# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 04:50:11 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: (5~{S},8~{S},9~{R})-2-[(~{E})-hex-1-enyl]-8-methoxy-3-methyl-9-oxidanyl-8-(phenylcarbonyl)-1-oxa-7-azaspiro[4.4]non-2-ene-4,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC\C=C\C1=C(C)C(=O)[C@@]2(O1)[C@@H](O)[C@](NC2=O)(OC)C(=O)c3ccccc3
#
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
 PZS  PZS  (5~{S},8~{S},9~{R})-2-[(~{E})-hex-1-enyl]-8-methoxy-3-methyl-9-oxidanyl-8-(phenylcarbonyl)-1-oxa-7-azaspiro[4.4]non-2-ene-4,6-dione  ligand  54  29  .  2021-08-20  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PZS
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
 PZS  C10  C  CH2   0  -0.420  -4.3035   1.4296  -0.2725
 PZS  C14  C  CH2   0  -0.420  -5.6704   2.0781  -0.4444
 PZS  C15  C  CH3   0  -0.663  -5.6416   3.5726  -0.1565
 PZS  C9   C  CH2   0  -0.491  -4.3083  -0.0694  -0.5795
 PZS  C8   C  C1    0  -0.138  -2.9395  -0.6431  -0.4826
 PZS  C7   C  C1    0  -0.387  -2.5939  -1.6752   0.2964
 PZS  C    C  CR5   0   0.452  -1.2447  -2.1689   0.4043
 PZS  O    O  O     0  -0.482  -0.3020  -1.4888  -0.2821
 PZS  C3   C  C     0  -0.121   0.9673  -2.0316   0.0402
 PZS  C2   C  CR5   0   0.408   0.6630  -3.2647   0.8777
 PZS  O1   O  O     0  -0.398   1.4753  -4.0875   1.2437
 PZS  C1   C  CR5   0  -0.188  -0.7582  -3.2198   1.1130
 PZS  C11  C  CH3   0  -0.727  -1.4903  -4.2088   1.9474
 PZS  C6   C  CR5   0   0.604   1.7047  -2.2584  -1.2814
 PZS  O2   O  O     0  -0.431   1.6110  -3.2382  -1.9825
 PZS  N    N  NR15  0  -0.659   2.4180  -1.1403  -1.5148
 PZS  C5   C  CR5   0   0.325   2.2498  -0.1015  -0.5272
 PZS  C4   C  CR15  0   0.015   1.7852  -0.9328   0.7096
 PZS  O3   O  OH1   0  -0.635   2.8672  -1.5345   1.3358
 PZS  O11  O  O2    0  -0.490   3.4325   0.5315  -0.1845
 PZS  C31  C  CH3   0  -0.437   4.0507   1.3396  -1.1746
 PZS  C12  C  C     0   0.364   1.1759   0.9170  -0.9982
 PZS  O4   O  O     0  -0.358   0.7426   0.8223  -2.1218
 PZS  C13  C  CR6   0  -0.025   0.6761   1.9628  -0.0690
 PZS  C28  C  CR16  0  -0.260  -0.5267   2.5917  -0.4065
 PZS  C27  C  CR16  0  -0.234  -1.0761   3.5539   0.4214
 PZS  C26  C  CR16  0  -0.242  -0.4222   3.9183   1.5923
 PZS  C25  C  CR16  0  -0.237   0.7801   3.3130   1.9295
 PZS  C24  C  CR16  0  -0.291   1.3255   2.3358   1.1104
 PZS  H6   H  HCH2  0   0.220  -3.5833   1.9278  -0.9301
 PZS  H16  H  HCH2  0   0.225  -3.9445   1.5913   0.7485
 PZS  H12  H  HCH2  0   0.216  -6.0261   1.9060  -1.4649
 PZS  H11  H  HCH2  0   0.217  -6.3927   1.5896   0.2162
 PZS  H13  H  HCH3  0   0.218  -5.3175   3.7702   0.8667
 PZS  H15  H  HCH3  0   0.218  -4.9511   4.0889  -0.8263
 PZS  H14  H  HCH3  0   0.229  -6.6262   4.0232  -0.2855
 PZS  H4   H  HCH2  0   0.245  -4.9961  -0.5956   0.0868
 PZS  H5   H  HCH2  0   0.250  -4.6765  -0.2152  -1.6013
 PZS  H3   H  H     0   0.265  -2.1831  -0.1535  -1.0895
 PZS  H2   H  H     0   0.275  -3.3394  -2.1772   0.9018
 PZS  H9   H  HCH3  0   0.249  -2.5472  -3.9648   2.0364
 PZS  H7   H  HCH3  0   0.253  -1.4170  -5.2110   1.5220
 PZS  H8   H  HCH3  0   0.252  -1.0751  -4.2547   2.9549
 PZS  H1   H  HNR5  0   0.416   2.8361  -0.9780  -2.4208
 PZS  H    H  HCR5  0   0.276   1.1738  -0.3426   1.4006
 PZS  H10  H  HOH1  0   0.467   3.5233  -0.8604   1.5487
 PZS  H38  H  HCH3  0   0.233   3.4332   2.1945  -1.4617
 PZS  H39  H  HCH3  0   0.266   4.9703   1.7154  -0.7342
 PZS  H37  H  HCH3  0   0.234   4.3076   0.7705  -2.0712
 PZS  H32  H  HCR6  0   0.265  -1.0390   2.3156  -1.3182
 PZS  H31  H  HCR6  0   0.263  -2.0158   4.0202   0.1554
 PZS  H30  H  HCR6  0   0.271  -0.8499   4.6727   2.2395
 PZS  H29  H  HCR6  0   0.270   1.2969   3.6000   2.8355
 PZS  H28  H  HCR6  0   0.274   2.2678   1.8912   1.3953

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
 PZS  C25  C26  aromatic  1.388  0.020  1.388
 PZS  C25  C24  aromatic  1.387  0.020  1.387
 PZS  C26  C27  aromatic  1.390  0.020  1.390
 PZS  C24  C13  aromatic  1.397  0.020  1.397
 PZS  C15  C14  single    1.522  0.020  1.522
 PZS  O4   C12  double    1.208  0.020  1.208
 PZS  C27  C28  aromatic  1.383  0.020  1.383
 PZS  C13  C12  single    1.486  0.020  1.486
 PZS  C13  C28  aromatic  1.399  0.020  1.399
 PZS  C12  C5   single    1.553  0.020  1.553
 PZS  C14  C10  single    1.523  0.020  1.523
 PZS  C4   O3   single    1.387  0.020  1.387
 PZS  C4   C5   single    1.561  0.020  1.561
 PZS  C4   C3   single    1.525  0.020  1.525
 PZS  C10  C9   single    1.530  0.020  1.530
 PZS  C5   O11  single    1.384  0.020  1.384
 PZS  C5   N    single    1.443  0.020  1.443
 PZS  O    C3   single    1.418  0.020  1.418
 PZS  O    C    single    1.350  0.020  1.350
 PZS  C8   C9   single    1.487  0.020  1.487
 PZS  C8   C7   double    1.338  0.020  1.338
 PZS  O11  C31  single    1.420  0.020  1.420
 PZS  C3   C6   single    1.530  0.020  1.530
 PZS  C3   C2   single    1.521  0.020  1.521
 PZS  N    C6   single    1.347  0.020  1.347
 PZS  C6   O2   double    1.208  0.020  1.208
 PZS  C    C7   single    1.441  0.020  1.441
 PZS  C    C1   double    1.358  0.020  1.358
 PZS  C2   C1   single    1.441  0.020  1.441
 PZS  C2   O1   double    1.213  0.020  1.213
 PZS  C1   C11  single    1.487  0.020  1.487
 PZS  C10  H6   single    0.970  0.020  1.090
 PZS  C10  H16  single    0.970  0.020  1.090
 PZS  C14  H12  single    0.970  0.020  1.090
 PZS  C14  H11  single    0.970  0.020  1.090
 PZS  C15  H13  single    0.970  0.020  1.090
 PZS  C15  H15  single    0.970  0.020  1.090
 PZS  C15  H14  single    0.970  0.020  1.090
 PZS  C9   H4   single    0.970  0.020  1.090
 PZS  C9   H5   single    0.970  0.020  1.090
 PZS  C8   H3   single    0.930  0.020  1.080
 PZS  C7   H2   single    0.930  0.020  1.080
 PZS  C11  H9   single    0.970  0.020  1.090
 PZS  C11  H7   single    0.970  0.020  1.090
 PZS  C11  H8   single    0.970  0.020  1.090
 PZS  N    H1   single    0.860  0.020  1.020
 PZS  C4   H    single    0.970  0.020  1.090
 PZS  O3   H10  single    0.850  0.020  0.980
 PZS  C31  H38  single    0.970  0.020  1.090
 PZS  C31  H39  single    0.970  0.020  1.090
 PZS  C31  H37  single    0.970  0.020  1.090
 PZS  C28  H32  single    0.930  0.020  1.080
 PZS  C27  H31  single    0.930  0.020  1.080
 PZS  C26  H30  single    0.930  0.020  1.080
 PZS  C25  H29  single    0.930  0.020  1.080
 PZS  C24  H28  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
 PZS  H16  C10  H6   106.10  3.000
 PZS  H16  C10  C9   109.45  3.000
 PZS  H6   C10  C9   109.10  3.000
 PZS  H16  C10  C14  109.69  3.000
 PZS  H6   C10  C14  109.20  3.000
 PZS  C9   C10  C14  113.07  3.000
 PZS  H11  C14  H12  106.16  3.000
 PZS  H11  C14  C15  109.68  3.000
 PZS  H12  C14  C15  109.69  3.000
 PZS  H11  C14  C10  109.53  3.000
 PZS  H12  C14  C10  109.27  3.000
 PZS  C15  C14  C10  112.32  3.000
 PZS  H14  C15  H15  107.64  3.000
 PZS  H14  C15  H13  107.71  3.000
 PZS  H15  C15  H13  107.56  3.000
 PZS  H14  C15  C14  111.48  3.000
 PZS  H15  C15  C14  111.12  3.000
 PZS  H13  C15  C14  111.15  3.000
 PZS  H5   C9   H4   107.03  3.000
 PZS  H5   C9   C8   108.58  3.000
 PZS  H4   C9   C8   110.72  3.000
 PZS  H5   C9   C10  108.57  3.000
 PZS  H4   C9   C10  110.57  3.000
 PZS  C8   C9   C10  111.22  3.000
 PZS  H3   C8   C7   119.53  3.000
 PZS  H3   C8   C9   115.50  3.000
 PZS  C7   C8   C9   124.97  3.000
 PZS  H2   C7   C    116.33  3.000
 PZS  H2   C7   C8   120.31  3.000
 PZS  C    C7   C8   123.35  3.000
 PZS  C1   C    O    113.90  3.000
 PZS  C1   C    C7   129.79  3.000
 PZS  O    C    C7   116.31  3.000
 PZS  C3   O    C    108.47  3.000
 PZS  C4   C3   C6   103.15  3.000
 PZS  C6   C3   C2   116.85  3.000
 PZS  C4   C3   C2   116.73  3.000
 PZS  C2   C3   O    104.86  3.000
 PZS  C6   C3   O    106.97  3.000
 PZS  C4   C3   O    107.71  3.000
 PZS  C1   C2   O1   129.22  3.000
 PZS  O1   C2   C3   125.60  3.000
 PZS  C1   C2   C3   105.18  3.000
 PZS  C11  C1   C2   123.82  3.000
 PZS  C11  C1   C    129.15  3.000
 PZS  C2   C1   C    106.99  3.000
 PZS  H8   C11  H7   107.21  3.000
 PZS  H8   C11  H9   107.68  3.000
 PZS  H7   C11  H9   107.64  3.000
 PZS  H8   C11  C1   111.03  3.000
 PZS  H7   C11  C1   111.04  3.000
 PZS  H9   C11  C1   112.02  3.000
 PZS  N    C6   O2   127.86  3.000
 PZS  O2   C6   C3   125.72  3.000
 PZS  N    C6   C3   106.37  3.000
 PZS  H1   N    C5   123.09  3.000
 PZS  H1   N    C6   120.51  3.000
 PZS  C5   N    C6   114.66  3.000
 PZS  C12  C5   O11  111.46  3.000
 PZS  O11  C5   C4   107.56  3.000
 PZS  C12  C5   C4   112.56  3.000
 PZS  O11  C5   N    113.51  3.000
 PZS  C4   C5   N    101.16  3.000
 PZS  C12  C5   N    110.18  3.000
 PZS  H    C4   O3   112.60  3.000
 PZS  H    C4   C5   112.27  3.000
 PZS  O3   C4   C5   110.88  3.000
 PZS  H    C4   C3   111.46  3.000
 PZS  C5   C4   C3   101.28  3.000
 PZS  O3   C4   C3   107.70  3.000
 PZS  H10  O3   C4   109.09  3.000
 PZS  C31  O11  C5   117.36  3.000
 PZS  H37  C31  H39  108.29  3.000
 PZS  H37  C31  H38  108.95  3.000
 PZS  H39  C31  H38  108.31  3.000
 PZS  H37  C31  O11  112.22  3.000
 PZS  H39  C31  O11  106.42  3.000
 PZS  H38  C31  O11  112.48  3.000
 PZS  C13  C12  O4   121.08  3.000
 PZS  C13  C12  C5   120.30  3.000
 PZS  O4   C12  C5   118.60  3.000
 PZS  C24  C13  C28  118.91  3.000
 PZS  C28  C13  C12  117.06  3.000
 PZS  C24  C13  C12  124.03  3.000
 PZS  H32  C28  C27  119.60  3.000
 PZS  H32  C28  C13  119.73  3.000
 PZS  C27  C28  C13  120.66  3.000
 PZS  H31  C27  C26  120.18  3.000
 PZS  H31  C27  C28  119.84  3.000
 PZS  C26  C27  C28  119.98  3.000
 PZS  H30  C26  C25  120.08  3.000
 PZS  H30  C26  C27  120.05  3.000
 PZS  C25  C26  C27  119.88  3.000
 PZS  H29  C25  C24  119.58  3.000
 PZS  H29  C25  C26  120.11  3.000
 PZS  C24  C25  C26  120.30  3.000
 PZS  H28  C24  C25  118.51  3.000
 PZS  H28  C24  C13  121.22  3.000
 PZS  C25  C24  C13  120.26  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
 PZS  CONST_01  C26  C25  C24  C13     0.00   0.0  0
 PZS  CONST_02  C26  C27  C28  C13     0.00   0.0  0
 PZS  CONST_03  C25  C26  C27  C28     0.00   0.0  0
 PZS  CONST_04  C25  C24  C13  C28     0.00   0.0  0
 PZS  CONST_05  C24  C25  C26  C27     0.00   0.0  0
 PZS  CONST_06  C24  C13  C28  C27     0.00   0.0  0
 PZS  CONST_07  C5   N    C6   C3      0.00   0.0  0
 PZS  CONST_08  C25  C24  C13  C12   180.00   0.0  0
 PZS  CONST_09  C27  C28  C13  C12   180.00   0.0  0
 PZS  CONST_10  C5   N    C6   O2    180.00   0.0  0
 PZS  CONST_11  H29  C25  C24  C13   180.00   0.0  0
 PZS  CONST_12  H31  C27  C28  C13   180.00   0.0  0
 PZS  CONST_13  H30  C26  C27  C28   180.00   0.0  0
 PZS  CONST_14  H28  C24  C13  C28   180.00   0.0  0
 PZS  CONST_15  H32  C28  C27  C26   180.00   0.0  0
 PZS  CONST_16  H1   N    C6   C3    180.00   0.0  0
 PZS  Var_01    C3   C2   C1   C       4.91  30.0  1
 PZS  Var_02    C2   C1   C    O      -0.39  30.0  1
 PZS  Var_03    C1   C    O    C3     -4.74  30.0  1
 PZS  Var_04    C24  C13  C12  C5     16.89  30.0  2
 PZS  Var_05    O    C    C7   C8      3.18  30.0  3
 PZS  Var_06    H9   C11  C1   C      -5.48  30.0  3
 PZS  Var_07    C    C7   C8   C9   -177.40   0.0  2
 PZS  Var_08    H38  C31  O11  C5     63.53  30.0  3
 PZS  Var_09    C7   C8   C9   C10   124.29  30.0  1
 PZS  Var_10    C8   C9   C10  C14   176.41  30.0  3
 PZS  Var_11    C9   C10  C14  C15  -179.08  30.0  3
 PZS  Var_12    H13  C15  C14  C10   -59.93  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
 PZS  chir_01  C3  O   C6  C2   positiv
 PZS  chir_02  C5  N   C4  C12  positiv
 PZS  chir_03  C4  O3  C5  C3   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
 PZS  plan-1  C3   0.020
 PZS  plan-1  C2   0.020
 PZS  plan-1  O1   0.020
 PZS  plan-1  C1   0.020
 PZS  plan-2  C12  0.020
 PZS  plan-2  C13  0.020
 PZS  plan-2  C28  0.020
 PZS  plan-2  C27  0.020
 PZS  plan-2  C26  0.020
 PZS  plan-2  C25  0.020
 PZS  plan-2  C24  0.020
 PZS  plan-2  H32  0.020
 PZS  plan-2  H31  0.020
 PZS  plan-2  H30  0.020
 PZS  plan-2  H29  0.020
 PZS  plan-2  H28  0.020
 PZS  plan-3  C3   0.020
 PZS  plan-3  C6   0.020
 PZS  plan-3  O2   0.020
 PZS  plan-3  N    0.020
 PZS  plan-3  C5   0.020
 PZS  plan-3  H1   0.020
 PZS  plan-4  C5   0.020
 PZS  plan-4  C12  0.020
 PZS  plan-4  O4   0.020
 PZS  plan-4  C13  0.020
 PZS  plan-5  C9   0.020
 PZS  plan-5  C8   0.020
 PZS  plan-5  C7   0.020
 PZS  plan-5  C    0.020
 PZS  plan-5  H3   0.020
 PZS  plan-5  H2   0.020

