# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 03:58:34 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  35  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 PERFECT
;

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  OH1   0  -0.589  -3.8771  -3.1766   0.3570
 W74  CAI  C  C     0   0.518  -2.9988  -2.2496   0.0219
 W74  OAK  O  O     0  -0.396  -1.8635  -2.4659  -0.3031
 W74  C4   C  CR6   0   0.285  -3.6079  -0.8813   0.0832
 W74  N3   N  NR16  0  -0.731  -4.9685  -0.8447  -0.0898
 W74  C2   C  CR6   0   0.671  -5.7093   0.3006  -0.0968
 W74  O2   O  O     0  -0.472  -6.9099   0.3163  -0.2671
 W74  N1   N  NR16  0  -0.716  -4.9659   1.4340   0.1057
 W74  C6   C  CR6   0   0.587  -3.6043   1.5151   0.3024
 W74  O6   O  O     0  -0.441  -3.0696   2.5940   0.4676
 W74  C5   C  CR6   0  -0.121  -2.8827   0.2388   0.2920
 W74  CAL  C  CH2   0  -0.499  -1.4024   0.3114   0.5071
 W74  CAM  C  CH2   0  -0.504  -0.6408   0.5895  -0.7976
 W74  CAN  C  CR6   0   0.117   0.8394   0.6657  -0.5580
 W74  CAO  C  CR16  0  -0.297   1.4630   1.8794  -0.2819
 W74  CAP  C  CR16  0  -0.311   2.8224   1.9462  -0.0274
 W74  CAQ  C  CR6   0   0.332   3.5795   0.7844  -0.0426
 W74  OAT  O  O2    0  -0.506   4.9234   0.9832   0.2263
 W74  CAU  C  CT    0   1.080   5.8334   0.0087   0.1737
 W74  FAW  F  F     0  -0.274   7.0099   0.5532   0.4423
 W74  FAX  F  F     0  -0.304   5.6141  -0.9590   1.0671
 W74  FAV  F  F     0  -0.304   5.9076  -0.5700  -1.0262
 W74  CAR  C  CR16  0  -0.326   2.9885  -0.4420  -0.3070
 W74  CAS  C  CR16  0  -0.295   1.6231  -0.4820  -0.5614
 W74  H1   H  HOH1  0   0.504  -3.4903  -4.0627   0.2772
 W74  H2   H  HNR6  0   0.431  -5.4787   2.3074   0.1018
 W74  H4   H  HCH2  0   0.264  -1.1975   1.1160   1.2152
 W74  H5   H  HCH2  0   0.266  -1.0265  -0.6035   0.9599
 W74  H6   H  HCH2  0   0.258  -0.8595  -0.2009  -1.5167
 W74  H7   H  HCH2  0   0.254  -0.9931   1.5265  -1.2338
 W74  H8   H  HCR6  0   0.257   0.8811   2.7932  -0.2718
 W74  H9   H  HCR6  0   0.279   3.2958   2.8971   0.1806
 W74  H10  H  HCR6  0   0.286   3.5402  -1.3707  -0.3236
 W74  H11  H  HCR6  0   0.259   1.1663  -1.4415  -0.7724
 W74  H12  H  HNR6  0   0.439  -5.4761  -1.7033  -0.2514

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    1.213  0.020  1.213
 W74  C2   N3   single    1.364  0.020  1.364
 W74  C2   N1   single    1.371  0.020  1.371
 W74  N3   C4   single    1.372  0.020  1.372
 W74  N1   C6   single    1.378  0.020  1.378
 W74  CAI  C4   single    1.499  0.020  1.499
 W74  CAI  OAK  double    1.201  0.020  1.201
 W74  CAI  OAJ  single    1.320  0.020  1.320
 W74  C4   C5   double    1.351  0.020  1.351
 W74  C6   C5   single    1.466  0.020  1.466
 W74  C6   O6   double    1.215  0.020  1.215
 W74  C5   CAL  single    1.498  0.020  1.498
 W74  FAX  CAU  single    1.335  0.020  1.335
 W74  CAL  CAM  single    1.536  0.020  1.536
 W74  CAU  FAV  single    1.334  0.020  1.334
 W74  CAU  FAW  single    1.324  0.020  1.324
 W74  CAU  OAT  single    1.334  0.020  1.334
 W74  CAO  CAP  aromatic  1.385  0.020  1.385
 W74  CAO  CAN  aromatic  1.392  0.020  1.392
 W74  CAP  CAQ  aromatic  1.387  0.020  1.387
 W74  CAM  CAN  single    1.501  0.020  1.501
 W74  CAN  CAS  aromatic  1.390  0.020  1.390
 W74  CAQ  OAT  single    1.385  0.020  1.385
 W74  CAQ  CAR  aromatic  1.387  0.020  1.387
 W74  CAS  CAR  aromatic  1.390  0.020  1.390
 W74  OAJ  H1   single    0.850  0.020  0.980
 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  H1   OAJ  CAI  110.81  3.000
 W74  C4   CAI  OAK  124.04  3.000
 W74  OAK  CAI  OAJ  124.84  3.000
 W74  C4   CAI  OAJ  111.12  3.000
 W74  C5   C4   N3   121.99  3.000
 W74  C5   C4   CAI  123.04  3.000
 W74  N3   C4   CAI  114.97  3.000
 W74  H12  N3   C2   116.09  3.000
 W74  H12  N3   C4   119.71  3.000
 W74  C2   N3   C4   124.17  3.000
 W74  N1   C2   O2   123.17  3.000
 W74  N1   C2   N3   113.51  3.000
 W74  O2   C2   N3   123.32  3.000
 W74  H2   N1   C6   116.75  3.000
 W74  H2   N1   C2   115.97  3.000
 W74  C6   N1   C2   127.28  3.000
 W74  C5   C6   O6   123.86  3.000
 W74  O6   C6   N1   120.41  3.000
 W74  C5   C6   N1   115.73  3.000
 W74  CAL  C5   C6   116.31  3.000
 W74  CAL  C5   C4   126.38  3.000
 W74  C6   C5   C4   117.31  3.000
 W74  H5   CAL  H4   106.56  3.000
 W74  H5   CAL  CAM  109.54  3.000
 W74  H4   CAL  CAM  108.94  3.000
 W74  H5   CAL  C5   111.14  3.000
 W74  H4   CAL  C5   108.33  3.000
 W74  CAM  CAL  C5   112.14  3.000
 W74  H7   CAM  H6   107.08  3.000
 W74  H7   CAM  CAN  109.77  3.000
 W74  H6   CAM  CAN  109.86  3.000
 W74  H7   CAM  CAL  109.55  3.000
 W74  H6   CAM  CAL  109.23  3.000
 W74  CAN  CAM  CAL  111.25  3.000
 W74  CAS  CAN  CAO  117.89  3.000
 W74  CAS  CAN  CAM  120.90  3.000
 W74  CAO  CAN  CAM  121.17  3.000
 W74  H8   CAO  CAP  119.01  3.000
 W74  H8   CAO  CAN  119.77  3.000
 W74  CAP  CAO  CAN  121.22  3.000
 W74  H9   CAP  CAQ  119.96  3.000
 W74  H9   CAP  CAO  120.47  3.000
 W74  CAQ  CAP  CAO  119.57  3.000
 W74  CAR  CAQ  OAT  125.28  3.000
 W74  CAR  CAQ  CAP  120.68  3.000
 W74  OAT  CAQ  CAP  114.04  3.000
 W74  CAU  OAT  CAQ  123.32  3.000
 W74  FAV  CAU  FAX  107.25  3.000
 W74  FAV  CAU  FAW  108.14  3.000
 W74  FAX  CAU  FAW  107.96  3.000
 W74  FAW  CAU  OAT  107.32  3.000
 W74  FAV  CAU  OAT  112.97  3.000
 W74  FAX  CAU  OAT  113.01  3.000
 W74  H10  CAR  CAS  118.31  3.000
 W74  H10  CAR  CAQ  123.06  3.000
 W74  CAS  CAR  CAQ  118.63  3.000
 W74  H11  CAS  CAR  118.39  3.000
 W74  H11  CAS  CAN  119.61  3.000
 W74  CAR  CAS  CAN  122.00  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  CONST_23  H1   OAJ  CAI  C4   180.00   0.0  0
 W74  Var_01    N3   C4   CAI  OAJ  -25.85  30.0  2
 W74  Var_02    CAM  CAL  C5   C4    94.73  30.0  3
 W74  Var_03    CAN  CAM  CAL  C5   179.68  30.0  3
 W74  Var_04    CAO  CAN  CAM  CAL  -91.71  30.0  2
 W74  Var_05    CAR  CAQ  OAT  CAU    4.64  30.0  2
 W74  Var_06    FAX  CAU  OAT  CAQ  -63.08  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
 W74  plan-3  H1   0.020

