# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 09:16:40 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 7-ethyl-3-(phenylmethyl)purine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCn1cnc2N(Cc3ccccc3)C(=O)NC(=O)c12
#
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
 DYZ  DYZ  7-ethyl-3-(phenylmethyl)purine-2,6-dione  ligand  34  20  .  2022-07-24  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_DYZ
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
 DYZ  C4   C  CR56  0   0.459   0.7426  -0.1471  -0.7812
 DYZ  C5   C  CR56  0   0.118   1.9329   0.1027  -0.1399
 DYZ  C6   C  CR6   0   0.542   2.1694   1.3103   0.5805
 DYZ  C8   C  CR15  0   0.138   1.9719  -1.8102  -1.1540
 DYZ  N1   N  NR16  0  -0.745   1.0423   2.1222   0.5442
 DYZ  N3   N  NR6   0  -0.576  -0.3026   0.7382  -0.7696
 DYZ  CAN  C  CH3   0  -0.667   4.0660  -1.6664   1.5541
 DYZ  N7   N  NR5   0  -0.470   2.7193  -0.9941  -0.4052
 DYZ  N9   N  N     0  -0.479   0.7651  -1.3334  -1.4088
 DYZ  O6   O  O     0  -0.456   3.1801   1.6510   1.1678
 DYZ  C2   C  CR6   0   0.711  -0.1748   1.9145  -0.0769
 DYZ  O2   O  O     0  -0.481  -1.0641   2.7400  -0.0101
 DYZ  CAK  C  CH2   0  -0.429  -1.5670   0.4231  -1.4313
 DYZ  CAL  C  CR6   0   0.136  -2.5819  -0.1597  -0.4827
 DYZ  CAP  C  CR16  0  -0.295  -3.6187   0.6227   0.0156
 DYZ  CAQ  C  CR16  0  -0.244  -4.5479   0.0856   0.8975
 DYZ  CAR  C  CR16  0  -0.263  -4.4465  -1.2411   1.2933
 DYZ  CAS  C  CR16  0  -0.242  -3.4160  -2.0302   0.7973
 DYZ  CAT  C  CR16  0  -0.298  -2.4918  -1.4931  -0.0875
 DYZ  H1   H  HCR5  0   0.303   2.3431  -2.7615  -1.5035
 DYZ  H2   H  HNR6  0   0.427   1.1137   3.0032   1.0384
 DYZ  H3   H  HCH3  0   0.247   5.0855  -1.8966   1.8616
 DYZ  H4   H  HCH3  0   0.241   3.6992  -0.8603   2.1875
 DYZ  H5   H  HCH3  0   0.237   3.4523  -2.5505   1.7247
 DYZ  H6   H  HCH2  0   0.271   4.6756  -0.3874  -0.0792
 DYZ  H7   H  HCH2  0   0.271   4.4631  -2.0688  -0.5289
 DYZ  H8   H  HCH2  0   0.290  -1.9450   1.3315  -1.8959
 DYZ  H9   H  HCH2  0   0.291  -1.3395  -0.2788  -2.2313
 DYZ  H10  H  HCR6  0   0.252  -3.7038   1.6580  -0.2888
 DYZ  H11  H  HCR6  0   0.256  -5.3505   0.7050   1.2767
 DYZ  H12  H  HCR6  0   0.257  -5.1700  -1.6612   1.9802
 DYZ  H13  H  HCR6  0   0.256  -3.3343  -3.0673   1.0960
 DYZ  H14  H  HCR6  0   0.255  -1.6984  -2.1174  -0.4805
 DYZ  CAM  C  CH2   0  -0.311   4.0602  -1.2687   0.0900

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
 DYZ  CAM  CAN  single    1.517  0.020  1.517
 DYZ  CAM  N7   single    1.456  0.020  1.456
 DYZ  C8   N7   aromatic  1.336  0.020  1.336
 DYZ  C8   N9   aromatic  1.322  0.020  1.322
 DYZ  N7   C5   aromatic  1.375  0.020  1.375
 DYZ  N9   C4   aromatic  1.342  0.020  1.342
 DYZ  C5   C6   single    1.426  0.020  1.426
 DYZ  C5   C4   aromatic  1.375  0.020  1.375
 DYZ  O6   C6   double    1.218  0.020  1.218
 DYZ  C6   N1   single    1.390  0.020  1.390
 DYZ  C4   N3   single    1.370  0.020  1.370
 DYZ  N1   C2   single    1.382  0.020  1.382
 DYZ  N3   C2   single    1.371  0.020  1.371
 DYZ  N3   CAK  single    1.461  0.020  1.461
 DYZ  C2   O2   double    1.215  0.020  1.215
 DYZ  CAK  CAL  single    1.506  0.020  1.506
 DYZ  CAT  CAL  aromatic  1.394  0.020  1.394
 DYZ  CAT  CAS  aromatic  1.388  0.020  1.388
 DYZ  CAL  CAP  aromatic  1.391  0.020  1.391
 DYZ  CAS  CAR  aromatic  1.389  0.020  1.389
 DYZ  CAP  CAQ  aromatic  1.389  0.020  1.389
 DYZ  CAR  CAQ  aromatic  1.388  0.020  1.388
 DYZ  C8   H1   single    0.930  0.020  1.080
 DYZ  N1   H2   single    0.860  0.020  1.020
 DYZ  CAN  H3   single    0.970  0.020  1.090
 DYZ  CAN  H4   single    0.970  0.020  1.090
 DYZ  CAN  H5   single    0.970  0.020  1.090
 DYZ  CAM  H6   single    0.970  0.020  1.090
 DYZ  CAM  H7   single    0.970  0.020  1.090
 DYZ  CAK  H8   single    0.970  0.020  1.090
 DYZ  CAK  H9   single    0.970  0.020  1.090
 DYZ  CAP  H10  single    0.930  0.020  1.080
 DYZ  CAQ  H11  single    0.930  0.020  1.080
 DYZ  CAR  H12  single    0.930  0.020  1.080
 DYZ  CAS  H13  single    0.930  0.020  1.080
 DYZ  CAT  H14  single    0.930  0.020  1.080

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
 DYZ  N9   C4   N3   126.01  3.000
 DYZ  N3   C4   C5   122.63  3.000
 DYZ  N9   C4   C5   111.36  3.000
 DYZ  N7   C5   C6   132.69  3.000
 DYZ  C6   C5   C4   122.22  3.000
 DYZ  N7   C5   C4   105.07  3.000
 DYZ  O6   C6   N1   121.50  3.000
 DYZ  N1   C6   C5   110.31  3.000
 DYZ  O6   C6   C5   128.19  3.000
 DYZ  H1   C8   N9   124.70  3.000
 DYZ  H1   C8   N7   121.83  3.000
 DYZ  N9   C8   N7   113.47  3.000
 DYZ  H2   N1   C2   114.34  3.000
 DYZ  H2   N1   C6   116.00  3.000
 DYZ  C2   N1   C6   129.66  3.000
 DYZ  CAK  N3   C2   119.63  3.000
 DYZ  CAK  N3   C4   121.13  3.000
 DYZ  C2   N3   C4   119.19  3.000
 DYZ  H5   CAN  H4   108.65  3.000
 DYZ  H5   CAN  H3   108.15  3.000
 DYZ  H4   CAN  H3   107.91  3.000
 DYZ  H5   CAN  CAM  111.20  3.000
 DYZ  H4   CAN  CAM  111.47  3.000
 DYZ  H3   CAN  CAM  109.34  3.000
 DYZ  CAM  N7   C8   126.21  3.000
 DYZ  C8   N7   C5   105.99  3.000
 DYZ  CAM  N7   C5   127.70  3.000
 DYZ  C8   N9   C4   104.11  3.000
 DYZ  O2   C2   N3   122.84  3.000
 DYZ  O2   C2   N1   121.18  3.000
 DYZ  N3   C2   N1   115.98  3.000
 DYZ  H9   CAK  H8   107.28  3.000
 DYZ  H9   CAK  CAL  110.75  3.000
 DYZ  H8   CAK  CAL  110.96  3.000
 DYZ  H9   CAK  N3   106.92  3.000
 DYZ  H8   CAK  N3   108.29  3.000
 DYZ  CAL  CAK  N3   112.41  3.000
 DYZ  CAT  CAL  CAP  118.99  3.000
 DYZ  CAP  CAL  CAK  120.67  3.000
 DYZ  CAT  CAL  CAK  120.34  3.000
 DYZ  H10  CAP  CAQ  119.72  3.000
 DYZ  H10  CAP  CAL  119.72  3.000
 DYZ  CAQ  CAP  CAL  120.56  3.000
 DYZ  H11  CAQ  CAR  120.09  3.000
 DYZ  H11  CAQ  CAP  119.81  3.000
 DYZ  CAR  CAQ  CAP  120.11  3.000
 DYZ  H12  CAR  CAS  120.12  3.000
 DYZ  H12  CAR  CAQ  120.20  3.000
 DYZ  CAS  CAR  CAQ  119.68  3.000
 DYZ  H13  CAS  CAT  119.77  3.000
 DYZ  H13  CAS  CAR  120.11  3.000
 DYZ  CAT  CAS  CAR  120.12  3.000
 DYZ  H14  CAT  CAS  119.74  3.000
 DYZ  H14  CAT  CAL  119.72  3.000
 DYZ  CAS  CAT  CAL  120.54  3.000
 DYZ  H7   CAM  H6   107.31  3.000
 DYZ  H7   CAM  N7   106.63  3.000
 DYZ  H6   CAM  N7   108.38  3.000
 DYZ  H7   CAM  CAN  110.76  3.000
 DYZ  H6   CAM  CAN  111.11  3.000
 DYZ  N7   CAM  CAN  112.41  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
 DYZ  CONST_01  N7   C8   N9   C4     0.00   0.0  0
 DYZ  CONST_02  C8   N7   C5   C4     0.00   0.0  0
 DYZ  CONST_03  N9   C8   N7   C5     0.00   0.0  0
 DYZ  CONST_04  C8   N9   C4   C5     0.00   0.0  0
 DYZ  CONST_05  N9   C4   C5   N7     0.00   0.0  0
 DYZ  CONST_06  CAR  CAS  CAT  CAL    0.00   0.0  0
 DYZ  CONST_07  CAR  CAQ  CAP  CAL    0.00   0.0  0
 DYZ  CONST_08  CAS  CAT  CAL  CAP    0.00   0.0  0
 DYZ  CONST_09  CAS  CAR  CAQ  CAP    0.00   0.0  0
 DYZ  CONST_10  CAT  CAL  CAP  CAQ    0.00   0.0  0
 DYZ  CONST_11  CAT  CAS  CAR  CAQ    0.00   0.0  0
 DYZ  CONST_12  N1   C2   N3   C4     0.00   0.0  0
 DYZ  CONST_13  C2   N1   C6   C5     0.00   0.0  0
 DYZ  CONST_14  N3   C2   N1   C6     0.00   0.0  0
 DYZ  CONST_15  CAM  N7   C5   C4   180.00   0.0  0
 DYZ  CONST_16  CAM  N7   C5   C6     0.00   0.0  0
 DYZ  CONST_17  N9   C8   N7   CAM  180.00   0.0  0
 DYZ  CONST_18  CAS  CAT  CAL  CAK  180.00   0.0  0
 DYZ  CONST_19  CAQ  CAP  CAL  CAK  180.00   0.0  0
 DYZ  CONST_20  O2   C2   N3   C4   180.00   0.0  0
 DYZ  CONST_21  O2   C2   N1   C6   180.00   0.0  0
 DYZ  CONST_22  CAK  N3   C2   N1   180.00   0.0  0
 DYZ  CONST_23  C2   N1   C6   O6   180.00   0.0  0
 DYZ  CONST_24  H1   C8   N9   C4   180.00   0.0  0
 DYZ  CONST_25  H13  CAS  CAT  CAL  180.00   0.0  0
 DYZ  CONST_26  H11  CAQ  CAP  CAL  180.00   0.0  0
 DYZ  CONST_27  H14  CAT  CAL  CAP  180.00   0.0  0
 DYZ  CONST_28  H12  CAR  CAQ  CAP  180.00   0.0  0
 DYZ  CONST_29  H10  CAP  CAQ  CAR  180.00   0.0  0
 DYZ  CONST_30  H2   N1   C6   C5   180.00   0.0  0
 DYZ  CONST_31  CAK  N3   C2   O2     0.00   0.0  0
 DYZ  Var_01    CAL  CAK  N3   C4    95.24  30.0  3
 DYZ  Var_02    CAT  CAL  CAK  N3   -77.66  30.0  2
 DYZ  Var_03    CAN  CAM  N7   C5    73.47  30.0  3
 DYZ  Var_04    H3   CAN  CAM  N7   177.85  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
 DYZ  plan-1  CAK  0.020
 DYZ  plan-1  CAL  0.020
 DYZ  plan-1  CAP  0.020
 DYZ  plan-1  CAQ  0.020
 DYZ  plan-1  CAR  0.020
 DYZ  plan-1  CAS  0.020
 DYZ  plan-1  CAT  0.020
 DYZ  plan-1  H10  0.020
 DYZ  plan-1  H11  0.020
 DYZ  plan-1  H12  0.020
 DYZ  plan-1  H13  0.020
 DYZ  plan-1  H14  0.020
 DYZ  plan-2  C4   0.020
 DYZ  plan-2  C5   0.020
 DYZ  plan-2  C6   0.020
 DYZ  plan-2  C8   0.020
 DYZ  plan-2  N1   0.020
 DYZ  plan-2  N3   0.020
 DYZ  plan-2  N7   0.020
 DYZ  plan-2  N9   0.020
 DYZ  plan-2  O6   0.020
 DYZ  plan-2  C2   0.020
 DYZ  plan-2  O2   0.020
 DYZ  plan-2  CAK  0.020
 DYZ  plan-2  H1   0.020
 DYZ  plan-2  H2   0.020
 DYZ  plan-2  CAM  0.020

