# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 13:26:58 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  34  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 PERFECT
;

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  -0.396   2.1582   2.6988  -0.0791
 WRO  CAP  C  C     0   0.525   3.1747   2.1001   0.1450
 WRO  OAD  O  OH1   0  -0.591   4.3329   2.6660   0.4307
 WRO  CAS  C  CR6   0   0.281   3.2934   0.6057   0.1189
 WRO  NAN  N  NR16  0  -0.732   4.5641   0.1283  -0.0820
 WRO  CAU  C  CR6   0   0.671   4.8844  -1.1954  -0.1561
 WRO  OAB  O  O     0  -0.472   6.0130  -1.5979  -0.3421
 WRO  NAO  N  NR16  0  -0.716   3.8072  -2.0283  -0.0030
 WRO  CAV  C  CR6   0   0.586   2.4938  -1.6638   0.1991
 WRO  OAC  O  O     0  -0.440   1.6290  -2.5120   0.2988
 WRO  CAT  C  CR6   0  -0.119   2.2369  -0.2218   0.2779
 WRO  CAM  C  CH2   0  -0.501   0.8150   0.1843   0.5150
 WRO  CAL  C  CH2   0  -0.506   0.0169   0.2895  -0.7933
 WRO  CAQ  C  CR6   0   0.144  -1.4018   0.7052  -0.5316
 WRO  CAK  C  CR16  0  -0.346  -2.4069  -0.2452  -0.3923
 WRO  CAR  C  CR6   0  -0.175  -3.7142   0.1409  -0.1191
 WRO  CAW  C  CT    0   1.050  -4.7729  -0.8987   0.0722
 WRO  FAF  F  F     0  -0.308  -5.9843  -0.4651  -0.2966
 WRO  FAG  F  F     0  -0.307  -4.5278  -2.0131  -0.6268
 WRO  FAE  F  F     0  -0.316  -4.8745  -1.2689   1.3595
 WRO  CAJ  C  CR16  0  -0.294  -4.0321   1.4859   0.0279
 WRO  CAH  C  CR16  0  -0.226  -3.0327   2.4378  -0.1084
 WRO  CAI  C  CR16  0  -0.296  -1.7304   2.0504  -0.3846
 WRO  H1   H  HOH1  0   0.504   4.2613   3.6330   0.4014
 WRO  H2   H  HNR6  0   0.431   4.0020  -3.0211  -0.0546
 WRO  H4   H  HCH2  0   0.266   0.3453  -0.5635   1.1553
 WRO  H5   H  HCH2  0   0.267   0.7620   1.1280   1.0529
 WRO  H6   H  HCH2  0   0.261   0.4988   1.0126  -1.4521
 WRO  H7   H  HCH2  0   0.257   0.0322  -0.6728  -1.3085
 WRO  H8   H  HCR6  0   0.263  -2.1547  -1.2921  -0.5095
 WRO  H9   H  HCR6  0   0.272  -5.0440   1.8022   0.2427
 WRO  H10  H  HCR6  0   0.267  -3.2743   3.4867  -0.0015
 WRO  H11  H  HCR6  0   0.258  -0.9567   2.8017  -0.4901
 WRO  H12  H  HNR6  0   0.439   5.3286   0.7771  -0.2056

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    1.338  0.020  1.338
 WRO  FAF  CAW  single    1.338  0.020  1.338
 WRO  CAW  CAR  single    1.496  0.020  1.496
 WRO  CAW  FAE  single    1.343  0.020  1.343
 WRO  CAR  CAK  aromatic  1.390  0.020  1.390
 WRO  CAR  CAJ  aromatic  1.390  0.020  1.390
 WRO  CAK  CAQ  aromatic  1.390  0.020  1.390
 WRO  CAJ  CAH  aromatic  1.387  0.020  1.387
 WRO  CAQ  CAL  single    1.501  0.020  1.501
 WRO  CAQ  CAI  aromatic  1.393  0.020  1.393
 WRO  CAH  CAI  aromatic  1.386  0.020  1.386
 WRO  CAL  CAM  single    1.536  0.020  1.536
 WRO  CAM  CAT  single    1.498  0.020  1.498
 WRO  OAC  CAV  double    1.215  0.020  1.215
 WRO  CAT  CAV  single    1.467  0.020  1.467
 WRO  CAT  CAS  double    1.351  0.020  1.351
 WRO  CAV  NAO  single    1.378  0.020  1.378
 WRO  CAS  CAP  single    1.499  0.020  1.499
 WRO  CAS  NAN  single    1.372  0.020  1.372
 WRO  CAP  OAA  double    1.201  0.020  1.201
 WRO  CAP  OAD  single    1.320  0.020  1.320
 WRO  NAO  CAU  single    1.370  0.020  1.370
 WRO  NAN  CAU  single    1.364  0.020  1.364
 WRO  CAU  OAB  double    1.213  0.020  1.213
 WRO  OAD  H1   single    0.850  0.020  0.980
 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  111.19  3.000
 WRO  OAD  CAP  OAA  124.70  3.000
 WRO  CAS  CAP  OAA  124.10  3.000
 WRO  H1   OAD  CAP  110.85  3.000
 WRO  CAT  CAS  NAN  121.88  3.000
 WRO  NAN  CAS  CAP  115.00  3.000
 WRO  CAT  CAS  CAP  123.12  3.000
 WRO  H12  NAN  CAU  116.03  3.000
 WRO  H12  NAN  CAS  119.68  3.000
 WRO  CAU  NAN  CAS  124.27  3.000
 WRO  NAO  CAU  OAB  123.17  3.000
 WRO  OAB  CAU  NAN  123.30  3.000
 WRO  NAO  CAU  NAN  113.53  3.000
 WRO  H2   NAO  CAV  116.74  3.000
 WRO  H2   NAO  CAU  116.03  3.000
 WRO  CAV  NAO  CAU  127.23  3.000
 WRO  CAT  CAV  OAC  123.85  3.000
 WRO  CAT  CAV  NAO  115.78  3.000
 WRO  OAC  CAV  NAO  120.38  3.000
 WRO  CAM  CAT  CAV  116.19  3.000
 WRO  CAV  CAT  CAS  117.30  3.000
 WRO  CAM  CAT  CAS  126.50  3.000
 WRO  H5   CAM  H4   106.47  3.000
 WRO  H5   CAM  CAL  109.66  3.000
 WRO  H4   CAM  CAL  108.85  3.000
 WRO  H5   CAM  CAT  111.09  3.000
 WRO  H4   CAM  CAT  108.42  3.000
 WRO  CAL  CAM  CAT  112.15  3.000
 WRO  H7   CAL  H6   107.04  3.000
 WRO  H7   CAL  CAQ  109.86  3.000
 WRO  H6   CAL  CAQ  109.83  3.000
 WRO  H7   CAL  CAM  109.53  3.000
 WRO  H6   CAL  CAM  109.29  3.000
 WRO  CAQ  CAL  CAM  111.19  3.000
 WRO  CAI  CAQ  CAK  118.63  3.000
 WRO  CAI  CAQ  CAL  120.59  3.000
 WRO  CAK  CAQ  CAL  120.75  3.000
 WRO  H8   CAK  CAR  120.58  3.000
 WRO  H8   CAK  CAQ  118.78  3.000
 WRO  CAR  CAK  CAQ  120.64  3.000
 WRO  CAJ  CAR  CAW  119.81  3.000
 WRO  CAJ  CAR  CAK  120.31  3.000
 WRO  CAW  CAR  CAK  119.84  3.000
 WRO  FAE  CAW  FAG  106.55  3.000
 WRO  FAE  CAW  FAF  106.55  3.000
 WRO  FAG  CAW  FAF  106.96  3.000
 WRO  FAE  CAW  CAR  111.56  3.000
 WRO  FAF  CAW  CAR  112.34  3.000
 WRO  FAG  CAW  CAR  112.48  3.000
 WRO  H9   CAJ  CAH  119.53  3.000
 WRO  H9   CAJ  CAR  121.19  3.000
 WRO  CAH  CAJ  CAR  119.28  3.000
 WRO  H10  CAH  CAI  120.03  3.000
 WRO  H10  CAH  CAJ  119.66  3.000
 WRO  CAI  CAH  CAJ  120.31  3.000
 WRO  H11  CAI  CAH  119.76  3.000
 WRO  H11  CAI  CAQ  119.41  3.000
 WRO  CAH  CAI  CAQ  120.84  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  CONST_23  H1   OAD  CAP  CAS   180.00   0.0  0
 WRO  Var_01    CAT  CAS  CAP  OAA   -22.46  30.0  2
 WRO  Var_02    CAL  CAM  CAT  CAS    93.06  30.0  2
 WRO  Var_03    CAQ  CAL  CAM  CAT  -179.67  30.0  1
 WRO  Var_04    CAK  CAQ  CAL  CAM   -94.20  30.0  2
 WRO  Var_05    FAG  CAW  CAR  CAK   -29.66  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
 WRO  plan-3  H1   0.020

