# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 11:50:40 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 2,6-dioxo-5-{2-[3-(trifluoromethyl)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(CCc2cccc(c2)C(F)(F)F)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
 WRO  WRO  '2,6-dioxo-5-{2-[3-(trifluoromethyl)phenyl]ethyl}-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  33  23  .  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_WRO
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
 WRO  OAA  O  O      0  -0.541   2.1008   2.6336   0.0422
 WRO  CAP  C  C      0   0.417   3.2162   2.1007   0.0342
 WRO  OAD  O  OC    -1  -0.584   4.3315   2.6477  -0.0386
 WRO  CAS  C  CR6    0   0.203   3.2759   0.5609   0.1025
 WRO  NAN  N  NR16   0  -0.706   4.5453   0.0948  -0.1019
 WRO  CAU  C  CR6    0   0.656   4.9122  -1.2119  -0.1203
 WRO  OAB  O  O      0  -0.492   6.0537  -1.5939  -0.2993
 WRO  NAO  N  NR16   0  -0.714   3.8614  -2.0681   0.0790
 WRO  CAV  C  CR6    0   0.563   2.5394  -1.7255   0.2939
 WRO  OAC  O  O      0  -0.466   1.7061  -2.6055   0.4378
 WRO  CAT  C  CR6    0  -0.159   2.2502  -0.2970   0.3259
 WRO  CAM  C  CH2    0  -0.477   0.8211   0.0890   0.5633
 WRO  CAL  C  CH2    0  -0.497   0.0304   0.2151  -0.7457
 WRO  CAQ  C  C      0   0.142  -1.3767   0.6738  -0.4974
 WRO  CAK  C  C1     0  -0.351  -2.4270  -0.2338  -0.4298
 WRO  CAR  C  C      0  -0.175  -3.7234   0.1982  -0.1683
 WRO  CAW  C  CT     0   1.049  -4.8252  -0.8065  -0.0495
 WRO  FAF  F  F      0  -0.308  -6.0232  -0.2912  -0.3491
 WRO  FAG  F  F      0  -0.309  -4.6424  -1.8617  -0.8530
 WRO  FAE  F  F      0  -0.317  -4.9175  -1.2911   1.2003
 WRO  CAJ  C  C1     0  -0.298  -3.9854   1.5468   0.0367
 WRO  CAH  C  C1     0  -0.226  -2.9402   2.4574  -0.0281
 WRO  CAI  C  C1     0  -0.296  -1.6499   2.0247  -0.2900
 WRO  H2   H  HNR6   0   0.420   4.0786  -3.0567   0.0601
 WRO  H4   H  HCH2   0   0.242   0.3480  -0.6684   1.1904
 WRO  H5   H  HCH2   0   0.255   0.7702   1.0304   1.1030
 WRO  H6   H  HCH2   0   0.252   0.5401   0.9292  -1.3937
 WRO  H7   H  HCH2   0   0.244   0.0245  -0.7460  -1.2647
 WRO  H8   H  H      0   0.261  -2.2196  -1.2849  -0.5910
 WRO  H9   H  H      0   0.270  -4.9872   1.8987   0.2425
 WRO  H10  H  H      0   0.265  -3.1380   3.5100   0.1247
 WRO  H11  H  H      0   0.260  -0.8377   2.7406  -0.3356
 WRO  H12  H  HNR6   0   0.417   5.2536   0.8096  -0.2259

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
 WRO  FAG  CAW  single    1.339  0.020  1.339
 WRO  FAF  CAW  single    1.338  0.020  1.338
 WRO  CAW  CAR  single    1.496  0.020  1.496
 WRO  CAW  FAE  single    1.344  0.020  1.344
 WRO  CAR  CAK  aromatic  1.391  0.020  1.391
 WRO  CAR  CAJ  aromatic  1.389  0.020  1.389
 WRO  CAK  CAQ  aromatic  1.390  0.020  1.390
 WRO  CAJ  CAH  aromatic  1.388  0.020  1.388
 WRO  CAQ  CAL  single    1.501  0.020  1.501
 WRO  CAQ  CAI  aromatic  1.394  0.020  1.394
 WRO  CAH  CAI  aromatic  1.386  0.020  1.386
 WRO  CAL  CAM  single    1.534  0.020  1.534
 WRO  CAM  CAT  single    1.499  0.020  1.499
 WRO  OAC  CAV  double    1.220  0.020  1.220
 WRO  CAT  CAV  single    1.458  0.020  1.458
 WRO  CAT  CAS  double    1.356  0.020  1.356
 WRO  CAV  NAO  single    1.383  0.020  1.383
 WRO  CAS  CAP  single    1.542  0.020  1.542
 WRO  CAS  NAN  single    1.368  0.020  1.368
 WRO  CAP  OAA  deloc     1.236  0.020  1.236
 WRO  CAP  OAD  deloc     1.244  0.020  1.244
 WRO  NAO  CAU  single    1.370  0.020  1.370
 WRO  NAN  CAU  single    1.357  0.020  1.357
 WRO  CAU  OAB  double    1.217  0.020  1.217
 WRO  NAO  H2   single    0.860  0.020  1.020
 WRO  CAM  H4   single    0.970  0.020  1.090
 WRO  CAM  H5   single    0.970  0.020  1.090
 WRO  CAL  H6   single    0.970  0.020  1.090
 WRO  CAL  H7   single    0.970  0.020  1.090
 WRO  CAK  H8   single    0.930  0.020  1.080
 WRO  CAJ  H9   single    0.930  0.020  1.080
 WRO  CAH  H10  single    0.930  0.020  1.080
 WRO  CAI  H11  single    0.930  0.020  1.080
 WRO  NAN  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
 WRO  CAS  CAP  OAD  114.00  3.000
 WRO  OAD  CAP  OAA  128.28  3.000
 WRO  CAS  CAP  OAA  117.71  3.000
 WRO  CAT  CAS  NAN  120.74  3.000
 WRO  NAN  CAS  CAP  111.69  3.000
 WRO  CAT  CAS  CAP  127.56  3.000
 WRO  H12  NAN  CAU  119.22  3.000
 WRO  H12  NAN  CAS  115.24  3.000
 WRO  CAU  NAN  CAS  125.52  3.000
 WRO  NAO  CAU  OAB  123.00  3.000
 WRO  OAB  CAU  NAN  123.90  3.000
 WRO  NAO  CAU  NAN  113.10  3.000
 WRO  H2   NAO  CAV  116.75  3.000
 WRO  H2   NAO  CAU  116.30  3.000
 WRO  CAV  NAO  CAU  126.95  3.000
 WRO  CAT  CAV  OAC  124.64  3.000
 WRO  CAT  CAV  NAO  115.85  3.000
 WRO  OAC  CAV  NAO  119.51  3.000
 WRO  CAM  CAT  CAV  116.42  3.000
 WRO  CAV  CAT  CAS  117.80  3.000
 WRO  CAM  CAT  CAS  125.76  3.000
 WRO  H5   CAM  H4   107.19  3.000
 WRO  H5   CAM  CAL  109.18  3.000
 WRO  H4   CAM  CAL  108.90  3.000
 WRO  H5   CAM  CAT  110.27  3.000
 WRO  H4   CAM  CAT  109.00  3.000
 WRO  CAL  CAM  CAT  112.17  3.000
 WRO  H7   CAL  H6   107.24  3.000
 WRO  H7   CAL  CAQ  110.03  3.000
 WRO  H6   CAL  CAQ  109.65  3.000
 WRO  H7   CAL  CAM  109.62  3.000
 WRO  H6   CAL  CAM  108.65  3.000
 WRO  CAQ  CAL  CAM  111.54  3.000
 WRO  CAI  CAQ  CAK  118.53  3.000
 WRO  CAI  CAQ  CAL  120.32  3.000
 WRO  CAK  CAQ  CAL  121.13  3.000
 WRO  H8   CAK  CAR  120.50  3.000
 WRO  H8   CAK  CAQ  118.79  3.000
 WRO  CAR  CAK  CAQ  120.70  3.000
 WRO  CAJ  CAR  CAW  120.10  3.000
 WRO  CAJ  CAR  CAK  120.33  3.000
 WRO  CAW  CAR  CAK  119.52  3.000
 WRO  FAE  CAW  FAG  106.46  3.000
 WRO  FAE  CAW  FAF  106.60  3.000
 WRO  FAG  CAW  FAF  106.94  3.000
 WRO  FAE  CAW  CAR  111.52  3.000
 WRO  FAF  CAW  CAR  112.52  3.000
 WRO  FAG  CAW  CAR  112.40  3.000
 WRO  H9   CAJ  CAH  119.53  3.000
 WRO  H9   CAJ  CAR  121.25  3.000
 WRO  CAH  CAJ  CAR  119.22  3.000
 WRO  H10  CAH  CAI  120.05  3.000
 WRO  H10  CAH  CAJ  119.61  3.000
 WRO  CAI  CAH  CAJ  120.34  3.000
 WRO  H11  CAI  CAH  119.97  3.000
 WRO  H11  CAI  CAQ  119.15  3.000
 WRO  CAH  CAI  CAQ  120.88  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
 WRO  CONST_01  CAJ  CAR  CAK  CAQ     0.00   0.0  0
 WRO  CONST_02  CAJ  CAH  CAI  CAQ     0.00   0.0  0
 WRO  CONST_03  CAH  CAJ  CAR  CAK     0.00   0.0  0
 WRO  CONST_04  CAH  CAI  CAQ  CAK     0.00   0.0  0
 WRO  CONST_05  CAI  CAQ  CAK  CAR     0.00   0.0  0
 WRO  CONST_06  CAI  CAH  CAJ  CAR     0.00   0.0  0
 WRO  CONST_07  NAO  CAU  NAN  CAS     0.00   0.0  0
 WRO  CONST_08  CAV  NAO  CAU  NAN     0.00   0.0  0
 WRO  CONST_09  CAT  CAV  NAO  CAU     0.00   0.0  0
 WRO  CONST_10  CAR  CAK  CAQ  CAL   180.00   0.0  0
 WRO  CONST_11  CAH  CAI  CAQ  CAL   180.00   0.0  0
 WRO  CONST_12  CAW  CAR  CAK  CAQ   180.00   0.0  0
 WRO  CONST_13  CAH  CAJ  CAR  CAW   180.00   0.0  0
 WRO  CONST_14  OAB  CAU  NAN  CAS   180.00   0.0  0
 WRO  CONST_15  OAC  CAV  NAO  CAU   180.00   0.0  0
 WRO  CONST_16  CAV  NAO  CAU  OAB   180.00   0.0  0
 WRO  CONST_17  H10  CAH  CAI  CAQ   180.00   0.0  0
 WRO  CONST_18  H9   CAJ  CAR  CAK   180.00   0.0  0
 WRO  CONST_19  H11  CAI  CAQ  CAK   180.00   0.0  0
 WRO  CONST_20  H8   CAK  CAR  CAJ   180.00   0.0  0
 WRO  CONST_21  H2   NAO  CAU  NAN   180.00   0.0  0
 WRO  CONST_22  H12  NAN  CAU  NAO   180.00   0.0  0
 WRO  Var_01    CAT  CAS  CAP  OAA    -8.27  30.0  2
 WRO  Var_02    CAL  CAM  CAT  CAS    88.24  30.0  2
 WRO  Var_03    CAQ  CAL  CAM  CAT  -176.91  30.0  1
 WRO  Var_04    CAK  CAQ  CAL  CAM   -97.54  30.0  2
 WRO  Var_05    FAG  CAW  CAR  CAK   -33.29  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
 WRO  plan-1  CAP  0.020
 WRO  plan-1  CAS  0.020
 WRO  plan-1  NAN  0.020
 WRO  plan-1  CAU  0.020
 WRO  plan-1  OAB  0.020
 WRO  plan-1  NAO  0.020
 WRO  plan-1  CAV  0.020
 WRO  plan-1  OAC  0.020
 WRO  plan-1  CAT  0.020
 WRO  plan-1  CAM  0.020
 WRO  plan-1  H2   0.020
 WRO  plan-1  H12  0.020
 WRO  plan-2  CAL  0.020
 WRO  plan-2  CAQ  0.020
 WRO  plan-2  CAK  0.020
 WRO  plan-2  CAR  0.020
 WRO  plan-2  CAW  0.020
 WRO  plan-2  CAJ  0.020
 WRO  plan-2  CAH  0.020
 WRO  plan-2  CAI  0.020
 WRO  plan-2  H8   0.020
 WRO  plan-2  H9   0.020
 WRO  plan-2  H10  0.020
 WRO  plan-2  H11  0.020
 WRO  plan-3  OAA  0.020
 WRO  plan-3  CAP  0.020
 WRO  plan-3  OAD  0.020
 WRO  plan-3  CAS  0.020

