# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 04:45:55 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 5-[2-(3-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(CCc2cccc(c2)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
 W7O  W7O  '5-[2-(3-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_W7O
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
 W7O  OAA  O  O      0  -0.593  -4.3727  -2.1736   0.0336
 W7O  CAO  C  C      0   0.394  -4.8994  -1.0513  -0.0940
 W7O  OAE  O  OC    -1  -0.597  -6.1028  -0.8141  -0.3163
 W7O  CAR  C  CR6    0  -0.081  -3.9783   0.1563   0.0360
 W7O  CAJ  C  CR16   0  -0.356  -2.6247  -0.0104   0.3123
 W7O  CAI  C  CR16   0  -0.312  -4.4730   1.4503  -0.1151
 W7O  CAG  C  CR16   0  -0.231  -3.6283   2.5440   0.0075
 W7O  CAH  C  CR16   0  -0.325  -2.2803   2.3582   0.2879
 W7O  CAQ  C  CR6    0   0.141  -1.7626   1.0756   0.4475
 W7O  CAK  C  CH2    0  -0.495  -0.2998   0.8544   0.7088
 W7O  CAL  C  CH2    0  -0.473   0.4708   0.5845  -0.5905
 W7O  CAS  C  CR6    0  -0.159   1.9267   0.3260  -0.3426
 W7O  CAV  C  CR6    0   0.563   2.7949   1.4968  -0.3089
 W7O  OAD  O  O      0  -0.465   2.4174   2.6463  -0.4677
 W7O  NAN  N  NR16   0  -0.714   4.1348   1.2478  -0.0730
 W7O  CAU  C  CR6    0   0.655   4.7217   0.0279   0.1369
 W7O  OAC  O  O      0  -0.494   5.9159  -0.1084   0.3308
 W7O  NAM  N  NR16   0  -0.706   3.8366  -0.9997   0.1097
 W7O  CAT  C  CR6    0   0.199   2.4899  -0.8845  -0.1056
 W7O  CAP  C  C      0   0.414   1.7826  -2.2534  -0.0347
 W7O  OAF  O  OC    -1  -0.587   2.5615  -3.2213   0.0451
 W7O  OAB  O  O      0  -0.537   0.5471  -2.2644  -0.0483
 W7O  H2   H  HCR6   0   0.234  -2.2299  -1.0132   0.4267
 W7O  H3   H  HCR6   0   0.238  -5.5236   1.5985  -0.3266
 W7O  H4   H  HCR6   0   0.243  -4.0199   3.5468  -0.1115
 W7O  H5   H  HCR6   0   0.239  -1.6260   3.2173   0.3864
 W7O  H6   H  HCH2   0   0.236   0.1279   1.7250   1.2121
 W7O  H7   H  HCH2   0   0.243  -0.1670  -0.0006   1.3731
 W7O  H8   H  HCH2   0   0.253   0.0192  -0.2621  -1.0996
 W7O  H9   H  HCH2   0   0.238   0.3719   1.4517  -1.2460
 W7O  H10  H  HNR6   0   0.419   4.7497   2.0510  -0.0450
 W7O  H11  H  HNR6   0   0.416   4.1724  -1.9465   0.2472

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
 W7O  OAA  CAO  deloc     1.246  0.020  1.246
 W7O  OAE  CAO  deloc     1.247  0.020  1.247
 W7O  CAO  CAR  single    1.524  0.020  1.524
 W7O  CAR  CAJ  aromatic  1.391  0.020  1.391
 W7O  CAR  CAI  aromatic  1.394  0.020  1.394
 W7O  CAJ  CAQ  aromatic  1.393  0.020  1.393
 W7O  CAI  CAG  aromatic  1.387  0.020  1.387
 W7O  CAQ  CAK  single    1.502  0.020  1.502
 W7O  CAQ  CAH  aromatic  1.392  0.020  1.392
 W7O  CAK  CAL  single    1.535  0.020  1.535
 W7O  CAG  CAH  aromatic  1.389  0.020  1.389
 W7O  CAL  CAS  single    1.499  0.020  1.499
 W7O  OAD  CAV  double    1.220  0.020  1.220
 W7O  CAS  CAV  single    1.458  0.020  1.458
 W7O  CAS  CAT  double    1.356  0.020  1.356
 W7O  CAV  NAN  single    1.383  0.020  1.383
 W7O  OAB  CAP  deloc     1.236  0.020  1.236
 W7O  CAP  CAT  single    1.543  0.020  1.543
 W7O  CAP  OAF  deloc     1.245  0.020  1.245
 W7O  CAT  NAM  single    1.369  0.020  1.369
 W7O  NAN  CAU  single    1.370  0.020  1.370
 W7O  NAM  CAU  single    1.357  0.020  1.357
 W7O  CAU  OAC  double    1.217  0.020  1.217
 W7O  CAJ  H2   single    0.930  0.020  1.080
 W7O  CAI  H3   single    0.930  0.020  1.080
 W7O  CAG  H4   single    0.930  0.020  1.080
 W7O  CAH  H5   single    0.930  0.020  1.080
 W7O  CAK  H6   single    0.970  0.020  1.090
 W7O  CAK  H7   single    0.970  0.020  1.090
 W7O  CAL  H8   single    0.970  0.020  1.090
 W7O  CAL  H9   single    0.970  0.020  1.090
 W7O  NAN  H10  single    0.860  0.020  1.020
 W7O  NAM  H11  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
 W7O  CAR  CAO  OAE  116.61  3.000
 W7O  CAR  CAO  OAA  116.70  3.000
 W7O  OAE  CAO  OAA  126.70  3.000
 W7O  CAI  CAR  CAJ  118.56  3.000
 W7O  CAI  CAR  CAO  120.79  3.000
 W7O  CAJ  CAR  CAO  120.65  3.000
 W7O  H2   CAJ  CAQ  119.05  3.000
 W7O  H2   CAJ  CAR  119.09  3.000
 W7O  CAQ  CAJ  CAR  121.86  3.000
 W7O  H3   CAI  CAG  120.04  3.000
 W7O  H3   CAI  CAR  119.54  3.000
 W7O  CAG  CAI  CAR  120.42  3.000
 W7O  H4   CAG  CAH  119.78  3.000
 W7O  H4   CAG  CAI  120.00  3.000
 W7O  CAH  CAG  CAI  120.21  3.000
 W7O  H5   CAH  CAQ  119.67  3.000
 W7O  H5   CAH  CAG  119.86  3.000
 W7O  CAQ  CAH  CAG  120.47  3.000
 W7O  CAK  CAQ  CAH  121.17  3.000
 W7O  CAH  CAQ  CAJ  118.48  3.000
 W7O  CAK  CAQ  CAJ  120.31  3.000
 W7O  H7   CAK  H6   107.24  3.000
 W7O  H7   CAK  CAL  108.46  3.000
 W7O  H6   CAK  CAL  109.48  3.000
 W7O  H7   CAK  CAQ  109.87  3.000
 W7O  H6   CAK  CAQ  110.11  3.000
 W7O  CAL  CAK  CAQ  111.56  3.000
 W7O  H9   CAL  H8   107.46  3.000
 W7O  H9   CAL  CAS  108.92  3.000
 W7O  H8   CAL  CAS  110.29  3.000
 W7O  H9   CAL  CAK  108.85  3.000
 W7O  H8   CAL  CAK  108.98  3.000
 W7O  CAS  CAL  CAK  112.21  3.000
 W7O  CAT  CAS  CAV  117.75  3.000
 W7O  CAT  CAS  CAL  125.88  3.000
 W7O  CAV  CAS  CAL  116.33  3.000
 W7O  NAN  CAV  OAD  119.44  3.000
 W7O  NAN  CAV  CAS  115.86  3.000
 W7O  OAD  CAV  CAS  124.70  3.000
 W7O  H10  NAN  CAU  116.24  3.000
 W7O  H10  NAN  CAV  116.78  3.000
 W7O  CAU  NAN  CAV  126.98  3.000
 W7O  NAM  CAU  OAC  123.95  3.000
 W7O  OAC  CAU  NAN  122.98  3.000
 W7O  NAM  CAU  NAN  113.07  3.000
 W7O  H11  NAM  CAT  115.21  3.000
 W7O  H11  NAM  CAU  119.24  3.000
 W7O  CAT  NAM  CAU  125.55  3.000
 W7O  CAP  CAT  NAM  111.67  3.000
 W7O  NAM  CAT  CAS  120.75  3.000
 W7O  CAP  CAT  CAS  127.58  3.000
 W7O  OAB  CAP  OAF  128.28  3.000
 W7O  OAF  CAP  CAT  113.95  3.000
 W7O  OAB  CAP  CAT  117.77  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
 W7O  CONST_01  CAH  CAQ  CAJ  CAR     0.00   0.0  0
 W7O  CONST_02  CAH  CAG  CAI  CAR     0.00   0.0  0
 W7O  CONST_03  CAG  CAI  CAR  CAJ     0.00   0.0  0
 W7O  CONST_04  CAG  CAH  CAQ  CAJ     0.00   0.0  0
 W7O  CONST_05  CAQ  CAJ  CAR  CAI     0.00   0.0  0
 W7O  CONST_06  CAQ  CAH  CAG  CAI     0.00   0.0  0
 W7O  CONST_07  CAU  NAN  CAV  CAS     0.00   0.0  0
 W7O  CONST_08  NAM  CAU  NAN  CAV     0.00   0.0  0
 W7O  CONST_09  CAT  NAM  CAU  NAN     0.00   0.0  0
 W7O  CONST_10  CAQ  CAJ  CAR  CAO   180.00   0.0  0
 W7O  CONST_11  CAG  CAI  CAR  CAO   180.00   0.0  0
 W7O  CONST_12  CAK  CAQ  CAJ  CAR   180.00   0.0  0
 W7O  CONST_13  CAK  CAQ  CAH  CAG   180.00   0.0  0
 W7O  CONST_14  OAC  CAU  NAN  CAV   180.00   0.0  0
 W7O  CONST_15  CAU  NAN  CAV  OAD   180.00   0.0  0
 W7O  CONST_16  CAT  NAM  CAU  OAC   180.00   0.0  0
 W7O  CONST_17  H4   CAG  CAI  CAR   180.00   0.0  0
 W7O  CONST_18  H3   CAI  CAR  CAJ   180.00   0.0  0
 W7O  CONST_19  H5   CAH  CAQ  CAJ   180.00   0.0  0
 W7O  CONST_20  H2   CAJ  CAR  CAI   180.00   0.0  0
 W7O  CONST_21  H10  NAN  CAV  CAS   180.00   0.0  0
 W7O  CONST_22  H11  NAM  CAU  NAN   180.00   0.0  0
 W7O  Var_01    CAJ  CAR  CAO  OAA    -1.33  30.0  2
 W7O  Var_02    CAL  CAK  CAQ  CAJ    83.28  30.0  2
 W7O  Var_03    CAS  CAL  CAK  CAQ  -178.50  30.0  3
 W7O  Var_04    CAV  CAS  CAL  CAK   -87.96  30.0  3
 W7O  Var_05    OAB  CAP  CAT  CAS    -8.59  30.0  3

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
 W7O  plan-1  CAO  0.020
 W7O  plan-1  CAR  0.020
 W7O  plan-1  CAJ  0.020
 W7O  plan-1  CAI  0.020
 W7O  plan-1  CAG  0.020
 W7O  plan-1  CAH  0.020
 W7O  plan-1  CAQ  0.020
 W7O  plan-1  CAK  0.020
 W7O  plan-1  H2   0.020
 W7O  plan-1  H3   0.020
 W7O  plan-1  H4   0.020
 W7O  plan-1  H5   0.020
 W7O  plan-2  CAL  0.020
 W7O  plan-2  CAS  0.020
 W7O  plan-2  CAV  0.020
 W7O  plan-2  OAD  0.020
 W7O  plan-2  NAN  0.020
 W7O  plan-2  CAU  0.020
 W7O  plan-2  OAC  0.020
 W7O  plan-2  NAM  0.020
 W7O  plan-2  CAT  0.020
 W7O  plan-2  CAP  0.020
 W7O  plan-2  H10  0.020
 W7O  plan-2  H11  0.020
 W7O  plan-3  OAA  0.020
 W7O  plan-3  CAO  0.020
 W7O  plan-3  OAE  0.020
 W7O  plan-3  CAR  0.020
 W7O  plan-4  CAT  0.020
 W7O  plan-4  CAP  0.020
 W7O  plan-4  OAF  0.020
 W7O  plan-4  OAB  0.020

