# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 10:11:23 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  33  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 OK
;

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  OC    -1  -0.584   3.6309   2.9401   0.3057
 ROD  CAP  C  C      0   0.418   2.5397   2.3633   0.1488
 ROD  OAD  O  O      0  -0.541   1.4069   2.8587   0.1423
 ROD  CAS  C  CR6    0   0.203   2.6579   0.8369  -0.0391
 ROD  NAN  N  NR16   0  -0.707   3.9325   0.3992   0.1949
 ROD  CAU  C  CR6    0   0.656   4.3473  -0.8915   0.1339
 ROD  OAB  O  O      0  -0.493   5.4911  -1.2476   0.3496
 ROD  NAO  N  NR16   0  -0.715   3.3432  -1.7637  -0.1934
 ROD  CAV  C  CR6    0   0.561   2.0229  -1.4494  -0.4624
 ROD  OAC  O  O      0  -0.458   1.2373  -2.3408  -0.7371
 ROD  CAT  C  CR6    0  -0.162   1.6788  -0.0339  -0.3874
 ROD  CAM  C  CH2    0  -0.474   0.2479   0.3174  -0.6667
 ROD  CAL  C  CH2    0  -0.525  -0.6088   0.2705   0.6071
 ROD  CAQ  C  CR6    0   0.145  -2.0201   0.7309   0.3446
 ROD  CAJ  C  CR16   0  -0.304  -2.2213   2.1053   0.2203
 ROD  CAH  C  CR16   0  -0.231  -3.4680   2.6408  -0.0565
 ROD  CAI  C  CR16   0  -0.259  -4.5581   1.7991  -0.2184
 ROD  CAK  C  CR16   0  -0.281  -4.3866   0.4304  -0.0985
 ROD  CAR  C  CR6    0  -0.279  -3.1308  -0.1067   0.1783
 ROD  CAW  C  CT     0   1.052  -2.9988  -1.5946   0.3136
 ROD  FAF  F  F      0  -0.318  -2.6236  -1.9596   1.5513
 ROD  FAG  F  F      0  -0.303  -4.1467  -2.2370   0.0682
 ROD  FAE  F  F      0  -0.312  -2.0922  -2.1064  -0.5305
 ROD  H2   H  HNR6   0   0.420   3.5981  -2.7420  -0.2438
 ROD  H4   H  HCH2   0   0.256   0.1807   1.3086  -1.1045
 ROD  H5   H  HCH2   0   0.247  -0.1544  -0.3861  -1.3955
 ROD  H6   H  HCH2   0   0.250  -0.5610  -0.7248   1.0436
 ROD  H7   H  HCH2   0   0.260  -0.1623   0.9478   1.3361
 ROD  H8   H  HCR6   0   0.265  -1.3691   2.7628   0.3444
 ROD  H9   H  HCR6   0   0.263  -3.5876   3.7129  -0.1431
 ROD  H10  H  HCR6   0   0.264  -5.5385   2.2011  -0.4352
 ROD  H11  H  HCR6   0   0.268  -5.2457  -0.2131  -0.2245
 ROD  H12  H  HNR6   0   0.417   4.6052   1.1259   0.4133

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  1.387  0.020  1.387
 ROD  CAI  CAK  aromatic  1.385  0.020  1.385
 ROD  CAH  CAJ  aromatic  1.385  0.020  1.385
 ROD  CAK  CAR  aromatic  1.394  0.020  1.394
 ROD  CAJ  CAQ  aromatic  1.395  0.020  1.395
 ROD  CAR  CAQ  aromatic  1.401  0.020  1.401
 ROD  CAR  CAW  single    1.500  0.020  1.500
 ROD  CAQ  CAL  single    1.507  0.020  1.507
 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    1.536  0.020  1.536
 ROD  CAM  CAT  single    1.500  0.020  1.500
 ROD  OAC  CAV  double    1.220  0.020  1.220
 ROD  CAT  CAV  single    1.459  0.020  1.459
 ROD  CAT  CAS  double    1.356  0.020  1.356
 ROD  CAV  NAO  single    1.384  0.020  1.384
 ROD  CAS  CAP  single    1.542  0.020  1.542
 ROD  CAS  NAN  single    1.368  0.020  1.368
 ROD  NAO  CAU  single    1.370  0.020  1.370
 ROD  OAD  CAP  deloc     1.236  0.020  1.236
 ROD  CAP  OAA  deloc     1.244  0.020  1.244
 ROD  NAN  CAU  single    1.357  0.020  1.357
 ROD  CAU  OAB  double    1.217  0.020  1.217
 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  CAS  CAP  OAD  117.78  3.000
 ROD  OAD  CAP  OAA  128.20  3.000
 ROD  CAS  CAP  OAA  114.01  3.000
 ROD  CAT  CAS  NAN  120.75  3.000
 ROD  NAN  CAS  CAP  111.54  3.000
 ROD  CAT  CAS  CAP  127.70  3.000
 ROD  H12  NAN  CAU  119.24  3.000
 ROD  H12  NAN  CAS  115.20  3.000
 ROD  CAU  NAN  CAS  125.55  3.000
 ROD  NAO  CAU  OAB  123.02  3.000
 ROD  OAB  CAU  NAN  123.88  3.000
 ROD  NAO  CAU  NAN  113.10  3.000
 ROD  H2   NAO  CAV  116.75  3.000
 ROD  H2   NAO  CAU  116.28  3.000
 ROD  CAV  NAO  CAU  126.97  3.000
 ROD  CAT  CAV  OAC  124.67  3.000
 ROD  CAT  CAV  NAO  115.82  3.000
 ROD  OAC  CAV  NAO  119.51  3.000
 ROD  CAM  CAT  CAV  116.29  3.000
 ROD  CAV  CAT  CAS  117.78  3.000
 ROD  CAM  CAT  CAS  125.90  3.000
 ROD  H5   CAM  H4   107.27  3.000
 ROD  H5   CAM  CAL  109.20  3.000
 ROD  H4   CAM  CAL  109.14  3.000
 ROD  H5   CAM  CAT  109.00  3.000
 ROD  H4   CAM  CAT  110.37  3.000
 ROD  CAL  CAM  CAT  111.76  3.000
 ROD  H7   CAL  H6   106.38  3.000
 ROD  H7   CAL  CAQ  108.05  3.000
 ROD  H6   CAL  CAQ  112.98  3.000
 ROD  H7   CAL  CAM  107.88  3.000
 ROD  H6   CAL  CAM  109.65  3.000
 ROD  CAQ  CAL  CAM  111.62  3.000
 ROD  CAR  CAQ  CAJ  117.66  3.000
 ROD  CAR  CAQ  CAL  125.47  3.000
 ROD  CAJ  CAQ  CAL  116.85  3.000
 ROD  H8   CAJ  CAH  119.76  3.000
 ROD  H8   CAJ  CAQ  118.31  3.000
 ROD  CAH  CAJ  CAQ  121.93  3.000
 ROD  H9   CAH  CAI  120.34  3.000
 ROD  H9   CAH  CAJ  119.90  3.000
 ROD  CAI  CAH  CAJ  119.76  3.000
 ROD  H10  CAI  CAK  119.80  3.000
 ROD  H10  CAI  CAH  120.69  3.000
 ROD  CAK  CAI  CAH  119.50  3.000
 ROD  H11  CAK  CAR  120.66  3.000
 ROD  H11  CAK  CAI  118.69  3.000
 ROD  CAR  CAK  CAI  120.65  3.000
 ROD  CAW  CAR  CAK  118.66  3.000
 ROD  CAW  CAR  CAQ  120.84  3.000
 ROD  CAK  CAR  CAQ  120.50  3.000
 ROD  FAE  CAW  FAG  106.35  3.000
 ROD  FAG  CAW  FAF  106.14  3.000
 ROD  FAE  CAW  FAF  106.70  3.000
 ROD  FAG  CAW  CAR  112.60  3.000
 ROD  FAF  CAW  CAR  112.16  3.000
 ROD  FAE  CAW  CAR  112.43  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  Var_01    CAT  CAS  CAP  OAA  -171.41  30.0  2
 ROD  Var_02    CAL  CAM  CAT  CAS   -89.40  30.0  2
 ROD  Var_03    CAQ  CAL  CAM  CAT   175.42  30.0  1
 ROD  Var_04    CAJ  CAQ  CAL  CAM   -76.76  30.0  2
 ROD  Var_05    FAE  CAW  CAR  CAQ   -57.30  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

