# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 00:58:19 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 2,6-dioxo-5-{2-[2-(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(CCc2ccccc2C(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
 ROD  ROD  '2,6-dioxo-5-{2-[2-(trifluoromethyl)phenyl]ethyl}-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  34  23  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ROD
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
 ROD  OAA  O  OH1   0  -0.590   3.6402   2.9778  -0.2358
 ROD  CAP  C  C     0   0.522   2.5065   2.3449   0.0022
 ROD  OAD  O  O     0  -0.396   1.4647   2.8822   0.2623
 ROD  CAS  C  CR6   0   0.284   2.6900   0.8590  -0.0770
 ROD  NAN  N  NR16  0  -0.732   3.9699   0.4227   0.1572
 ROD  CAU  C  CR6   0   0.671   4.3461  -0.8886   0.1574
 ROD  OAB  O  O     0  -0.472   5.4803  -1.2554   0.3807
 ROD  NAO  N  NR16  0  -0.716   3.3187  -1.7519  -0.1168
 ROD  CAV  C  CR6   0   0.584   2.0036  -1.4290  -0.3774
 ROD  OAC  O  O     0  -0.432   1.1903  -2.3021  -0.6040
 ROD  CAT  C  CR6   0  -0.124   1.6828   0.0025  -0.3558
 ROD  CAM  C  CH2   0  -0.498   0.2577   0.3666  -0.6409
 ROD  CAL  C  CH2   0  -0.533  -0.6143   0.2910   0.6229
 ROD  CAQ  C  CR6   0   0.149  -2.0260   0.7452   0.3475
 ROD  CAJ  C  CR16  0  -0.301  -2.2463   2.1200   0.2801
 ROD  CAH  C  CR16  0  -0.229  -3.4937   2.6495  -0.0053
 ROD  CAI  C  CR16  0  -0.257  -4.5654   1.7999  -0.2313
 ROD  CAK  C  CR16  0  -0.279  -4.3756   0.4298  -0.1650
 ROD  CAR  C  CR6   0  -0.276  -3.1194  -0.1012   0.1191
 ROD  CAW  C  CT    0   1.054  -2.9700  -1.5919   0.1970
 ROD  FAF  F  F     0  -0.317  -2.6026  -1.9993   1.4236
 ROD  FAG  F  F     0  -0.302  -4.1071  -2.2375  -0.0852
 ROD  FAE  F  F     0  -0.311  -2.0484  -2.0583  -0.6567
 ROD  H1   H  HOH1  0   0.504   3.5257   3.9371  -0.1468
 ROD  H2   H  HNR6  0   0.431   3.5559  -2.7369  -0.1237
 ROD  H4   H  HCH2  0   0.268   0.1888   1.3605  -1.0756
 ROD  H5   H  HCH2  0   0.269  -0.1320  -0.3254  -1.3871
 ROD  H6   H  HCH2  0   0.262  -0.5661  -0.7134   1.0367
 ROD  H7   H  HCH2  0   0.269  -0.1876   0.9516   1.3789
 ROD  H8   H  HCR6  0   0.261  -1.4122   2.7878   0.4598
 ROD  H9   H  HCR6  0   0.265  -3.6274   3.7224  -0.0474
 ROD  H10  H  HCR6  0   0.266  -5.5463   2.1964  -0.4555
 ROD  H11  H  HCR6  0   0.270  -5.2223  -0.2192  -0.3378
 ROD  H12  H  HNR6  0   0.439   4.6980   1.0930   0.3607

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
 ROD  CAI  CAH  aromatic  1.386  0.020  1.386
 ROD  CAI  CAK  aromatic  1.385  0.020  1.385
 ROD  CAH  CAJ  aromatic  1.385  0.020  1.385
 ROD  CAK  CAR  aromatic  1.393  0.020  1.393
 ROD  CAJ  CAQ  aromatic  1.394  0.020  1.394
 ROD  CAR  CAQ  aromatic  1.401  0.020  1.401
 ROD  CAR  CAW  single    1.500  0.020  1.500
 ROD  CAQ  CAL  single    1.508  0.020  1.508
 ROD  FAE  CAW  single    1.340  0.020  1.340
 ROD  FAF  CAW  single    1.344  0.020  1.344
 ROD  CAW  FAG  single    1.338  0.020  1.338
 ROD  CAL  CAM  single    1.537  0.020  1.537
 ROD  CAM  CAT  single    1.498  0.020  1.498
 ROD  OAC  CAV  double    1.215  0.020  1.215
 ROD  CAT  CAV  single    1.467  0.020  1.467
 ROD  CAT  CAS  double    1.351  0.020  1.351
 ROD  CAV  NAO  single    1.379  0.020  1.379
 ROD  CAS  CAP  single    1.499  0.020  1.499
 ROD  CAS  NAN  single    1.372  0.020  1.372
 ROD  NAO  CAU  single    1.370  0.020  1.370
 ROD  OAD  CAP  double    1.201  0.020  1.201
 ROD  CAP  OAA  single    1.320  0.020  1.320
 ROD  NAN  CAU  single    1.364  0.020  1.364
 ROD  CAU  OAB  double    1.213  0.020  1.213
 ROD  OAA  H1   single    0.850  0.020  0.980
 ROD  NAO  H2   single    0.860  0.020  1.020
 ROD  CAM  H4   single    0.970  0.020  1.090
 ROD  CAM  H5   single    0.970  0.020  1.090
 ROD  CAL  H6   single    0.970  0.020  1.090
 ROD  CAL  H7   single    0.970  0.020  1.090
 ROD  CAJ  H8   single    0.930  0.020  1.080
 ROD  CAH  H9   single    0.930  0.020  1.080
 ROD  CAI  H10  single    0.930  0.020  1.080
 ROD  CAK  H11  single    0.930  0.020  1.080
 ROD  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
 ROD  H1   OAA  CAP  110.87  3.000
 ROD  CAS  CAP  OAD  124.14  3.000
 ROD  OAD  CAP  OAA  124.73  3.000
 ROD  CAS  CAP  OAA  111.13  3.000
 ROD  CAT  CAS  NAN  121.93  3.000
 ROD  NAN  CAS  CAP  114.85  3.000
 ROD  CAT  CAS  CAP  123.22  3.000
 ROD  H12  NAN  CAU  116.03  3.000
 ROD  H12  NAN  CAS  119.71  3.000
 ROD  CAU  NAN  CAS  124.25  3.000
 ROD  NAO  CAU  OAB  123.21  3.000
 ROD  OAB  CAU  NAN  123.28  3.000
 ROD  NAO  CAU  NAN  113.52  3.000
 ROD  H2   NAO  CAV  116.72  3.000
 ROD  H2   NAO  CAU  116.01  3.000
 ROD  CAV  NAO  CAU  127.27  3.000
 ROD  CAT  CAV  OAC  123.89  3.000
 ROD  CAT  CAV  NAO  115.73  3.000
 ROD  OAC  CAV  NAO  120.37  3.000
 ROD  CAM  CAT  CAV  116.25  3.000
 ROD  CAV  CAT  CAS  117.29  3.000
 ROD  CAM  CAT  CAS  126.46  3.000
 ROD  H5   CAM  H4   106.51  3.000
 ROD  H5   CAM  CAL  109.20  3.000
 ROD  H4   CAM  CAL  109.74  3.000
 ROD  H5   CAM  CAT  108.43  3.000
 ROD  H4   CAM  CAT  111.01  3.000
 ROD  CAL  CAM  CAT  111.79  3.000
 ROD  H7   CAL  H6   106.16  3.000
 ROD  H7   CAL  CAQ  108.08  3.000
 ROD  H6   CAL  CAQ  112.90  3.000
 ROD  H7   CAL  CAM  108.55  3.000
 ROD  H6   CAL  CAM  109.45  3.000
 ROD  CAQ  CAL  CAM  111.47  3.000
 ROD  CAR  CAQ  CAJ  117.68  3.000
 ROD  CAR  CAQ  CAL  125.32  3.000
 ROD  CAJ  CAQ  CAL  116.98  3.000
 ROD  H8   CAJ  CAH  119.47  3.000
 ROD  H8   CAJ  CAQ  118.57  3.000
 ROD  CAH  CAJ  CAQ  121.96  3.000
 ROD  H9   CAH  CAI  120.39  3.000
 ROD  H9   CAH  CAJ  119.90  3.000
 ROD  CAI  CAH  CAJ  119.71  3.000
 ROD  H10  CAI  CAK  119.79  3.000
 ROD  H10  CAI  CAH  120.69  3.000
 ROD  CAK  CAI  CAH  119.52  3.000
 ROD  H11  CAK  CAR  120.68  3.000
 ROD  H11  CAK  CAI  118.63  3.000
 ROD  CAR  CAK  CAI  120.69  3.000
 ROD  CAW  CAR  CAK  118.63  3.000
 ROD  CAW  CAR  CAQ  120.93  3.000
 ROD  CAK  CAR  CAQ  120.44  3.000
 ROD  FAE  CAW  FAG  106.39  3.000
 ROD  FAG  CAW  FAF  106.18  3.000
 ROD  FAE  CAW  FAF  106.74  3.000
 ROD  FAG  CAW  CAR  112.58  3.000
 ROD  FAF  CAW  CAR  112.08  3.000
 ROD  FAE  CAW  CAR  112.41  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
 ROD  CONST_01  CAI  CAH  CAJ  CAQ     0.00   0.0  0
 ROD  CONST_02  CAI  CAK  CAR  CAQ     0.00   0.0  0
 ROD  CONST_03  CAK  CAI  CAH  CAJ     0.00   0.0  0
 ROD  CONST_04  CAK  CAR  CAQ  CAJ     0.00   0.0  0
 ROD  CONST_05  CAR  CAK  CAI  CAH     0.00   0.0  0
 ROD  CONST_06  CAR  CAQ  CAJ  CAH     0.00   0.0  0
 ROD  CONST_07  NAO  CAU  NAN  CAS     0.00   0.0  0
 ROD  CONST_08  CAV  NAO  CAU  NAN     0.00   0.0  0
 ROD  CONST_09  CAT  CAV  NAO  CAU     0.00   0.0  0
 ROD  CONST_10  CAH  CAJ  CAQ  CAL   180.00   0.0  0
 ROD  CONST_11  CAK  CAR  CAQ  CAL   180.00   0.0  0
 ROD  CONST_12  CAW  CAR  CAQ  CAJ   180.00   0.0  0
 ROD  CONST_13  CAW  CAR  CAK  CAI   180.00   0.0  0
 ROD  CONST_14  OAB  CAU  NAN  CAS   180.00   0.0  0
 ROD  CONST_15  OAC  CAV  NAO  CAU   180.00   0.0  0
 ROD  CONST_16  CAV  NAO  CAU  OAB   180.00   0.0  0
 ROD  CONST_17  H9   CAH  CAJ  CAQ   180.00   0.0  0
 ROD  CONST_18  H11  CAK  CAR  CAQ   180.00   0.0  0
 ROD  CONST_19  H10  CAI  CAH  CAJ   180.00   0.0  0
 ROD  CONST_20  H8   CAJ  CAH  CAI   180.00   0.0  0
 ROD  CONST_21  H2   NAO  CAU  NAN   180.00   0.0  0
 ROD  CONST_22  H12  NAN  CAU  NAO   180.00   0.0  0
 ROD  CONST_23  H1   OAA  CAP  CAS   180.00   0.0  0
 ROD  Var_01    CAT  CAS  CAP  OAA  -155.38  30.0  2
 ROD  Var_02    CAL  CAM  CAT  CAS   -94.90  30.0  2
 ROD  Var_03    CAQ  CAL  CAM  CAT   176.29  30.0  1
 ROD  Var_04    CAJ  CAQ  CAL  CAM   -78.56  30.0  2
 ROD  Var_05    FAE  CAW  CAR  CAQ   -58.15  30.0  2

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
 ROD  plan-1  CAP  0.020
 ROD  plan-1  CAS  0.020
 ROD  plan-1  NAN  0.020
 ROD  plan-1  CAU  0.020
 ROD  plan-1  OAB  0.020
 ROD  plan-1  NAO  0.020
 ROD  plan-1  CAV  0.020
 ROD  plan-1  OAC  0.020
 ROD  plan-1  CAT  0.020
 ROD  plan-1  CAM  0.020
 ROD  plan-1  H2   0.020
 ROD  plan-1  H12  0.020
 ROD  plan-2  CAL  0.020
 ROD  plan-2  CAQ  0.020
 ROD  plan-2  CAJ  0.020
 ROD  plan-2  CAH  0.020
 ROD  plan-2  CAI  0.020
 ROD  plan-2  CAK  0.020
 ROD  plan-2  CAR  0.020
 ROD  plan-2  CAW  0.020
 ROD  plan-2  H8   0.020
 ROD  plan-2  H9   0.020
 ROD  plan-2  H10  0.020
 ROD  plan-2  H11  0.020
 ROD  plan-3  OAA  0.020
 ROD  plan-3  CAP  0.020
 ROD  plan-3  OAD  0.020
 ROD  plan-3  CAS  0.020
 ROD  plan-3  H1   0.020

