# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 09:35:29 2022
#   Inital geometry file: a 128 line input string
#   Ligand name: 5-({4-[(1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydro-7H-purin-7-yl)methyl]phenyl}methyl)pyrimidine-2,4,6(1H,3H,5H)-trione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2ncn(Cc3ccc(CC4C(=O)NC(=O)NC4=O)cc3)c2C1=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
 WDA  WDA  5-({4-[(1,3-dimethyl-2,6-dioxo-1,2,3,6-tetrahydro-7H-purin-7-yl)methyl]phenyl}methyl)pyrimidine-2,4,6(1H,3H,5H)-trione  ligand  48  30  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_WDA
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
 WDA  C10  C  CH2   0  -0.394  5.9024   2.2709  -25.1323
 WDA  C13  C  CR16  0  -0.283  3.5514  -0.3608  -23.7363
 WDA  C15  C  CH2   0  -0.516  3.3887  -1.4917  -21.4976
 WDA  C17  C  C     0   0.584  3.3938   0.1381  -19.5934
 WDA  C21  C  C     0   0.590  1.5384   0.1682  -21.3380
 WDA  C26  C  CR16  0  -0.267  5.9005   0.9063  -23.0191
 WDA  C28  C  CR6   0   0.583  3.6896   4.4044  -24.1323
 WDA  C03  C  CR6   0   0.735  3.7528   6.4346  -22.6908
 WDA  C06  C  CR56  0   0.433  5.7719   5.3161  -23.2210
 WDA  C08  C  CR15  0   0.132  7.2411   4.0132  -23.9641
 WDA  C11  C  CR6   0   0.100  5.3006   1.2203  -24.2352
 WDA  C12  C  CR16  0  -0.273  4.1343   0.5595  -24.5953
 WDA  C14  C  CR6   0   0.079  4.1128  -0.6297  -22.4920
 WDA  C16  C  CH1   0  -0.546  2.5100  -0.6491  -20.5264
 WDA  C19  C  C     0   0.709  2.8130   2.1972  -20.7982
 WDA  C25  C  CR16  0  -0.288  5.3151  -0.0078  -22.1592
 WDA  C27  C  CR56  0   0.130  5.1006   4.3650  -23.9433
 WDA  N02  N  NR6   0  -0.601  3.0975   5.4695  -23.4496
 WDA  N04  N  NR6   0  -0.588  5.1183   6.3378  -22.5955
 WDA  N07  N  N     0  -0.470  7.0998   5.1038  -23.2344
 WDA  N09  N  NR5   0  -0.470  6.0816   3.5271  -24.4256
 WDA  N18  N  NH1   0  -0.695  3.5106   1.4774  -19.8556
 WDA  N20  N  NH1   0  -0.698  1.8308   1.5016  -21.4639
 WDA  O22  O  O     0  -0.406  0.5904  -0.3251  -21.8994
 WDA  O23  O  O     0  -0.429  3.0275   3.3668  -21.0023
 WDA  O24  O  O     0  -0.408  4.0060  -0.3830  -18.6924
 WDA  O30  O  O     0  -0.486  3.1551   7.3370  -22.1366
 WDA  H1   H  HCH2  0   0.293  5.2792   2.4393  -26.0086
 WDA  H2   H  HCH2  0   0.295  6.8883   1.9673  -25.4869
 WDA  H3   H  HCR6  0   0.258  2.6321  -0.8534  -24.0298
 WDA  H4   H  HCH2  0   0.290  2.7302  -2.1978  -22.0037
 WDA  H5   H  HCH2  0   0.290  4.0845  -2.0769  -20.8950
 WDA  H6   H  HCR6  0   0.256  6.8272   1.3867  -22.7270
 WDA  H7   H  HCH3  0   0.267  1.2824   6.3218  -22.8816
 WDA  H8   H  HCH3  0   0.252  1.3405   5.7904  -24.5648
 WDA  H9   H  HCH3  0   0.255  1.1988   4.6004  -23.2620
 WDA  H10  H  HCH3  0   0.267  6.8909   7.0886  -21.8371
 WDA  H11  H  HCH3  0   0.257  5.7018   8.3288  -22.2513
 WDA  H12  H  HCH3  0   0.257  5.4908   7.3463  -20.7905
 WDA  H13  H  HCR5  0   0.304  8.1843   3.5347  -24.1833
 WDA  H14  H  HCR6  0   0.254  3.6634   0.7768  -25.5454
 WDA  H15  H  HCH1  0   0.346  1.9326  -1.3467  -19.9156
 WDA  H16  H  HCR6  0   0.259  5.7963  -0.2325  -21.2145
 WDA  H17  H  HNH1  0   0.433  4.1760   2.0059  -19.3031
 WDA  H18  H  HNH1  0   0.436  1.2640   2.0472  -22.1033
 WDA  O29  O  O     0  -0.461  3.0228   3.6406  -24.8067
 WDA  C01  C  CH3   0  -0.535  1.6455   5.5500  -23.5478
 WDA  C05  C  CH3   0  -0.530  5.8353   7.3376  -21.8224

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
 WDA  O29  C28  double    1.218  0.020  1.218
 WDA  C01  N02  single    1.458  0.020  1.458
 WDA  C10  N09  single    1.452  0.020  1.452
 WDA  C10  C11  single    1.507  0.020  1.507
 WDA  C28  N02  single    1.397  0.020  1.397
 WDA  C28  C27  single    1.424  0.020  1.424
 WDA  N02  C03  single    1.392  0.020  1.392
 WDA  C12  C11  aromatic  1.388  0.020  1.388
 WDA  C12  C13  aromatic  1.387  0.020  1.387
 WDA  N09  C27  aromatic  1.377  0.020  1.377
 WDA  N09  C08  aromatic  1.339  0.020  1.339
 WDA  C27  C06  aromatic  1.370  0.020  1.370
 WDA  C11  C26  aromatic  1.392  0.020  1.392
 WDA  C03  O30  double    1.216  0.020  1.216
 WDA  C03  N04  single    1.372  0.020  1.372
 WDA  C08  N07  aromatic  1.320  0.020  1.320
 WDA  C06  N04  single    1.365  0.020  1.365
 WDA  C06  N07  aromatic  1.345  0.020  1.345
 WDA  C13  C14  aromatic  1.391  0.020  1.391
 WDA  N04  C05  single    1.453  0.020  1.453
 WDA  C26  C25  aromatic  1.385  0.020  1.385
 WDA  C14  C25  aromatic  1.394  0.020  1.394
 WDA  C14  C15  single    1.502  0.020  1.502
 WDA  C15  C16  single    1.557  0.020  1.557
 WDA  O22  C21  double    1.207  0.020  1.207
 WDA  C16  C21  single    1.507  0.020  1.507
 WDA  C16  C17  single    1.507  0.020  1.507
 WDA  C21  N20  single    1.371  0.020  1.371
 WDA  O24  C17  double    1.208  0.020  1.208
 WDA  C17  N18  single    1.370  0.020  1.370
 WDA  N20  C19  single    1.375  0.020  1.375
 WDA  N18  C19  single    1.376  0.020  1.376
 WDA  C19  O23  double    1.206  0.020  1.206
 WDA  C10  H1   single    0.970  0.020  1.090
 WDA  C10  H2   single    0.970  0.020  1.090
 WDA  C13  H3   single    0.930  0.020  1.080
 WDA  C15  H4   single    0.970  0.020  1.090
 WDA  C15  H5   single    0.970  0.020  1.090
 WDA  C26  H6   single    0.930  0.020  1.080
 WDA  C01  H7   single    0.970  0.020  1.090
 WDA  C01  H8   single    0.970  0.020  1.090
 WDA  C01  H9   single    0.970  0.020  1.090
 WDA  C05  H10  single    0.970  0.020  1.090
 WDA  C05  H11  single    0.970  0.020  1.090
 WDA  C05  H12  single    0.970  0.020  1.090
 WDA  C08  H13  single    0.930  0.020  1.080
 WDA  C12  H14  single    0.930  0.020  1.080
 WDA  C16  H15  single    0.970  0.020  1.090
 WDA  C25  H16  single    0.930  0.020  1.080
 WDA  N18  H17  single    0.860  0.020  1.020
 WDA  N20  H18  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
 WDA  H2   C10  H1   107.39  3.000
 WDA  H2   C10  N09  106.70  3.000
 WDA  H1   C10  N09  109.18  3.000
 WDA  H2   C10  C11  111.12  3.000
 WDA  H1   C10  C11  111.01  3.000
 WDA  N09  C10  C11  111.26  3.000
 WDA  H3   C13  C14  119.79  3.000
 WDA  H3   C13  C12  119.36  3.000
 WDA  C14  C13  C12  120.82  3.000
 WDA  H5   C15  H4   107.12  3.000
 WDA  H5   C15  C16  107.80  3.000
 WDA  H4   C15  C16  107.40  3.000
 WDA  H5   C15  C14  111.48  3.000
 WDA  H4   C15  C14  110.82  3.000
 WDA  C16  C15  C14  111.99  3.000
 WDA  O24  C17  N18  121.43  3.000
 WDA  N18  C17  C16  116.25  3.000
 WDA  O24  C17  C16  122.27  3.000
 WDA  O22  C21  N20  121.48  3.000
 WDA  N20  C21  C16  116.07  3.000
 WDA  O22  C21  C16  122.36  3.000
 WDA  H6   C26  C25  119.12  3.000
 WDA  H6   C26  C11  120.26  3.000
 WDA  C25  C26  C11  120.62  3.000
 WDA  O29  C28  N02  121.12  3.000
 WDA  N02  C28  C27  112.10  3.000
 WDA  O29  C28  C27  126.77  3.000
 WDA  O30  C03  N04  120.65  3.000
 WDA  N04  C03  N02  117.23  3.000
 WDA  O30  C03  N02  122.12  3.000
 WDA  N07  C06  N04  126.56  3.000
 WDA  N07  C06  C27  111.65  3.000
 WDA  N04  C06  C27  121.78  3.000
 WDA  H13  C08  N09  121.69  3.000
 WDA  H13  C08  N07  124.88  3.000
 WDA  N09  C08  N07  113.44  3.000
 WDA  C12  C11  C26  118.78  3.000
 WDA  C26  C11  C10  120.35  3.000
 WDA  C12  C11  C10  120.87  3.000
 WDA  H14  C12  C11  119.84  3.000
 WDA  H14  C12  C13  119.60  3.000
 WDA  C11  C12  C13  120.55  3.000
 WDA  C25  C14  C15  120.91  3.000
 WDA  C15  C14  C13  120.56  3.000
 WDA  C25  C14  C13  118.38  3.000
 WDA  H15  C16  C21  107.86  3.000
 WDA  H15  C16  C17  107.30  3.000
 WDA  C21  C16  C17  115.35  3.000
 WDA  H15  C16  C15  107.55  3.000
 WDA  C17  C16  C15  109.74  3.000
 WDA  C21  C16  C15  108.75  3.000
 WDA  O23  C19  N20  122.37  3.000
 WDA  O23  C19  N18  122.20  3.000
 WDA  N20  C19  N18  115.41  3.000
 WDA  H16  C25  C14  119.91  3.000
 WDA  H16  C25  C26  119.37  3.000
 WDA  C14  C25  C26  120.72  3.000
 WDA  N09  C27  C06  104.95  3.000
 WDA  C06  C27  C28  122.43  3.000
 WDA  N09  C27  C28  132.54  3.000
 WDA  C03  N02  C01  117.87  3.000
 WDA  C03  N02  C28  126.56  3.000
 WDA  C01  N02  C28  115.56  3.000
 WDA  C06  N04  C05  121.51  3.000
 WDA  C05  N04  C03  118.65  3.000
 WDA  C06  N04  C03  119.84  3.000
 WDA  C08  N07  C06  103.99  3.000
 WDA  C27  N09  C08  105.97  3.000
 WDA  C08  N09  C10  126.04  3.000
 WDA  C27  N09  C10  127.49  3.000
 WDA  H17  N18  C19  115.69  3.000
 WDA  H17  N18  C17  117.48  3.000
 WDA  C19  N18  C17  126.83  3.000
 WDA  H18  N20  C19  115.61  3.000
 WDA  H18  N20  C21  117.53  3.000
 WDA  C19  N20  C21  126.85  3.000
 WDA  H9   C01  H8   108.86  3.000
 WDA  H9   C01  H7   108.85  3.000
 WDA  H8   C01  H7   108.87  3.000
 WDA  H9   C01  N02  110.08  3.000
 WDA  H8   C01  N02  110.75  3.000
 WDA  H7   C01  N02  109.40  3.000
 WDA  H12  C05  H11  109.13  3.000
 WDA  H12  C05  H10  108.83  3.000
 WDA  H11  C05  H10  108.86  3.000
 WDA  H12  C05  N04  110.73  3.000
 WDA  H11  C05  N04  110.89  3.000
 WDA  H10  C05  N04  108.36  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
 WDA  CONST_01  C26  C11  C12  C13    0.00   0.0  0
 WDA  CONST_02  C26  C25  C14  C13    0.00   0.0  0
 WDA  CONST_03  C08  N09  C27  C06    0.00   0.0  0
 WDA  CONST_04  N09  C08  N07  C06    0.00   0.0  0
 WDA  CONST_05  C27  C06  N07  C08    0.00   0.0  0
 WDA  CONST_06  C14  C13  C12  C11    0.00   0.0  0
 WDA  CONST_07  C14  C25  C26  C11    0.00   0.0  0
 WDA  CONST_08  C25  C26  C11  C12    0.00   0.0  0
 WDA  CONST_09  C25  C14  C13  C12    0.00   0.0  0
 WDA  CONST_10  N07  C08  N09  C27    0.00   0.0  0
 WDA  CONST_11  N09  C27  C06  N07    0.00   0.0  0
 WDA  CONST_12  N20  C19  N18  C17    0.00   0.0  0
 WDA  CONST_13  N18  C19  N20  C21    0.00   0.0  0
 WDA  CONST_14  N04  C03  N02  C28    0.00   0.0  0
 WDA  CONST_15  C27  C28  N02  C03    0.00   0.0  0
 WDA  CONST_16  N02  C03  N04  C06    0.00   0.0  0
 WDA  CONST_17  C19  N20  C21  C16    0.00   0.0  0
 WDA  CONST_18  C19  N18  C17  C16    0.00   0.0  0
 WDA  CONST_19  C28  C27  N09  C10    0.00   0.0  0
 WDA  CONST_20  C06  C27  N09  C10  180.00   0.0  0
 WDA  CONST_21  N07  C08  N09  C10  180.00   0.0  0
 WDA  CONST_22  C13  C12  C11  C10  180.00   0.0  0
 WDA  CONST_23  C25  C26  C11  C10  180.00   0.0  0
 WDA  CONST_24  C12  C13  C14  C15  180.00   0.0  0
 WDA  CONST_25  C26  C25  C14  C15  180.00   0.0  0
 WDA  CONST_26  O23  C19  N18  C17  180.00   0.0  0
 WDA  CONST_27  O23  C19  N20  C21  180.00   0.0  0
 WDA  CONST_28  O30  C03  N02  C28  180.00   0.0  0
 WDA  CONST_29  C27  C28  N02  C01  180.00   0.0  0
 WDA  CONST_30  N04  C03  N02  C01  180.00   0.0  0
 WDA  CONST_31  O29  C28  N02  C03  180.00   0.0  0
 WDA  CONST_32  N02  C03  N04  C05  180.00   0.0  0
 WDA  CONST_33  O30  C03  N04  C06  180.00   0.0  0
 WDA  CONST_34  O22  C21  N20  C19  180.00   0.0  0
 WDA  CONST_35  O24  C17  N18  C19  180.00   0.0  0
 WDA  CONST_36  H16  C25  C14  C13  180.00   0.0  0
 WDA  CONST_37  H14  C12  C11  C26  180.00   0.0  0
 WDA  CONST_38  H13  C08  N07  C06  180.00   0.0  0
 WDA  CONST_39  H3   C13  C12  C11  180.00   0.0  0
 WDA  CONST_40  H6   C26  C11  C12  180.00   0.0  0
 WDA  CONST_41  H18  N20  C21  C16  180.00   0.0  0
 WDA  CONST_42  H17  N18  C17  C16  180.00   0.0  0
 WDA  CONST_43  O29  C28  N02  C01    0.00   0.0  0
 WDA  CONST_44  O30  C03  N02  C01    0.00   0.0  0
 WDA  CONST_45  O30  C03  N04  C05    0.00   0.0  0
 WDA  Var_01    C16  C15  C14  C13  -92.52  30.0  2
 WDA  Var_02    N09  C10  C11  C26  -54.55  30.0  3
 WDA  Var_03    C11  C10  N09  C08  103.84  30.0  2
 WDA  Var_04    H7   C01  N02  C28  172.44  30.0  3
 WDA  Var_05    H10  C05  N04  C03  178.56  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 WDA  chir_01  C16  C15  C21  C17  positiv

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
 WDA  plan-1  C10  0.020
 WDA  plan-1  C13  0.020
 WDA  plan-1  C15  0.020
 WDA  plan-1  C26  0.020
 WDA  plan-1  C11  0.020
 WDA  plan-1  C12  0.020
 WDA  plan-1  C14  0.020
 WDA  plan-1  C25  0.020
 WDA  plan-1  H3   0.020
 WDA  plan-1  H6   0.020
 WDA  plan-1  H14  0.020
 WDA  plan-1  H16  0.020
 WDA  plan-2  C10  0.020
 WDA  plan-2  C28  0.020
 WDA  plan-2  C03  0.020
 WDA  plan-2  C06  0.020
 WDA  plan-2  C08  0.020
 WDA  plan-2  C27  0.020
 WDA  plan-2  N02  0.020
 WDA  plan-2  N04  0.020
 WDA  plan-2  N07  0.020
 WDA  plan-2  N09  0.020
 WDA  plan-2  O30  0.020
 WDA  plan-2  H13  0.020
 WDA  plan-2  O29  0.020
 WDA  plan-2  C01  0.020
 WDA  plan-2  C05  0.020
 WDA  plan-3  C17  0.020
 WDA  plan-3  C21  0.020
 WDA  plan-3  C16  0.020
 WDA  plan-3  C19  0.020
 WDA  plan-3  N18  0.020
 WDA  plan-3  N20  0.020
 WDA  plan-3  O22  0.020
 WDA  plan-3  O23  0.020
 WDA  plan-3  O24  0.020
 WDA  plan-3  H17  0.020
 WDA  plan-3  H18  0.020

