# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 24 03:43:15 2021
#   Inital geometry file: a 94 line input string
#   Ligand name: 2,6-dioxo-5-{2-[4-(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(CCc2ccc(cc2)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
 ZRO  ZRO  '2,6-dioxo-5-{2-[4-(trifluoromethyl)phenyl]ethyl}-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  34  23  .  2021-08-25  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZRO
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
 ZRO  OAA  O  O     0  -0.396  -4.2069  -15.0911  13.3587
 ZRO  CAP  C  C     0   0.523  -4.5996  -14.4050  14.2623
 ZRO  OAD  O  OH1   0  -0.591  -4.2720  -14.5712  15.5306
 ZRO  CAS  C  CR6   0   0.282  -5.5175  -13.2321  14.0900
 ZRO  NAN  N  NR16  0  -0.732  -5.4603  -12.2979  15.0936
 ZRO  CAU  C  CR6   0   0.671  -6.1989  -11.1513  15.1181
 ZRO  OAB  O  O     0  -0.472  -6.1328  -10.3349  16.0123
 ZRO  NAO  N  NR16  0  -0.716  -7.0218  -11.0078  14.0319
 ZRO  CAV  C  CR6   0   0.587  -7.1619  -11.8758  12.9710
 ZRO  OAC  O  O     0  -0.440  -7.9244  -11.6157  12.0610
 ZRO  CAT  C  CR6   0  -0.120  -6.3436  -13.0914  13.0299
 ZRO  CAM  C  CH2   0  -0.500  -6.5059  -14.0490  11.8899
 ZRO  CAL  C  CH2   0  -0.506  -5.6063  -13.6873  10.6982
 ZRO  CAQ  C  CR6   0   0.130  -5.8211  -14.6334   9.5537
 ZRO  CAH  C  CR16  0  -0.290  -5.1359  -15.8465   9.4946
 ZRO  CAJ  C  CR16  0  -0.253  -5.3528  -16.7363   8.4577
 ZRO  CAR  C  CR6   0  -0.210  -6.2697  -16.4265   7.4564
 ZRO  CAW  C  CT    0   1.049  -6.4710  -17.4006   6.3417
 ZRO  FAF  F  F     0  -0.303  -7.3901  -16.9979   5.4593
 ZRO  FAG  F  F     0  -0.316  -5.3367  -17.6104   5.6546
 ZRO  FAE  F  F     0  -0.316  -6.8628  -18.6023   6.7928
 ZRO  CAK  C  CR16  0  -0.269  -6.9644  -15.2259   7.5051
 ZRO  CAI  C  CR16  0  -0.294  -6.7378  -14.3414   8.5499
 ZRO  H1   H  HOH1  0   0.504  -3.6473  -15.3064  15.6332
 ZRO  H2   H  HNR6  0   0.431  -7.5832  -10.1648  14.0091
 ZRO  H4   H  HCH2  0   0.266  -7.5473  -14.0207  11.5651
 ZRO  H5   H  HCH2  0   0.267  -6.3068  -15.0713  12.2030
 ZRO  H6   H  HCH2  0   0.261  -4.5626  -13.7138  11.0138
 ZRO  H7   H  HCH2  0   0.258  -5.8196  -12.6666  10.3748
 ZRO  H8   H  HCR6  0   0.258  -4.4197  -16.0949  10.2687
 ZRO  H9   H  HCR6  0   0.272  -4.7996  -17.6670   8.4364
 ZRO  H10  H  HCR6  0   0.269  -7.6806  -14.9632   6.7386
 ZRO  H11  H  HCR6  0   0.257  -7.2830  -13.4056   8.5779
 ZRO  H12  H  HNR6  0   0.439  -4.8298  -12.4376  15.8708

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
 ZRO  FAF  CAW  single    1.336  0.020  1.336
 ZRO  FAG  CAW  single    1.343  0.020  1.343
 ZRO  CAW  FAE  single    1.342  0.020  1.342
 ZRO  CAW  CAR  single    1.494  0.020  1.494
 ZRO  CAR  CAK  aromatic  1.388  0.020  1.388
 ZRO  CAR  CAJ  aromatic  1.393  0.020  1.393
 ZRO  CAK  CAI  aromatic  1.388  0.020  1.388
 ZRO  CAJ  CAH  aromatic  1.383  0.020  1.383
 ZRO  CAI  CAQ  aromatic  1.390  0.020  1.390
 ZRO  CAH  CAQ  aromatic  1.394  0.020  1.394
 ZRO  CAQ  CAL  single    1.500  0.020  1.500
 ZRO  CAL  CAM  single    1.536  0.020  1.536
 ZRO  CAM  CAT  single    1.498  0.020  1.498
 ZRO  OAC  CAV  double    1.215  0.020  1.215
 ZRO  CAT  CAV  single    1.467  0.020  1.467
 ZRO  CAT  CAS  double    1.351  0.020  1.351
 ZRO  CAV  NAO  single    1.378  0.020  1.378
 ZRO  CAS  CAP  single    1.499  0.020  1.499
 ZRO  CAS  NAN  single    1.372  0.020  1.372
 ZRO  OAA  CAP  double    1.201  0.020  1.201
 ZRO  CAP  OAD  single    1.320  0.020  1.320
 ZRO  NAO  CAU  single    1.370  0.020  1.370
 ZRO  NAN  CAU  single    1.364  0.020  1.364
 ZRO  CAU  OAB  double    1.213  0.020  1.213
 ZRO  OAD  H1   single    0.850  0.020  0.980
 ZRO  NAO  H2   single    0.860  0.020  1.020
 ZRO  CAM  H4   single    0.970  0.020  1.090
 ZRO  CAM  H5   single    0.970  0.020  1.090
 ZRO  CAL  H6   single    0.970  0.020  1.090
 ZRO  CAL  H7   single    0.970  0.020  1.090
 ZRO  CAH  H8   single    0.930  0.020  1.080
 ZRO  CAJ  H9   single    0.930  0.020  1.080
 ZRO  CAK  H10  single    0.930  0.020  1.080
 ZRO  CAI  H11  single    0.930  0.020  1.080
 ZRO  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
 ZRO  CAS  CAP  OAD  111.15  3.000
 ZRO  OAD  CAP  OAA  124.74  3.000
 ZRO  CAS  CAP  OAA  124.11  3.000
 ZRO  H1   OAD  CAP  110.90  3.000
 ZRO  CAT  CAS  NAN  121.89  3.000
 ZRO  NAN  CAS  CAP  115.02  3.000
 ZRO  CAT  CAS  CAP  123.09  3.000
 ZRO  H12  NAN  CAU  116.12  3.000
 ZRO  H12  NAN  CAS  119.63  3.000
 ZRO  CAU  NAN  CAS  124.24  3.000
 ZRO  NAO  CAU  OAB  123.14  3.000
 ZRO  OAB  CAU  NAN  123.34  3.000
 ZRO  NAO  CAU  NAN  113.52  3.000
 ZRO  H2   NAO  CAV  116.77  3.000
 ZRO  H2   NAO  CAU  115.97  3.000
 ZRO  CAV  NAO  CAU  127.26  3.000
 ZRO  CAT  CAV  OAC  123.89  3.000
 ZRO  CAT  CAV  NAO  115.75  3.000
 ZRO  OAC  CAV  NAO  120.36  3.000
 ZRO  CAM  CAT  CAV  116.03  3.000
 ZRO  CAV  CAT  CAS  117.32  3.000
 ZRO  CAM  CAT  CAS  126.64  3.000
 ZRO  H5   CAM  H4   106.55  3.000
 ZRO  H5   CAM  CAL  109.72  3.000
 ZRO  H4   CAM  CAL  108.78  3.000
 ZRO  H5   CAM  CAT  111.23  3.000
 ZRO  H4   CAM  CAT  108.26  3.000
 ZRO  CAL  CAM  CAT  112.11  3.000
 ZRO  H7   CAL  H6   107.18  3.000
 ZRO  H7   CAL  CAQ  109.61  3.000
 ZRO  H6   CAL  CAQ  110.02  3.000
 ZRO  H7   CAL  CAM  109.60  3.000
 ZRO  H6   CAL  CAM  109.28  3.000
 ZRO  CAQ  CAL  CAM  111.06  3.000
 ZRO  CAI  CAQ  CAH  118.43  3.000
 ZRO  CAH  CAQ  CAL  120.70  3.000
 ZRO  CAI  CAQ  CAL  120.84  3.000
 ZRO  H8   CAH  CAJ  119.44  3.000
 ZRO  H8   CAH  CAQ  119.61  3.000
 ZRO  CAJ  CAH  CAQ  120.95  3.000
 ZRO  H9   CAJ  CAR  120.89  3.000
 ZRO  H9   CAJ  CAH  119.18  3.000
 ZRO  CAR  CAJ  CAH  119.93  3.000
 ZRO  CAK  CAR  CAW  121.52  3.000
 ZRO  CAK  CAR  CAJ  119.79  3.000
 ZRO  CAW  CAR  CAJ  118.70  3.000
 ZRO  FAE  CAW  FAG  106.18  3.000
 ZRO  FAE  CAW  FAF  106.92  3.000
 ZRO  FAG  CAW  FAF  106.88  3.000
 ZRO  FAE  CAW  CAR  111.86  3.000
 ZRO  FAG  CAW  CAR  111.71  3.000
 ZRO  FAF  CAW  CAR  112.89  3.000
 ZRO  H10  CAK  CAI  119.14  3.000
 ZRO  H10  CAK  CAR  121.11  3.000
 ZRO  CAI  CAK  CAR  119.74  3.000
 ZRO  H11  CAI  CAK  119.20  3.000
 ZRO  H11  CAI  CAQ  119.64  3.000
 ZRO  CAK  CAI  CAQ  121.15  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
 ZRO  CONST_01  CAR  CAK  CAI  CAQ     0.00   0.0  0
 ZRO  CONST_02  CAR  CAJ  CAH  CAQ     0.00   0.0  0
 ZRO  CONST_03  CAK  CAR  CAJ  CAH     0.00   0.0  0
 ZRO  CONST_04  CAK  CAI  CAQ  CAH     0.00   0.0  0
 ZRO  CONST_05  CAI  CAK  CAR  CAJ     0.00   0.0  0
 ZRO  CONST_06  CAI  CAQ  CAH  CAJ     0.00   0.0  0
 ZRO  CONST_07  NAO  CAU  NAN  CAS     0.00   0.0  0
 ZRO  CONST_08  CAV  NAO  CAU  NAN     0.00   0.0  0
 ZRO  CONST_09  CAT  CAV  NAO  CAU     0.00   0.0  0
 ZRO  CONST_10  CAK  CAI  CAQ  CAL   180.00   0.0  0
 ZRO  CONST_11  CAJ  CAH  CAQ  CAL   180.00   0.0  0
 ZRO  CONST_12  CAW  CAR  CAJ  CAH   180.00   0.0  0
 ZRO  CONST_13  CAI  CAK  CAR  CAW   180.00   0.0  0
 ZRO  CONST_14  OAB  CAU  NAN  CAS   180.00   0.0  0
 ZRO  CONST_15  OAC  CAV  NAO  CAU   180.00   0.0  0
 ZRO  CONST_16  CAV  NAO  CAU  OAB   180.00   0.0  0
 ZRO  CONST_17  H10  CAK  CAI  CAQ   180.00   0.0  0
 ZRO  CONST_18  H9   CAJ  CAH  CAQ   180.00   0.0  0
 ZRO  CONST_19  H11  CAI  CAQ  CAH   180.00   0.0  0
 ZRO  CONST_20  H8   CAH  CAJ  CAR   180.00   0.0  0
 ZRO  CONST_21  H2   NAO  CAU  NAN   180.00   0.0  0
 ZRO  CONST_22  H12  NAN  CAU  NAO   180.00   0.0  0
 ZRO  CONST_23  H1   OAD  CAP  CAS   180.00   0.0  0
 ZRO  Var_01    CAT  CAS  CAP  OAA    23.31  30.0  2
 ZRO  Var_02    CAL  CAM  CAT  CAS   -93.88  30.0  1
 ZRO  Var_03    CAQ  CAL  CAM  CAT  -178.10  30.0  2
 ZRO  Var_04    CAI  CAQ  CAL  CAM    92.80  30.0  3
 ZRO  Var_05    FAF  CAW  CAR  CAJ   178.97  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
 ZRO  plan-1  CAP  0.020
 ZRO  plan-1  CAS  0.020
 ZRO  plan-1  NAN  0.020
 ZRO  plan-1  CAU  0.020
 ZRO  plan-1  OAB  0.020
 ZRO  plan-1  NAO  0.020
 ZRO  plan-1  CAV  0.020
 ZRO  plan-1  OAC  0.020
 ZRO  plan-1  CAT  0.020
 ZRO  plan-1  CAM  0.020
 ZRO  plan-1  H2   0.020
 ZRO  plan-1  H12  0.020
 ZRO  plan-2  CAL  0.020
 ZRO  plan-2  CAQ  0.020
 ZRO  plan-2  CAH  0.020
 ZRO  plan-2  CAJ  0.020
 ZRO  plan-2  CAR  0.020
 ZRO  plan-2  CAW  0.020
 ZRO  plan-2  CAK  0.020
 ZRO  plan-2  CAI  0.020
 ZRO  plan-2  H8   0.020
 ZRO  plan-2  H9   0.020
 ZRO  plan-2  H10  0.020
 ZRO  plan-2  H11  0.020
 ZRO  plan-3  OAA  0.020
 ZRO  plan-3  CAP  0.020
 ZRO  plan-3  OAD  0.020
 ZRO  plan-3  CAS  0.020
 ZRO  plan-3  H1   0.020

