# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 03:24:01 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 5-{2-[3,5-bis(trifluoromethyl)phenyl]ethyl}-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=C(CCc2cc(cc(c2)C(F)(F)F)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
 ROU  ROU  '5-{2-[3,5-bis(trifluoromethyl)phenyl]ethyl}-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  37  27  .  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_ROU
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
 ROU  OAA  O  OH1   0  -0.588  -4.2121   3.0204  -0.4438
 ROU  CAR  C  C     0   0.521  -3.2583   2.1759  -0.0998
 ROU  OAD  O  O     0  -0.397  -2.1356   2.4894   0.1896
 ROU  CAV  C  CR6   0   0.288  -3.7602   0.7633  -0.0976
 ROU  NAP  N  NR16  0  -0.731  -5.1073   0.6277   0.1210
 ROU  CAX  C  CR6   0   0.672  -5.7550  -0.5710   0.1948
 ROU  OAB  O  O     0  -0.471  -6.9445  -0.6734   0.4070
 ROU  NAQ  N  NR16  0  -0.717  -4.9305  -1.6499   0.0078
 ROU  CAY  C  CR6   0   0.588  -3.5734  -1.6321  -0.2308
 ROU  OAC  O  O     0  -0.440  -2.9594  -2.6714  -0.3736
 ROU  CAW  C  CR6   0  -0.121  -2.9561  -0.3042  -0.2918
 ROU  CAO  C  CH2   0  -0.507  -1.4809  -0.2662  -0.5469
 ROU  CAN  C  CH2   0  -0.510  -0.6716  -0.4410   0.7478
 ROU  CAS  C  CR6   0   0.164   0.8003  -0.2970   0.4954
 ROU  CAK  C  CR16  0  -0.333   1.6264  -1.4070   0.3854
 ROU  CAT  C  CR6   0  -0.148   2.9839  -1.2580   0.1262
 ROU  CAZ  C  CT    0   1.060   3.8262  -2.4921   0.0220
 ROU  FAF  F  F     0  -0.299   5.1142  -2.2228  -0.1998
 ROU  FAG  F  F     0  -0.312   3.7635  -3.2249   1.1422
 ROU  FAE  F  F     0  -0.313   3.4115  -3.2853  -0.9755
 ROU  CAM  C  CR16  0  -0.357   3.5385   0.0024  -0.0298
 ROU  CAU  C  CR6   0  -0.146   2.7148   1.1142   0.0780
 ROU  CBA  C  CT    0   1.059   3.2608   2.4999  -0.0817
 ROU  FAI  F  F     0  -0.312   2.7076   3.1276  -1.1284
 ROU  FAJ  F  F     0  -0.312   3.0043   3.2547   0.9953
 ROU  FAH  F  F     0  -0.300   4.5826   2.5167  -0.2673
 ROU  CAL  C  CR16  0  -0.322   1.3599   0.9664   0.3362
 ROU  H1   H  HOH1  0   0.504  -3.8934   3.9359  -0.4017
 ROU  H2   H  HNR6  0   0.439  -5.6755   1.4501   0.2702
 ROU  H3   H  HNR6  0   0.431  -5.3706  -2.5605   0.0640
 ROU  H4   H  HCH2  0   0.269  -1.2277  -1.0718  -1.2377
 ROU  H5   H  HCH2  0   0.271  -1.1949   0.6614  -1.0371
 ROU  H6   H  HCH2  0   0.268  -0.9915   0.3040   1.4775
 ROU  H7   H  HCH2  0   0.263  -0.8802  -1.4207   1.1795
 ROU  H8   H  HCR6  0   0.277   1.1973  -2.3937   0.5133
 ROU  H9   H  HCR6  0   0.283   4.5948   0.1190  -0.2255
 ROU  H10  H  HCR6  0   0.277   0.7178   1.8357   0.4223

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
 ROU  FAE  CAZ  single    1.340  0.020  1.340
 ROU  FAG  CAZ  single    1.340  0.020  1.340
 ROU  CAZ  CAT  single    1.498  0.020  1.498
 ROU  CAZ  FAF  single    1.334  0.020  1.334
 ROU  FAI  CBA  single    1.340  0.020  1.340
 ROU  CAT  CAM  aromatic  1.386  0.020  1.386
 ROU  CAT  CAK  aromatic  1.390  0.020  1.390
 ROU  CAM  CAU  aromatic  1.388  0.020  1.388
 ROU  CAK  CAS  aromatic  1.388  0.020  1.388
 ROU  CAU  CBA  single    1.498  0.020  1.498
 ROU  CAU  CAL  aromatic  1.387  0.020  1.387
 ROU  CAS  CAL  aromatic  1.391  0.020  1.391
 ROU  CAS  CAN  single    1.500  0.020  1.500
 ROU  CBA  FAH  single    1.335  0.020  1.335
 ROU  CBA  FAJ  single    1.340  0.020  1.340
 ROU  CAN  CAO  single    1.537  0.020  1.537
 ROU  CAO  CAW  single    1.498  0.020  1.498
 ROU  OAC  CAY  double    1.216  0.020  1.216
 ROU  CAW  CAY  single    1.466  0.020  1.466
 ROU  CAW  CAV  double    1.351  0.020  1.351
 ROU  CAY  NAQ  single    1.378  0.020  1.378
 ROU  OAD  CAR  double    1.201  0.020  1.201
 ROU  OAA  CAR  single    1.320  0.020  1.320
 ROU  CAR  CAV  single    1.499  0.020  1.499
 ROU  CAV  NAP  single    1.371  0.020  1.371
 ROU  NAQ  CAX  single    1.371  0.020  1.371
 ROU  NAP  CAX  single    1.365  0.020  1.365
 ROU  CAX  OAB  double    1.213  0.020  1.213
 ROU  OAA  H1   single    0.850  0.020  0.980
 ROU  NAP  H2   single    0.860  0.020  1.020
 ROU  NAQ  H3   single    0.860  0.020  1.020
 ROU  CAO  H4   single    0.970  0.020  1.090
 ROU  CAO  H5   single    0.970  0.020  1.090
 ROU  CAN  H6   single    0.970  0.020  1.090
 ROU  CAN  H7   single    0.970  0.020  1.090
 ROU  CAK  H8   single    0.930  0.020  1.080
 ROU  CAM  H9   single    0.930  0.020  1.080
 ROU  CAL  H10  single    0.930  0.020  1.080

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
 ROU  H1   OAA  CAR  110.81  3.000
 ROU  CAV  CAR  OAD  123.96  3.000
 ROU  CAV  CAR  OAA  111.19  3.000
 ROU  OAD  CAR  OAA  124.85  3.000
 ROU  CAW  CAV  NAP  121.98  3.000
 ROU  NAP  CAV  CAR  114.98  3.000
 ROU  CAW  CAV  CAR  123.04  3.000
 ROU  H2   NAP  CAX  116.11  3.000
 ROU  H2   NAP  CAV  119.69  3.000
 ROU  CAX  NAP  CAV  124.17  3.000
 ROU  NAQ  CAX  OAB  123.19  3.000
 ROU  OAB  CAX  NAP  123.31  3.000
 ROU  NAQ  CAX  NAP  113.49  3.000
 ROU  H3   NAQ  CAY  116.69  3.000
 ROU  H3   NAQ  CAX  116.02  3.000
 ROU  CAY  NAQ  CAX  127.29  3.000
 ROU  CAW  CAY  OAC  123.85  3.000
 ROU  CAW  CAY  NAQ  115.71  3.000
 ROU  OAC  CAY  NAQ  120.45  3.000
 ROU  CAO  CAW  CAY  116.42  3.000
 ROU  CAY  CAW  CAV  117.35  3.000
 ROU  CAO  CAW  CAV  126.22  3.000
 ROU  H5   CAO  H4   106.46  3.000
 ROU  H5   CAO  CAN  109.77  3.000
 ROU  H4   CAO  CAN  109.10  3.000
 ROU  H5   CAO  CAW  110.95  3.000
 ROU  H4   CAO  CAW  108.52  3.000
 ROU  CAN  CAO  CAW  111.86  3.000
 ROU  H7   CAN  H6   107.01  3.000
 ROU  H7   CAN  CAS  109.91  3.000
 ROU  H6   CAN  CAS  109.56  3.000
 ROU  H7   CAN  CAO  109.57  3.000
 ROU  H6   CAN  CAO  109.35  3.000
 ROU  CAS  CAN  CAO  111.35  3.000
 ROU  CAL  CAS  CAK  118.54  3.000
 ROU  CAL  CAS  CAN  120.08  3.000
 ROU  CAK  CAS  CAN  121.36  3.000
 ROU  H8   CAK  CAT  120.41  3.000
 ROU  H8   CAK  CAS  118.90  3.000
 ROU  CAT  CAK  CAS  120.69  3.000
 ROU  CAM  CAT  CAZ  121.10  3.000
 ROU  CAM  CAT  CAK  120.62  3.000
 ROU  CAZ  CAT  CAK  118.29  3.000
 ROU  FAE  CAZ  FAG  106.50  3.000
 ROU  FAG  CAZ  FAF  107.12  3.000
 ROU  FAE  CAZ  FAF  107.12  3.000
 ROU  FAF  CAZ  CAT  112.84  3.000
 ROU  FAG  CAZ  CAT  111.48  3.000
 ROU  FAE  CAZ  CAT  111.43  3.000
 ROU  H9   CAM  CAU  120.52  3.000
 ROU  H9   CAM  CAT  120.65  3.000
 ROU  CAU  CAM  CAT  118.83  3.000
 ROU  CAL  CAU  CBA  118.33  3.000
 ROU  CAL  CAU  CAM  120.58  3.000
 ROU  CBA  CAU  CAM  121.09  3.000
 ROU  FAH  CBA  FAJ  107.11  3.000
 ROU  FAJ  CBA  FAI  106.55  3.000
 ROU  FAH  CBA  FAI  107.11  3.000
 ROU  FAJ  CBA  CAU  111.44  3.000
 ROU  FAH  CBA  CAU  112.80  3.000
 ROU  FAI  CBA  CAU  111.48  3.000
 ROU  H10  CAL  CAU  120.52  3.000
 ROU  H10  CAL  CAS  118.74  3.000
 ROU  CAU  CAL  CAS  120.74  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
 ROU  CONST_01  CAM  CAT  CAK  CAS     0.00   0.0  0
 ROU  CONST_02  CAM  CAU  CAL  CAS     0.00   0.0  0
 ROU  CONST_03  CAU  CAM  CAT  CAK     0.00   0.0  0
 ROU  CONST_04  CAU  CAL  CAS  CAK     0.00   0.0  0
 ROU  CONST_05  CAL  CAU  CAM  CAT     0.00   0.0  0
 ROU  CONST_06  CAL  CAS  CAK  CAT     0.00   0.0  0
 ROU  CONST_07  NAQ  CAX  NAP  CAV     0.00   0.0  0
 ROU  CONST_08  CAY  NAQ  CAX  NAP     0.00   0.0  0
 ROU  CONST_09  CAW  CAY  NAQ  CAX     0.00   0.0  0
 ROU  CONST_10  CAT  CAK  CAS  CAN   180.00   0.0  0
 ROU  CONST_11  CAU  CAL  CAS  CAN   180.00   0.0  0
 ROU  CONST_12  CAZ  CAT  CAK  CAS   180.00   0.0  0
 ROU  CONST_13  CBA  CAU  CAL  CAS   180.00   0.0  0
 ROU  CONST_14  CBA  CAU  CAM  CAT   180.00   0.0  0
 ROU  CONST_15  CAU  CAM  CAT  CAZ   180.00   0.0  0
 ROU  CONST_16  OAB  CAX  NAP  CAV   180.00   0.0  0
 ROU  CONST_17  OAC  CAY  NAQ  CAX   180.00   0.0  0
 ROU  CONST_18  CAY  NAQ  CAX  OAB   180.00   0.0  0
 ROU  CONST_19  H9   CAM  CAT  CAK   180.00   0.0  0
 ROU  CONST_20  H10  CAL  CAS  CAK   180.00   0.0  0
 ROU  CONST_21  H8   CAK  CAT  CAM   180.00   0.0  0
 ROU  CONST_22  H3   NAQ  CAX  NAP   180.00   0.0  0
 ROU  CONST_23  H2   NAP  CAX  NAQ   180.00   0.0  0
 ROU  CONST_24  H1   OAA  CAR  CAV   180.00   0.0  0
 ROU  Var_01    CAW  CAV  CAR  OAA   153.87  30.0  2
 ROU  Var_02    CAN  CAO  CAW  CAV    94.78  30.0  1
 ROU  Var_03    CAS  CAN  CAO  CAW  -175.67  30.0  1
 ROU  Var_04    CAK  CAS  CAN  CAO  -100.74  30.0  2
 ROU  Var_05    FAE  CAZ  CAT  CAK    60.79  30.0  3
 ROU  Var_06    FAI  CBA  CAU  CAM   117.71  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
 ROU  plan-1  CAR  0.020
 ROU  plan-1  CAV  0.020
 ROU  plan-1  NAP  0.020
 ROU  plan-1  CAX  0.020
 ROU  plan-1  OAB  0.020
 ROU  plan-1  NAQ  0.020
 ROU  plan-1  CAY  0.020
 ROU  plan-1  OAC  0.020
 ROU  plan-1  CAW  0.020
 ROU  plan-1  CAO  0.020
 ROU  plan-1  H2   0.020
 ROU  plan-1  H3   0.020
 ROU  plan-2  CAN  0.020
 ROU  plan-2  CAS  0.020
 ROU  plan-2  CAK  0.020
 ROU  plan-2  CAT  0.020
 ROU  plan-2  CAZ  0.020
 ROU  plan-2  CAM  0.020
 ROU  plan-2  CAU  0.020
 ROU  plan-2  CBA  0.020
 ROU  plan-2  CAL  0.020
 ROU  plan-2  H8   0.020
 ROU  plan-2  H9   0.020
 ROU  plan-2  H10  0.020
 ROU  plan-3  OAA  0.020
 ROU  plan-3  CAR  0.020
 ROU  plan-3  OAD  0.020
 ROU  plan-3  CAV  0.020
 ROU  plan-3  H1   0.020

