
 JXM  C14  H141  single    0.970  0.020  1.090
 JXM  C14  H142  single    0.970  0.020  1.090
 JXM  C16  H161  single    0.970  0.020  1.090
 JXM  C16  H162  single    0.970  0.020  1.090
 JXM  C18  H181  single    0.970  0.020  1.090
 JXM  C18  H182  single    0.970  0.020  1.090
 JXM  O27  H27   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
 JXM  H1    C1   C3    120.22  3.000
 JXM  H1    C1   C2    120.20  3.000
 JXM  C3    C1   C2    119.58  3.000
 JXM  H2    C2   C4    119.83  3.000
 JXM  H2    C2   C1    120.14  3.000
 JXM  C4    C2   C1    120.03  3.000
 JXM  H3    C3   C5    119.74  3.000
 JXM  H3    C3   C1    120.02  3.000
 JXM  C5    C3   C1    120.24  3.000
 JXM  H4    C4   C6    119.59  3.000
 JXM  H4    C4   C2    119.62  3.000
 JXM  C6    C4   C2    120.79  3.000
 JXM  H5    C5   C6    120.60  3.000
 JXM  H5    C5   C3    118.86  3.000
 JXM  C6    C5   C3    120.54  3.000
 JXM  C19   C6   C5    121.31  3.000
 JXM  C19   C6   C4    119.81  3.000
 JXM  C5    C6   C4    118.82  3.000
 JXM  H7    C7   C9    117.02  3.000
 JXM  H7    C7   C8    123.45  3.000
 JXM  C9    C7   C8    119.52  3.000
 JXM  N22   C8   N21   115.01  3.000
 JXM  N22   C8   C7    123.87  3.000
 JXM  N21   C8   C7    121.10  3.000
 JXM  O25   C9   N23   118.25  3.000
 JXM  O25   C9   C7    125.86  3.000
 JXM  N23   C9   C7    115.89  3.000
 JXM  N24   C10  N23   120.73  3.000
 JXM  N24   C10  N21   117.11  3.000
 JXM  N23   C10  N21   122.16  3.000
 JXM  H112  C11  H111  108.12  3.000
 JXM  H112  C11  C17   110.36  3.000
 JXM  H111  C11  C17   110.55  3.000
 JXM  H112  C11  C12   110.07  3.000
 JXM  H111  C11  C12   108.04  3.000
 JXM  C17   C11  C12   109.65  3.000
 JXM  H122  C12  H121  107.69  3.000
 JXM  H122  C12  N23   109.50  3.000
 JXM  H121  C12  N23   108.55  3.000
 JXM  H122  C12  C11   110.97  3.000
 JXM  H121  C12  C11   109.83  3.000
 JXM  N23   C12  C11   110.22  3.000
 JXM  H132  C13  H131  107.36  3.000
 JXM  H132  C13  N22   110.10  3.000
 JXM  H131  C13  N22   109.79  3.000
 JXM  H132  C13  C15   109.58  3.000
 JXM  H131  C13  C15   109.76  3.000
 JXM  N22   C13  C15   110.21  3.000
 JXM  H142  C14  H141  107.74  3.000
 JXM  H142  C14  N22   110.77  3.000
 JXM  H141  C14  N22   110.52  3.000
 JXM  H142  C14  C16   110.55  3.000
 JXM  H141  C14  C16   107.44  3.000
 JXM  N22   C14  C16   109.74  3.000
 JXM  H152  C15  H151  108.09  3.000
 JXM  H152  C15  O26   107.63  3.000
 JXM  H151  C15  O26   110.38  3.000
 JXM  H152  C15  C13   109.57  3.000
 JXM  H151  C15  C13   109.61  3.000
 JXM  O26   C15  C13   111.48  3.000
 JXM  H162  C16  H161  108.03  3.000
 JXM  H162  C16  O26   110.42  3.000
 JXM  H161  C16  O26   107.68  3.000
 JXM  H162  C16  C14   108.93  3.000
 JXM  H161  C16  C14   109.42  3.000
 JXM  O26   C16  C14   112.27  3.000
 JXM  H17   C17  N24   110.81  3.000
 JXM  H17   C17  C20   106.29  3.000
 JXM  N24   C17  C20   112.54  3.000
 JXM  H17   C17  C11   109.23  3.000
 JXM  N24   C17  C11   108.83  3.000
 JXM  C20   C17  C11   109.06  3.000
 JXM  H182  C18  H181  104.95  3.000
 JXM  H182  C18  N24   110.73  3.000
 JXM  H181  C18  N24   107.72  3.000
 JXM  H182  C18  C19   109.44  3.000
 JXM  H181  C18  C19   109.73  3.000
 JXM  N24   C18  C19   113.87  3.000
 JXM  H19   C19  O27   105.87  3.000
 JXM  H19   C19  C18   109.26  3.000
 JXM  O27   C19  C18   112.42  3.000
 JXM  H19   C19  C6    108.07  3.000
 JXM  O27   C19  C6    113.36  3.000
 JXM  C18   C19  C6    107.73  3.000
 JXM  F30   C20  F29   105.76  3.000
 JXM  F30   C20  F28   107.36  3.000
 JXM  F29   C20  F28   107.49  3.000
 JXM  F30   C20  C17   110.15  3.000
 JXM  F29   C20  C17   113.23  3.000
 JXM  F28   C20  C17   112.46  3.000
 JXM  C10   N21  C8    120.50  3.000
 JXM  C14   N22  C13   113.37  3.000
 JXM  C14   N22  C8    121.96  3.000
 JXM  C13   N22  C8    121.58  3.000
 JXM  C12   N23  C10   122.16  3.000
 JXM  C12   N23  C9    116.98  3.000
 JXM  C10   N23  C9    120.76  3.000
 JXM  C18   N24  C17   120.29  3.000
 JXM  C18   N24  C10   116.17  3.000
 JXM  C17   N24  C10   120.90  3.000
 JXM  C16   O26  C15   110.53  3.000
 JXM  H27   O27  C19   108.97  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
 JXM  CONST_01  C6    C4   C2   C1      0.00   0.0  0
 JXM  CONST_02  C6    C5   C3   C1      0.00   0.0  0
 JXM  CONST_03  C5    C3   C1   C2      0.00   0.0  0
 JXM  CONST_04  C5    C6   C4   C2      0.00   0.0  0
 JXM  CONST_05  C4    C2   C1   C3      0.00   0.0  0
 JXM  CONST_06  C4    C6   C5   C3      0.00   0.0  0
 JXM  CONST_07  C10   N21  C8   C7      0.00   0.0  0
 JXM  CONST_09  C14   N22  C8   C7      0.00   0.0  0
 JXM  CONST_10  C10   N23  C9   C7      0.00   0.0  0
 JXM  CONST_11  C12   N23  C9   C7    180.00   0.0  0
 JXM  CONST_12  N23   C10  N21  C8      0.00   0.0  0
 JXM  CONST_13  N24   C10  N21  C8    180.00   0.0  0
 JXM  CONST_14  N21   C10  N23  C9      0.00   0.0  0
 JXM  CONST_15  N24   C10  N23  C9    180.00   0.0  0
 JXM  CONST_16  N22   C8   N21  C10   180.00   0.0  0
 JXM  CONST_17  N21   C10  N23  C12   180.00   0.0  0
 JXM  CONST_18  N24   C10  N23  C12     0.00   0.0  0
 JXM  CONST_20  N21   C8   N22  C14   180.00   0.0  0
 JXM  CONST_21  N21   C10  N24  C17   180.00   0.0  0
 JXM  CONST_22  N23   C10  N24  C17     0.00   0.0  0
 JXM  CONST_23  C19   C6   C4   C2    180.00   0.0  0
 JXM  CONST_24  C19   C6   C5   C3    180.00   0.0  0
 JXM  CONST_25  O25   C9   N23  C10   180.00   0.0  0
 JXM  CONST_26  O25   C9   N23  C12     0.00   0.0  0
 JXM  CONST_27  N21   C10  N24  C18     0.00   0.0  0
 JXM  CONST_28  N23   C10  N24  C18   180.00   0.0  0
 JXM  CONST_29  H4    C4   C2   C1    180.00   0.0  0
 JXM  CONST_30  H5    C5   C3   C1    180.00   0.0  0
 JXM  CONST_31  H3    C3   C1   C2    180.00   0.0  0
 JXM  CONST_32  H2    C2   C1   C3    180.00   0.0  0
 JXM  CONST_33  H1    C1   C2   C4    180.00   0.0  0
 JXM  Var_01    C15   C13  N22  C8   -147.79  30.0  1
 JXM  Var_02    C16   C14  N22  C8    148.63  30.0  1
 JXM  Var_03    C11   C12  N23  C9    156.18  30.0  1
 JXM  Var_04    N23   C12  C11  C17    53.57  30.0  1
 JXM  Var_05    O26   C15  C13  N22   -55.17  30.0  1
 JXM  Var_06    O26   C16  C14  N22    54.45  30.0  1
 JXM  Var_07    H161  C16  O26  C15  -179.83  30.0  1
 JXM  Var_08    H151  C15  O26  C16   -62.67  30.0  1
 JXM  Var_09    C19   C18  N24  C10    85.89  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
 JXM  chir_01  C17  C11  C20  N24  negativ
 JXM  chir_02  C19  O27  C6   C18  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
 JXM  plan-1  C1   0.020
 JXM  plan-1  C2   0.020
 JXM  plan-1  C3   0.020
 JXM  plan-1  C4   0.020
 JXM  plan-1  C5   0.020
 JXM  plan-1  C6   0.020
 JXM  plan-1  C19  0.020
 JXM  plan-1  H1   0.020
 JXM  plan-1  H2   0.020
 JXM  plan-1  H3   0.020
 JXM  plan-1  H4   0.020
 JXM  plan-1  H5   0.020
 JXM  plan-2  C7   0.020
 JXM  plan-2  C8   0.020
 JXM  plan-2  C9   0.020
 JXM  plan-2  C10  0.020
 JXM  plan-2  C12  0.020
 JXM  plan-2  C13  0.020
 JXM  plan-2  C14  0.020
 JXM  plan-2  C17  0.020
 JXM  plan-2  C18  0.020
 JXM  plan-2  N21  0.020
 JXM  plan-2  N22  0.020
 JXM  plan-2  N23  0.020
 JXM  plan-2  N24  0.020
 JXM  plan-2  H7   0.020
 JXM  plan-2  O25  0.020

