# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 07:42:21 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 2,6-dioxo-5-{2-[4-(trifluoromethoxy)phenyl]ethyl}-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=C(CCc2ccc(OC(F)(F)F)cc2)C(=O)NC(=O)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
 W74  W74  '2,6-dioxo-5-{2-[4-(trifluoromethoxy)phenyl]ethyl}-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  34  24  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_W74
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
 W74  OAJ  O  OC    -1  -0.586  -3.9701  -3.1511   0.1521
 W74  CAI  C  C      0   0.414  -3.0890  -2.2726   0.1644
 W74  OAK  O  O      0  -0.538  -1.8621  -2.4191   0.2005
 W74  C4   C  CR6    0   0.203  -3.6391  -0.8329   0.1058
 W74  N3   N  NR16   0  -0.707  -4.9778  -0.8142  -0.1753
 W74  C2   C  CR6    0   0.655  -5.7372   0.3012  -0.3199
 W74  O2   O  O      0  -0.493  -6.9278   0.2844  -0.5724
 W74  N1   N  NR16   0  -0.715  -5.0259   1.4609  -0.1568
 W74  C6   C  CR6    0   0.564  -3.6798   1.5760   0.1377
 W74  O6   O  O      0  -0.466  -3.1798   2.6841   0.2443
 W74  C5   C  CR6    0  -0.159  -2.9544   0.3218   0.2936
 W74  CAL  C  CH2    0  -0.478  -1.4925   0.4311   0.6071
 W74  CAM  C  CH2    0  -0.493  -0.6390   0.5593  -0.6625
 W74  CAN  C  CR6    0   0.124   0.8301   0.5482  -0.3528
 W74  CAO  C  CR16   0  -0.321   1.5863   1.7158  -0.3632
 W74  CAP  C  CR16   0  -0.288   2.9403   1.7004  -0.0536
 W74  CAQ  C  CR6    0   0.289   3.5367   0.4963   0.2723
 W74  OAT  O  O2     0  -0.524   4.8826   0.4764   0.6356
 W74  CAU  C  CT     0   1.070   5.7838   0.2867  -0.3331
 W74  FAW  F  F      0  -0.279   6.9845   0.2872   0.2255
 W74  FAX  F  F      0  -0.300   5.6211  -0.8731  -0.9740
 W74  FAV  F  F      0  -0.301   5.7556   1.2445  -1.2629
 W74  CAR  C  CR16   0  -0.296   2.8111  -0.6831   0.3035
 W74  CAS  C  CR16   0  -0.314   1.4614  -0.6469  -0.0082
 W74  H2   H  HNR6   0   0.419  -5.5424   2.3232  -0.2749
 W74  H4   H  HCH2   0   0.240  -1.3279   1.3086   1.2357
 W74  H5   H  HCH2   0   0.258  -1.1640  -0.4357   1.1716
 W74  H6   H  HCH2   0   0.249  -0.8758  -0.2713  -1.3295
 W74  H7   H  HCH2   0   0.242  -0.9029   1.4792  -1.1874
 W74  H8   H  HCR6   0   0.255   1.1177   2.6572  -0.6226
 W74  H9   H  HCR6   0   0.280   3.5130   2.6187  -0.0547
 W74  H10  H  HCR6   0   0.293   3.2859  -1.6155   0.5794
 W74  H11  H  HCR6   0   0.280   0.8848  -1.5641   0.0151
 W74  H12  H  HNR6   0   0.420  -5.4142  -1.7249  -0.2664

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
 W74  O2   C2   double    1.217  0.020  1.217
 W74  C2   N3   single    1.357  0.020  1.357
 W74  C2   N1   single    1.370  0.020  1.370
 W74  N3   C4   single    1.368  0.020  1.368
 W74  N1   C6   single    1.383  0.020  1.383
 W74  CAI  C4   single    1.542  0.020  1.542
 W74  CAI  OAK  deloc     1.236  0.020  1.236
 W74  CAI  OAJ  deloc     1.244  0.020  1.244
 W74  C4   C5   double    1.356  0.020  1.356
 W74  C6   C5   single    1.457  0.020  1.457
 W74  C6   O6   double    1.220  0.020  1.220
 W74  C5   CAL  single    1.499  0.020  1.499
 W74  FAX  CAU  single    1.335  0.020  1.335
 W74  CAL  CAM  single    1.535  0.020  1.535
 W74  CAU  FAV  single    1.335  0.020  1.335
 W74  CAU  FAW  single    1.324  0.020  1.324
 W74  CAU  OAT  single    1.337  0.020  1.337
 W74  CAO  CAP  aromatic  1.389  0.020  1.389
 W74  CAO  CAN  aromatic  1.391  0.020  1.391
 W74  CAP  CAQ  aromatic  1.383  0.020  1.383
 W74  CAM  CAN  single    1.501  0.020  1.501
 W74  CAN  CAS  aromatic  1.395  0.020  1.395
 W74  CAQ  OAT  single    1.394  0.020  1.394
 W74  CAQ  CAR  aromatic  1.385  0.020  1.385
 W74  CAS  CAR  aromatic  1.386  0.020  1.386
 W74  N1   H2   single    0.860  0.020  1.020
 W74  CAL  H4   single    0.970  0.020  1.090
 W74  CAL  H5   single    0.970  0.020  1.090
 W74  CAM  H6   single    0.970  0.020  1.090
 W74  CAM  H7   single    0.970  0.020  1.090
 W74  CAO  H8   single    0.930  0.020  1.080
 W74  CAP  H9   single    0.930  0.020  1.080
 W74  CAR  H10  single    0.930  0.020  1.080
 W74  CAS  H11  single    0.930  0.020  1.080
 W74  N3   H12  single    0.860  0.020  1.020

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
 W74  C4   CAI  OAK  117.76  3.000
 W74  OAK  CAI  OAJ  128.27  3.000
 W74  C4   CAI  OAJ  113.96  3.000
 W74  C5   C4   N3   120.74  3.000
 W74  C5   C4   CAI  127.57  3.000
 W74  N3   C4   CAI  111.69  3.000
 W74  H12  N3   C2   119.20  3.000
 W74  H12  N3   C4   115.29  3.000
 W74  C2   N3   C4   125.50  3.000
 W74  N1   C2   O2   122.97  3.000
 W74  N1   C2   N3   113.11  3.000
 W74  O2   C2   N3   123.92  3.000
 W74  H2   N1   C6   116.79  3.000
 W74  H2   N1   C2   116.25  3.000
 W74  C6   N1   C2   126.95  3.000
 W74  C5   C6   O6   124.62  3.000
 W74  O6   C6   N1   119.54  3.000
 W74  C5   C6   N1   115.84  3.000
 W74  CAL  C5   C6   116.43  3.000
 W74  CAL  C5   C4   125.71  3.000
 W74  C6   C5   C4   117.83  3.000
 W74  H5   CAL  H4   107.27  3.000
 W74  H5   CAL  CAM  109.18  3.000
 W74  H4   CAL  CAM  108.97  3.000
 W74  H5   CAL  C5   110.23  3.000
 W74  H4   CAL  C5   109.03  3.000
 W74  CAM  CAL  C5   112.04  3.000
 W74  H7   CAM  H6   107.16  3.000
 W74  H7   CAM  CAN  110.00  3.000
 W74  H6   CAM  CAN  109.44  3.000
 W74  H7   CAM  CAL  109.49  3.000
 W74  H6   CAM  CAL  108.73  3.000
 W74  CAN  CAM  CAL  111.89  3.000
 W74  CAS  CAN  CAO  118.36  3.000
 W74  CAS  CAN  CAM  120.01  3.000
 W74  CAO  CAN  CAM  121.61  3.000
 W74  H8   CAO  CAP  119.00  3.000
 W74  H8   CAO  CAN  119.74  3.000
 W74  CAP  CAO  CAN  121.26  3.000
 W74  H9   CAP  CAQ  120.72  3.000
 W74  H9   CAP  CAO  120.41  3.000
 W74  CAQ  CAP  CAO  118.86  3.000
 W74  CAR  CAQ  OAT  119.19  3.000
 W74  CAR  CAQ  CAP  121.39  3.000
 W74  OAT  CAQ  CAP  119.36  3.000
 W74  CAU  OAT  CAQ  117.65  3.000
 W74  FAV  CAU  FAX  106.64  3.000
 W74  FAV  CAU  FAW  108.22  3.000
 W74  FAX  CAU  FAW  108.26  3.000
 W74  FAW  CAU  OAT  107.79  3.000
 W74  FAV  CAU  OAT  112.87  3.000
 W74  FAX  CAU  OAT  112.90  3.000
 W74  H10  CAR  CAS  120.48  3.000
 W74  H10  CAR  CAQ  120.63  3.000
 W74  CAS  CAR  CAQ  118.88  3.000
 W74  H11  CAS  CAR  119.42  3.000
 W74  H11  CAS  CAN  119.33  3.000
 W74  CAR  CAS  CAN  121.25  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
 W74  CONST_01  CAQ  CAP  CAO  CAN     0.00   0.0  0
 W74  CONST_02  CAQ  CAR  CAS  CAN     0.00   0.0  0
 W74  CONST_03  CAR  CAQ  CAP  CAO     0.00   0.0  0
 W74  CONST_04  CAR  CAS  CAN  CAO     0.00   0.0  0
 W74  CONST_05  CAS  CAN  CAO  CAP     0.00   0.0  0
 W74  CONST_06  CAS  CAR  CAQ  CAP     0.00   0.0  0
 W74  CONST_07  N1   C2   N3   C4      0.00   0.0  0
 W74  CONST_08  C6   N1   C2   N3      0.00   0.0  0
 W74  CONST_09  C5   C6   N1   C2      0.00   0.0  0
 W74  CONST_10  CAP  CAO  CAN  CAM   180.00   0.0  0
 W74  CONST_11  CAR  CAS  CAN  CAM   180.00   0.0  0
 W74  CONST_12  OAT  CAQ  CAP  CAO   180.00   0.0  0
 W74  CONST_13  CAS  CAR  CAQ  OAT   180.00   0.0  0
 W74  CONST_14  O2   C2   N3   C4    180.00   0.0  0
 W74  CONST_15  O6   C6   N1   C2    180.00   0.0  0
 W74  CONST_16  C6   N1   C2   O2    180.00   0.0  0
 W74  CONST_17  H9   CAP  CAO  CAN   180.00   0.0  0
 W74  CONST_18  H10  CAR  CAS  CAN   180.00   0.0  0
 W74  CONST_19  H11  CAS  CAN  CAO   180.00   0.0  0
 W74  CONST_20  H8   CAO  CAP  CAQ   180.00   0.0  0
 W74  CONST_21  H2   N1   C2   N3    180.00   0.0  0
 W74  CONST_22  H12  N3   C2   N1    180.00   0.0  0
 W74  Var_01    N3   C4   CAI  OAJ   -10.30  30.0  2
 W74  Var_02    CAM  CAL  C5   C4     91.39  30.0  3
 W74  Var_03    CAN  CAM  CAL  C5   -175.03  30.0  3
 W74  Var_04    CAO  CAN  CAM  CAL  -103.40  30.0  2
 W74  Var_05    CAR  CAQ  OAT  CAU    91.65  30.0  3
 W74  Var_06    FAX  CAU  OAT  CAQ   -59.76  30.0  3

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
 W74  plan-1  CAI  0.020
 W74  plan-1  C4   0.020
 W74  plan-1  N3   0.020
 W74  plan-1  C2   0.020
 W74  plan-1  O2   0.020
 W74  plan-1  N1   0.020
 W74  plan-1  C6   0.020
 W74  plan-1  O6   0.020
 W74  plan-1  C5   0.020
 W74  plan-1  CAL  0.020
 W74  plan-1  H2   0.020
 W74  plan-1  H12  0.020
 W74  plan-2  CAM  0.020
 W74  plan-2  CAN  0.020
 W74  plan-2  CAO  0.020
 W74  plan-2  CAP  0.020
 W74  plan-2  CAQ  0.020
 W74  plan-2  OAT  0.020
 W74  plan-2  CAR  0.020
 W74  plan-2  CAS  0.020
 W74  plan-2  H8   0.020
 W74  plan-2  H9   0.020
 W74  plan-2  H10  0.020
 W74  plan-2  H11  0.020
 W74  plan-3  OAJ  0.020
 W74  plan-3  CAI  0.020
 W74  plan-3  OAK  0.020
 W74  plan-3  C4   0.020

