# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 05:31:39 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 5-[2-(4-carboxyphenyl)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(CCc2ccc(cc2)C(O)=O)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
 W7P  W7P  '5-[2-(4-carboxyphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  32  22  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_W7P
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
 W7P  OAB  O  OC    -1  -0.586  -3.3769  -3.1016   0.0112
 W7P  CAP  C  C      0   0.415  -2.4370  -2.2865   0.0392
 W7P  OAF  O  O      0  -0.540  -1.2235  -2.5171  -0.0067
 W7P  CAT  C  CR6    0   0.202  -2.8850  -0.8134   0.1239
 W7P  NAM  N  NR16   0  -0.707  -4.2348  -0.6838  -0.0593
 W7P  CAU  C  CR6    0   0.656  -4.9207   0.4869  -0.0678
 W7P  OAC  O  O      0  -0.493  -6.1235   0.5679  -0.2371
 W7P  NAN  N  NR16   0  -0.715  -4.1199   1.5804   0.1314
 W7P  CAV  C  CR6    0   0.564  -2.7529   1.5828   0.3395
 W7P  OAD  O  O      0  -0.466  -2.1713   2.6439   0.4988
 W7P  CAS  C  CR6    0  -0.159  -2.1080   0.2753   0.3458
 W7P  CAL  C  CH2    0  -0.475  -0.6234   0.2659   0.5553
 W7P  CAK  C  CH2    0  -0.494   0.1474   0.4372  -0.7619
 W7P  CAQ  C  CR6    0   0.115   1.6315   0.3474  -0.5530
 W7P  CAG  C  CR16   0  -0.310   2.4326   1.4848  -0.5054
 W7P  CAI  C  CR16   0  -0.276   3.7976   1.3880  -0.2695
 W7P  CAR  C  CR6    0  -0.116   4.4062   0.1511  -0.0759
 W7P  CAO  C  C      0   0.391   5.9017   0.0456   0.1866
 W7P  OAE  O  O      0  -0.597   6.5354   1.1172   0.2523
 W7P  OAA  O  OC    -1  -0.597   6.3685  -1.1032   0.3157
 W7P  CAJ  C  CR16   0  -0.277   3.6045  -0.9880  -0.1283
 W7P  CAH  C  CR16   0  -0.296   2.2413  -0.8921  -0.3603
 W7P  H2   H  HNR6   0   0.420  -4.5803   2.4817   0.1201
 W7P  H4   H  HCH2   0   0.237  -0.3555   1.0797   1.2319
 W7P  H5   H  HCH2   0   0.255  -0.3165  -0.6625   1.0270
 W7P  H6   H  HCH2   0   0.243  -0.1777  -0.3410  -1.4547
 W7P  H7   H  HCH2   0   0.238  -0.1098   1.3984  -1.2121
 W7P  H8   H  HCR6   0   0.236   1.9836   2.4601  -0.6588
 W7P  H9   H  HCR6   0   0.238   4.4010   2.2860  -0.2370
 W7P  H11  H  HCR6   0   0.236   4.0559  -1.9611   0.0153
 W7P  H12  H  HCR6   0   0.242   1.6327  -1.7894  -0.3926
 W7P  H13  H  HNR6   0   0.416  -4.7410  -1.5527  -0.1872

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
 W7P  CAG  CAI  aromatic  1.389  0.020  1.389
 W7P  CAG  CAQ  aromatic  1.392  0.020  1.392
 W7P  CAI  CAR  aromatic  1.392  0.020  1.392
 W7P  CAK  CAQ  single    1.501  0.020  1.501
 W7P  CAK  CAL  single    1.536  0.020  1.536
 W7P  CAQ  CAH  aromatic  1.395  0.020  1.395
 W7P  CAR  CAO  single    1.522  0.020  1.522
 W7P  CAR  CAJ  aromatic  1.394  0.020  1.394
 W7P  CAO  OAE  deloc     1.247  0.020  1.247
 W7P  CAO  OAA  deloc     1.247  0.020  1.247
 W7P  CAH  CAJ  aromatic  1.386  0.020  1.386
 W7P  CAL  CAS  single    1.499  0.020  1.499
 W7P  OAD  CAV  double    1.221  0.020  1.221
 W7P  CAS  CAV  single    1.458  0.020  1.458
 W7P  CAS  CAT  double    1.356  0.020  1.356
 W7P  CAV  NAN  single    1.383  0.020  1.383
 W7P  OAF  CAP  deloc     1.236  0.020  1.236
 W7P  CAT  CAP  single    1.542  0.020  1.542
 W7P  CAT  NAM  single    1.368  0.020  1.368
 W7P  NAN  CAU  single    1.370  0.020  1.370
 W7P  CAP  OAB  deloc     1.244  0.020  1.244
 W7P  NAM  CAU  single    1.357  0.020  1.357
 W7P  CAU  OAC  double    1.217  0.020  1.217
 W7P  NAN  H2   single    0.860  0.020  1.020
 W7P  CAL  H4   single    0.970  0.020  1.090
 W7P  CAL  H5   single    0.970  0.020  1.090
 W7P  CAK  H6   single    0.970  0.020  1.090
 W7P  CAK  H7   single    0.970  0.020  1.090
 W7P  CAG  H8   single    0.930  0.020  1.080
 W7P  CAI  H9   single    0.930  0.020  1.080
 W7P  CAJ  H11  single    0.930  0.020  1.080
 W7P  CAH  H12  single    0.930  0.020  1.080
 W7P  NAM  H13  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
 W7P  CAT  CAP  OAF  117.74  3.000
 W7P  CAT  CAP  OAB  114.05  3.000
 W7P  OAF  CAP  OAB  128.20  3.000
 W7P  CAS  CAT  NAM  120.74  3.000
 W7P  NAM  CAT  CAP  111.70  3.000
 W7P  CAS  CAT  CAP  127.56  3.000
 W7P  H13  NAM  CAU  119.10  3.000
 W7P  H13  NAM  CAT  115.36  3.000
 W7P  CAU  NAM  CAT  125.54  3.000
 W7P  NAN  CAU  OAC  123.00  3.000
 W7P  OAC  CAU  NAM  123.91  3.000
 W7P  NAN  CAU  NAM  113.10  3.000
 W7P  H2   NAN  CAV  116.73  3.000
 W7P  H2   NAN  CAU  116.31  3.000
 W7P  CAV  NAN  CAU  126.95  3.000
 W7P  CAS  CAV  OAD  124.63  3.000
 W7P  CAS  CAV  NAN  115.88  3.000
 W7P  OAD  CAV  NAN  119.49  3.000
 W7P  CAL  CAS  CAV  116.37  3.000
 W7P  CAV  CAS  CAT  117.77  3.000
 W7P  CAL  CAS  CAT  125.83  3.000
 W7P  H5   CAL  H4   107.39  3.000
 W7P  H5   CAL  CAK  109.03  3.000
 W7P  H4   CAL  CAK  108.98  3.000
 W7P  H5   CAL  CAS  110.24  3.000
 W7P  H4   CAL  CAS  108.96  3.000
 W7P  CAK  CAL  CAS  112.11  3.000
 W7P  H7   CAK  H6   107.20  3.000
 W7P  H7   CAK  CAQ  110.04  3.000
 W7P  H6   CAK  CAQ  109.89  3.000
 W7P  H7   CAK  CAL  109.48  3.000
 W7P  H6   CAK  CAL  108.38  3.000
 W7P  CAQ  CAK  CAL  111.72  3.000
 W7P  CAH  CAQ  CAG  118.02  3.000
 W7P  CAH  CAQ  CAK  120.30  3.000
 W7P  CAG  CAQ  CAK  121.65  3.000
 W7P  H8   CAG  CAI  119.58  3.000
 W7P  H8   CAG  CAQ  119.45  3.000
 W7P  CAI  CAG  CAQ  120.97  3.000
 W7P  H9   CAI  CAR  119.29  3.000
 W7P  H9   CAI  CAG  119.69  3.000
 W7P  CAR  CAI  CAG  121.02  3.000
 W7P  CAJ  CAR  CAO  121.00  3.000
 W7P  CAJ  CAR  CAI  117.99  3.000
 W7P  CAO  CAR  CAI  121.01  3.000
 W7P  OAA  CAO  OAE  126.61  3.000
 W7P  OAA  CAO  CAR  116.72  3.000
 W7P  OAE  CAO  CAR  116.68  3.000
 W7P  H11  CAJ  CAH  119.64  3.000
 W7P  H11  CAJ  CAR  119.33  3.000
 W7P  CAH  CAJ  CAR  121.02  3.000
 W7P  H12  CAH  CAJ  119.97  3.000
 W7P  H12  CAH  CAQ  119.06  3.000
 W7P  CAJ  CAH  CAQ  120.97  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
 W7P  CONST_01  CAR  CAI  CAG  CAQ     0.00   0.0  0
 W7P  CONST_02  CAR  CAJ  CAH  CAQ     0.00   0.0  0
 W7P  CONST_03  CAJ  CAR  CAI  CAG     0.00   0.0  0
 W7P  CONST_04  CAJ  CAH  CAQ  CAG     0.00   0.0  0
 W7P  CONST_05  CAH  CAQ  CAG  CAI     0.00   0.0  0
 W7P  CONST_06  CAH  CAJ  CAR  CAI     0.00   0.0  0
 W7P  CONST_07  NAN  CAU  NAM  CAT     0.00   0.0  0
 W7P  CONST_08  CAV  NAN  CAU  NAM     0.00   0.0  0
 W7P  CONST_09  CAS  CAV  NAN  CAU     0.00   0.0  0
 W7P  CONST_10  CAI  CAG  CAQ  CAK   180.00   0.0  0
 W7P  CONST_11  CAJ  CAH  CAQ  CAK   180.00   0.0  0
 W7P  CONST_12  CAO  CAR  CAI  CAG   180.00   0.0  0
 W7P  CONST_13  CAH  CAJ  CAR  CAO   180.00   0.0  0
 W7P  CONST_14  OAC  CAU  NAM  CAT   180.00   0.0  0
 W7P  CONST_15  OAD  CAV  NAN  CAU   180.00   0.0  0
 W7P  CONST_16  CAV  NAN  CAU  OAC   180.00   0.0  0
 W7P  CONST_17  H9   CAI  CAG  CAQ   180.00   0.0  0
 W7P  CONST_18  H11  CAJ  CAH  CAQ   180.00   0.0  0
 W7P  CONST_19  H12  CAH  CAQ  CAG   180.00   0.0  0
 W7P  CONST_20  H8   CAG  CAI  CAR   180.00   0.0  0
 W7P  CONST_21  H2   NAN  CAU  NAM   180.00   0.0  0
 W7P  CONST_22  H13  NAM  CAU  NAN   180.00   0.0  0
 W7P  Var_01    CAS  CAT  CAP  OAB   170.54  30.0  2
 W7P  Var_02    CAK  CAL  CAS  CAT    91.26  30.0  3
 W7P  Var_03    CAQ  CAK  CAL  CAS  -176.72  30.0  1
 W7P  Var_04    CAG  CAQ  CAK  CAL  -101.40  30.0  2
 W7P  Var_05    OAE  CAO  CAR  CAI     1.80  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
 W7P  plan-1  CAP  0.020
 W7P  plan-1  CAT  0.020
 W7P  plan-1  NAM  0.020
 W7P  plan-1  CAU  0.020
 W7P  plan-1  OAC  0.020
 W7P  plan-1  NAN  0.020
 W7P  plan-1  CAV  0.020
 W7P  plan-1  OAD  0.020
 W7P  plan-1  CAS  0.020
 W7P  plan-1  CAL  0.020
 W7P  plan-1  H2   0.020
 W7P  plan-1  H13  0.020
 W7P  plan-2  CAK  0.020
 W7P  plan-2  CAQ  0.020
 W7P  plan-2  CAG  0.020
 W7P  plan-2  CAI  0.020
 W7P  plan-2  CAR  0.020
 W7P  plan-2  CAO  0.020
 W7P  plan-2  CAJ  0.020
 W7P  plan-2  CAH  0.020
 W7P  plan-2  H8   0.020
 W7P  plan-2  H9   0.020
 W7P  plan-2  H11  0.020
 W7P  plan-2  H12  0.020
 W7P  plan-3  OAB  0.020
 W7P  plan-3  CAP  0.020
 W7P  plan-3  OAF  0.020
 W7P  plan-3  CAT  0.020
 W7P  plan-4  CAR  0.020
 W7P  plan-4  CAO  0.020
 W7P  plan-4  OAE  0.020
 W7P  plan-4  OAA  0.020

