# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 15:42:46 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: (2S,8S)-8-benzyl-2-(4-bromobenzyl)-2-hydroperoxy-6-(4-hydroxyphenyl)-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(Br)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
 CZB  CZB  (2S,8S)-8-benzyl-2-(4-bromobenzyl)-2-hydroperoxy-6-(4-hydroxyphenyl)-7,8-dihydroimidazo[1,2-a]pyrazin-3(2H)-one  ligand  56  34  .  2021-08-07  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CZB
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
 CZB  O18   O   O     0  -0.425  -1.1797   2.6015  -2.2282
 CZB  C3    C   CR5   0   0.510  -0.8933   1.7013  -1.4767
 CZB  N4    N   NR5   0  -0.566  -1.7462   0.9144  -0.7636
 CZB  C5    C   C1    0  -0.154  -3.1410   1.0012  -0.6642
 CZB  C9    C   CR5   0   0.546  -0.9908  -0.0138  -0.0521
 CZB  C8    C   CH1   0  -0.203  -1.7621  -1.0069   0.7585
 CZB  C26   C   CH2   0  -0.523  -2.1080  -2.2643  -0.0721
 CZB  C27   C   CR6   0   0.146  -0.9014  -3.0483  -0.4979
 CZB  C28   C   CR16  0  -0.315  -0.2289  -3.8576   0.4161
 CZB  C29   C   CR16  0  -0.241   0.9004  -4.5692   0.0376
 CZB  C30   C   CR16  0  -0.274   1.3746  -4.4811  -1.2658
 CZB  C31   C   CR16  0  -0.242   0.7112  -3.6785  -2.1837
 CZB  C32   C   CR16  0  -0.278  -0.4177  -2.9680  -1.7993
 CZB  N7    N   NH1   0  -0.665  -2.9420  -0.3318   1.2563
 CZB  C6    C   C     0   0.262  -3.7271   0.3860   0.3788
 CZB  C19   C   CR6   0   0.038  -5.1747   0.4566   0.6182
 CZB  C20   C   CR16  0  -0.288  -5.8882   1.6245   0.3499
 CZB  C21   C   CR16  0  -0.368  -7.2564   1.6909   0.5444
 CZB  C24   C   CR16  0  -0.297  -5.8794  -0.6424   1.1133
 CZB  C23   C   CR16  0  -0.325  -7.2461  -0.5869   1.3187
 CZB  C22   C   CR6   0   0.353  -7.9473   0.5827   1.0314
 CZB  O25   O   OH1   0  -0.626  -9.2748   0.5904   1.2451
 CZB  N1    N   N     0  -0.406   0.2667   0.0697  -0.1952
 CZB  C2    C   CR5   0   0.235   0.5061   1.2060  -1.0597
 CZB  O33   O   O2    0  -0.284   1.2990   0.8969  -2.1642
 CZB  O34   O   OH1   0  -0.432   0.5927  -0.0118  -2.9772
 CZB  C10   C   CH2   0  -0.567   1.2427   2.3207  -0.3058
 CZB  C11   C   CR6   0   0.150   2.6204   1.9113   0.1313
 CZB  C12   C   CR16  0  -0.301   3.7310   2.2154  -0.6490
 CZB  C13   C   CR16  0  -0.214   5.0088   1.8338  -0.2642
 CZB  C14   C   CR6   0  -0.124   5.1724   1.1337   0.9210
 CZB  BR17  BR  BR    0  -0.051   6.9052   0.6059   1.4589
 CZB  C15   C   CR16  0  -0.215   4.0841   0.8212   1.7224
 CZB  C16   C   CR16  0  -0.288   2.8161   1.2126   1.3193
 CZB  H5    H   H     0   0.294  -3.6638   1.5347  -1.4407
 CZB  H8    H   HCH1  0   0.300  -1.1490  -1.3010   1.6113
 CZB  H261  H   HCH2  0   0.272  -2.7527  -2.8816   0.5590
 CZB  H262  H   HCH2  0   0.262  -2.7020  -1.9715  -0.9415
 CZB  H28   H   HCR6  0   0.247  -0.5951  -3.9380   1.4335
 CZB  H29   H   HCR6  0   0.252   1.4080  -5.1978   0.7580
 CZB  H30   H   HCR6  0   0.252   2.2546  -5.0369  -1.5633
 CZB  H31   H   HCR6  0   0.251   1.0716  -3.6051  -3.2018
 CZB  H32   H   HCR6  0   0.238  -0.9271  -2.3403  -2.5190
 CZB  HN7   H   HNH1  0   0.398  -3.3981  -0.7737   2.0374
 CZB  H20   H   HCR6  0   0.263  -5.3666   2.5047  -0.0034
 CZB  H21   H   HCR6  0   0.277  -7.7843   2.6131   0.3293
 CZB  H24   H   HCR6  0   0.255  -5.3655  -1.5721   1.3251
 CZB  H23   H   HCR6  0   0.269  -7.7745  -1.4540   1.6941
 CZB  H25   H   HOH1  0   0.477  -9.6520   1.4418   0.9960
 CZB  H34   H   HOH1  0   0.478   0.4020   0.5272  -3.7592
 CZB  H101  H   HCH2  0   0.283   1.2927   3.1989  -0.9534
 CZB  H102  H   HCH2  0   0.292   0.6358   2.5987   0.5587
 CZB  H12   H   HCR6  0   0.261   3.6076   2.7691  -1.5715
 CZB  H13   H   HCR6  0   0.278   5.8564   2.0848  -0.8878
 CZB  H15   H   HCR6  0   0.278   4.2108   0.2808   2.6510
 CZB  H16   H   HCR6  0   0.257   1.9692   0.9703   1.9480

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
 CZB  O18  C3    double    1.207  0.020  1.207
 CZB  C3   N4    single    1.362  0.020  1.362
 CZB  C3   C2    single    1.542  0.020  1.542
 CZB  N4   C5    single    1.401  0.020  1.401
 CZB  N4   C9    single    1.392  0.020  1.392
 CZB  C5   C6    double    1.345  0.020  1.345
 CZB  C5   H5    single    0.930  0.020  1.080
 CZB  C9   C8    single    1.496  0.020  1.496
 CZB  C9   N1    double    1.268  0.020  1.268
 CZB  C8   C26   single    1.546  0.020  1.546
 CZB  C8   N7    single    1.448  0.020  1.448
 CZB  C8   H8    single    0.970  0.020  1.090
 CZB  C26  C27   single    1.501  0.020  1.501
 CZB  C26  H261  single    0.970  0.020  1.090
 CZB  C26  H262  single    0.970  0.020  1.090
 CZB  C27  C28   aromatic  1.394  0.020  1.394
 CZB  C27  C32   aromatic  1.391  0.020  1.391
 CZB  C28  C29   aromatic  1.387  0.020  1.387
 CZB  C28  H28   single    0.930  0.020  1.080
 CZB  C29  C30   aromatic  1.390  0.020  1.390
 CZB  C29  H29   single    0.930  0.020  1.080
 CZB  C30  C31   aromatic  1.388  0.020  1.388
 CZB  C30  H30   single    0.930  0.020  1.080
 CZB  C31  C32   aromatic  1.388  0.020  1.388
 CZB  C31  H31   single    0.930  0.020  1.080
 CZB  C32  H32   single    0.930  0.020  1.080
 CZB  N7   C6    single    1.379  0.020  1.379
 CZB  N7   HN7   single    0.890  0.020  1.040
 CZB  C6   C19   single    1.469  0.020  1.469
 CZB  C19  C20   aromatic  1.395  0.020  1.395
 CZB  C19  C24   aromatic  1.396  0.020  1.396
 CZB  C20  C21   aromatic  1.383  0.020  1.383
 CZB  C20  H20   single    0.930  0.020  1.080
 CZB  C21  C22   aromatic  1.394  0.020  1.394
 CZB  C21  H21   single    0.930  0.020  1.080
 CZB  C24  C23   aromatic  1.383  0.020  1.383
 CZB  C24  H24   single    0.930  0.020  1.080
 CZB  C23  C22   aromatic  1.394  0.020  1.394
 CZB  C23  H23   single    0.930  0.020  1.080
 CZB  C22  O25   single    1.345  0.020  1.345
 CZB  O25  H25   single    0.850  0.020  0.980
 CZB  N1   C2    single    1.448  0.020  1.448
 CZB  C2   O33   single    1.394  0.020  1.394
 CZB  C2   C10   single    1.534  0.020  1.534
 CZB  O33  O34   single    1.409  0.020  1.409
 CZB  O34  H34   single    0.850  0.020  0.980
 CZB  C10  C11   single    1.502  0.020  1.502
 CZB  C10  H101  single    0.970  0.020  1.090
 CZB  C10  H102  single    0.970  0.020  1.090
 CZB  C11  C12   aromatic  1.391  0.020  1.391
 CZB  C11  C16   aromatic  1.392  0.020  1.392
 CZB  C12  C13   aromatic  1.388  0.020  1.388
 CZB  C12  H12   single    0.930  0.020  1.080
 CZB  C13  C14   aromatic  1.386  0.020  1.386
 CZB  C13  H13   single    0.930  0.020  1.080
 CZB  C14  BR17  single    1.890  0.020  1.890
 CZB  C14  C15   aromatic  1.387  0.020  1.387
 CZB  C15  C16   aromatic  1.387  0.020  1.387
 CZB  C15  H15   single    0.930  0.020  1.080
 CZB  C16  H16   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
 CZB  C2    C3   N4    103.95  3.000
 CZB  C2    C3   O18   128.55  3.000
 CZB  N4    C3   O18   127.46  3.000
 CZB  C9    N4   C5    123.04  3.000
 CZB  C9    N4   C3    108.24  3.000
 CZB  C5    N4   C3    128.66  3.000
 CZB  H5    C5   C6    125.01  3.000
 CZB  H5    C5   N4    117.56  3.000
 CZB  C6    C5   N4    117.41  3.000
 CZB  N1    C9   C8    128.02  3.000
 CZB  N1    C9   N4    115.87  3.000
 CZB  C8    C9   N4    116.09  3.000
 CZB  H8    C8   N7    108.37  3.000
 CZB  H8    C8   C26   109.05  3.000
 CZB  N7    C8   C26   112.43  3.000
 CZB  H8    C8   C9    108.23  3.000
 CZB  N7    C8   C9    107.27  3.000
 CZB  C26   C8   C9    111.35  3.000
 CZB  H262  C26  H261  106.86  3.000
 CZB  H262  C26  C27   110.57  3.000
 CZB  H261  C26  C27   110.06  3.000
 CZB  H262  C26  C8    109.33  3.000
 CZB  H261  C26  C8    106.32  3.000
 CZB  C27   C26  C8    113.42  3.000
 CZB  C32   C27  C28   118.64  3.000
 CZB  C32   C27  C26   121.00  3.000
 CZB  C28   C27  C26   120.35  3.000
 CZB  H28   C28  C29   119.53  3.000
 CZB  H28   C28  C27   119.70  3.000
 CZB  C29   C28  C27   120.77  3.000
 CZB  H29   C29  C30   120.07  3.000
 CZB  H29   C29  C28   119.86  3.000
 CZB  C30   C29  C28   120.07  3.000
 CZB  H30   C30  C31   120.24  3.000
 CZB  H30   C30  C29   120.17  3.000
 CZB  C31   C30  C29   119.59  3.000
 CZB  H31   C31  C32   119.77  3.000
 CZB  H31   C31  C30   120.14  3.000
 CZB  C32   C31  C30   120.10  3.000
 CZB  H32   C32  C31   119.70  3.000
 CZB  H32   C32  C27   119.47  3.000
 CZB  C31   C32  C27   120.83  3.000
 CZB  HN7   N7   C6    117.67  3.000
 CZB  HN7   N7   C8    115.55  3.000
 CZB  C6    N7   C8    119.21  3.000
 CZB  C19   C6   N7    118.84  3.000
 CZB  C19   C6   C5    122.26  3.000
 CZB  N7    C6   C5    118.90  3.000
 CZB  C24   C19  C20   117.98  3.000
 CZB  C24   C19  C6    121.15  3.000
 CZB  C20   C19  C6    120.87  3.000
 CZB  H20   C20  C21   118.91  3.000
 CZB  H20   C20  C19   119.82  3.000
 CZB  C21   C20  C19   121.27  3.000
 CZB  H21   C21  C22   120.28  3.000
 CZB  H21   C21  C20   119.63  3.000
 CZB  C22   C21  C20   120.08  3.000
 CZB  H24   C24  C23   118.31  3.000
 CZB  H24   C24  C19   120.36  3.000
 CZB  C23   C24  C19   121.32  3.000
 CZB  H23   C23  C22   119.88  3.000
 CZB  H23   C23  C24   120.11  3.000
 CZB  C22   C23  C24   120.01  3.000
 CZB  O25   C22  C23   117.96  3.000
 CZB  O25   C22  C21   122.71  3.000
 CZB  C23   C22  C21   119.34  3.000
 CZB  H25   O25  C22   110.51  3.000
 CZB  C2    N1   C9    106.44  3.000
 CZB  C10   C2   O33   106.10  3.000
 CZB  C10   C2   N1    110.87  3.000
 CZB  O33   C2   N1    113.15  3.000
 CZB  C10   C2   C3    109.59  3.000
 CZB  O33   C2   C3    111.91  3.000
 CZB  N1    C2   C3    105.28  3.000
 CZB  O34   O33  C2    108.36  3.000
 CZB  H34   O34  O33   101.87  3.000
 CZB  H102  C10  H101  106.85  3.000
 CZB  H102  C10  C11   110.41  3.000
 CZB  H101  C10  C11   110.47  3.000
 CZB  H102  C10  C2    107.88  3.000
 CZB  H101  C10  C2    108.35  3.000
 CZB  C11   C10  C2    112.66  3.000
 CZB  C16   C11  C12   118.44  3.000
 CZB  C16   C11  C10   120.94  3.000
 CZB  C12   C11  C10   120.62  3.000
 CZB  H12   C12  C13   118.79  3.000
 CZB  H12   C12  C11   119.91  3.000
 CZB  C13   C12  C11   121.29  3.000
 CZB  H13   C13  C14   121.17  3.000
 CZB  H13   C13  C12   119.85  3.000
 CZB  C14   C13  C12   118.98  3.000
 CZB  C15   C14  BR17  119.47  3.000
 CZB  C15   C14  C13   121.01  3.000
 CZB  BR17  C14  C13   119.52  3.000
 CZB  H15   C15  C16   119.84  3.000
 CZB  H15   C15  C14   121.10  3.000
 CZB  C16   C15  C14   119.06  3.000
 CZB  H16   C16  C15   118.91  3.000
 CZB  H16   C16  C11   119.88  3.000
 CZB  C15   C16  C11   121.22  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
 CZB  CONST_01  C30   C29  C28  C27      0.00   0.0  0
 CZB  CONST_02  C30   C31  C32  C27      0.00   0.0  0
 CZB  CONST_03  C31   C32  C27  C28      0.00   0.0  0
 CZB  CONST_04  C31   C30  C29  C28      0.00   0.0  0
 CZB  CONST_05  C32   C27  C28  C29      0.00   0.0  0
 CZB  CONST_06  C32   C31  C30  C29      0.00   0.0  0
 CZB  CONST_07  C22   C21  C20  C19      0.00   0.0  0
 CZB  CONST_08  C22   C23  C24  C19      0.00   0.0  0
 CZB  CONST_09  C23   C24  C19  C20      0.00   0.0  0
 CZB  CONST_10  C23   C22  C21  C20      0.00   0.0  0
 CZB  CONST_11  C24   C19  C20  C21      0.00   0.0  0
 CZB  CONST_12  C24   C23  C22  C21      0.00   0.0  0
 CZB  CONST_13  C14   C13  C12  C11      0.00   0.0  0
 CZB  CONST_14  C14   C15  C16  C11      0.00   0.0  0
 CZB  CONST_15  C15   C16  C11  C12      0.00   0.0  0
 CZB  CONST_16  C15   C14  C13  C12      0.00   0.0  0
 CZB  CONST_17  C16   C11  C12  C13      0.00   0.0  0
 CZB  CONST_18  C16   C15  C14  C13      0.00   0.0  0
 CZB  CONST_19  C21   C20  C19  C6     180.00   0.0  0
 CZB  CONST_20  C23   C24  C19  C6     180.00   0.0  0
 CZB  CONST_21  C8    C9   N4   C3     180.00   0.0  0
 CZB  CONST_22  N1    C9   N4   C3       0.00   0.0  0
 CZB  CONST_23  C2    N1   C9   N4       0.00   0.0  0
 CZB  CONST_24  C2    C3   N4   C5     180.00   0.0  0
 CZB  CONST_25  C8    C9   N4   C5       0.00   0.0  0
 CZB  CONST_26  N1    C9   N4   C5     180.00   0.0  0
 CZB  CONST_27  C2    C3   N4   C9       0.00   0.0  0
 CZB  CONST_28  C2    N1   C9   C8     180.00   0.0  0
 CZB  CONST_29  C29   C28  C27  C26    180.00   0.0  0
 CZB  CONST_30  C31   C32  C27  C26    180.00   0.0  0
 CZB  CONST_31  O25   C22  C21  C20    180.00   0.0  0
 CZB  CONST_32  O25   C22  C23  C24    180.00   0.0  0
 CZB  CONST_33  C13   C12  C11  C10    180.00   0.0  0
 CZB  CONST_34  C15   C16  C11  C10    180.00   0.0  0
 CZB  CONST_35  BR17  C14  C13  C12    180.00   0.0  0
 CZB  CONST_36  C16   C15  C14  BR17   180.00   0.0  0
 CZB  CONST_37  C5    N4   C3   O18      0.00   0.0  0
 CZB  CONST_38  C9    N4   C3   O18    180.00   0.0  0
 CZB  CONST_39  H29   C29  C28  C27    180.00   0.0  0
 CZB  CONST_40  H31   C31  C32  C27    180.00   0.0  0
 CZB  CONST_41  H32   C32  C27  C28    180.00   0.0  0
 CZB  CONST_42  H30   C30  C29  C28    180.00   0.0  0
 CZB  CONST_43  H28   C28  C29  C30    180.00   0.0  0
 CZB  CONST_44  H20   C20  C19  C6       0.00   0.0  0
 CZB  CONST_45  H24   C24  C19  C6       0.00   0.0  0
 CZB  CONST_46  H21   C21  C20  C19    180.00   0.0  0
 CZB  CONST_47  H23   C23  C24  C19    180.00   0.0  0
 CZB  CONST_48  H13   C13  C12  C11    180.00   0.0  0
 CZB  CONST_49  H15   C15  C16  C11    180.00   0.0  0
 CZB  CONST_50  H16   C16  C11  C12    180.00   0.0  0
 CZB  CONST_51  H12   C12  C13  C14    180.00   0.0  0
 CZB  Var_01    C6    C5   N4   C3    -160.97  30.0  1
 CZB  Var_02    N7    C6   C5   N4      -2.44  30.0  1
 CZB  Var_03    C8    N7   C6   C5     -32.52  30.0  1
 CZB  Var_04    C20   C19  C6   C5     -36.57  30.0  2
 CZB  Var_05    C28   C27  C26  C8      76.20  30.0  2
 CZB  Var_06    C12   C11  C10  C2      95.08  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
 CZB  chir_01  C8  C9  C26  N7  positiv
 CZB  chir_02  C2  N1  C10  C3  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
 CZB  plan-1  C26   0.020
 CZB  plan-1  C27   0.020
 CZB  plan-1  C28   0.020
 CZB  plan-1  C29   0.020
 CZB  plan-1  C30   0.020
 CZB  plan-1  C31   0.020
 CZB  plan-1  C32   0.020
 CZB  plan-1  H28   0.020
 CZB  plan-1  H29   0.020
 CZB  plan-1  H30   0.020
 CZB  plan-1  H31   0.020
 CZB  plan-1  H32   0.020
 CZB  plan-2  C6    0.020
 CZB  plan-2  C19   0.020
 CZB  plan-2  C20   0.020
 CZB  plan-2  C21   0.020
 CZB  plan-2  C24   0.020
 CZB  plan-2  C23   0.020
 CZB  plan-2  C22   0.020
 CZB  plan-2  O25   0.020
 CZB  plan-2  H20   0.020
 CZB  plan-2  H21   0.020
 CZB  plan-2  H24   0.020
 CZB  plan-2  H23   0.020
 CZB  plan-3  C10   0.020
 CZB  plan-3  C11   0.020
 CZB  plan-3  C12   0.020
 CZB  plan-3  C13   0.020
 CZB  plan-3  C14   0.020
 CZB  plan-3  BR17  0.020
 CZB  plan-3  C15   0.020
 CZB  plan-3  C16   0.020
 CZB  plan-3  H12   0.020
 CZB  plan-3  H13   0.020
 CZB  plan-3  H15   0.020
 CZB  plan-3  H16   0.020
 CZB  plan-4  O18   0.020
 CZB  plan-4  C3    0.020
 CZB  plan-4  N4    0.020
 CZB  plan-4  C5    0.020
 CZB  plan-4  C9    0.020
 CZB  plan-4  C8    0.020
 CZB  plan-4  N1    0.020
 CZB  plan-4  C2    0.020
 CZB  plan-5  C8    0.020
 CZB  plan-5  N7    0.020
 CZB  plan-5  C6    0.020
 CZB  plan-5  HN7   0.020

