# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 03:59:10 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 5-[2-(3-methoxyphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(CCC2=C(NC(=O)NC2=O)C(O)=O)c1
#
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
 W76  W76  '5-[2-(3-methoxyphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  34  21  .  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_W76
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
 W76  OAJ  O  OC    -1  -0.585  -2.4386  -3.1962  -0.0705
 W76  CAI  C  C      0   0.416  -1.6306  -2.2524  -0.0003
 W76  OAK  O  O      0  -0.540  -0.3956  -2.3000  -0.0124
 W76  C4   C  CR6    0   0.202  -2.2954  -0.8637   0.0944
 W76  N3   N  NR16   0  -0.706  -3.6453  -0.9327  -0.1197
 W76  C2   C  CR6    0   0.656  -4.4974   0.1232  -0.1260
 W76  O2   O  O      0  -0.493  -5.6955   0.0284  -0.3192
 W76  N1   N  NR16   0  -0.714  -3.8719   1.3200   0.1058
 W76  C6   C  CR6    0   0.564  -2.5247   1.5223   0.3421
 W76  O6   O  O      0  -0.467  -2.1097   2.6558   0.5221
 W76  C5   C  CR6    0  -0.159  -1.6942   0.3242   0.3503
 W76  CAL  C  CH2    0  -0.475  -0.2297   0.5279   0.5990
 W76  CAM  C  CH2    0  -0.497   0.5446   0.7968  -0.6987
 W76  CAN  C  CR6    0   0.134   2.0208   0.9181  -0.4479
 W76  CAS  C  CR16   0  -0.400   2.7894  -0.2287  -0.3012
 W76  CAO  C  CR16   0  -0.341   2.6331   2.1650  -0.3180
 W76  CAP  C  CR16   0  -0.227   3.9899   2.2442  -0.0506
 W76  CAQ  C  CR16   0  -0.401   4.7639   1.0979   0.0921
 W76  CAR  C  CR6    0   0.397   4.1565  -0.1498  -0.0339
 W76  OAT  O  O2     0  -0.474   4.8070  -1.3253   0.0859
 W76  CAU  C  CH3    0  -0.435   6.1988  -1.3040   0.3263
 W76  H2   H  HNR6   0   0.420  -4.4623   2.1420   0.0968
 W76  H4   H  HCH2   0   0.239  -0.0975   1.3765   1.2727
 W76  H5   H  HCH2   0   0.255   0.1917  -0.3443   1.0900
 W76  H6   H  HCH2   0   0.246   0.3549  -0.0230  -1.3927
 W76  H7   H  HCH2   0   0.240   0.1695   1.7105  -1.1653
 W76  H8   H  HCR6   0   0.253   2.3219  -1.2030  -0.3962
 W76  H9   H  HCR6   0   0.240   2.0474   3.0691  -0.4326
 W76  H10  H  HCR6   0   0.254   4.4646   3.2123   0.0475
 W76  H11  H  HCR6   0   0.274   5.8217   1.1964   0.2940
 W76  H12  H  HCH3   0   0.226   6.4455  -0.8146   1.2725
 W76  H13  H  HCH3   0   0.257   6.5201  -2.3416   0.3766
 W76  H14  H  HCH3   0   0.226   6.7466  -0.8063  -0.4788
 W76  H15  H  HNR6   0   0.416  -4.0136  -1.8657  -0.2681

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
 W76  CAO  CAP  aromatic  1.385  0.020  1.385
 W76  CAO  CAN  aromatic  1.395  0.020  1.395
 W76  CAP  CAQ  aromatic  1.390  0.020  1.390
 W76  CAM  CAN  single    1.502  0.020  1.502
 W76  CAM  CAL  single    1.535  0.020  1.535
 W76  CAN  CAS  aromatic  1.388  0.020  1.388
 W76  CAQ  CAR  aromatic  1.393  0.020  1.393
 W76  CAS  CAR  aromatic  1.395  0.020  1.395
 W76  CAR  OAT  single    1.349  0.020  1.349
 W76  OAT  CAU  single    1.413  0.020  1.413
 W76  CAL  C5   single    1.499  0.020  1.499
 W76  O6   C6   double    1.220  0.020  1.220
 W76  C5   C6   single    1.458  0.020  1.458
 W76  C5   C4   double    1.356  0.020  1.356
 W76  C6   N1   single    1.383  0.020  1.383
 W76  C4   CAI  single    1.543  0.020  1.543
 W76  C4   N3   single    1.368  0.020  1.368
 W76  N1   C2   single    1.370  0.020  1.370
 W76  OAK  CAI  deloc     1.236  0.020  1.236
 W76  CAI  OAJ  deloc     1.244  0.020  1.244
 W76  C2   N3   single    1.357  0.020  1.357
 W76  C2   O2   double    1.217  0.020  1.217
 W76  N1   H2   single    0.860  0.020  1.020
 W76  CAL  H4   single    0.970  0.020  1.090
 W76  CAL  H5   single    0.970  0.020  1.090
 W76  CAM  H6   single    0.970  0.020  1.090
 W76  CAM  H7   single    0.970  0.020  1.090
 W76  CAS  H8   single    0.930  0.020  1.080
 W76  CAO  H9   single    0.930  0.020  1.080
 W76  CAP  H10  single    0.930  0.020  1.080
 W76  CAQ  H11  single    0.930  0.020  1.080
 W76  CAU  H12  single    0.970  0.020  1.090
 W76  CAU  H13  single    0.970  0.020  1.090
 W76  CAU  H14  single    0.970  0.020  1.090
 W76  N3   H15  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
 W76  C4   CAI  OAK  117.77  3.000
 W76  OAK  CAI  OAJ  128.25  3.000
 W76  C4   CAI  OAJ  113.98  3.000
 W76  C5   C4   N3   120.74  3.000
 W76  N3   C4   CAI  111.72  3.000
 W76  C5   C4   CAI  127.54  3.000
 W76  H15  N3   C2   119.16  3.000
 W76  H15  N3   C4   115.32  3.000
 W76  C2   N3   C4   125.51  3.000
 W76  N1   C2   O2   122.97  3.000
 W76  O2   C2   N3   123.93  3.000
 W76  N1   C2   N3   113.10  3.000
 W76  H2   N1   C6   116.81  3.000
 W76  H2   N1   C2   116.21  3.000
 W76  C6   N1   C2   126.98  3.000
 W76  C5   C6   O6   124.67  3.000
 W76  C5   C6   N1   115.84  3.000
 W76  O6   C6   N1   119.49  3.000
 W76  CAL  C5   C6   116.47  3.000
 W76  C6   C5   C4   117.80  3.000
 W76  CAL  C5   C4   125.70  3.000
 W76  H5   CAL  H4   107.36  3.000
 W76  H5   CAL  CAM  109.10  3.000
 W76  H4   CAL  CAM  108.93  3.000
 W76  H5   CAL  C5   110.17  3.000
 W76  H4   CAL  C5   109.05  3.000
 W76  CAM  CAL  C5   112.11  3.000
 W76  H7   CAM  H6   107.28  3.000
 W76  H7   CAM  CAN  109.95  3.000
 W76  H6   CAM  CAN  109.75  3.000
 W76  H7   CAM  CAL  109.54  3.000
 W76  H6   CAM  CAL  108.57  3.000
 W76  CAN  CAM  CAL  111.64  3.000
 W76  CAO  CAN  CAS  119.04  3.000
 W76  CAS  CAN  CAM  119.67  3.000
 W76  CAO  CAN  CAM  121.26  3.000
 W76  H8   CAS  CAR  119.33  3.000
 W76  H8   CAS  CAN  119.61  3.000
 W76  CAR  CAS  CAN  121.07  3.000
 W76  H9   CAO  CAP  120.15  3.000
 W76  H9   CAO  CAN  119.91  3.000
 W76  CAP  CAO  CAN  119.93  3.000
 W76  H10  CAP  CAQ  118.93  3.000
 W76  H10  CAP  CAO  119.88  3.000
 W76  CAQ  CAP  CAO  121.19  3.000
 W76  H11  CAQ  CAR  121.66  3.000
 W76  H11  CAQ  CAP  119.25  3.000
 W76  CAR  CAQ  CAP  119.10  3.000
 W76  OAT  CAR  CAQ  124.20  3.000
 W76  OAT  CAR  CAS  116.12  3.000
 W76  CAQ  CAR  CAS  119.67  3.000
 W76  CAU  OAT  CAR  118.50  3.000
 W76  H14  CAU  H13  108.68  3.000
 W76  H14  CAU  H12  108.69  3.000
 W76  H13  CAU  H12  108.68  3.000
 W76  H14  CAU  OAT  112.03  3.000
 W76  H13  CAU  OAT  106.54  3.000
 W76  H12  CAU  OAT  112.10  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
 W76  CONST_01  CAQ  CAP  CAO  CAN     0.00   0.0  0
 W76  CONST_02  CAQ  CAR  CAS  CAN     0.00   0.0  0
 W76  CONST_03  CAP  CAO  CAN  CAS     0.00   0.0  0
 W76  CONST_04  CAP  CAQ  CAR  CAS     0.00   0.0  0
 W76  CONST_05  CAR  CAQ  CAP  CAO     0.00   0.0  0
 W76  CONST_06  CAR  CAS  CAN  CAO     0.00   0.0  0
 W76  CONST_07  N1   C2   N3   C4      0.00   0.0  0
 W76  CONST_08  C6   N1   C2   N3      0.00   0.0  0
 W76  CONST_09  C5   C6   N1   C2      0.00   0.0  0
 W76  CONST_10  CAP  CAO  CAN  CAM   180.00   0.0  0
 W76  CONST_11  CAR  CAS  CAN  CAM   180.00   0.0  0
 W76  CONST_12  OAT  CAR  CAS  CAN   180.00   0.0  0
 W76  CONST_13  OAT  CAR  CAQ  CAP   180.00   0.0  0
 W76  CONST_14  O2   C2   N3   C4    180.00   0.0  0
 W76  CONST_15  O6   C6   N1   C2    180.00   0.0  0
 W76  CONST_16  C6   N1   C2   O2    180.00   0.0  0
 W76  CONST_17  H10  CAP  CAO  CAN   180.00   0.0  0
 W76  CONST_18  H9   CAO  CAN  CAS   180.00   0.0  0
 W76  CONST_19  H11  CAQ  CAR  CAS   180.00   0.0  0
 W76  CONST_20  H8   CAS  CAN  CAO   180.00   0.0  0
 W76  CONST_21  H2   N1   C2   N3    180.00   0.0  0
 W76  CONST_22  H15  N3   C2   N1    180.00   0.0  0
 W76  Var_01    C5   C4   CAI  OAJ   170.96  30.0  2
 W76  Var_02    CAM  CAL  C5   C4     89.85  30.0  1
 W76  Var_03    CAN  CAM  CAL  C5   -176.61  30.0  1
 W76  Var_04    CAO  CAN  CAM  CAL   -97.81  30.0  2
 W76  Var_05    H12  CAU  OAT  CAR    61.87  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
 W76  plan-1  CAI  0.020
 W76  plan-1  C4   0.020
 W76  plan-1  N3   0.020
 W76  plan-1  C2   0.020
 W76  plan-1  O2   0.020
 W76  plan-1  N1   0.020
 W76  plan-1  C6   0.020
 W76  plan-1  O6   0.020
 W76  plan-1  C5   0.020
 W76  plan-1  CAL  0.020
 W76  plan-1  H2   0.020
 W76  plan-1  H15  0.020
 W76  plan-2  CAM  0.020
 W76  plan-2  CAN  0.020
 W76  plan-2  CAS  0.020
 W76  plan-2  CAO  0.020
 W76  plan-2  CAP  0.020
 W76  plan-2  CAQ  0.020
 W76  plan-2  CAR  0.020
 W76  plan-2  OAT  0.020
 W76  plan-2  H8   0.020
 W76  plan-2  H9   0.020
 W76  plan-2  H10  0.020
 W76  plan-2  H11  0.020
 W76  plan-3  OAJ  0.020
 W76  plan-3  CAI  0.020
 W76  plan-3  OAK  0.020
 W76  plan-3  C4   0.020

