# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 09:02:09 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (8S)-9-[(5-chlorothiophen-2-yl)methyl]-2-[(3R,5R)-3,5-dimethylmorpholin-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: C[C@@H]1COC[C@@H](C)N1C2=CC(=O)N3CC[C@H](N(Cc4sc(Cl)cc4)C3=N2)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
 UJB  UJB  (8S)-9-[(5-chlorothiophen-2-yl)methyl]-2-[(3R,5R)-3,5-dimethylmorpholin-4-yl]-8-(trifluoromethyl)-6,7,8,9-tetrahydro-4H-pyrimido[1,2-a]pyrimidin-4-one  ligand  52  30  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UJB
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
 UJB  C1    C   CH1   0  -0.286   3.0920   0.0475   0.0749
 UJB  C2    C   CR6   0   0.755   0.7376   0.8169   0.0315
 UJB  N3    N   NR6   0  -0.567   1.0445   1.7732  -0.8764
 UJB  N4    N   NT    0  -0.531   1.6714  -0.1583   0.2671
 UJB  N5    N   N     0  -0.518  -0.3980   0.7515   0.6545
 UJB  C6    C   CR6   0   0.574   0.1362   2.8049  -1.1787
 UJB  C7    C   CH2   0  -0.324   2.2631   1.6122  -1.6572
 UJB  C8    C   CR6   0   0.555  -1.3310   1.7049   0.4114
 UJB  C9    C   CR16  0  -0.576  -1.0964   2.7278  -0.4783
 UJB  O10   O   O     0  -0.508   0.4338   3.6435  -2.0216
 UJB  C11   C   CH2   0  -0.505   3.4005   1.3255  -0.7103
 UJB  C12   C   CH1   0  -0.123  -3.4641   2.6489   1.1648
 UJB  C13   C   CH2   0  -0.168  -4.6302   2.2897   2.0920
 UJB  O14   O   O2    0  -0.476  -5.1585   1.0061   1.9003
 UJB  C15   C   CH2   0  -0.196  -4.1481   0.0539   2.1316
 UJB  C16   C   CH1   0  -0.138  -3.0455   0.1821   1.1018
 UJB  N17   N   NT    0  -0.505  -2.4971   1.5505   1.1245
 UJB  C18   C   CT    0   1.036   3.7856   0.1001   1.4344
 UJB  F19   F   F     0  -0.304   3.6694  -1.0398   2.1275
 UJB  F20   F   F     0  -0.305   5.0954   0.3334   1.2902
 UJB  F21   F   F     0  -0.303   3.2837   1.0704   2.2055
 UJB  S22   S   S2    0   0.264  -0.2454  -1.6617  -1.9837
 UJB  C23   C   CR5   0  -0.125   0.9990  -2.1852  -0.9047
 UJB  C24   C   CR15  0  -0.232   1.7605  -3.1592  -1.4733
 UJB  C25   C   CR15  0  -0.132   1.3522  -3.5052  -2.7913
 UJB  C26   C   CR5   0  -0.244   0.2863  -2.7667  -3.1912
 UJB  CL    CL  CL    0  -0.076  -0.5227  -2.8545  -4.6923
 UJB  C28   C   CH2   0  -0.430   1.1854  -1.5283   0.4249
 UJB  C30   C   CH3   0  -0.673  -3.5313  -0.2130  -0.2913
 UJB  H1    H   HCH1  0   0.312   3.4987  -0.8081  -0.4747
 UJB  H111  H   HCH2  0   0.277   3.5239   2.1892  -0.0547
 UJB  H112  H   HCH2  0   0.294   4.3293   1.1994  -1.2631
 UJB  H71C  H   HCH2  0   0.269   2.1241   0.8023  -2.3790
 UJB  H72C  H   HCH2  0   0.295   2.4403   2.5281  -2.2104
 UJB  H281  H   HCH2  0   0.295   1.8970  -2.1135   1.0018
 UJB  H282  H   HCH2  0   0.310   0.2629  -1.5071   1.0017
 UJB  H9    H   HCR6  0   0.274  -1.8476   3.4601  -0.7279
 UJB  H12   H   HCH1  0   0.234  -3.8643   2.8532   0.1607
 UJB  H131  H   HCH2  0   0.200  -4.2944   2.4019   3.1342
 UJB  H132  H   HCH2  0   0.250  -5.4326   3.0099   1.9247
 UJB  H151  H   HCH2  0   0.221  -3.7345   0.1693   3.1440
 UJB  H152  H   HCH2  0   0.242  -4.5986  -0.9377   2.0650
 UJB  H16   H   HCH1  0   0.272  -2.2431  -0.4931   1.3994
 UJB  H301  H   HCH3  0   0.233  -4.3742   0.3959  -0.6194
 UJB  H302  H   HCH3  0   0.235  -2.7369  -0.1124  -1.0309
 UJB  H303  H   HCH3  0   0.235  -3.8511  -1.2559  -0.2952
 UJB  H24   H   HCR5  0   0.279   2.5952  -3.6215  -0.9646
 UJB  H25   H   HCR5  0   0.290   1.8294  -4.2556  -3.4038
 UJB  C29   C   CH3   0  -0.684  -2.8671   3.9286   1.7471
 UJB  H291  H   HCH3  0   0.233  -2.4564   3.7353   2.7389
 UJB  H292  H   HCH3  0   0.257  -2.0818   4.3668   1.1393
 UJB  H293  H   HCH3  0   0.241  -3.6529   4.6787   1.8491

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
 UJB  C1   N4    single    1.448  0.020  1.448
 UJB  C1   C11   single    1.531  0.020  1.531
 UJB  C1   C18   single    1.527  0.020  1.527
 UJB  C2   N3    single    1.354  0.020  1.354
 UJB  C2   N4    single    1.371  0.020  1.371
 UJB  C2   N5    double    1.297  0.020  1.297
 UJB  N3   C6    single    1.407  0.020  1.407
 UJB  N3   C7    single    1.456  0.020  1.456
 UJB  N4   C28   single    1.462  0.020  1.462
 UJB  N5   C8    single    1.356  0.020  1.356
 UJB  C6   C9    single    1.420  0.020  1.420
 UJB  C6   O10   double    1.226  0.020  1.226
 UJB  C7   C11   single    1.507  0.020  1.507
 UJB  C8   C9    double    1.376  0.020  1.376
 UJB  C8   N17   single    1.376  0.020  1.376
 UJB  C12  C13   single    1.533  0.020  1.533
 UJB  C12  N17   single    1.464  0.020  1.464
 UJB  C12  C29   single    1.527  0.020  1.527
 UJB  C13  O14   single    1.401  0.020  1.401
 UJB  O14  C15   single    1.407  0.020  1.407
 UJB  C15  C16   single    1.514  0.020  1.514
 UJB  C16  N17   single    1.474  0.020  1.474
 UJB  C16  C30   single    1.527  0.020  1.527
 UJB  C18  F19   single    1.339  0.020  1.339
 UJB  C18  F20   single    1.338  0.020  1.338
 UJB  C18  F21   single    1.337  0.020  1.337
 UJB  S22  C23   aromatic  1.728  0.020  1.728
 UJB  S22  C26   aromatic  1.721  0.020  1.721
 UJB  C23  C24   aromatic  1.361  0.020  1.361
 UJB  C23  C28   single    1.495  0.020  1.495
 UJB  C24  C25   aromatic  1.422  0.020  1.422
 UJB  C25  C26   aromatic  1.357  0.020  1.357
 UJB  C26  CL    single    1.707  0.020  1.707
 UJB  C1   H1    single    0.970  0.020  1.090
 UJB  C11  H111  single    0.970  0.020  1.090
 UJB  C11  H112  single    0.970  0.020  1.090
 UJB  C7   H71C  single    0.970  0.020  1.090
 UJB  C7   H72C  single    0.970  0.020  1.090
 UJB  C28  H281  single    0.970  0.020  1.090
 UJB  C28  H282  single    0.970  0.020  1.090
 UJB  C9   H9    single    0.930  0.020  1.080
 UJB  C12  H12   single    0.970  0.020  1.090
 UJB  C13  H131  single    0.970  0.020  1.090
 UJB  C13  H132  single    0.970  0.020  1.090
 UJB  C29  H291  single    0.970  0.020  1.090
 UJB  C29  H292  single    0.970  0.020  1.090
 UJB  C29  H293  single    0.970  0.020  1.090
 UJB  C15  H151  single    0.970  0.020  1.090
 UJB  C15  H152  single    0.970  0.020  1.090
 UJB  C16  H16   single    0.970  0.020  1.090
 UJB  C30  H301  single    0.970  0.020  1.090
 UJB  C30  H302  single    0.970  0.020  1.090
 UJB  C30  H303  single    0.970  0.020  1.090
 UJB  C24  H24   single    0.930  0.020  1.080
 UJB  C25  H25   single    0.930  0.020  1.080

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
 UJB  H1    C1   C18   107.75  3.000
 UJB  H1    C1   C11   108.66  3.000
 UJB  C18   C1   C11   109.65  3.000
 UJB  H1    C1   N4    108.65  3.000
 UJB  C18   C1   N4    109.41  3.000
 UJB  C11   C1   N4    112.60  3.000
 UJB  N5    C2   N4    118.56  3.000
 UJB  N5    C2   N3    123.80  3.000
 UJB  N4    C2   N3    117.60  3.000
 UJB  C7    N3   C6    120.40  3.000
 UJB  C7    N3   C2    118.11  3.000
 UJB  C6    N3   C2    121.03  3.000
 UJB  C28   N4   C2    117.31  3.000
 UJB  C28   N4   C1    118.26  3.000
 UJB  C2    N4   C1    122.98  3.000
 UJB  C8    N5   C2    118.74  3.000
 UJB  O10   C6   C9    125.96  3.000
 UJB  O10   C6   N3    119.51  3.000
 UJB  C9    C6   N3    114.49  3.000
 UJB  H72C  C7   H71C  108.03  3.000
 UJB  H72C  C7   C11   110.96  3.000
 UJB  H71C  C7   C11   111.69  3.000
 UJB  H72C  C7   N3    108.47  3.000
 UJB  H71C  C7   N3    109.23  3.000
 UJB  C11   C7   N3    108.40  3.000
 UJB  N17   C8   C9    124.28  3.000
 UJB  N17   C8   N5    114.29  3.000
 UJB  C9    C8   N5    121.43  3.000
 UJB  H9    C9   C8    122.40  3.000
 UJB  H9    C9   C6    116.98  3.000
 UJB  C8    C9   C6    120.49  3.000
 UJB  H112  C11  H111  107.48  3.000
 UJB  H112  C11  C7    110.30  3.000
 UJB  H111  C11  C7    108.19  3.000
 UJB  H112  C11  C1    109.62  3.000
 UJB  H111  C11  C1    112.04  3.000
 UJB  C7    C11  C1    109.20  3.000
 UJB  H12   C12  C29   109.54  3.000
 UJB  H12   C12  N17   110.77  3.000
 UJB  C29   C12  N17   112.40  3.000
 UJB  H12   C12  C13   108.60  3.000
 UJB  C29   C12  C13   105.25  3.000
 UJB  N17   C12  C13   110.08  3.000
 UJB  H132  C13  H131  107.60  3.000
 UJB  H132  C13  O14   107.84  3.000
 UJB  H131  C13  O14   109.75  3.000
 UJB  H132  C13  C12   108.19  3.000
 UJB  H131  C13  C12   108.47  3.000
 UJB  O14   C13  C12   114.76  3.000
 UJB  C15   O14  C13   109.07  3.000
 UJB  H152  C15  H151  107.87  3.000
 UJB  H152  C15  C16   109.63  3.000
 UJB  H151  C15  C16   110.08  3.000
 UJB  H152  C15  O14   107.97  3.000
 UJB  H151  C15  O14   110.51  3.000
 UJB  C16   C15  O14   110.72  3.000
 UJB  H16   C16  C30   108.84  3.000
 UJB  H16   C16  N17   107.27  3.000
 UJB  C30   C16  N17   111.86  3.000
 UJB  H16   C16  C15   107.33  3.000
 UJB  C30   C16  C15   111.51  3.000
 UJB  N17   C16  C15   109.81  3.000
 UJB  C16   N17  C12   116.82  3.000
 UJB  C16   N17  C8    114.30  3.000
 UJB  C12   N17  C8    119.34  3.000
 UJB  F21   C18  F20   107.64  3.000
 UJB  F21   C18  F19   106.65  3.000
 UJB  F20   C18  F19   106.80  3.000
 UJB  F21   C18  C1    111.58  3.000
 UJB  F20   C18  C1    110.77  3.000
 UJB  F19   C18  C1    113.08  3.000
 UJB  C26   S22  C23    91.21  3.000
 UJB  C28   C23  C24   128.06  3.000
 UJB  C28   C23  S22   120.80  3.000
 UJB  C24   C23  S22   111.03  3.000
 UJB  H24   C24  C25   123.61  3.000
 UJB  H24   C24  C23   122.78  3.000
 UJB  C25   C24  C23   113.61  3.000
 UJB  H25   C25  C26   123.93  3.000
 UJB  H25   C25  C24   124.59  3.000
 UJB  C26   C25  C24   111.48  3.000
 UJB  CL    C26  C25   127.10  3.000
 UJB  CL    C26  S22   120.23  3.000
 UJB  C25   C26  S22   112.66  3.000
 UJB  H282  C28  H281  106.51  3.000
 UJB  H282  C28  C23   111.98  3.000
 UJB  H281  C28  C23   108.49  3.000
 UJB  H282  C28  N4    108.71  3.000
 UJB  H281  C28  N4    110.13  3.000
 UJB  C23   C28  N4    110.93  3.000
 UJB  H303  C30  H302  107.42  3.000
 UJB  H303  C30  H301  107.83  3.000
 UJB  H302  C30  H301  107.92  3.000
 UJB  H303  C30  C16   110.11  3.000
 UJB  H302  C30  C16   111.29  3.000
 UJB  H301  C30  C16   112.08  3.000
 UJB  H293  C29  H292  107.21  3.000
 UJB  H293  C29  H291  107.94  3.000
 UJB  H292  C29  H291  107.95  3.000
 UJB  H293  C29  C12   109.28  3.000
 UJB  H292  C29  C12   114.05  3.000
 UJB  H291  C29  C12   110.20  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
 UJB  CONST_01  C25   C24  C23  S22    0.00   0.0  0
 UJB  CONST_02  C24   C25  C26  S22    0.00   0.0  0
 UJB  CONST_03  C25   C26  S22  C23    0.00   0.0  0
 UJB  CONST_04  C26   C25  C24  C23    0.00   0.0  0
 UJB  CONST_05  C26   S22  C23  C24    0.00   0.0  0
 UJB  CONST_08  C9    C6   N3   C2     0.00   0.0  0
 UJB  CONST_09  C9    C8   N5   C2     0.00   0.0  0
 UJB  CONST_10  N17   C8   N5   C2   180.00   0.0  0
 UJB  CONST_11  C8    N5   C2   N3     0.00   0.0  0
 UJB  CONST_12  C6    N3   C2   N4   180.00   0.0  0
 UJB  CONST_13  C7    N3   C2   N4     0.00   0.0  0
 UJB  CONST_14  C8    N5   C2   N4   180.00   0.0  0
 UJB  CONST_15  C6    N3   C2   N5     0.00   0.0  0
 UJB  CONST_16  C7    N3   C2   N5   180.00   0.0  0
 UJB  CONST_17  C12   N17  C8   N5   180.00   0.0  0
 UJB  CONST_19  C9    C6   N3   C7   180.00   0.0  0
 UJB  CONST_20  C12   N17  C8   C9     0.00   0.0  0
 UJB  CONST_22  CL    C26  S22  C23  180.00   0.0  0
 UJB  CONST_23  CL    C26  C25  C24  180.00   0.0  0
 UJB  CONST_24  C28   C23  C24  C25  180.00   0.0  0
 UJB  CONST_25  C28   C23  S22  C26  180.00   0.0  0
 UJB  CONST_26  O10   C6   N3   C2   180.00   0.0  0
 UJB  CONST_29  O10   C6   N3   C7     0.00   0.0  0
 UJB  CONST_30  H24   C24  C23  S22  180.00   0.0  0
 UJB  CONST_31  H25   C25  C26  S22  180.00   0.0  0
 UJB  Var_01    N3    C7   C11  C1    59.49  30.0  1
 UJB  Var_02    C11   C7   N3   C2   -50.42  30.0  1
 UJB  Var_03    C16   C15  O14  C13  -64.93  30.0  1
 UJB  Var_04    C23   C28  N4   C1   -82.85  30.0  3
 UJB  Var_05    S22   C23  C28  N4   -68.44  30.0  3
 UJB  Var_06    H131  C13  O14  C15  -62.12  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
 UJB  chir_01  C1   N4   C11  C18  negativ
 UJB  chir_02  C12  C13  N17  C29  positiv
 UJB  chir_03  C16  N17  C30  C15  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
 UJB  plan-1  S22  0.020
 UJB  plan-1  C23  0.020
 UJB  plan-1  C24  0.020
 UJB  plan-1  C25  0.020
 UJB  plan-1  C26  0.020
 UJB  plan-1  CL   0.020
 UJB  plan-1  C28  0.020
 UJB  plan-1  H24  0.020
 UJB  plan-1  H25  0.020
 UJB  plan-2  C1   0.020
 UJB  plan-2  C2   0.020
 UJB  plan-2  N3   0.020
 UJB  plan-2  N4   0.020
 UJB  plan-2  N5   0.020
 UJB  plan-2  C6   0.020
 UJB  plan-2  C7   0.020
 UJB  plan-2  C8   0.020
 UJB  plan-2  C9   0.020
 UJB  plan-2  O10  0.020
 UJB  plan-2  C12  0.020
 UJB  plan-2  C16  0.020
 UJB  plan-2  N17  0.020
 UJB  plan-2  C28  0.020
 UJB  plan-2  H9   0.020

