# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 21:38:45 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 5-amino-1-benzyl-6-hydroxypyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=C(O)N(Cc2ccccc2)C(=O)NC1=O
#
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
 4WF  4WF  5-amino-1-benzyl-6-hydroxypyrimidine-2,4(1H,3H)-dione  ligand  28  17  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4WF
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
 4WF  C     C  CR6   0   0.670   1.0975  -0.7878  -0.3679
 4WF  N     N  NH2   0  -0.857   2.8268  -1.9674   0.7162
 4WF  O     O  OH1   0  -0.578   0.5025  -1.9386  -0.5756
 4WF  CA    C  CR6   0  -0.129   2.2947  -0.7295   0.2867
 4WF  CB    C  CR6   0   0.538   2.9177   0.5380   0.4884
 4WF  OAC   O  O     0  -0.482   0.4398   2.5802  -1.0747
 4WF  CAE   C  CR16  0  -0.265  -4.1026  -0.5152   1.1925
 4WF  CAF   C  CR16  0  -0.240  -3.4193   0.6948   1.2115
 4WF  CAG   C  CR16  0  -0.242  -3.7310  -1.5001   0.2883
 4WF  CAH   C  CR16  0  -0.294  -2.3694   0.9158   0.3324
 4WF  CAI   C  CR16  0  -0.297  -2.6743  -1.2790  -0.5862
 4WF  CA0   C  CR6   0   0.734   0.9902   1.5727  -0.6782
 4WF  CAJ   C  CH2   0  -0.416  -0.8454   0.1684  -1.5280
 4WF  NAL   N  NR6   0  -0.579   0.4474   0.3105  -0.8492
 4WF  OAN   O  O     0  -0.476   3.9814   0.7367   1.0534
 4WF  NAB   N  NR16  0  -0.742   2.1909   1.6067  -0.0315
 4WF  CAQ   C  CR6   0   0.127  -1.9836  -0.0726  -0.5713
 4WF  HN1   H  HNH2  0   0.373   2.9424  -2.0061   1.7207
 4WF  HN2   H  HNH2  0   0.373   3.7264  -2.1651   0.2970
 4WF  HAB   H  HNR6  0   0.424   2.5866   2.5297   0.0950
 4WF  HAF   H  HCR6  0   0.257  -3.7093   1.4710   1.9078
 4WF  HAG   H  HCR6  0   0.257  -4.2596  -2.4442   0.2659
 4WF  HAH   H  HCR6  0   0.254  -1.8555   1.8691   0.3445
 4WF  HAI   H  HCR6  0   0.253  -2.3863  -2.0535  -1.2864
 4WF  HAJ1  H  HCH2  0   0.300  -1.0065   1.0842  -2.0910
 4WF  HAJ2  H  HCH2  0   0.295  -0.7703  -0.6392  -2.2539
 4WF  HO    H  HOH1  0   0.486   1.1038  -2.6055  -0.1783
 4WF  HAE   H  HCR6  0   0.258  -4.9235  -0.6851   1.8771

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
 4WF  C    O     single    1.312  0.020  1.312
 4WF  O    HO    single    0.850  0.020  0.980
 4WF  C    CA    double    1.366  0.020  1.366
 4WF  C    NAL   single    1.364  0.020  1.364
 4WF  N    CA    single    1.414  0.020  1.414
 4WF  CA   CB    single    1.427  0.020  1.427
 4WF  CB   OAN   double    1.221  0.020  1.221
 4WF  CB   NAB   single    1.393  0.020  1.393
 4WF  OAC  CA0   double    1.215  0.020  1.215
 4WF  CAE  CAF   aromatic  1.390  0.020  1.390
 4WF  CAE  CAG   aromatic  1.388  0.020  1.388
 4WF  CAF  CAH   aromatic  1.387  0.020  1.387
 4WF  CAG  CAI   aromatic  1.389  0.020  1.389
 4WF  CAH  CAQ   aromatic  1.394  0.020  1.394
 4WF  CAI  CAQ   aromatic  1.390  0.020  1.390
 4WF  CAJ  NAL   single    1.467  0.020  1.467
 4WF  CAJ  CAQ   single    1.506  0.020  1.506
 4WF  NAL  CA0   single    1.385  0.020  1.385
 4WF  CA0  NAB   single    1.364  0.020  1.364
 4WF  N    HN1   single    0.890  0.020  1.040
 4WF  N    HN2   single    0.890  0.020  1.040
 4WF  NAB  HAB   single    0.860  0.020  1.020
 4WF  CAE  HAE   single    0.930  0.020  1.080
 4WF  CAF  HAF   single    0.930  0.020  1.080
 4WF  CAG  HAG   single    0.930  0.020  1.080
 4WF  CAH  HAH   single    0.930  0.020  1.080
 4WF  CAI  HAI   single    0.930  0.020  1.080
 4WF  CAJ  HAJ1  single    0.970  0.020  1.090
 4WF  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
 4WF  NAL   C    CA    123.54  3.000
 4WF  NAL   C    O     115.73  3.000
 4WF  CA    C    O     120.72  3.000
 4WF  HN2   N    HN1   107.59  3.000
 4WF  HN2   N    CA    112.31  3.000
 4WF  HN1   N    CA    112.21  3.000
 4WF  HO    O    C     104.71  3.000
 4WF  CB    CA   N     124.78  3.000
 4WF  CB    CA   C     119.24  3.000
 4WF  N     CA   C     115.98  3.000
 4WF  NAB   CB   OAN   120.17  3.000
 4WF  NAB   CB   CA    113.64  3.000
 4WF  OAN   CB   CA    126.20  3.000
 4WF  HAE   CAE  CAG   120.25  3.000
 4WF  HAE   CAE  CAF   120.07  3.000
 4WF  CAG   CAE  CAF   119.68  3.000
 4WF  HAF   CAF  CAH   119.76  3.000
 4WF  HAF   CAF  CAE   120.09  3.000
 4WF  CAH   CAF  CAE   120.15  3.000
 4WF  HAG   CAG  CAI   119.82  3.000
 4WF  HAG   CAG  CAE   120.12  3.000
 4WF  CAI   CAG  CAE   120.06  3.000
 4WF  HAH   CAH  CAQ   120.01  3.000
 4WF  HAH   CAH  CAF   119.49  3.000
 4WF  CAQ   CAH  CAF   120.50  3.000
 4WF  HAI   CAI  CAQ   119.69  3.000
 4WF  HAI   CAI  CAG   119.69  3.000
 4WF  CAQ   CAI  CAG   120.61  3.000
 4WF  NAB   CA0  NAL   115.24  3.000
 4WF  NAB   CA0  OAC   122.20  3.000
 4WF  NAL   CA0  OAC   122.56  3.000
 4WF  HAJ2  CAJ  HAJ1  106.85  3.000
 4WF  HAJ2  CAJ  CAQ   110.91  3.000
 4WF  HAJ1  CAJ  CAQ   110.60  3.000
 4WF  HAJ2  CAJ  NAL   108.64  3.000
 4WF  HAJ1  CAJ  NAL   106.78  3.000
 4WF  CAQ   CAJ  NAL   112.80  3.000
 4WF  CAJ   NAL  CA0   119.40  3.000
 4WF  CA0   NAL  C     120.23  3.000
 4WF  CAJ   NAL  C     120.35  3.000
 4WF  HAB   NAB  CA0   115.22  3.000
 4WF  HAB   NAB  CB    116.68  3.000
 4WF  CA0   NAB  CB    128.10  3.000
 4WF  CAJ   CAQ  CAI   120.50  3.000
 4WF  CAJ   CAQ  CAH   120.50  3.000
 4WF  CAI   CAQ  CAH   119.00  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
 4WF  CONST_01  CAQ  CAH  CAF  CAE     0.00   0.0  0
 4WF  CONST_02  CAQ  CAI  CAG  CAE     0.00   0.0  0
 4WF  CONST_03  CAI  CAG  CAE  CAF     0.00   0.0  0
 4WF  CONST_04  CAI  CAQ  CAH  CAF     0.00   0.0  0
 4WF  CONST_05  CAH  CAF  CAE  CAG     0.00   0.0  0
 4WF  CONST_06  CAH  CAQ  CAI  CAG     0.00   0.0  0
 4WF  CONST_07  NAB  CA0  NAL  C       0.00   0.0  0
 4WF  CONST_08  CA0  NAB  CB   CA      0.00   0.0  0
 4WF  CONST_09  NAL  CA0  NAB  CB      0.00   0.0  0
 4WF  CONST_10  CAJ  CAQ  CAH  CAF   180.00   0.0  0
 4WF  CONST_11  CAJ  CAQ  CAI  CAG   180.00   0.0  0
 4WF  CONST_12  OAC  CA0  NAL  C     180.00   0.0  0
 4WF  CONST_13  OAC  CA0  NAB  CB    180.00   0.0  0
 4WF  CONST_14  OAN  CB   NAB  CA0   180.00   0.0  0
 4WF  CONST_15  NAB  CA0  NAL  CAJ   180.00   0.0  0
 4WF  CONST_16  HAH  CAH  CAF  CAE   180.00   0.0  0
 4WF  CONST_17  HAI  CAI  CAG  CAE   180.00   0.0  0
 4WF  CONST_18  HAG  CAG  CAE  CAF   180.00   0.0  0
 4WF  CONST_19  HAF  CAF  CAE  CAG   180.00   0.0  0
 4WF  CONST_20  HAE  CAE  CAF  CAH   180.00   0.0  0
 4WF  CONST_21  HAB  NAB  CB   CA    180.00   0.0  0
 4WF  CONST_22  CAJ  NAL  CA0  OAC     0.00   0.0  0
 4WF  Var_01    CAQ  CAJ  NAL  C      76.28  30.0  3
 4WF  Var_02    NAL  CAJ  CAQ  CAH    66.13  30.0  2
 4WF  Var_03    HN1  N    CA   C    -119.41  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
 4WF  plan-1  C    0.020
 4WF  plan-1  N    0.020
 4WF  plan-1  O    0.020
 4WF  plan-1  CA   0.020
 4WF  plan-1  CB   0.020
 4WF  plan-1  OAC  0.020
 4WF  plan-1  CA0  0.020
 4WF  plan-1  CAJ  0.020
 4WF  plan-1  NAL  0.020
 4WF  plan-1  OAN  0.020
 4WF  plan-1  NAB  0.020
 4WF  plan-1  HAB  0.020
 4WF  plan-2  CAE  0.020
 4WF  plan-2  CAF  0.020
 4WF  plan-2  CAG  0.020
 4WF  plan-2  CAH  0.020
 4WF  plan-2  CAI  0.020
 4WF  plan-2  CAJ  0.020
 4WF  plan-2  CAQ  0.020
 4WF  plan-2  HAF  0.020
 4WF  plan-2  HAG  0.020
 4WF  plan-2  HAH  0.020
 4WF  plan-2  HAI  0.020
 4WF  plan-2  HAE  0.020

