# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 13:27:01 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  36  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 OK
;

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  OC    -1  -0.583  -4.2324   3.0049  -0.0680
 ROU  CAR  C  C      0   0.418  -3.2954   2.1870  -0.0641
 ROU  OAD  O  O      0  -0.541  -2.0807   2.4133  -0.0141
 ROU  CAV  C  CR6    0   0.207  -3.7475   0.7130  -0.1036
 ROU  NAP  N  NR16   0  -0.706  -5.0895   0.5867   0.1254
 ROU  CAX  C  CR6    0   0.657  -5.7735  -0.5854   0.1704
 ROU  OAB  O  O      0  -0.491  -6.9730  -0.6633   0.3601
 ROU  NAQ  N  NR16   0  -0.715  -4.9731  -1.6829  -0.0083
 ROU  CAY  C  CR6    0   0.565  -3.6109  -1.6890  -0.2449
 ROU  OAC  O  O      0  -0.466  -3.0263  -2.7526  -0.3727
 ROU  CAW  C  CR6    0  -0.160  -2.9753  -0.3801  -0.3186
 ROU  CAO  C  CH2    0  -0.481  -1.4980  -0.3655  -0.5722
 ROU  CAN  C  CH2    0  -0.501  -0.6940  -0.4672   0.7319
 ROU  CAS  C  C      0   0.161   0.7771  -0.3135   0.4871
 ROU  CAK  C  C1     0  -0.343   1.6214  -1.4159   0.4257
 ROU  CAT  C  C      0  -0.152   2.9774  -1.2568   0.1718
 ROU  CAZ  C  CT     0   1.059   3.8526  -2.4670   0.0590
 ROU  FAF  F  F      0  -0.305   5.1341  -2.1961   0.3258
 ROU  FAG  F  F      0  -0.306   3.4740  -3.4421   0.8921
 ROU  FAE  F  F      0  -0.313   3.8156  -2.9814  -1.1797
 ROU  CAM  C  C1     0  -0.350   3.5143   0.0068  -0.0299
 ROU  CAU  C  C      0  -0.148   2.6740   1.1083   0.0263
 ROU  CBA  C  CT     0   1.058   3.2015   2.4953  -0.1755
 ROU  FAI  F  F      0  -0.313   2.6296   3.0890  -1.2323
 ROU  FAJ  F  F      0  -0.312   2.9475   3.2759   0.8838
 ROU  FAH  F  F      0  -0.300   4.5211   2.5235  -0.3756
 ROU  CAL  C  C1     0  -0.325   1.3182   0.9502   0.2803
 ROU  H2   H  HNR6   0   0.417  -5.5988   1.4579   0.2220
 ROU  H3   H  HNR6   0   0.421  -5.4315  -2.5841   0.0384
 ROU  H4   H  HCH2   0   0.245  -1.2386  -1.2072  -1.2170
 ROU  H5   H  HCH2   0   0.260  -1.2152   0.5409  -1.0992
 ROU  H6   H  HCH2   0   0.258  -1.0334   0.3126   1.4141
 ROU  H7   H  HCH2   0   0.251  -0.8934  -1.4258   1.2135
 ROU  H8   H  H      0   0.273   1.2043  -2.4024   0.5869
 ROU  H9   H  H      0   0.283   4.5712   0.1295  -0.2192
 ROU  H10  H  H      0   0.279   0.6571   1.8085   0.3204

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    1.342  0.020  1.342
 ROU  FAG  CAZ  single    1.337  0.020  1.337
 ROU  CAZ  CAT  single    1.498  0.020  1.498
 ROU  CAZ  FAF  single    1.337  0.020  1.337
 ROU  FAI  CBA  single    1.340  0.020  1.340
 ROU  CAT  CAM  aromatic  1.388  0.020  1.388
 ROU  CAT  CAK  aromatic  1.389  0.020  1.389
 ROU  CAM  CAU  aromatic  1.387  0.020  1.387
 ROU  CAK  CAS  aromatic  1.390  0.020  1.390
 ROU  CAU  CBA  single    1.498  0.020  1.498
 ROU  CAU  CAL  aromatic  1.388  0.020  1.388
 ROU  CAS  CAL  aromatic  1.390  0.020  1.390
 ROU  CAS  CAN  single    1.499  0.020  1.499
 ROU  CBA  FAH  single    1.335  0.020  1.335
 ROU  CBA  FAJ  single    1.340  0.020  1.340
 ROU  CAN  CAO  single    1.535  0.020  1.535
 ROU  CAO  CAW  single    1.499  0.020  1.499
 ROU  OAC  CAY  double    1.220  0.020  1.220
 ROU  CAW  CAY  single    1.457  0.020  1.457
 ROU  CAW  CAV  double    1.356  0.020  1.356
 ROU  CAY  NAQ  single    1.383  0.020  1.383
 ROU  OAD  CAR  deloc     1.237  0.020  1.237
 ROU  OAA  CAR  deloc     1.244  0.020  1.244
 ROU  CAR  CAV  single    1.542  0.020  1.542
 ROU  CAV  NAP  single    1.367  0.020  1.367
 ROU  NAQ  CAX  single    1.370  0.020  1.370
 ROU  NAP  CAX  single    1.358  0.020  1.358
 ROU  CAX  OAB  double    1.217  0.020  1.217
 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  CAV  CAR  OAD  117.64  3.000
 ROU  CAV  CAR  OAA  114.05  3.000
 ROU  OAD  CAR  OAA  128.30  3.000
 ROU  CAW  CAV  NAP  120.74  3.000
 ROU  NAP  CAV  CAR  111.83  3.000
 ROU  CAW  CAV  CAR  127.43  3.000
 ROU  H2   NAP  CAX  119.05  3.000
 ROU  H2   NAP  CAV  115.44  3.000
 ROU  CAX  NAP  CAV  125.43  3.000
 ROU  NAQ  CAX  OAB  123.02  3.000
 ROU  OAB  CAX  NAP  123.84  3.000
 ROU  NAQ  CAX  NAP  113.14  3.000
 ROU  H3   NAQ  CAY  116.75  3.000
 ROU  H3   NAQ  CAX  116.28  3.000
 ROU  CAY  NAQ  CAX  126.97  3.000
 ROU  CAW  CAY  OAC  124.66  3.000
 ROU  CAW  CAY  NAQ  115.75  3.000
 ROU  OAC  CAY  NAQ  119.59  3.000
 ROU  CAO  CAW  CAY  116.57  3.000
 ROU  CAY  CAW  CAV  117.90  3.000
 ROU  CAO  CAW  CAV  125.47  3.000
 ROU  H5   CAO  H4   107.16  3.000
 ROU  H5   CAO  CAN  109.33  3.000
 ROU  H4   CAO  CAN  109.04  3.000
 ROU  H5   CAO  CAW  110.30  3.000
 ROU  H4   CAO  CAW  109.06  3.000
 ROU  CAN  CAO  CAW  111.82  3.000
 ROU  H7   CAN  H6   107.18  3.000
 ROU  H7   CAN  CAS  109.96  3.000
 ROU  H6   CAN  CAS  109.53  3.000
 ROU  H7   CAN  CAO  109.72  3.000
 ROU  H6   CAN  CAO  108.73  3.000
 ROU  CAS  CAN  CAO  111.61  3.000
 ROU  CAL  CAS  CAK  118.56  3.000
 ROU  CAL  CAS  CAN  119.96  3.000
 ROU  CAK  CAS  CAN  121.46  3.000
 ROU  H8   CAK  CAT  120.50  3.000
 ROU  H8   CAK  CAS  118.81  3.000
 ROU  CAT  CAK  CAS  120.68  3.000
 ROU  CAM  CAT  CAZ  119.92  3.000
 ROU  CAM  CAT  CAK  120.58  3.000
 ROU  CAZ  CAT  CAK  119.46  3.000
 ROU  FAE  CAZ  FAG  106.73  3.000
 ROU  FAG  CAZ  FAF  107.15  3.000
 ROU  FAE  CAZ  FAF  106.77  3.000
 ROU  FAF  CAZ  CAT  112.42  3.000
 ROU  FAG  CAZ  CAT  112.13  3.000
 ROU  FAE  CAZ  CAT  111.30  3.000
 ROU  H9   CAM  CAU  120.64  3.000
 ROU  H9   CAM  CAT  120.48  3.000
 ROU  CAU  CAM  CAT  118.88  3.000
 ROU  CAL  CAU  CBA  118.30  3.000
 ROU  CAL  CAU  CAM  120.58  3.000
 ROU  CBA  CAU  CAM  121.12  3.000
 ROU  FAH  CBA  FAJ  107.07  3.000
 ROU  FAJ  CBA  FAI  106.52  3.000
 ROU  FAH  CBA  FAI  107.11  3.000
 ROU  FAJ  CBA  CAU  111.48  3.000
 ROU  FAH  CBA  CAU  112.83  3.000
 ROU  FAI  CBA  CAU  111.48  3.000
 ROU  H10  CAL  CAU  120.80  3.000
 ROU  H10  CAL  CAS  118.48  3.000
 ROU  CAU  CAL  CAS  120.72  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  Var_01    CAW  CAV  CAR  OAA   168.77  30.0  2
 ROU  Var_02    CAN  CAO  CAW  CAV    90.09  30.0  2
 ROU  Var_03    CAS  CAN  CAO  CAW  -174.27  30.0  1
 ROU  Var_04    CAK  CAS  CAN  CAO  -100.23  30.0  2
 ROU  Var_05    FAE  CAZ  CAT  CAK    84.29  30.0  2
 ROU  Var_06    FAI  CBA  CAU  CAM   119.25  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

