# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 17:41:33 2022
#   Inital geometry file: a 148 line input string
#   Ligand name: (2S,8R)-8-benzyl-2-hydroperoxy-6-(4-hydroxyphenyl)-2-(4-iodobenzyl)-7,8-dihydroimidazo[1,2-a]pyrazin-3(2H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OO[C@]1(Cc2ccc(I)cc2)N=C3[C@@H](Cc4ccccc4)NC(=CN3C1=O)c5ccc(O)cc5
#
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
 CZI  CZI  (2S,8R)-8-benzyl-2-hydroperoxy-6-(4-hydroxyphenyl)-2-(4-iodobenzyl)-7,8-dihydroimidazo[1,2-a]pyrazin-3(2H)-one  ligand  56  34  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CZI
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
 CZI  I     I  I     0   0.048   6.9615  -0.8695  -0.2354
 CZI  C14   C  CR6   0  -0.234   5.1298   0.0544   0.2346
 CZI  C15   C  CR16  0  -0.211   5.0385   1.4378   0.2200
 CZI  C16   C  CR16  0  -0.295   3.8251   2.0366   0.5310
 CZI  C13   C  CR16  0  -0.212   4.0325  -0.7298   0.5604
 CZI  C12   C  CR16  0  -0.285   2.8291  -0.1116   0.8682
 CZI  C11   C  CR6   0   0.150   2.7085   1.2747   0.8585
 CZI  C10   C  CH2   0  -0.566   1.3999   1.9357   1.1855
 CZI  C2    C  CR5   0   0.231   0.4749   2.0545  -0.0317
 CZI  O33   O  O2    0  -0.282   1.1556   2.8292  -0.9697
 CZI  O34   O  OH1   0  -0.443   0.2996   3.0322  -2.0712
 CZI  N1    N  N     0  -0.414   0.1166   0.7494  -0.5429
 CZI  C9    C  CR5   0   0.521  -1.1340   0.6272  -0.3676
 CZI  N4    N  NR5   0  -0.567  -1.7838   1.7226   0.1852
 CZI  C3    C  CR5   0   0.515  -0.8611   2.7069   0.3844
 CZI  O18   O  O     0  -0.420  -1.0536   3.8186   0.8102
 CZI  C5    C  C1    0  -0.111  -3.1751   1.7795   0.3355
 CZI  C8    C  CH1   0  -0.206  -1.9644  -0.5874  -0.6086
 CZI  C26   C  CH2   0  -0.528  -1.9495  -1.4635   0.6689
 CZI  C27   C  CR6   0   0.120  -2.7832  -2.6975   0.4858
 CZI  C28   C  CR16  0  -0.300  -2.2340  -3.8453  -0.0831
 CZI  C29   C  CR16  0  -0.240  -3.0148  -4.9709  -0.3047
 CZI  C30   C  CR16  0  -0.267  -4.3621  -4.9632   0.0354
 CZI  C31   C  CR16  0  -0.238  -4.9203  -3.8256   0.6022
 CZI  C32   C  CR16  0  -0.314  -4.1349  -2.7019   0.8253
 CZI  N7    N  NH1   0  -0.654  -3.2926  -0.1616  -1.0084
 CZI  C6    C  C     0   0.229  -3.9141   0.8238  -0.2516
 CZI  C19   C  CR6   0   0.027  -5.3817   0.8097  -0.1785
 CZI  C20   C  CR16  0  -0.294  -6.0533   1.2580   0.9607
 CZI  C21   C  CR16  0  -0.321  -7.4338   1.2529   1.0305
 CZI  C24   C  CR16  0  -0.289  -6.1481   0.3429  -1.2461
 CZI  C23   C  CR16  0  -0.369  -7.5317   0.3293  -1.1864
 CZI  C22   C  CR6   0   0.350  -8.1864   0.7846  -0.0454
 CZI  O25   O  OH1   0  -0.627  -9.5263   0.7905   0.0725
 CZI  H15   H  HCR6  0   0.278   5.8919   2.0543  -0.0278
 CZI  H16   H  HCR6  0   0.261   3.7590   3.1175   0.5242
 CZI  H13   H  HCR6  0   0.278   4.1000  -1.8090   0.5787
 CZI  H12   H  HCR6  0   0.255   1.9745  -0.7254   1.1234
 CZI  H101  H  HCH2  0   0.286   1.5661   2.9368   1.5902
 CZI  H102  H  HCH2  0   0.292   0.8685   1.3675   1.9522
 CZI  H34   H  HOH1  0   0.482   0.1312   3.9847  -2.0218
 CZI  H5    H  H     0   0.296  -3.5760   2.6180   0.8810
 CZI  H8    H  HCH1  0   0.308  -1.5191  -1.1521  -1.4287
 CZI  H261  H  HCH2  0   0.276  -0.9134  -1.7304   0.8868
 CZI  H262  H  HCH2  0   0.270  -2.3191  -0.8803   1.5159
 CZI  H28   H  HCR6  0   0.251  -1.1835  -3.8601  -0.3500
 CZI  H29   H  HCR6  0   0.257  -2.5709  -5.8560  -0.7415
 CZI  H30   H  HCR6  0   0.257  -4.9727  -5.8398  -0.1387
 CZI  H31   H  HCR6  0   0.257  -5.9682  -3.8117   0.8730
 CZI  H32   H  HCR6  0   0.253  -4.5781  -1.8211   1.2760
 CZI  HN7   H  HNH1  0   0.394  -3.8875  -0.9444  -1.2384
 CZI  H20   H  HCR6  0   0.258  -5.4922   1.6014   1.8204
 CZI  H21   H  HCR6  0   0.269  -7.9325   1.5992   1.9268
 CZI  H24   H  HCR6  0   0.264  -5.6728   0.0004  -2.1569
 CZI  H23   H  HCR6  0   0.276  -8.0981  -0.0336  -2.0361
 CZI  H25   H  HOH1  0   0.477  -9.9370   0.4366  -0.7246

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
 CZI  I    C14   single    2.105  0.020  2.105
 CZI  C14  C15   aromatic  1.387  0.020  1.387
 CZI  C14  C13   aromatic  1.387  0.020  1.387
 CZI  C15  C16   aromatic  1.388  0.020  1.388
 CZI  C15  H15   single    0.930  0.020  1.080
 CZI  C16  C11   aromatic  1.391  0.020  1.391
 CZI  C16  H16   single    0.930  0.020  1.080
 CZI  C13  C12   aromatic  1.387  0.020  1.387
 CZI  C13  H13   single    0.930  0.020  1.080
 CZI  C12  C11   aromatic  1.392  0.020  1.392
 CZI  C12  H12   single    0.930  0.020  1.080
 CZI  C11  C10   single    1.502  0.020  1.502
 CZI  C10  C2    single    1.533  0.020  1.533
 CZI  C10  H101  single    0.970  0.020  1.090
 CZI  C10  H102  single    0.970  0.020  1.090
 CZI  C2   O33   single    1.394  0.020  1.394
 CZI  C2   N1    single    1.447  0.020  1.447
 CZI  C2   C3    single    1.544  0.020  1.544
 CZI  O33  O34   single    1.410  0.020  1.410
 CZI  O34  H34   single    0.850  0.020  0.980
 CZI  N1   C9    double    1.269  0.020  1.269
 CZI  C9   N4    single    1.388  0.020  1.388
 CZI  C9   C8    single    1.491  0.020  1.491
 CZI  N4   C3    single    1.364  0.020  1.364
 CZI  N4   C5    single    1.401  0.020  1.401
 CZI  C3   O18   double    1.206  0.020  1.206
 CZI  C5   C6    double    1.343  0.020  1.343
 CZI  C5   H5    single    0.930  0.020  1.080
 CZI  C8   C26   single    1.549  0.020  1.549
 CZI  C8   N7    single    1.451  0.020  1.451
 CZI  C8   H8    single    0.970  0.020  1.090
 CZI  C26  C27   single    1.500  0.020  1.500
 CZI  C26  H261  single    0.970  0.020  1.090
 CZI  C26  H262  single    0.970  0.020  1.090
 CZI  C27  C28   aromatic  1.394  0.020  1.394
 CZI  C27  C32   aromatic  1.394  0.020  1.394
 CZI  C28  C29   aromatic  1.388  0.020  1.388
 CZI  C28  H28   single    0.930  0.020  1.080
 CZI  C29  C30   aromatic  1.390  0.020  1.390
 CZI  C29  H29   single    0.930  0.020  1.080
 CZI  C30  C31   aromatic  1.388  0.020  1.388
 CZI  C30  H30   single    0.930  0.020  1.080
 CZI  C31  C32   aromatic  1.389  0.020  1.389
 CZI  C31  H31   single    0.930  0.020  1.080
 CZI  C32  H32   single    0.930  0.020  1.080
 CZI  N7   C6    single    1.389  0.020  1.389
 CZI  N7   HN7   single    0.890  0.020  1.040
 CZI  C6   C19   single    1.469  0.020  1.469
 CZI  C19  C20   aromatic  1.396  0.020  1.396
 CZI  C19  C24   aromatic  1.395  0.020  1.395
 CZI  C20  C21   aromatic  1.382  0.020  1.382
 CZI  C20  H20   single    0.930  0.020  1.080
 CZI  C21  C22   aromatic  1.394  0.020  1.394
 CZI  C21  H21   single    0.930  0.020  1.080
 CZI  C24  C23   aromatic  1.385  0.020  1.385
 CZI  C24  H24   single    0.930  0.020  1.080
 CZI  C23  C22   aromatic  1.392  0.020  1.392
 CZI  C23  H23   single    0.930  0.020  1.080
 CZI  C22  O25   single    1.345  0.020  1.345
 CZI  O25  H25   single    0.850  0.020  0.980

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
 CZI  C13   C14  C15   120.95  3.000
 CZI  C13   C14  I     119.51  3.000
 CZI  C15   C14  I     119.53  3.000
 CZI  H15   C15  C16   119.67  3.000
 CZI  H15   C15  C14   121.28  3.000
 CZI  C16   C15  C14   119.05  3.000
 CZI  H16   C16  C11   119.95  3.000
 CZI  H16   C16  C15   118.85  3.000
 CZI  C11   C16  C15   121.20  3.000
 CZI  H13   C13  C12   119.67  3.000
 CZI  H13   C13  C14   121.24  3.000
 CZI  C12   C13  C14   119.09  3.000
 CZI  H12   C12  C11   119.87  3.000
 CZI  H12   C12  C13   118.97  3.000
 CZI  C11   C12  C13   121.16  3.000
 CZI  C10   C11  C12   120.82  3.000
 CZI  C10   C11  C16   120.64  3.000
 CZI  C12   C11  C16   118.54  3.000
 CZI  H102  C10  H101  106.90  3.000
 CZI  H102  C10  C2    107.70  3.000
 CZI  H101  C10  C2    108.35  3.000
 CZI  H102  C10  C11   110.35  3.000
 CZI  H101  C10  C11   110.57  3.000
 CZI  C2    C10  C11   112.76  3.000
 CZI  C3    C2   N1    105.20  3.000
 CZI  C3    C2   O33   111.66  3.000
 CZI  N1    C2   O33   112.61  3.000
 CZI  C3    C2   C10   109.92  3.000
 CZI  N1    C2   C10   111.10  3.000
 CZI  O33   C2   C10   106.42  3.000
 CZI  O34   O33  C2    108.01  3.000
 CZI  H34   O34  O33   101.97  3.000
 CZI  C9    N1   C2    106.39  3.000
 CZI  C8    C9   N4    116.52  3.000
 CZI  C8    C9   N1    127.24  3.000
 CZI  N4    C9   N1    116.13  3.000
 CZI  C5    N4   C3    128.83  3.000
 CZI  C5    N4   C9    122.66  3.000
 CZI  C3    N4   C9    108.12  3.000
 CZI  O18   C3   N4    127.51  3.000
 CZI  O18   C3   C2    128.52  3.000
 CZI  N4    C3   C2    103.95  3.000
 CZI  H5    C5   C6    124.76  3.000
 CZI  H5    C5   N4    117.10  3.000
 CZI  C6    C5   N4    118.08  3.000
 CZI  H8    C8   N7    108.57  3.000
 CZI  H8    C8   C26   108.86  3.000
 CZI  N7    C8   C26   113.71  3.000
 CZI  H8    C8   C9    108.42  3.000
 CZI  N7    C8   C9    108.38  3.000
 CZI  C26   C8   C9    108.79  3.000
 CZI  H262  C26  H261  107.27  3.000
 CZI  H262  C26  C27   110.22  3.000
 CZI  H261  C26  C27   110.52  3.000
 CZI  H262  C26  C8    109.51  3.000
 CZI  H261  C26  C8    108.17  3.000
 CZI  C27   C26  C8    111.05  3.000
 CZI  C32   C27  C28   118.62  3.000
 CZI  C32   C27  C26   120.78  3.000
 CZI  C28   C27  C26   120.54  3.000
 CZI  H28   C28  C29   119.66  3.000
 CZI  H28   C28  C27   119.58  3.000
 CZI  C29   C28  C27   120.76  3.000
 CZI  H29   C29  C30   120.07  3.000
 CZI  H29   C29  C28   119.80  3.000
 CZI  C30   C29  C28   120.13  3.000
 CZI  H30   C30  C31   120.17  3.000
 CZI  H30   C30  C29   120.20  3.000
 CZI  C31   C30  C29   119.63  3.000
 CZI  H31   C31  C32   119.79  3.000
 CZI  H31   C31  C30   120.13  3.000
 CZI  C32   C31  C30   120.08  3.000
 CZI  H32   C32  C31   119.53  3.000
 CZI  H32   C32  C27   119.68  3.000
 CZI  C31   C32  C27   120.79  3.000
 CZI  HN7   N7   C6    114.23  3.000
 CZI  HN7   N7   C8    112.00  3.000
 CZI  C6    N7   C8    117.87  3.000
 CZI  C19   C6   N7    117.85  3.000
 CZI  C19   C6   C5    122.32  3.000
 CZI  N7    C6   C5    119.77  3.000
 CZI  C24   C19  C20   117.89  3.000
 CZI  C24   C19  C6    120.93  3.000
 CZI  C20   C19  C6    121.18  3.000
 CZI  H20   C20  C21   118.60  3.000
 CZI  H20   C20  C19   120.03  3.000
 CZI  C21   C20  C19   121.35  3.000
 CZI  H21   C21  C22   119.85  3.000
 CZI  H21   C21  C20   120.05  3.000
 CZI  C22   C21  C20   120.10  3.000
 CZI  H24   C24  C23   118.14  3.000
 CZI  H24   C24  C19   120.56  3.000
 CZI  C23   C24  C19   121.29  3.000
 CZI  H23   C23  C22   120.42  3.000
 CZI  H23   C23  C24   119.45  3.000
 CZI  C22   C23  C24   120.13  3.000
 CZI  O25   C22  C23   122.81  3.000
 CZI  O25   C22  C21   117.95  3.000
 CZI  C23   C22  C21   119.24  3.000
 CZI  H25   O25  C22   110.50  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
 CZI  CONST_01  C11  C16  C15  C14    0.00   0.0  0
 CZI  CONST_02  C11  C12  C13  C14    0.00   0.0  0
 CZI  CONST_03  C12  C13  C14  C15    0.00   0.0  0
 CZI  CONST_04  C12  C11  C16  C15    0.00   0.0  0
 CZI  CONST_05  C13  C14  C15  C16    0.00   0.0  0
 CZI  CONST_06  C13  C12  C11  C16    0.00   0.0  0
 CZI  CONST_07  C30  C29  C28  C27    0.00   0.0  0
 CZI  CONST_08  C30  C31  C32  C27    0.00   0.0  0
 CZI  CONST_09  C31  C32  C27  C28    0.00   0.0  0
 CZI  CONST_10  C31  C30  C29  C28    0.00   0.0  0
 CZI  CONST_11  C32  C27  C28  C29    0.00   0.0  0
 CZI  CONST_12  C32  C31  C30  C29    0.00   0.0  0
 CZI  CONST_13  C22  C21  C20  C19    0.00   0.0  0
 CZI  CONST_14  C22  C23  C24  C19    0.00   0.0  0
 CZI  CONST_15  C23  C24  C19  C20    0.00   0.0  0
 CZI  CONST_16  C23  C22  C21  C20    0.00   0.0  0
 CZI  CONST_17  C24  C19  C20  C21    0.00   0.0  0
 CZI  CONST_18  C24  C23  C22  C21    0.00   0.0  0
 CZI  CONST_19  C21  C20  C19  C6   180.00   0.0  0
 CZI  CONST_20  C23  C24  C19  C6   180.00   0.0  0
 CZI  CONST_21  N4   C9   N1   C2     0.00   0.0  0
 CZI  CONST_22  C8   C9   N1   C2   180.00   0.0  0
 CZI  CONST_23  C9   N4   C3   C2     0.00   0.0  0
 CZI  CONST_24  C5   N4   C3   C2   180.00   0.0  0
 CZI  CONST_25  C3   N4   C9   N1     0.00   0.0  0
 CZI  CONST_26  C5   N4   C9   N1   180.00   0.0  0
 CZI  CONST_27  C8   C9   N4   C3   180.00   0.0  0
 CZI  CONST_28  C8   C9   N4   C5     0.00   0.0  0
 CZI  CONST_29  C16  C15  C14  I    180.00   0.0  0
 CZI  CONST_30  C12  C13  C14  I    180.00   0.0  0
 CZI  CONST_31  C10  C11  C16  C15  180.00   0.0  0
 CZI  CONST_32  C10  C11  C12  C13  180.00   0.0  0
 CZI  CONST_33  C29  C28  C27  C26  180.00   0.0  0
 CZI  CONST_34  C31  C32  C27  C26  180.00   0.0  0
 CZI  CONST_35  O25  C22  C21  C20  180.00   0.0  0
 CZI  CONST_36  O25  C22  C23  C24  180.00   0.0  0
 CZI  CONST_37  O18  C3   N4   C9   180.00   0.0  0
 CZI  CONST_38  C5   N4   C3   O18    0.00   0.0  0
 CZI  CONST_39  H16  C16  C15  C14  180.00   0.0  0
 CZI  CONST_40  H12  C12  C13  C14  180.00   0.0  0
 CZI  CONST_41  H13  C13  C14  C15  180.00   0.0  0
 CZI  CONST_42  H15  C15  C14  C13  180.00   0.0  0
 CZI  CONST_43  H29  C29  C28  C27  180.00   0.0  0
 CZI  CONST_44  H31  C31  C32  C27  180.00   0.0  0
 CZI  CONST_45  H32  C32  C27  C28  180.00   0.0  0
 CZI  CONST_46  H30  C30  C29  C28  180.00   0.0  0
 CZI  CONST_47  H28  C28  C29  C30  180.00   0.0  0
 CZI  CONST_48  H20  C20  C19  C6     0.00   0.0  0
 CZI  CONST_49  H24  C24  C19  C6     0.00   0.0  0
 CZI  CONST_50  H21  C21  C20  C19  180.00   0.0  0
 CZI  CONST_51  H23  C23  C24  C19  180.00   0.0  0
 CZI  Var_01    C6   C5   N4   C9    -9.78  30.0  1
 CZI  Var_02    N7   C6   C5   N4    -1.60  30.0  1
 CZI  Var_03    C8   N7   C6   C5    32.45  30.0  1
 CZI  Var_04    C20  C19  C6   C5   -34.31  30.0  2
 CZI  Var_05    C2   C10  C11  C16   94.18  30.0  2
 CZI  Var_06    C28  C27  C26  C8    86.46  30.0  2

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
 CZI  chir_01  C2  O33  N1   C3  positiv
 CZI  chir_02  C8  N7   C26  C9  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
 CZI  plan-1  I    0.020
 CZI  plan-1  C14  0.020
 CZI  plan-1  C15  0.020
 CZI  plan-1  C16  0.020
 CZI  plan-1  C13  0.020
 CZI  plan-1  C12  0.020
 CZI  plan-1  C11  0.020
 CZI  plan-1  C10  0.020
 CZI  plan-1  H15  0.020
 CZI  plan-1  H16  0.020
 CZI  plan-1  H13  0.020
 CZI  plan-1  H12  0.020
 CZI  plan-2  C26  0.020
 CZI  plan-2  C27  0.020
 CZI  plan-2  C28  0.020
 CZI  plan-2  C29  0.020
 CZI  plan-2  C30  0.020
 CZI  plan-2  C31  0.020
 CZI  plan-2  C32  0.020
 CZI  plan-2  H28  0.020
 CZI  plan-2  H29  0.020
 CZI  plan-2  H30  0.020
 CZI  plan-2  H31  0.020
 CZI  plan-2  H32  0.020
 CZI  plan-3  C6   0.020
 CZI  plan-3  C19  0.020
 CZI  plan-3  C20  0.020
 CZI  plan-3  C21  0.020
 CZI  plan-3  C24  0.020
 CZI  plan-3  C23  0.020
 CZI  plan-3  C22  0.020
 CZI  plan-3  O25  0.020
 CZI  plan-3  H20  0.020
 CZI  plan-3  H21  0.020
 CZI  plan-3  H24  0.020
 CZI  plan-3  H23  0.020
 CZI  plan-4  C2   0.020
 CZI  plan-4  N1   0.020
 CZI  plan-4  C9   0.020
 CZI  plan-4  N4   0.020
 CZI  plan-4  C3   0.020
 CZI  plan-4  O18  0.020
 CZI  plan-4  C5   0.020
 CZI  plan-4  C8   0.020
 CZI  plan-5  C8   0.020
 CZI  plan-5  N7   0.020
 CZI  plan-5  C6   0.020
 CZI  plan-5  HN7  0.020

