# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 03:36:22 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (8S,9aS)-9-[(5-chloropyridin-3-yl)methyl]-2-[(3R)-3-methylmorpholin-4-yl]-8-(trifluoromethyl)-3,6,7,8,9,9a-hexahydro-4H-pyrimido[1,2-a]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1COCCN1C2=N[C@@H]3N(Cc4cncc(Cl)c4)[C@@H](CCN3C(=O)C2)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
 1TT  1TT  (8S,9aS)-9-[(5-chloropyridin-3-yl)methyl]-2-[(3R)-3-methylmorpholin-4-yl]-8-(trifluoromethyl)-3,6,7,8,9,9a-hexahydro-4H-pyrimido[1,2-a]pyrimidin-4-one  ligand  53  30  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1TT
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
 1TT  C1   C   C     0   0.575  -2.5099   2.0926  -1.5314
 1TT  C2   C   CH2   0  -0.722  -3.2219   0.7754  -1.7156
 1TT  C3   C   C     0   0.478  -2.7405  -0.2043  -0.6752
 1TT  C8   C   CH1   0  -0.343   1.1835   1.5774   0.1535
 1TT  C9   C   CH2   0  -0.470   0.9727   2.9293  -0.5121
 1TT  C10  C   CH2   0  -0.280  -0.4762   3.1841  -0.8843
 1TT  C13  C   CT    0   1.022   0.6484   1.4996   1.5808
 1TT  C20  C   CH2   0  -0.172  -4.3024  -3.0605   1.1367
 1TT  C21  C   CH1   0  -0.094  -3.1356  -2.1965   0.6581
 1TT  C24  C   CR16  0  -0.138   3.5369  -1.2973   0.2076
 1TT  C30  C   CH3   0  -0.698  -2.2500  -3.1010  -0.1902
 1TT  N4   N   N     0  -0.408  -1.5012  -0.2592  -0.4073
 1TT  N5   N   NT    0  -0.518  -1.1957   1.9691  -1.2542
 1TT  C6   C   CH1   0   0.280  -0.6619   0.6080  -1.2017
 1TT  N7   N   NT    0  -0.472   0.7029   0.5801  -0.7615
 1TT  N11  N   NT    0  -0.497  -3.6625  -1.0542  -0.0989
 1TT  O12  O   O     0  -0.490  -3.0789   3.1708  -1.6059
 1TT  F14  F   F     0  -0.299  -0.6702   1.6982   1.6831
 1TT  F15  F   F     0  -0.308   0.9056   0.3088   2.1423
 1TT  F16  F   F     0  -0.313   1.2369   2.4247   2.3585
 1TT  C17  C   CH2   0  -0.322  -4.7758  -0.3759   0.5711
 1TT  C18  C   CH2   0  -0.194  -5.8415  -1.3611   0.9901
 1TT  O19  O   O2    0  -0.480  -5.2994  -2.3531   1.8274
 1TT  C23  C   CR6   0  -0.024   2.7476  -0.7544  -0.7938
 1TT  C25  C   CR6   0  -0.102   4.9131  -1.2728   0.0497
 1TT  C26  C   CR16  0  -0.039   5.4630  -0.7069  -1.0892
 1TT  N27  N   N     0  -0.394   4.7078  -0.1813  -2.0445
 1TT  C28  C   CR16  0  -0.062   3.3919  -0.2035  -1.8991
 1TT  CL1  CL  CL    0  -0.110   5.9449  -1.9348   1.2645
 1TT  H1   H   HCH2  0   0.300  -4.2958   0.9329  -1.7469
 1TT  H2   H   HCH2  0   0.319  -2.9362   0.3536  -2.6894
 1TT  H3   H   HCH1  0   0.307   2.2640   1.4357   0.2555
 1TT  H4   H   HCH2  0   0.270   1.3298   3.7543   0.1038
 1TT  H5   H   HCH2  0   0.267   1.5963   2.9147  -1.4060
 1TT  H6   H   HCH2  0   0.245  -0.9993   3.6527  -0.0490
 1TT  H7   H   HCH2  0   0.259  -0.5142   3.8926  -1.7124
 1TT  H8   H   HCH2  0   0.199  -4.7381  -3.5747   0.2658
 1TT  H9   H   HCH2  0   0.245  -3.9135  -3.8243   1.8121
 1TT  H10  H   HCH1  0   0.230  -2.5712  -1.8397   1.5310
 1TT  H11  H   HCH2  0   0.248   0.9298  -1.3265   0.1802
 1TT  H12  H   HCH2  0   0.269   0.8534  -1.3092  -1.5627
 1TT  H14  H   HCH3  0   0.265  -1.2947  -2.6439  -0.4224
 1TT  H15  H   HCH3  0   0.234  -2.0537  -4.0303   0.3471
 1TT  H16  H   HCH3  0   0.225  -2.7504  -3.3561  -1.1258
 1TT  H17  H   HCH1  0   0.261  -0.6527   0.2101  -2.2296
 1TT  H19  H   HCH2  0   0.231  -4.4172   0.1644   1.4578
 1TT  H20  H   HCH2  0   0.260  -5.2296   0.3574  -0.0935
 1TT  H21  H   HCH2  0   0.245  -6.6189  -0.8378   1.5477
 1TT  H22  H   HCH2  0   0.209  -6.3047  -1.8127   0.1011
 1TT  H23  H   HCR6  0   0.286   6.5375  -0.6805  -1.2293
 1TT  H24  H   HCR6  0   0.269   2.8077   0.2386  -2.6994
 1TT  C22  C   CH2   0  -0.340   1.2473  -0.7623  -0.7015
 1TT  H13  H   HCR6  0   0.291   3.0868  -1.7312   1.0915

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
 1TT  F16  C13  single    1.344  0.020  1.344
 1TT  F15  C13  single    1.341  0.020  1.341
 1TT  F14  C13  single    1.337  0.020  1.337
 1TT  C13  C8   single    1.526  0.020  1.526
 1TT  C8   C9   single    1.522  0.020  1.522
 1TT  C8   N7   single    1.436  0.020  1.436
 1TT  C30  C21  single    1.524  0.020  1.524
 1TT  C10  C9   single    1.517  0.020  1.517
 1TT  C10  N5   single    1.460  0.020  1.460
 1TT  C22  N7   single    1.450  0.020  1.450
 1TT  C22  C23  single    1.503  0.020  1.503
 1TT  N7   C6   single    1.434  0.020  1.434
 1TT  N5   C6   single    1.463  0.020  1.463
 1TT  N5   C1   single    1.349  0.020  1.349
 1TT  O12  C1   double    1.221  0.020  1.221
 1TT  C6   N4   single    1.445  0.020  1.445
 1TT  C1   C2   single    1.509  0.020  1.509
 1TT  N4   C3   double    1.269  0.020  1.269
 1TT  C2   C3   single    1.508  0.020  1.508
 1TT  C3   N11  single    1.380  0.020  1.380
 1TT  C21  N11  single    1.468  0.020  1.468
 1TT  C21  C20  single    1.529  0.020  1.529
 1TT  N11  C17  single    1.466  0.020  1.466
 1TT  C17  C18  single    1.511  0.020  1.511
 1TT  C23  C24  aromatic  1.386  0.020  1.386
 1TT  C23  C28  aromatic  1.393  0.020  1.393
 1TT  C24  C25  aromatic  1.385  0.020  1.385
 1TT  O19  C20  single    1.404  0.020  1.404
 1TT  O19  C18  single    1.407  0.020  1.407
 1TT  C28  N27  aromatic  1.324  0.020  1.324
 1TT  C25  CL1  single    1.726  0.020  1.726
 1TT  C25  C26  aromatic  1.386  0.020  1.386
 1TT  N27  C26  aromatic  1.326  0.020  1.326
 1TT  C2   H1   single    0.970  0.020  1.090
 1TT  C2   H2   single    0.970  0.020  1.090
 1TT  C8   H3   single    0.970  0.020  1.090
 1TT  C9   H4   single    0.970  0.020  1.090
 1TT  C9   H5   single    0.970  0.020  1.090
 1TT  C10  H6   single    0.970  0.020  1.090
 1TT  C10  H7   single    0.970  0.020  1.090
 1TT  C20  H8   single    0.970  0.020  1.090
 1TT  C20  H9   single    0.970  0.020  1.090
 1TT  C21  H10  single    0.970  0.020  1.090
 1TT  C22  H11  single    0.970  0.020  1.090
 1TT  C22  H12  single    0.970  0.020  1.090
 1TT  C24  H13  single    0.930  0.020  1.080
 1TT  C30  H14  single    0.970  0.020  1.090
 1TT  C30  H15  single    0.970  0.020  1.090
 1TT  C30  H16  single    0.970  0.020  1.090
 1TT  C6   H17  single    0.970  0.020  1.090
 1TT  C17  H19  single    0.970  0.020  1.090
 1TT  C17  H20  single    0.970  0.020  1.090
 1TT  C18  H21  single    0.970  0.020  1.090
 1TT  C18  H22  single    0.970  0.020  1.090
 1TT  C26  H23  single    0.930  0.020  1.080
 1TT  C28  H24  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
 1TT  O12  C1   N5   123.18  3.000
 1TT  O12  C1   C2   122.92  3.000
 1TT  N5   C1   C2   113.89  3.000
 1TT  H2   C2   H1   106.69  3.000
 1TT  H2   C2   C3   106.20  3.000
 1TT  H1   C2   C3   115.46  3.000
 1TT  H2   C2   C1   108.70  3.000
 1TT  H1   C2   C1   110.10  3.000
 1TT  C3   C2   C1   109.41  3.000
 1TT  N11  C3   N4   122.52  3.000
 1TT  N11  C3   C2   118.35  3.000
 1TT  N4   C3   C2   119.04  3.000
 1TT  H3   C8   N7   107.45  3.000
 1TT  H3   C8   C13  104.62  3.000
 1TT  N7   C8   C13  116.30  3.000
 1TT  H3   C8   C9   107.01  3.000
 1TT  N7   C8   C9   106.97  3.000
 1TT  C13  C8   C9   113.94  3.000
 1TT  H5   C9   H4   106.63  3.000
 1TT  H5   C9   C10  110.33  3.000
 1TT  H4   C9   C10  108.93  3.000
 1TT  H5   C9   C8   105.51  3.000
 1TT  H4   C9   C8   112.33  3.000
 1TT  C10  C9   C8   112.88  3.000
 1TT  H7   C10  H6   106.60  3.000
 1TT  H7   C10  N5   109.34  3.000
 1TT  H6   C10  N5   108.37  3.000
 1TT  H7   C10  C9   109.18  3.000
 1TT  H6   C10  C9   110.00  3.000
 1TT  N5   C10  C9   113.14  3.000
 1TT  F16  C13  F15  106.55  3.000
 1TT  F15  C13  F14  106.78  3.000
 1TT  F16  C13  F14  106.57  3.000
 1TT  F14  C13  C8   114.18  3.000
 1TT  F15  C13  C8   111.68  3.000
 1TT  F16  C13  C8   110.64  3.000
 1TT  H9   C20  H8   107.67  3.000
 1TT  H9   C20  O19  107.53  3.000
 1TT  H8   C20  O19  110.08  3.000
 1TT  H9   C20  C21  108.50  3.000
 1TT  H8   C20  C21  108.56  3.000
 1TT  O19  C20  C21  114.28  3.000
 1TT  H10  C21  N11  109.95  3.000
 1TT  H10  C21  C30  109.66  3.000
 1TT  N11  C21  C30  112.54  3.000
 1TT  H10  C21  C20  109.08  3.000
 1TT  N11  C21  C20  109.11  3.000
 1TT  C30  C21  C20  106.40  3.000
 1TT  H13  C24  C25  120.87  3.000
 1TT  H13  C24  C23  120.67  3.000
 1TT  C25  C24  C23  118.46  3.000
 1TT  H16  C30  H15  107.79  3.000
 1TT  H16  C30  H14  108.60  3.000
 1TT  H15  C30  H14  107.82  3.000
 1TT  H16  C30  C21  110.46  3.000
 1TT  H15  C30  C21  109.63  3.000
 1TT  H14  C30  C21  112.40  3.000
 1TT  C6   N4   C3   115.17  3.000
 1TT  C6   N5   C10  125.83  3.000
 1TT  C6   N5   C1   116.62  3.000
 1TT  C10  N5   C1   117.14  3.000
 1TT  H17  C6   N7   105.74  3.000
 1TT  H17  C6   N5   107.78  3.000
 1TT  N7   C6   N5   112.11  3.000
 1TT  H17  C6   N4   107.51  3.000
 1TT  N5   C6   N4   111.48  3.000
 1TT  N7   C6   N4   111.86  3.000
 1TT  C6   N7   C22  112.83  3.000
 1TT  C6   N7   C8   120.03  3.000
 1TT  C22  N7   C8   119.40  3.000
 1TT  C17  N11  C21  113.38  3.000
 1TT  C17  N11  C3   114.42  3.000
 1TT  C21  N11  C3   117.05  3.000
 1TT  H20  C17  H19  107.31  3.000
 1TT  H20  C17  C18  108.33  3.000
 1TT  H19  C17  C18  109.10  3.000
 1TT  H20  C17  N11  110.44  3.000
 1TT  H19  C17  N11  110.40  3.000
 1TT  C18  C17  N11  111.15  3.000
 1TT  H22  C18  H21  108.07  3.000
 1TT  H22  C18  O19  110.74  3.000
 1TT  H21  C18  O19  107.99  3.000
 1TT  H22  C18  C17  109.93  3.000
 1TT  H21  C18  C17  109.37  3.000
 1TT  O19  C18  C17  110.68  3.000
 1TT  C18  O19  C20  109.64  3.000
 1TT  C28  C23  C24  117.70  3.000
 1TT  C28  C23  C22  120.83  3.000
 1TT  C24  C23  C22  121.47  3.000
 1TT  CL1  C25  C26  119.87  3.000
 1TT  C26  C25  C24  119.68  3.000
 1TT  CL1  C25  C24  120.46  3.000
 1TT  H23  C26  N27  117.49  3.000
 1TT  H23  C26  C25  120.64  3.000
 1TT  N27  C26  C25  121.87  3.000
 1TT  C28  N27  C26  118.69  3.000
 1TT  H24  C28  N27  116.57  3.000
 1TT  H24  C28  C23  119.83  3.000
 1TT  N27  C28  C23  123.61  3.000
 1TT  H12  C22  H11  105.79  3.000
 1TT  H12  C22  C23  108.29  3.000
 1TT  H11  C22  C23  110.00  3.000
 1TT  H12  C22  N7   107.17  3.000
 1TT  H11  C22  N7   113.70  3.000
 1TT  C23  C22  N7   111.56  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
 1TT  CONST_01  N27  C28  C23  C24    0.00   0.0  0
 1TT  CONST_02  N27  C26  C25  C24    0.00   0.0  0
 1TT  CONST_03  C26  C25  C24  C23    0.00   0.0  0
 1TT  CONST_04  C26  N27  C28  C23    0.00   0.0  0
 1TT  CONST_05  C28  C23  C24  C25    0.00   0.0  0
 1TT  CONST_06  C28  N27  C26  C25    0.00   0.0  0
 1TT  CONST_07  C10  N5   C1   C2   180.00   0.0  0
 1TT  CONST_08  C6   N5   C1   C2     0.00   0.0  0
 1TT  CONST_09  C6   N4   C3   C2     0.00   0.0  0
 1TT  CONST_10  C21  N11  C3   C2   180.00   0.0  0
 1TT  CONST_12  N4   C3   N11  C21    0.00   0.0  0
 1TT  CONST_14  N11  C3   N4   C6   180.00   0.0  0
 1TT  CONST_15  C25  C24  C23  C22  180.00   0.0  0
 1TT  CONST_16  N27  C28  C23  C22  180.00   0.0  0
 1TT  CONST_17  CL1  C25  C24  C23  180.00   0.0  0
 1TT  CONST_18  CL1  C25  C26  N27  180.00   0.0  0
 1TT  CONST_19  O12  C1   N5   C10    0.00   0.0  0
 1TT  CONST_20  O12  C1   N5   C6   180.00   0.0  0
 1TT  CONST_21  H24  C28  C23  C24  180.00   0.0  0
 1TT  CONST_22  H23  C26  C25  C24  180.00   0.0  0
 1TT  CONST_23  H13  C24  C25  C26  180.00   0.0  0
 1TT  Var_01    C9   C10  N5   C1   176.57  30.0  1
 1TT  Var_02    N4   C3   C2   C1   -42.26  30.0  1
 1TT  Var_03    N5   C1   C2   C3    41.39  30.0  1
 1TT  Var_04    C18  C17  N11  C3   171.39  30.0  1
 1TT  Var_05    N5   C10  C9   C8   -32.66  30.0  1
 1TT  Var_06    C17  C18  O19  C20  -60.98  30.0  1
 1TT  Var_07    O19  C18  C17  N11   57.07  30.0  1
 1TT  Var_08    C23  C22  N7   C8   -53.77  30.0  1
 1TT  Var_09    N7   C22  C23  C24  121.52  30.0  2
 1TT  Var_10    H8   C20  O19  C18  -62.43  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
 1TT  chir_01  C8   C13  C9   N7   positiv
 1TT  chir_02  C21  C30  N11  C20  negativ
 1TT  chir_03  C6   N4   N5   N7   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
 1TT  plan-1  C24  0.020
 1TT  plan-1  C23  0.020
 1TT  plan-1  C25  0.020
 1TT  plan-1  C26  0.020
 1TT  plan-1  N27  0.020
 1TT  plan-1  C28  0.020
 1TT  plan-1  CL1  0.020
 1TT  plan-1  H23  0.020
 1TT  plan-1  H24  0.020
 1TT  plan-1  C22  0.020
 1TT  plan-1  H13  0.020
 1TT  plan-2  C1   0.020
 1TT  plan-2  C2   0.020
 1TT  plan-2  C10  0.020
 1TT  plan-2  N5   0.020
 1TT  plan-2  C6   0.020
 1TT  plan-2  O12  0.020
 1TT  plan-3  C2   0.020
 1TT  plan-3  C3   0.020
 1TT  plan-3  C21  0.020
 1TT  plan-3  N4   0.020
 1TT  plan-3  C6   0.020
 1TT  plan-3  N11  0.020
 1TT  plan-3  C17  0.020

