# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 09:22:14 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 2,6-dioxo-5-{2-[4-(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(CCc2ccc(cc2)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
 ZRO  ZRO  '2,6-dioxo-5-{2-[4-(trifluoromethyl)phenyl]ethyl}-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  33  23  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ZRO
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
 ZRO  OAA  O  O      0  -0.541   1.6237   2.4725  -0.0496
 ZRO  CAP  C  C      0   0.417   2.8399   2.2598   0.0158
 ZRO  OAD  O  OC    -1  -0.584   3.7685   3.0874  -0.0030
 ZRO  CAS  C  CR6    0   0.204   3.3071   0.7935   0.1157
 ZRO  NAN  N  NR16   0  -0.707   4.6594   0.6791  -0.0543
 ZRO  CAU  C  CR6    0   0.656   5.3592  -0.4839  -0.0478
 ZRO  OAB  O  O      0  -0.492   6.5644  -0.5516  -0.2036
 ZRO  NAO  N  NR16   0  -0.715   4.5693  -1.5859   0.1492
 ZRO  CAV  C  CR6    0   0.565   3.2006  -1.6033   0.3443
 ZRO  OAC  O  O      0  -0.466   2.6286  -2.6697   0.5032
 ZRO  CAT  C  CR6    0  -0.158   2.5419  -0.3033   0.3382
 ZRO  CAM  C  CH2    0  -0.480   1.0568  -0.3063   0.5418
 ZRO  CAL  C  CH2    0  -0.497   0.2944  -0.4775  -0.7805
 ZRO  CAQ  C  C      0   0.130  -1.1882  -0.3705  -0.5793
 ZRO  CAH  C  C1     0  -0.291  -1.7733   0.8760  -0.3519
 ZRO  CAJ  C  C1     0  -0.256  -3.1328   0.9961  -0.1298
 ZRO  CAR  C  C      0  -0.214  -3.9404  -0.1390  -0.1322
 ZRO  CAW  C  CT     0   1.048  -5.3999   0.0078   0.1500
 ZRO  FAF  F  F      0  -0.313  -5.9426   1.0341  -0.5207
 ZRO  FAG  F  F      0  -0.305  -6.1018  -1.0840  -0.1715
 ZRO  FAE  F  F      0  -0.317  -5.6321   0.2454   1.4522
 ZRO  CAK  C  C1     0  -0.266  -3.3735  -1.3861  -0.3545
 ZRO  CAI  C  C1     0  -0.307  -2.0072  -1.4937  -0.5762
 ZRO  H2   H  HNR6   0   0.420   5.0408  -2.4815   0.1472
 ZRO  H4   H  HCH2   0   0.242   0.7918  -1.1245   1.2138
 ZRO  H5   H  HCH2   0   0.258   0.7430   0.6178   1.0176
 ZRO  H6   H  HCH2   0   0.252   0.6267   0.2951  -1.4754
 ZRO  H7   H  HCH2   0   0.245   0.5434  -1.4427  -1.2254
 ZRO  H8   H  H      0   0.263  -1.1501   1.7623  -0.3509
 ZRO  H9   H  H      0   0.269  -3.5545   1.9784   0.0418
 ZRO  H10  H  H      0   0.268  -3.9796  -2.2820  -0.3604
 ZRO  H11  H  H      0   0.256  -1.5780  -2.4720  -0.7555
 ZRO  H12  H  HNR6   0   0.417   5.1575   1.5529  -0.1814

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
 ZRO  FAF  CAW  single    1.341  0.020  1.341
 ZRO  FAG  CAW  single    1.337  0.020  1.337
 ZRO  CAW  FAE  single    1.344  0.020  1.344
 ZRO  CAW  CAR  single    1.494  0.020  1.494
 ZRO  CAR  CAK  aromatic  1.388  0.020  1.388
 ZRO  CAR  CAJ  aromatic  1.393  0.020  1.393
 ZRO  CAK  CAI  aromatic  1.388  0.020  1.388
 ZRO  CAJ  CAH  aromatic  1.383  0.020  1.383
 ZRO  CAI  CAQ  aromatic  1.390  0.020  1.390
 ZRO  CAH  CAQ  aromatic  1.396  0.020  1.396
 ZRO  CAQ  CAL  single    1.500  0.020  1.500
 ZRO  CAL  CAM  single    1.536  0.020  1.536
 ZRO  CAM  CAT  single    1.499  0.020  1.499
 ZRO  OAC  CAV  double    1.221  0.020  1.221
 ZRO  CAT  CAV  single    1.457  0.020  1.457
 ZRO  CAT  CAS  double    1.356  0.020  1.356
 ZRO  CAV  NAO  single    1.383  0.020  1.383
 ZRO  CAS  CAP  single    1.542  0.020  1.542
 ZRO  CAS  NAN  single    1.368  0.020  1.368
 ZRO  OAA  CAP  deloc     1.236  0.020  1.236
 ZRO  CAP  OAD  deloc     1.244  0.020  1.244
 ZRO  NAO  CAU  single    1.370  0.020  1.370
 ZRO  NAN  CAU  single    1.357  0.020  1.357
 ZRO  CAU  OAB  double    1.217  0.020  1.217
 ZRO  NAO  H2   single    0.860  0.020  1.020
 ZRO  CAM  H4   single    0.970  0.020  1.090
 ZRO  CAM  H5   single    0.970  0.020  1.090
 ZRO  CAL  H6   single    0.970  0.020  1.090
 ZRO  CAL  H7   single    0.970  0.020  1.090
 ZRO  CAH  H8   single    0.930  0.020  1.080
 ZRO  CAJ  H9   single    0.930  0.020  1.080
 ZRO  CAK  H10  single    0.930  0.020  1.080
 ZRO  CAI  H11  single    0.930  0.020  1.080
 ZRO  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
 ZRO  CAS  CAP  OAD  114.04  3.000
 ZRO  OAD  CAP  OAA  128.24  3.000
 ZRO  CAS  CAP  OAA  117.71  3.000
 ZRO  CAT  CAS  NAN  120.72  3.000
 ZRO  NAN  CAS  CAP  111.77  3.000
 ZRO  CAT  CAS  CAP  127.51  3.000
 ZRO  H12  NAN  CAU  119.07  3.000
 ZRO  H12  NAN  CAS  115.42  3.000
 ZRO  CAU  NAN  CAS  125.51  3.000
 ZRO  NAO  CAU  OAB  123.00  3.000
 ZRO  OAB  CAU  NAN  123.89  3.000
 ZRO  NAO  CAU  NAN  113.12  3.000
 ZRO  H2   NAO  CAV  116.76  3.000
 ZRO  H2   NAO  CAU  116.29  3.000
 ZRO  CAV  NAO  CAU  126.95  3.000
 ZRO  CAT  CAV  OAC  124.62  3.000
 ZRO  CAT  CAV  NAO  115.82  3.000
 ZRO  OAC  CAV  NAO  119.56  3.000
 ZRO  CAM  CAT  CAV  116.45  3.000
 ZRO  CAV  CAT  CAS  117.85  3.000
 ZRO  CAM  CAT  CAS  125.67  3.000
 ZRO  H5   CAM  H4   107.35  3.000
 ZRO  H5   CAM  CAL  109.19  3.000
 ZRO  H4   CAM  CAL  109.02  3.000
 ZRO  H5   CAM  CAT  110.13  3.000
 ZRO  H4   CAM  CAT  109.01  3.000
 ZRO  CAL  CAM  CAT  112.03  3.000
 ZRO  H7   CAL  H6   107.28  3.000
 ZRO  H7   CAL  CAQ  110.07  3.000
 ZRO  H6   CAL  CAQ  109.63  3.000
 ZRO  H7   CAL  CAM  109.64  3.000
 ZRO  H6   CAL  CAM  108.56  3.000
 ZRO  CAQ  CAL  CAM  111.54  3.000
 ZRO  CAI  CAQ  CAH  118.32  3.000
 ZRO  CAH  CAQ  CAL  120.00  3.000
 ZRO  CAI  CAQ  CAL  121.67  3.000
 ZRO  H8   CAH  CAJ  119.62  3.000
 ZRO  H8   CAH  CAQ  119.32  3.000
 ZRO  CAJ  CAH  CAQ  121.06  3.000
 ZRO  H9   CAJ  CAR  120.91  3.000
 ZRO  H9   CAJ  CAH  119.16  3.000
 ZRO  CAR  CAJ  CAH  119.93  3.000
 ZRO  CAK  CAR  CAW  121.18  3.000
 ZRO  CAK  CAR  CAJ  119.71  3.000
 ZRO  CAW  CAR  CAJ  119.08  3.000
 ZRO  FAE  CAW  FAG  106.65  3.000
 ZRO  FAE  CAW  FAF  106.22  3.000
 ZRO  FAG  CAW  FAF  106.99  3.000
 ZRO  FAE  CAW  CAR  111.67  3.000
 ZRO  FAG  CAW  CAR  112.78  3.000
 ZRO  FAF  CAW  CAR  112.10  3.000
 ZRO  H10  CAK  CAI  119.10  3.000
 ZRO  H10  CAK  CAR  121.08  3.000
 ZRO  CAI  CAK  CAR  119.82  3.000
 ZRO  H11  CAI  CAK  119.10  3.000
 ZRO  H11  CAI  CAQ  119.73  3.000
 ZRO  CAK  CAI  CAQ  121.16  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
 ZRO  CONST_01  CAR  CAK  CAI  CAQ     0.00   0.0  0
 ZRO  CONST_02  CAR  CAJ  CAH  CAQ     0.00   0.0  0
 ZRO  CONST_03  CAK  CAR  CAJ  CAH     0.00   0.0  0
 ZRO  CONST_04  CAK  CAI  CAQ  CAH     0.00   0.0  0
 ZRO  CONST_05  CAI  CAK  CAR  CAJ     0.00   0.0  0
 ZRO  CONST_06  CAI  CAQ  CAH  CAJ     0.00   0.0  0
 ZRO  CONST_07  NAO  CAU  NAN  CAS     0.00   0.0  0
 ZRO  CONST_08  CAV  NAO  CAU  NAN     0.00   0.0  0
 ZRO  CONST_09  CAT  CAV  NAO  CAU     0.00   0.0  0
 ZRO  CONST_10  CAK  CAI  CAQ  CAL   180.00   0.0  0
 ZRO  CONST_11  CAJ  CAH  CAQ  CAL   180.00   0.0  0
 ZRO  CONST_12  CAW  CAR  CAJ  CAH   180.00   0.0  0
 ZRO  CONST_13  CAI  CAK  CAR  CAW   180.00   0.0  0
 ZRO  CONST_14  OAB  CAU  NAN  CAS   180.00   0.0  0
 ZRO  CONST_15  OAC  CAV  NAO  CAU   180.00   0.0  0
 ZRO  CONST_16  CAV  NAO  CAU  OAB   180.00   0.0  0
 ZRO  CONST_17  H10  CAK  CAI  CAQ   180.00   0.0  0
 ZRO  CONST_18  H9   CAJ  CAH  CAQ   180.00   0.0  0
 ZRO  CONST_19  H11  CAI  CAQ  CAH   180.00   0.0  0
 ZRO  CONST_20  H8   CAH  CAJ  CAR   180.00   0.0  0
 ZRO  CONST_21  H2   NAO  CAU  NAN   180.00   0.0  0
 ZRO  CONST_22  H12  NAN  CAU  NAO   180.00   0.0  0
 ZRO  Var_01    CAT  CAS  CAP  OAA   -10.54  30.0  2
 ZRO  Var_02    CAL  CAM  CAT  CAS    90.79  30.0  3
 ZRO  Var_03    CAQ  CAL  CAM  CAT  -175.50  30.0  1
 ZRO  Var_04    CAI  CAQ  CAL  CAM  -103.73  30.0  2
 ZRO  Var_05    FAF  CAW  CAR  CAJ    45.15  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
 ZRO  plan-1  CAP  0.020
 ZRO  plan-1  CAS  0.020
 ZRO  plan-1  NAN  0.020
 ZRO  plan-1  CAU  0.020
 ZRO  plan-1  OAB  0.020
 ZRO  plan-1  NAO  0.020
 ZRO  plan-1  CAV  0.020
 ZRO  plan-1  OAC  0.020
 ZRO  plan-1  CAT  0.020
 ZRO  plan-1  CAM  0.020
 ZRO  plan-1  H2   0.020
 ZRO  plan-1  H12  0.020
 ZRO  plan-2  CAL  0.020
 ZRO  plan-2  CAQ  0.020
 ZRO  plan-2  CAH  0.020
 ZRO  plan-2  CAJ  0.020
 ZRO  plan-2  CAR  0.020
 ZRO  plan-2  CAW  0.020
 ZRO  plan-2  CAK  0.020
 ZRO  plan-2  CAI  0.020
 ZRO  plan-2  H8   0.020
 ZRO  plan-2  H9   0.020
 ZRO  plan-2  H10  0.020
 ZRO  plan-2  H11  0.020
 ZRO  plan-3  OAA  0.020
 ZRO  plan-3  CAP  0.020
 ZRO  plan-3  OAD  0.020
 ZRO  plan-3  CAS  0.020

