# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 21:25:28 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: (2S,8S)-8-(cyclopentylmethyl)-2-hydroperoxy-2-(4-hydroxybenzyl)-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(O)cc2)N=C3[C@H](CC4CCCC4)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
 CZP  CZP  (2S,8S)-8-(cyclopentylmethyl)-2-hydroperoxy-2-(4-hydroxybenzyl)-6-(4-hydroxyphenyl)-7,8-dihydroimidazo[1,2-a]pyrazin-3(2H)-one  ligand  60  33  .  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_CZP
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
 CZP  O25   O  OH1   0  -0.627   2.5681   5.6252   -0.0393
 CZP  C22   C  CR6   0   0.351   2.3987   4.7586   -1.0539
 CZP  C23   C  CR16  0  -0.370   1.2500   4.7323   -1.8399
 CZP  C24   C  CR16  0  -0.293   1.1320   3.8116   -2.8683
 CZP  C21   C  CR16  0  -0.321   3.4230   3.8486   -1.3128
 CZP  C20   C  CR16  0  -0.298   3.2907   2.9301   -2.3367
 CZP  C19   C  CR6   0   0.022   2.1482   2.8951   -3.1399
 CZP  C6    C  C     0   0.243   2.0225   1.9302   -4.2414
 CZP  N7    N  NH1   0  -0.665   0.7478   1.5038   -4.5852
 CZP  C8    C  CH1   0  -0.220   0.5969   0.1917   -5.1945
 CZP  C26   C  CH2   0  -0.420   0.7303  -0.9796   -4.2036
 CZP  C27   C  CH1   0  -0.255  -0.2794  -0.9364   -3.0691
 CZP  C28   C  CH2   0  -0.442  -1.7472  -0.9692   -3.4981
 CZP  C29   C  CH2   0  -0.444  -2.5118  -1.3632   -2.2250
 CZP  C30   C  CH2   0  -0.450  -1.4865  -2.0937   -1.3244
 CZP  C31   C  CH2   0  -0.422  -0.1868  -2.1435   -2.1353
 CZP  C9    C  CR5   0   0.530   1.6357   0.0348   -6.2526
 CZP  N4    N  NR5   0  -0.569   2.8637   0.6363   -6.0202
 CZP  C5    C  C1    0  -0.116   3.0834   1.5205   -4.9565
 CZP  N1    N  N     0  -0.423   1.5496  -0.6663   -7.3080
 CZP  C2    C  CR5   0   0.219   2.8594  -0.6458   -7.9210
 CZP  C3    C  CR5   0   0.529   3.6956   0.3203   -7.0552
 CZP  O18   O  O     0  -0.423   4.8306   0.6920   -7.2203
 CZP  O32   O  O2    0  -0.280   2.8168  -0.2349   -9.2550
 CZP  C10   C  CH2   0  -0.565   3.5008  -2.0387   -7.9104
 CZP  C11   C  CR6   0   0.127   2.6959  -3.0701   -8.6473
 CZP  C12   C  CR16  0  -0.285   1.6893  -3.7825   -8.0038
 CZP  C13   C  CR16  0  -0.374   0.9347  -4.7332   -8.6733
 CZP  C14   C  CR6   0   0.341   1.1759  -4.9899  -10.0205
 CZP  O17   O  OH1   0  -0.633   0.4747  -5.9021  -10.7246
 CZP  C15   C  CR16  0  -0.327   2.1819  -4.2876  -10.6793
 CZP  C16   C  CR16  0  -0.292   2.9259  -3.3401   -9.9937
 CZP  O1    O  OH1   0  -0.445   2.3409   1.0880   -9.2966
 CZP  H25   H  HOH1  0   0.476   1.7918   6.1884    0.0562
 CZP  H23   H  HCR6  0   0.276   0.4452   5.4349   -1.6558
 CZP  H24   H  HCR6  0   0.265   0.2356   3.8353   -3.4756
 CZP  H21   H  HCR6  0   0.269   4.3147   3.8531   -0.6985
 CZP  H20   H  HCR6  0   0.258   4.0854   2.2136   -2.5003
 CZP  HN7   H  HNH1  0   0.391   0.0490   1.6772   -3.8783
 CZP  H8    H  HCH1  0   0.300  -0.3826   0.1464   -5.6749
 CZP  H261  H  HCH2  0   0.244   0.6025  -1.9094   -4.7666
 CZP  H262  H  HCH2  0   0.246   1.7448  -0.9974   -3.7924
 CZP  H27   H  HCH1  0   0.220  -0.1126  -0.0365   -2.4626
 CZP  H281  H  HCH2  0   0.220  -1.8737  -1.7320   -4.2737
 CZP  H282  H  HCH2  0   0.234  -2.1007  -0.0251   -3.9180
 CZP  H291  H  HCH2  0   0.229  -3.3767  -1.9865   -2.4546
 CZP  H292  H  HCH2  0   0.227  -2.8938  -0.4745   -1.7204
 CZP  H301  H  HCH2  0   0.226  -1.3307  -1.5369   -0.3984
 CZP  H302  H  HCH2  0   0.229  -1.8241  -3.0897   -1.0368
 CZP  H311  H  HCH2  0   0.233   0.7078  -2.1288   -1.5102
 CZP  H312  H  HCH2  0   0.215  -0.1467  -3.0573   -2.7373
 CZP  H5    H  H     0   0.295   4.0944   1.8612   -4.8052
 CZP  H101  H  HCH2  0   0.283   3.6279  -2.3334   -6.8659
 CZP  H102  H  HCH2  0   0.279   4.5045  -1.9530   -8.3334
 CZP  H12   H  HCR6  0   0.249   1.4878  -3.5983   -6.9557
 CZP  H13   H  HCR6  0   0.268   0.1587  -5.2737   -8.1430
 CZP  H17   H  HOH1  0   0.473  -0.1828  -6.3257  -10.1618
 CZP  H15   H  HCR6  0   0.261   2.3803  -4.4859  -11.7254
 CZP  H16   H  HCR6  0   0.249   3.7077  -2.8090  -10.5234
 CZP  HO1   H  HOH1  0   0.478   1.3857   0.9709   -9.4139

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
 CZP  O25  C22   single    1.345  0.020  1.345
 CZP  O25  H25   single    0.850  0.020  0.980
 CZP  C22  C23   aromatic  1.392  0.020  1.392
 CZP  C22  C21   aromatic  1.394  0.020  1.394
 CZP  C23  C24   aromatic  1.385  0.020  1.385
 CZP  C23  H23   single    0.930  0.020  1.080
 CZP  C24  C19   aromatic  1.395  0.020  1.395
 CZP  C24  H24   single    0.930  0.020  1.080
 CZP  C21  C20   aromatic  1.382  0.020  1.382
 CZP  C21  H21   single    0.930  0.020  1.080
 CZP  C20  C19   aromatic  1.397  0.020  1.397
 CZP  C20  H20   single    0.930  0.020  1.080
 CZP  C19  C6    single    1.470  0.020  1.470
 CZP  C6   N7    single    1.387  0.020  1.387
 CZP  C6   C5    double    1.343  0.020  1.343
 CZP  N7   C8    single    1.454  0.020  1.454
 CZP  N7   HN7   single    0.890  0.020  1.040
 CZP  C8   C26   single    1.540  0.020  1.540
 CZP  C8   C9    single    1.491  0.020  1.491
 CZP  C8   H8    single    0.970  0.020  1.090
 CZP  C26  C27   single    1.519  0.020  1.519
 CZP  C26  H261  single    0.970  0.020  1.090
 CZP  C26  H262  single    0.970  0.020  1.090
 CZP  C27  C28   single    1.530  0.020  1.530
 CZP  C27  C31   single    1.529  0.020  1.529
 CZP  C27  H27   single    0.970  0.020  1.090
 CZP  C28  C29   single    1.536  0.020  1.536
 CZP  C28  H281  single    0.970  0.020  1.090
 CZP  C28  H282  single    0.970  0.020  1.090
 CZP  C29  C30   single    1.548  0.020  1.548
 CZP  C29  H291  single    0.970  0.020  1.090
 CZP  C29  H292  single    0.970  0.020  1.090
 CZP  C30  C31   single    1.533  0.020  1.533
 CZP  C30  H301  single    0.970  0.020  1.090
 CZP  C30  H302  single    0.970  0.020  1.090
 CZP  C31  H311  single    0.970  0.020  1.090
 CZP  C31  H312  single    0.970  0.020  1.090
 CZP  C9   N4    single    1.387  0.020  1.387
 CZP  C9   N1    double    1.270  0.020  1.270
 CZP  N4   C5    single    1.401  0.020  1.401
 CZP  N4   C3    single    1.365  0.020  1.365
 CZP  C5   H5    single    0.930  0.020  1.080
 CZP  N1   C2    single    1.446  0.020  1.446
 CZP  C2   C3    single    1.543  0.020  1.543
 CZP  C2   O32   single    1.396  0.020  1.396
 CZP  C2   C10   single    1.533  0.020  1.533
 CZP  C3   O18   double    1.206  0.020  1.206
 CZP  O32  O1    single    1.406  0.020  1.406
 CZP  C10  C11   single    1.501  0.020  1.501
 CZP  C10  H101  single    0.970  0.020  1.090
 CZP  C10  H102  single    0.970  0.020  1.090
 CZP  C11  C12   aromatic  1.391  0.020  1.391
 CZP  C11  C16   aromatic  1.392  0.020  1.392
 CZP  C12  C13   aromatic  1.386  0.020  1.386
 CZP  C12  H12   single    0.930  0.020  1.080
 CZP  C13  C14   aromatic  1.393  0.020  1.393
 CZP  C13  H13   single    0.930  0.020  1.080
 CZP  C14  O17   single    1.349  0.020  1.349
 CZP  C14  C15   aromatic  1.393  0.020  1.393
 CZP  O17  H17   single    0.850  0.020  0.980
 CZP  C15  C16   aromatic  1.386  0.020  1.386
 CZP  C15  H15   single    0.930  0.020  1.080
 CZP  C16  H16   single    0.930  0.020  1.080
 CZP  O1   HO1   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
 CZP  H25   O25  C22   110.48  3.000
 CZP  C21   C22  C23   119.27  3.000
 CZP  C21   C22  O25   117.90  3.000
 CZP  C23   C22  O25   122.82  3.000
 CZP  H23   C23  C24   119.58  3.000
 CZP  H23   C23  C22   120.29  3.000
 CZP  C24   C23  C22   120.13  3.000
 CZP  H24   C24  C19   120.54  3.000
 CZP  H24   C24  C23   118.18  3.000
 CZP  C19   C24  C23   121.27  3.000
 CZP  H21   C21  C20   120.13  3.000
 CZP  H21   C21  C22   119.80  3.000
 CZP  C20   C21  C22   120.06  3.000
 CZP  H20   C20  C19   119.80  3.000
 CZP  H20   C20  C21   118.79  3.000
 CZP  C19   C20  C21   121.40  3.000
 CZP  C6    C19  C20   121.15  3.000
 CZP  C6    C19  C24   120.99  3.000
 CZP  C20   C19  C24   117.86  3.000
 CZP  C5    C6   N7    120.00  3.000
 CZP  C5    C6   C19   122.11  3.000
 CZP  N7    C6   C19   117.78  3.000
 CZP  HN7   N7   C8    112.13  3.000
 CZP  HN7   N7   C6    114.20  3.000
 CZP  C8    N7   C6    118.45  3.000
 CZP  H8    C8   C9    107.96  3.000
 CZP  H8    C8   C26   109.23  3.000
 CZP  C9    C8   C26   108.43  3.000
 CZP  H8    C8   N7    108.35  3.000
 CZP  C9    C8   N7    108.66  3.000
 CZP  C26   C8   N7    114.05  3.000
 CZP  H262  C26  H261  106.71  3.000
 CZP  H262  C26  C27   109.62  3.000
 CZP  H261  C26  C27   109.31  3.000
 CZP  H262  C26  C8    109.53  3.000
 CZP  H261  C26  C8    107.76  3.000
 CZP  C27   C26  C8    113.66  3.000
 CZP  H27   C27  C31   107.49  3.000
 CZP  H27   C27  C28   108.56  3.000
 CZP  C31   C27  C28   102.27  3.000
 CZP  H27   C27  C26   109.56  3.000
 CZP  C31   C27  C26   113.16  3.000
 CZP  C28   C27  C26   115.32  3.000
 CZP  H282  C28  H281  107.00  3.000
 CZP  H282  C28  C29   112.29  3.000
 CZP  H281  C28  C29   110.53  3.000
 CZP  H282  C28  C27   113.58  3.000
 CZP  H281  C28  C27   108.93  3.000
 CZP  C29   C28  C27   104.51  3.000
 CZP  H292  C29  H291  106.57  3.000
 CZP  H292  C29  C30   110.32  3.000
 CZP  H291  C29  C30   112.22  3.000
 CZP  H292  C29  C28   110.40  3.000
 CZP  H291  C29  C28   111.52  3.000
 CZP  C30   C29  C28   105.87  3.000
 CZP  H302  C30  H301  106.64  3.000
 CZP  H302  C30  C31   111.86  3.000
 CZP  H301  C30  C31   110.14  3.000
 CZP  H302  C30  C29   112.30  3.000
 CZP  H301  C30  C29   110.33  3.000
 CZP  C31   C30  C29   105.62  3.000
 CZP  H312  C31  H311  107.22  3.000
 CZP  H312  C31  C30   110.42  3.000
 CZP  H311  C31  C30   113.05  3.000
 CZP  H312  C31  C27   108.99  3.000
 CZP  H311  C31  C27   112.89  3.000
 CZP  C30   C31  C27   104.24  3.000
 CZP  N1    C9   N4    116.02  3.000
 CZP  N1    C9   C8    126.91  3.000
 CZP  N4    C9   C8    116.89  3.000
 CZP  C3    N4   C5    128.79  3.000
 CZP  C3    N4   C9    108.18  3.000
 CZP  C5    N4   C9    122.68  3.000
 CZP  H5    C5   N4    116.97  3.000
 CZP  H5    C5   C6    124.74  3.000
 CZP  N4    C5   C6    118.22  3.000
 CZP  C2    N1   C9    106.44  3.000
 CZP  C10   C2   O32   106.66  3.000
 CZP  C10   C2   C3    109.76  3.000
 CZP  O32   C2   C3    111.60  3.000
 CZP  C10   C2   N1    111.28  3.000
 CZP  O32   C2   N1    112.42  3.000
 CZP  C3    C2   N1    105.17  3.000
 CZP  O18   C3   C2    128.77  3.000
 CZP  O18   C3   N4    127.32  3.000
 CZP  C2    C3   N4    103.89  3.000
 CZP  O1    O32  C2    108.38  3.000
 CZP  H102  C10  H101  106.52  3.000
 CZP  H102  C10  C11   110.87  3.000
 CZP  H101  C10  C11   110.26  3.000
 CZP  H102  C10  C2    108.08  3.000
 CZP  H101  C10  C2    107.48  3.000
 CZP  C11   C10  C2    113.35  3.000
 CZP  C16   C11  C12   117.87  3.000
 CZP  C16   C11  C10   121.28  3.000
 CZP  C12   C11  C10   120.84  3.000
 CZP  H12   C12  C13   118.86  3.000
 CZP  H12   C12  C11   119.68  3.000
 CZP  C13   C12  C11   121.45  3.000
 CZP  H13   C13  C14   120.35  3.000
 CZP  H13   C13  C12   119.69  3.000
 CZP  C14   C13  C12   119.96  3.000
 CZP  C15   C14  O17   118.01  3.000
 CZP  C15   C14  C13   119.33  3.000
 CZP  O17   C14  C13   122.66  3.000
 CZP  H17   O17  C14   110.31  3.000
 CZP  H15   C15  C16   120.31  3.000
 CZP  H15   C15  C14   119.79  3.000
 CZP  C16   C15  C14   119.90  3.000
 CZP  H16   C16  C15   118.72  3.000
 CZP  H16   C16  C11   119.80  3.000
 CZP  C15   C16  C11   121.49  3.000
 CZP  HO1   O1   O32   102.91  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
 CZP  CONST_01  C19  C24  C23  C22     0.00   0.0  0
 CZP  CONST_02  C19  C20  C21  C22     0.00   0.0  0
 CZP  CONST_03  C20  C21  C22  C23     0.00   0.0  0
 CZP  CONST_04  C20  C19  C24  C23     0.00   0.0  0
 CZP  CONST_05  C21  C22  C23  C24     0.00   0.0  0
 CZP  CONST_06  C21  C20  C19  C24     0.00   0.0  0
 CZP  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 CZP  CONST_08  C14  C15  C16  C11     0.00   0.0  0
 CZP  CONST_09  C15  C16  C11  C12     0.00   0.0  0
 CZP  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 CZP  CONST_11  C16  C11  C12  C13     0.00   0.0  0
 CZP  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 CZP  CONST_13  C6   C19  C24  C23   180.00   0.0  0
 CZP  CONST_14  C6   C19  C20  C21   180.00   0.0  0
 CZP  CONST_15  C5   N4   C9   C8      0.00   0.0  0
 CZP  CONST_16  C3   N4   C9   C8    180.00   0.0  0
 CZP  CONST_17  C2   N1   C9   C8    180.00   0.0  0
 CZP  CONST_18  C2   C3   N4   C9      0.00   0.0  0
 CZP  CONST_19  C2   N1   C9   N4      0.00   0.0  0
 CZP  CONST_20  N1   C9   N4   C5    180.00   0.0  0
 CZP  CONST_21  C2   C3   N4   C5    180.00   0.0  0
 CZP  CONST_22  C3   N4   C9   N1      0.00   0.0  0
 CZP  CONST_23  C24  C23  C22  O25   180.00   0.0  0
 CZP  CONST_24  C20  C21  C22  O25   180.00   0.0  0
 CZP  CONST_25  C13  C12  C11  C10   180.00   0.0  0
 CZP  CONST_26  C15  C16  C11  C10   180.00   0.0  0
 CZP  CONST_27  O17  C14  C13  C12   180.00   0.0  0
 CZP  CONST_28  C16  C15  C14  O17   180.00   0.0  0
 CZP  CONST_29  O18  C3   N4   C9    180.00   0.0  0
 CZP  CONST_30  O18  C3   N4   C5      0.00   0.0  0
 CZP  CONST_31  H24  C24  C23  C22   180.00   0.0  0
 CZP  CONST_32  H20  C20  C21  C22   180.00   0.0  0
 CZP  CONST_33  H21  C21  C22  C23   180.00   0.0  0
 CZP  CONST_34  H23  C23  C22  C21   180.00   0.0  0
 CZP  CONST_35  H13  C13  C12  C11   180.00   0.0  0
 CZP  CONST_36  H15  C15  C16  C11   180.00   0.0  0
 CZP  CONST_37  H16  C16  C11  C12   180.00   0.0  0
 CZP  CONST_38  H12  C12  C13  C14   180.00   0.0  0
 CZP  Var_01    N7   C6   C19  C24   -29.66  30.0  2
 CZP  Var_02    C8   N7   C6   C19  -152.99  30.0  1
 CZP  Var_03    N4   C5   C6   C19  -177.68  30.0  1
 CZP  Var_04    C9   N4   C5   C6     -8.71  30.0  1
 CZP  Var_05    C30  C29  C28  C27   -22.98  30.0  1
 CZP  Var_06    C29  C30  C31  C27    26.65  30.0  1
 CZP  Var_07    C31  C30  C29  C28    -2.25  30.0  1
 CZP  Var_08    C12  C11  C10  C2    -87.28  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
 CZP  chir_01  C8   N7   C26  C9   positiv
 CZP  chir_02  C27  C31  C28  C26  positiv
 CZP  chir_03  C2   N1   C3   C10  negativ

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
 CZP  plan-1  O25  0.020
 CZP  plan-1  C22  0.020
 CZP  plan-1  C23  0.020
 CZP  plan-1  C24  0.020
 CZP  plan-1  C21  0.020
 CZP  plan-1  C20  0.020
 CZP  plan-1  C19  0.020
 CZP  plan-1  C6   0.020
 CZP  plan-1  H23  0.020
 CZP  plan-1  H24  0.020
 CZP  plan-1  H21  0.020
 CZP  plan-1  H20  0.020
 CZP  plan-2  C10  0.020
 CZP  plan-2  C11  0.020
 CZP  plan-2  C12  0.020
 CZP  plan-2  C13  0.020
 CZP  plan-2  C14  0.020
 CZP  plan-2  O17  0.020
 CZP  plan-2  C15  0.020
 CZP  plan-2  C16  0.020
 CZP  plan-2  H12  0.020
 CZP  plan-2  H13  0.020
 CZP  plan-2  H15  0.020
 CZP  plan-2  H16  0.020
 CZP  plan-3  C6   0.020
 CZP  plan-3  N7   0.020
 CZP  plan-3  C8   0.020
 CZP  plan-3  HN7  0.020
 CZP  plan-4  C8   0.020
 CZP  plan-4  C9   0.020
 CZP  plan-4  N4   0.020
 CZP  plan-4  C5   0.020
 CZP  plan-4  N1   0.020
 CZP  plan-4  C2   0.020
 CZP  plan-4  C3   0.020
 CZP  plan-4  O18  0.020

