# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 04:54:38 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 5-[2-(3,5-dimethoxyphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(CCC2=C(NC(=O)NC2=O)C(O)=O)cc(OC)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
 W75  W75  '5-[2-(3,5-dimethoxyphenyl)ethyl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  39  23  .  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_W75
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
 W75  OAJ  O  OH1   0  -0.589  -3.4614  -3.0621   0.3418
 W75  CAI  C  C     0   0.519  -2.5000  -2.2171   0.0177
 W75  OAK  O  O     0  -0.396  -1.3853  -2.5350  -0.2958
 W75  C4   C  CR6   0   0.285  -2.9827  -0.7994   0.0766
 W75  N3   N  NR16  0  -0.732  -4.3322  -0.6393  -0.1136
 W75  C2   C  CR6   0   0.671  -4.9668   0.5681  -0.1277
 W75  O2   O  O     0  -0.472  -6.1587   0.6920  -0.3138
 W75  N1   N  NR16  0  -0.716  -4.1266   1.6291   0.0870
 W75  C6   C  CR6   0   0.587  -2.7661   1.5862   0.3033
 W75  O6   O  O     0  -0.440  -2.1397   2.6128   0.4798
 W75  C5   C  CR6   0  -0.120  -2.1617   0.2502   0.2986
 W75  CAL  C  CH2   0  -0.501  -0.6837   0.1888   0.5317
 W75  CAM  C  CH2   0  -0.506   0.1161   0.4028  -0.7627
 W75  CAN  C  CR6   0   0.154   1.5949   0.3094  -0.5117
 W75  CAS  C  CR16  0  -0.441   2.3567   1.4605  -0.3657
 W75  CAO  C  CR16  0  -0.431   2.1934  -0.9394  -0.3876
 W75  CAP  C  CR6   0   0.432   3.5555  -1.0340  -0.1189
 W75  OAU  O  O2    0  -0.475   4.0556  -2.2806  -0.0163
 W75  CAW  C  CH3   0  -0.439   5.4347  -2.4464   0.2453
 W75  CAQ  C  CR16  0  -0.548   4.3315   0.1167   0.0272
 W75  CAR  C  CR6   0   0.432   3.7211   1.3636  -0.0982
 W75  OAT  O  O2    0  -0.475   4.3849   2.5288   0.0257
 W75  CAV  C  CH3   0  -0.438   5.7772   2.5006   0.2664
 W75  H1   H  HOH1  0   0.504  -3.1536  -3.9789   0.2656
 W75  H2   H  HNR6  0   0.431  -4.5572   2.5460   0.0798
 W75  H4   H  HCH2  0   0.263  -0.4161   0.9687   1.2462
 W75  H5   H  HCH2  0   0.266  -0.3986  -0.7580   0.9842
 W75  H6   H  HCH2  0   0.256  -0.1836  -0.3477  -1.4958
 W75  H7   H  HCH2  0   0.253  -0.1285   1.3796  -1.1837
 W75  H8   H  HCR6  0   0.247   1.8998   2.4380  -0.4664
 W75  H9   H  HCR6  0   0.249   1.6041  -1.8420  -0.5006
 W75  H10  H  HCH3  0   0.228   6.0557  -2.0263  -0.5503
 W75  H11  H  HCH3  0   0.228   5.7279  -1.9950   1.1966
 W75  H12  H  HCH3  0   0.261   5.6123  -3.5177   0.2973
 W75  H13  H  HCR6  0   0.299   5.3891   0.0415   0.2336
 W75  H14  H  HCH3  0   0.228   6.3222   2.0022  -0.5398
 W75  H15  H  HCH3  0   0.261   6.1021   3.5368   0.3177
 W75  H16  H  HCH3  0   0.228   6.0210   2.0098   1.2123
 W75  H17  H  HNR6  0   0.439  -4.9137  -1.4486  -0.2805

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
 W75  O2   C2   double    1.213  0.020  1.213
 W75  N3   C2   single    1.364  0.020  1.364
 W75  N3   C4   single    1.372  0.020  1.372
 W75  C2   N1   single    1.370  0.020  1.370
 W75  OAK  CAI  double    1.201  0.020  1.201
 W75  CAI  C4   single    1.499  0.020  1.499
 W75  CAI  OAJ  single    1.320  0.020  1.320
 W75  C4   C5   double    1.351  0.020  1.351
 W75  N1   C6   single    1.378  0.020  1.378
 W75  C5   C6   single    1.466  0.020  1.466
 W75  C5   CAL  single    1.498  0.020  1.498
 W75  C6   O6   double    1.216  0.020  1.216
 W75  CAV  OAT  single    1.413  0.020  1.413
 W75  CAL  CAM  single    1.537  0.020  1.537
 W75  OAT  CAR  single    1.347  0.020  1.347
 W75  CAR  CAS  aromatic  1.394  0.020  1.394
 W75  CAR  CAQ  aromatic  1.394  0.020  1.394
 W75  CAS  CAN  aromatic  1.388  0.020  1.388
 W75  CAQ  CAP  aromatic  1.396  0.020  1.396
 W75  CAN  CAM  single    1.503  0.020  1.503
 W75  CAN  CAO  aromatic  1.390  0.020  1.390
 W75  CAP  CAO  aromatic  1.391  0.020  1.391
 W75  CAP  OAU  single    1.347  0.020  1.347
 W75  OAU  CAW  single    1.413  0.020  1.413
 W75  OAJ  H1   single    0.850  0.020  0.980
 W75  N1   H2   single    0.860  0.020  1.020
 W75  CAL  H4   single    0.970  0.020  1.090
 W75  CAL  H5   single    0.970  0.020  1.090
 W75  CAM  H6   single    0.970  0.020  1.090
 W75  CAM  H7   single    0.970  0.020  1.090
 W75  CAS  H8   single    0.930  0.020  1.080
 W75  CAO  H9   single    0.930  0.020  1.080
 W75  CAW  H10  single    0.970  0.020  1.090
 W75  CAW  H11  single    0.970  0.020  1.090
 W75  CAW  H12  single    0.970  0.020  1.090
 W75  CAQ  H13  single    0.930  0.020  1.080
 W75  CAV  H14  single    0.970  0.020  1.090
 W75  CAV  H15  single    0.970  0.020  1.090
 W75  CAV  H16  single    0.970  0.020  1.090
 W75  N3   H17  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
 W75  H1   OAJ  CAI  110.76  3.000
 W75  C4   CAI  OAK  124.03  3.000
 W75  C4   CAI  OAJ  111.17  3.000
 W75  OAK  CAI  OAJ  124.79  3.000
 W75  C5   C4   N3   121.99  3.000
 W75  C5   C4   CAI  123.07  3.000
 W75  N3   C4   CAI  114.94  3.000
 W75  H17  N3   C2   116.07  3.000
 W75  H17  N3   C4   119.70  3.000
 W75  C2   N3   C4   124.21  3.000
 W75  N1   C2   O2   123.20  3.000
 W75  N1   C2   N3   113.49  3.000
 W75  O2   C2   N3   123.31  3.000
 W75  H2   N1   C6   116.67  3.000
 W75  H2   N1   C2   116.05  3.000
 W75  C6   N1   C2   127.28  3.000
 W75  C5   C6   O6   123.89  3.000
 W75  O6   C6   N1   120.35  3.000
 W75  C5   C6   N1   115.77  3.000
 W75  CAL  C5   C6   116.34  3.000
 W75  CAL  C5   C4   126.41  3.000
 W75  C6   C5   C4   117.25  3.000
 W75  H5   CAL  H4   106.59  3.000
 W75  H5   CAL  CAM  109.60  3.000
 W75  H4   CAL  CAM  108.94  3.000
 W75  H5   CAL  C5   111.05  3.000
 W75  H4   CAL  C5   108.34  3.000
 W75  CAM  CAL  C5   112.14  3.000
 W75  H7   CAM  H6   107.15  3.000
 W75  H7   CAM  CAN  109.91  3.000
 W75  H6   CAM  CAN  109.86  3.000
 W75  H7   CAM  CAL  109.45  3.000
 W75  H6   CAM  CAL  109.10  3.000
 W75  CAN  CAM  CAL  111.27  3.000
 W75  CAO  CAN  CAS  119.95  3.000
 W75  CAO  CAN  CAM  119.63  3.000
 W75  CAS  CAN  CAM  120.40  3.000
 W75  H8   CAS  CAR  119.56  3.000
 W75  H8   CAS  CAN  120.46  3.000
 W75  CAR  CAS  CAN  119.98  3.000
 W75  H9   CAO  CAP  119.72  3.000
 W75  H9   CAO  CAN  120.30  3.000
 W75  CAP  CAO  CAN  119.98  3.000
 W75  CAQ  CAP  OAU  123.27  3.000
 W75  OAU  CAP  CAO  116.17  3.000
 W75  CAQ  CAP  CAO  120.56  3.000
 W75  CAW  OAU  CAP  119.00  3.000
 W75  H12  CAW  H11  108.76  3.000
 W75  H12  CAW  H10  108.70  3.000
 W75  H11  CAW  H10  108.81  3.000
 W75  H12  CAW  OAU  106.49  3.000
 W75  H11  CAW  OAU  111.99  3.000
 W75  H10  CAW  OAU  111.99  3.000
 W75  H13  CAQ  CAR  120.55  3.000
 W75  H13  CAQ  CAP  120.46  3.000
 W75  CAR  CAQ  CAP  118.99  3.000
 W75  OAT  CAR  CAQ  123.35  3.000
 W75  CAQ  CAR  CAS  120.54  3.000
 W75  OAT  CAR  CAS  116.10  3.000
 W75  CAV  OAT  CAR  118.95  3.000
 W75  H16  CAV  H15  108.68  3.000
 W75  H16  CAV  H14  108.80  3.000
 W75  H15  CAV  H14  108.68  3.000
 W75  H16  CAV  OAT  112.09  3.000
 W75  H15  CAV  OAT  106.46  3.000
 W75  H14  CAV  OAT  112.01  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
 W75  CONST_01  CAQ  CAR  CAS  CAN     0.00   0.0  0
 W75  CONST_02  CAQ  CAP  CAO  CAN     0.00   0.0  0
 W75  CONST_03  CAP  CAQ  CAR  CAS     0.00   0.0  0
 W75  CONST_04  CAP  CAO  CAN  CAS     0.00   0.0  0
 W75  CONST_05  CAR  CAS  CAN  CAO     0.00   0.0  0
 W75  CONST_06  CAR  CAQ  CAP  CAO     0.00   0.0  0
 W75  CONST_07  N1   C2   N3   C4      0.00   0.0  0
 W75  CONST_08  C6   N1   C2   N3      0.00   0.0  0
 W75  CONST_09  C5   C6   N1   C2      0.00   0.0  0
 W75  CONST_10  CAR  CAS  CAN  CAM   180.00   0.0  0
 W75  CONST_11  CAP  CAO  CAN  CAM   180.00   0.0  0
 W75  CONST_12  OAT  CAR  CAS  CAN   180.00   0.0  0
 W75  CONST_13  OAU  CAP  CAO  CAN   180.00   0.0  0
 W75  CONST_14  OAT  CAR  CAQ  CAP   180.00   0.0  0
 W75  CONST_15  CAR  CAQ  CAP  OAU   180.00   0.0  0
 W75  CONST_16  O2   C2   N3   C4    180.00   0.0  0
 W75  CONST_17  O6   C6   N1   C2    180.00   0.0  0
 W75  CONST_18  C6   N1   C2   O2    180.00   0.0  0
 W75  CONST_19  H13  CAQ  CAR  CAS   180.00   0.0  0
 W75  CONST_20  H9   CAO  CAN  CAS   180.00   0.0  0
 W75  CONST_21  H8   CAS  CAN  CAO   180.00   0.0  0
 W75  CONST_22  H2   N1   C2   N3    180.00   0.0  0
 W75  CONST_23  H17  N3   C2   N1    180.00   0.0  0
 W75  CONST_24  H1   OAJ  CAI  C4    180.00   0.0  0
 W75  Var_01    N3   C4   CAI  OAJ   -26.04  30.0  2
 W75  Var_02    CAM  CAL  C5   C4     94.80  30.0  3
 W75  Var_03    CAN  CAM  CAL  C5   -178.83  30.0  3
 W75  Var_04    CAS  CAN  CAM  CAL   -99.23  30.0  2
 W75  Var_05    CAQ  CAP  OAU  CAW    -0.34  30.0  2
 W75  Var_06    H10  CAW  OAU  CAP   -61.92  30.0  3
 W75  Var_07    H14  CAV  OAT  CAR    60.63  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
 W75  plan-1  CAI  0.020
 W75  plan-1  C4   0.020
 W75  plan-1  N3   0.020
 W75  plan-1  C2   0.020
 W75  plan-1  O2   0.020
 W75  plan-1  N1   0.020
 W75  plan-1  C6   0.020
 W75  plan-1  O6   0.020
 W75  plan-1  C5   0.020
 W75  plan-1  CAL  0.020
 W75  plan-1  H2   0.020
 W75  plan-1  H17  0.020
 W75  plan-2  CAM  0.020
 W75  plan-2  CAN  0.020
 W75  plan-2  CAS  0.020
 W75  plan-2  CAO  0.020
 W75  plan-2  CAP  0.020
 W75  plan-2  OAU  0.020
 W75  plan-2  CAQ  0.020
 W75  plan-2  CAR  0.020
 W75  plan-2  OAT  0.020
 W75  plan-2  H8   0.020
 W75  plan-2  H9   0.020
 W75  plan-2  H13  0.020
 W75  plan-3  OAJ  0.020
 W75  plan-3  CAI  0.020
 W75  plan-3  OAK  0.020
 W75  plan-3  C4   0.020
 W75  plan-3  H1   0.020

