# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 08:50:34 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  34  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 PERFECT
;

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  -0.439  -4.4655  -2.1219   0.2041
 W7O  CAO  C  C     0   0.532  -4.8517  -0.9943   0.0069
 W7O  OAE  O  OH1   0  -0.594  -6.1099  -0.7022  -0.2920
 W7O  CAR  C  CR6   0  -0.062  -3.9765   0.2026   0.0713
 W7O  CAJ  C  CR16  0  -0.318  -2.6293   0.0148   0.3697
 W7O  CAI  C  CR16  0  -0.279  -4.4616   1.4904  -0.1534
 W7O  CAG  C  CR16  0  -0.226  -3.5954   2.5694  -0.0768
 W7O  CAH  C  CR16  0  -0.299  -2.2547   2.3713   0.2228
 W7O  CAQ  C  CR6   0   0.142  -1.7550   1.0919   0.4526
 W7O  CAK  C  CH2   0  -0.506  -0.2972   0.8673   0.7331
 W7O  CAL  C  CH2   0  -0.502   0.4723   0.5584  -0.5606
 W7O  CAS  C  CR6   0  -0.120   1.9259   0.3056  -0.3050
 W7O  CAV  C  CR6   0   0.587   2.7914   1.4884  -0.2522
 W7O  OAD  O  O     0  -0.440   2.3917   2.6273  -0.3942
 W7O  NAN  N  NR16  0  -0.716   4.1278   1.2427  -0.0226
 W7O  CAU  C  CR6   0   0.671   4.7262   0.0253   0.1714
 W7O  OAC  O  O     0  -0.472   5.9143  -0.1048   0.3769
 W7O  NAM  N  NR16  0  -0.732   3.8563  -1.0238   0.1139
 W7O  CAT  C  CR6   0   0.282   2.5073  -0.8974  -0.1033
 W7O  CAP  C  C     0   0.523   1.7423  -2.1869  -0.0978
 W7O  OAF  O  OH1   0  -0.591   2.5307  -3.2098  -0.3728
 W7O  OAB  O  O     0  -0.395   0.5683  -2.2722   0.1391
 W7O  H1   H  HOH1  0   0.487  -6.6387  -1.5133  -0.3267
 W7O  H2   H  HCR6  0   0.256  -2.2542  -0.9865   0.5439
 W7O  H3   H  HCR6  0   0.267  -5.5038   1.6620  -0.3832
 W7O  H4   H  HCR6  0   0.264  -3.9677   3.5704  -0.2492
 W7O  H5   H  HCR6  0   0.257  -1.5877   3.2233   0.2822
 W7O  H6   H  HCH2  0   0.256   0.1302   1.7514   1.2103
 W7O  H7   H  HCH2  0   0.260  -0.1761   0.0378   1.4306
 W7O  H8   H  HCH2  0   0.268   0.0114  -0.2877  -1.0656
 W7O  H9   H  HCH2  0   0.265   0.3827   1.4105  -1.2363
 W7O  H10  H  HNR6  0   0.431   4.7386   2.0494   0.0214
 W7O  H11  H  HNR6  0   0.439   4.2539  -1.9401   0.2671
 W7O  H12  H  HOH1  0   0.504   2.0389  -4.0449  -0.3301

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  double    1.208  0.020  1.208
 W7O  OAE  CAO  single    1.326  0.020  1.326
 W7O  CAO  CAR  single    1.484  0.020  1.484
 W7O  CAR  CAJ  aromatic  1.393  0.020  1.393
 W7O  CAR  CAI  aromatic  1.394  0.020  1.394
 W7O  CAJ  CAQ  aromatic  1.390  0.020  1.390
 W7O  CAI  CAG  aromatic  1.386  0.020  1.386
 W7O  CAQ  CAK  single    1.501  0.020  1.501
 W7O  CAQ  CAH  aromatic  1.393  0.020  1.393
 W7O  CAK  CAL  single    1.537  0.020  1.537
 W7O  CAG  CAH  aromatic  1.388  0.020  1.388
 W7O  CAL  CAS  single    1.497  0.020  1.497
 W7O  OAD  CAV  double    1.215  0.020  1.215
 W7O  CAS  CAV  single    1.467  0.020  1.467
 W7O  CAS  CAT  double    1.351  0.020  1.351
 W7O  CAV  NAN  single    1.378  0.020  1.378
 W7O  OAB  CAP  double    1.201  0.020  1.201
 W7O  CAP  CAT  single    1.499  0.020  1.499
 W7O  CAP  OAF  single    1.320  0.020  1.320
 W7O  CAT  NAM  single    1.372  0.020  1.372
 W7O  NAN  CAU  single    1.370  0.020  1.370
 W7O  NAM  CAU  single    1.364  0.020  1.364
 W7O  CAU  OAC  double    1.213  0.020  1.213
 W7O  OAE  H1   single    0.850  0.020  0.980
 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
 W7O  OAF  H12  single    0.850  0.020  0.980

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  113.06  3.000
 W7O  CAR  CAO  OAA  123.85  3.000
 W7O  OAE  CAO  OAA  123.08  3.000
 W7O  H1   OAE  CAO  109.97  3.000
 W7O  CAI  CAR  CAJ  119.72  3.000
 W7O  CAI  CAR  CAO  122.18  3.000
 W7O  CAJ  CAR  CAO  118.10  3.000
 W7O  H2   CAJ  CAQ  119.27  3.000
 W7O  H2   CAJ  CAR  119.61  3.000
 W7O  CAQ  CAJ  CAR  121.12  3.000
 W7O  H3   CAI  CAG  119.40  3.000
 W7O  H3   CAI  CAR  121.09  3.000
 W7O  CAG  CAI  CAR  119.52  3.000
 W7O  H4   CAG  CAH  119.92  3.000
 W7O  H4   CAG  CAI  119.77  3.000
 W7O  CAH  CAG  CAI  120.31  3.000
 W7O  H5   CAH  CAQ  119.50  3.000
 W7O  H5   CAH  CAG  119.62  3.000
 W7O  CAQ  CAH  CAG  120.89  3.000
 W7O  CAK  CAQ  CAH  121.11  3.000
 W7O  CAH  CAQ  CAJ  118.45  3.000
 W7O  CAK  CAQ  CAJ  120.40  3.000
 W7O  H7   CAK  H6   107.04  3.000
 W7O  H7   CAK  CAL  109.27  3.000
 W7O  H6   CAK  CAL  109.55  3.000
 W7O  H7   CAK  CAQ  109.94  3.000
 W7O  H6   CAK  CAQ  109.91  3.000
 W7O  CAL  CAK  CAQ  111.04  3.000
 W7O  H9   CAL  H8   106.58  3.000
 W7O  H9   CAL  CAS  108.49  3.000
 W7O  H8   CAL  CAS  111.05  3.000
 W7O  H9   CAL  CAK  108.86  3.000
 W7O  H8   CAL  CAK  109.57  3.000
 W7O  CAS  CAL  CAK  112.11  3.000
 W7O  CAT  CAS  CAV  117.30  3.000
 W7O  CAT  CAS  CAL  126.40  3.000
 W7O  CAV  CAS  CAL  116.29  3.000
 W7O  NAN  CAV  OAD  120.37  3.000
 W7O  NAN  CAV  CAS  115.76  3.000
 W7O  OAD  CAV  CAS  123.88  3.000
 W7O  H10  NAN  CAU  115.98  3.000
 W7O  H10  NAN  CAV  116.75  3.000
 W7O  CAU  NAN  CAV  127.26  3.000
 W7O  NAM  CAU  OAC  123.33  3.000
 W7O  OAC  CAU  NAN  123.17  3.000
 W7O  NAM  CAU  NAN  113.50  3.000
 W7O  H11  NAM  CAT  119.62  3.000
 W7O  H11  NAM  CAU  116.11  3.000
 W7O  CAT  NAM  CAU  124.25  3.000
 W7O  CAP  CAT  NAM  114.95  3.000
 W7O  NAM  CAT  CAS  121.91  3.000
 W7O  CAP  CAT  CAS  123.14  3.000
 W7O  OAB  CAP  OAF  124.74  3.000
 W7O  OAF  CAP  CAT  111.15  3.000
 W7O  OAB  CAP  CAT  124.10  3.000
 W7O  H12  OAF  CAP  110.80  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  CONST_23  H1   OAE  CAO  CAR   180.00   0.0  0
 W7O  CONST_24  H12  OAF  CAP  CAT   180.00   0.0  0
 W7O  Var_01    CAJ  CAR  CAO  OAA     0.35  30.0  2
 W7O  Var_02    CAL  CAK  CAQ  CAJ    84.82  30.0  2
 W7O  Var_03    CAS  CAL  CAK  CAQ  -178.96  30.0  3
 W7O  Var_04    CAV  CAS  CAL  CAK   -85.61  30.0  3
 W7O  Var_05    OAB  CAP  CAT  CAS   -23.77  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
 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-3  H1   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
 W7O  plan-4  H12  0.020

