# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 21:43:55 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 1-(2-phenylethyl)pyrimidine-2,4,6(1H,3H,5H)-trione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CC(=O)N(CCc2ccccc2)C(=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
 GJB  GJB  1-(2-phenylethyl)pyrimidine-2,4,6(1H,3H,5H)-trione  ligand  29  17  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GJB
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
 GJB  C     C  C     0   0.592   1.7881  -1.2978  -0.1148
 GJB  O     O  O     0  -0.426   1.1543  -2.3240  -0.0479
 GJB  CA    C  CH2   0  -0.721   3.2858  -1.2988  -0.0213
 GJB  CB    C  C     0   0.569   3.9554   0.0132   0.2347
 GJB  OAC   O  O     0  -0.446   1.2403   2.1841  -0.4020
 GJB  CAE   C  CR16  0  -0.240  -4.5652  -1.1692  -0.0609
 GJB  CAF   C  CR16  0  -0.301  -3.2125  -1.1390   0.2485
 GJB  CAG   C  CR16  0  -0.270  -5.2752   0.0174  -0.1963
 GJB  CAH   C  CR6   0   0.124  -2.5478   0.0730   0.4262
 GJB  CA0   C  C     0   0.759   1.8188   1.1354  -0.2479
 GJB  CAJ   C  CH2   0  -0.310  -0.2733  -0.0642  -0.5724
 GJB  NAL   N  NT    0  -0.569   1.1718  -0.0845  -0.3395
 GJB  OAN   O  O     0  -0.424   5.1167   0.1135   0.5513
 GJB  NAB   N  NH1   0  -0.717   3.1629   1.1108   0.0497
 GJB  CAQ   C  CH2   0  -0.523  -1.0736   0.0974   0.7193
 GJB  CAP   C  CR16  0  -0.240  -4.6232   1.2306  -0.0221
 GJB  CAO   C  CR16  0  -0.309  -3.2687   1.2558   0.2856
 GJB  HA1C  H  HCH2  0   0.334   3.5970  -2.0205   0.7336
 GJB  HA2C  H  HCH2  0   0.349   3.6636  -1.6768  -0.9787
 GJB  HAB   H  HNH1  0   0.434   3.5904   2.0212   0.1720
 GJB  HAF   H  HCR6  0   0.248  -2.6660  -2.0691   0.3581
 GJB  HAG   H  HCR6  0   0.255  -6.3316  -0.0044  -0.4313
 GJB  HAP   H  HCR6  0   0.255  -5.1694   2.1597  -0.1244
 GJB  HAQ1  H  HCH2  0   0.259  -0.8034   1.0382   1.2017
 GJB  HAQ2  H  HCH2  0   0.260  -0.8161  -0.7079   1.4105
 GJB  HAO   H  HCR6  0   0.248  -2.7676   2.2067   0.4251
 GJB  HAJ1  H  HCH2  0   0.280  -0.4952   0.7451  -1.2643
 GJB  HAJ2  H  HCH2  0   0.277  -0.5395  -0.9941  -1.0691
 GJB  HAE   H  HCR6  0   0.255  -5.0664  -2.1194  -0.1937

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
 GJB  C    O     double    1.208  0.020  1.208
 GJB  C    CA    single    1.501  0.020  1.501
 GJB  C    NAL   single    1.379  0.020  1.379
 GJB  CA   CB    single    1.495  0.020  1.495
 GJB  CB   OAN   double    1.208  0.020  1.208
 GJB  CB   NAB   single    1.366  0.020  1.366
 GJB  OAC  CA0   double    1.208  0.020  1.208
 GJB  CAE  CAF   aromatic  1.388  0.020  1.388
 GJB  CAE  CAG   aromatic  1.389  0.020  1.389
 GJB  CAF  CAH   aromatic  1.394  0.020  1.394
 GJB  CAG  CAP   aromatic  1.388  0.020  1.388
 GJB  CAH  CAQ   single    1.503  0.020  1.503
 GJB  CAH  CAO   aromatic  1.392  0.020  1.392
 GJB  CA0  NAL   single    1.384  0.020  1.384
 GJB  CA0  NAB   single    1.377  0.020  1.377
 GJB  CAJ  NAL   single    1.464  0.020  1.464
 GJB  CAJ  CAQ   single    1.528  0.020  1.528
 GJB  CAP  CAO   aromatic  1.389  0.020  1.389
 GJB  CA   HA1C  single    0.970  0.020  1.090
 GJB  CA   HA2C  single    0.970  0.020  1.090
 GJB  NAB  HAB   single    0.860  0.020  1.020
 GJB  CAE  HAE   single    0.930  0.020  1.080
 GJB  CAF  HAF   single    0.930  0.020  1.080
 GJB  CAG  HAG   single    0.930  0.020  1.080
 GJB  CAP  HAP   single    0.930  0.020  1.080
 GJB  CAQ  HAQ1  single    0.970  0.020  1.090
 GJB  CAQ  HAQ2  single    0.970  0.020  1.090
 GJB  CAO  HAO   single    0.930  0.020  1.080
 GJB  CAJ  HAJ1  single    0.970  0.020  1.090
 GJB  CAJ  HAJ2  single    0.970  0.020  1.090

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
 GJB  NAL   C    CA    117.18  3.000
 GJB  NAL   C    O     121.46  3.000
 GJB  CA    C    O     121.30  3.000
 GJB  HA2C  CA   HA1C  106.15  3.000
 GJB  HA2C  CA   CB    107.32  3.000
 GJB  HA1C  CA   CB    109.55  3.000
 GJB  HA2C  CA   C     106.83  3.000
 GJB  HA1C  CA   C     109.19  3.000
 GJB  CB    CA   C     117.20  3.000
 GJB  NAB   CB   OAN   121.76  3.000
 GJB  NAB   CB   CA    114.96  3.000
 GJB  OAN   CB   CA    123.25  3.000
 GJB  HAE   CAE  CAG   120.07  3.000
 GJB  HAE   CAE  CAF   119.85  3.000
 GJB  CAG   CAE  CAF   120.08  3.000
 GJB  HAF   CAF  CAH   119.52  3.000
 GJB  HAF   CAF  CAE   119.68  3.000
 GJB  CAH   CAF  CAE   120.80  3.000
 GJB  HAG   CAG  CAP   120.21  3.000
 GJB  HAG   CAG  CAE   120.18  3.000
 GJB  CAP   CAG  CAE   119.61  3.000
 GJB  CAO   CAH  CAQ   120.91  3.000
 GJB  CAO   CAH  CAF   118.62  3.000
 GJB  CAQ   CAH  CAF   120.44  3.000
 GJB  NAB   CA0  NAL   117.07  3.000
 GJB  NAB   CA0  OAC   120.71  3.000
 GJB  NAL   CA0  OAC   122.21  3.000
 GJB  HAJ2  CAJ  HAJ1  107.21  3.000
 GJB  HAJ2  CAJ  CAQ   110.39  3.000
 GJB  HAJ1  CAJ  CAQ   110.62  3.000
 GJB  HAJ2  CAJ  NAL   107.61  3.000
 GJB  HAJ1  CAJ  NAL   108.24  3.000
 GJB  CAQ   CAJ  NAL   112.58  3.000
 GJB  CAJ   NAL  CA0   117.38  3.000
 GJB  CAJ   NAL  C     118.63  3.000
 GJB  CA0   NAL  C     123.76  3.000
 GJB  HAB   NAB  CA0   114.96  3.000
 GJB  HAB   NAB  CB    117.43  3.000
 GJB  CA0   NAB  CB    127.57  3.000
 GJB  HAQ2  CAQ  HAQ1  107.31  3.000
 GJB  HAQ2  CAQ  CAJ   109.48  3.000
 GJB  HAQ1  CAQ  CAJ   109.58  3.000
 GJB  HAQ2  CAQ  CAH   110.04  3.000
 GJB  HAQ1  CAQ  CAH   110.06  3.000
 GJB  CAJ   CAQ  CAH   110.31  3.000
 GJB  HAP   CAP  CAO   119.82  3.000
 GJB  HAP   CAP  CAG   120.08  3.000
 GJB  CAO   CAP  CAG   120.10  3.000
 GJB  HAO   CAO  CAP   119.68  3.000
 GJB  HAO   CAO  CAH   119.53  3.000
 GJB  CAP   CAO  CAH   120.78  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
 GJB  CONST_01  CAO   CAH  CAF  CAE     0.00   0.0  0
 GJB  CONST_02  CAO   CAP  CAG  CAE     0.00   0.0  0
 GJB  CONST_03  CAP   CAG  CAE  CAF     0.00   0.0  0
 GJB  CONST_04  CAP   CAO  CAH  CAF     0.00   0.0  0
 GJB  CONST_05  CAH   CAF  CAE  CAG     0.00   0.0  0
 GJB  CONST_06  CAH   CAO  CAP  CAG     0.00   0.0  0
 GJB  CONST_07  NAB   CA0  NAL  C       0.00   0.0  0
 GJB  CONST_08  CA0   NAL  C    CA      0.00   0.0  0
 GJB  CONST_09  CA0   NAB  CB   CA      0.00   0.0  0
 GJB  CONST_10  NAL   CA0  NAB  CB      0.00   0.0  0
 GJB  CONST_11  CAQ   CAH  CAF  CAE   180.00   0.0  0
 GJB  CONST_12  CAP   CAO  CAH  CAQ   180.00   0.0  0
 GJB  CONST_13  OAC   CA0  NAL  C     180.00   0.0  0
 GJB  CONST_14  CA0   NAL  C    O     180.00   0.0  0
 GJB  CONST_15  CAJ   NAL  C    CA    180.00   0.0  0
 GJB  CONST_16  OAC   CA0  NAB  CB    180.00   0.0  0
 GJB  CONST_17  OAN   CB   NAB  CA0   180.00   0.0  0
 GJB  CONST_18  NAB   CA0  NAL  CAJ   180.00   0.0  0
 GJB  CONST_19  HAP   CAP  CAG  CAE   180.00   0.0  0
 GJB  CONST_20  HAG   CAG  CAE  CAF   180.00   0.0  0
 GJB  CONST_21  HAO   CAO  CAH  CAF   180.00   0.0  0
 GJB  CONST_22  HAF   CAF  CAE  CAG   180.00   0.0  0
 GJB  CONST_23  HAE   CAE  CAF  CAH   180.00   0.0  0
 GJB  CONST_24  HAB   NAB  CB   CA    180.00   0.0  0
 GJB  CONST_25  CAJ   NAL  C    O       0.00   0.0  0
 GJB  CONST_26  CAJ   NAL  CA0  OAC     0.00   0.0  0
 GJB  Var_01    HA1C  CA   C    NAL   143.22  30.0  1
 GJB  Var_02    CAQ   CAJ  NAL  C      90.38  30.0  3
 GJB  Var_03    CAJ   CAQ  CAH  CAF    81.05  30.0  2
 GJB  Var_04    NAL   CAJ  CAQ  CAH  -178.42  30.0  1

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
 GJB  plan-1  CAE  0.020
 GJB  plan-1  CAF  0.020
 GJB  plan-1  CAG  0.020
 GJB  plan-1  CAH  0.020
 GJB  plan-1  CAQ  0.020
 GJB  plan-1  CAP  0.020
 GJB  plan-1  CAO  0.020
 GJB  plan-1  HAF  0.020
 GJB  plan-1  HAG  0.020
 GJB  plan-1  HAP  0.020
 GJB  plan-1  HAO  0.020
 GJB  plan-1  HAE  0.020
 GJB  plan-2  C    0.020
 GJB  plan-2  O    0.020
 GJB  plan-2  CA   0.020
 GJB  plan-2  CB   0.020
 GJB  plan-2  OAC  0.020
 GJB  plan-2  CA0  0.020
 GJB  plan-2  CAJ  0.020
 GJB  plan-2  NAL  0.020
 GJB  plan-2  OAN  0.020
 GJB  plan-2  NAB  0.020
 GJB  plan-2  HAB  0.020

