# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 15:30:44 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: (6E,8E)-11-{[(3S)-hexahydropyridazine-3-carbonyl]oxy}undeca-6,8-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCC\C=C\C=C\CCOC(=O)[C@@H]1CCCNN1
#
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
 78D  78D  '(6E,8E)-11-{[(3S)-hexahydropyridazine-3-carbonyl]oxy}undeca-6,8-dienoic acid'  ligand  48  22  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_78D
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
 78D  N2   N  NR16  0  -0.483  -6.6985  -1.7330  -0.2112
 78D  C2   C  C     0  -0.455  -7.9730   0.8645  -0.0966
 78D  N1   N  NR16  0  -0.470  -8.0590  -1.5889  -0.5456
 78D  C4   C  CR16  0  -0.217  -5.9111  -0.5143  -0.3365
 78D  C5   C  C     0   0.601  -4.5173  -0.7714   0.1881
 78D  C16  C  CH2   0  -0.161  -2.3356   0.1418   0.3149
 78D  C18  C  C1    0  -0.241  -0.2473   1.4710   0.4101
 78D  C15  C  C     0   0.550   9.1208  -0.9594   0.0813
 78D  C17  C  CH2   0  -0.529  -1.6418   1.4191  -0.1258
 78D  C19  C  C1    0  -0.236   0.8541   1.4604  -0.3459
 78D  C1   C  C     0  -0.444  -6.5304   0.7038   0.3649
 78D  C3   C  C     0  -0.305  -8.7215  -0.4497   0.0758
 78D  C20  C  C1    0  -0.250   2.2063   1.5078   0.1826
 78D  O1   O  O2    0  -0.458  -3.6849   0.1941  -0.1679
 78D  C21  C  C1    0  -0.212   3.3023   1.4989  -0.5820
 78D  O2   O  O     0  -0.447  -4.2023  -1.7138   0.8711
 78D  O5   O  O     0  -0.446   9.6967  -0.0301   0.5908
 78D  C22  C  CH2   0  -0.486   4.7051   1.5269  -0.0734
 78D  C23  C  CH2   0  -0.418   5.4698   0.2449  -0.4074
 78D  C29  C  CH2   0  -0.420   6.9334   0.3169   0.0082
 78D  C30  C  CH2   0  -0.581   7.6692  -0.9742  -0.3078
 78D  H1   H  HNR6  0   0.347  -6.6503  -2.0901   0.7354
 78D  H2   H  H     0   0.239  -8.4661   1.6585   0.4685
 78D  H3   H  H     0   0.223  -7.9923   1.1641  -1.1496
 78D  H4   H  HCR6  0   0.268  -5.8289  -0.2818  -1.4054
 78D  H6   H  HCH2  0   0.241  -1.8290  -0.7341  -0.0963
 78D  H7   H  HCH2  0   0.238  -2.3312   0.0563   1.4042
 78D  H9   H  H     0   0.246  -0.1435   1.5130   1.4920
 78D  H12  H  HCH2  0   0.252  -1.6317   1.4815  -1.2166
 78D  H13  H  HCH2  0   0.250  -2.2107   2.2764   0.2479
 78D  H18  H  H     0   0.242   0.7534   1.4181  -1.4282
 78D  H19  H  H     0   0.248  -5.9522   1.6031   0.1466
 78D  H20  H  H     0   0.231  -6.5009   0.5532   1.4495
 78D  H21  H  H     0   0.218  -8.8378  -0.6668   1.1431
 78D  H22  H  H     0   0.239  -9.7273  -0.3850  -0.3439
 78D  H26  H  H     0   0.239   2.3110   1.5524   1.2643
 78D  H27  H  H     0   0.239   3.1842   1.4488  -1.6627
 78D  H31  H  HCH2  0   0.232   5.2347   2.3755  -0.5206
 78D  H32  H  HCH2  0   0.233   4.7112   1.6870   1.0085
 78D  H33  H  HCH2  0   0.223   4.9837  -0.6020   0.0867
 78D  H34  H  HCH2  0   0.222   5.4036   0.0502  -1.4829
 78D  H39  H  HCH2  0   0.228   7.4138   1.1553  -0.5030
 78D  H40  H  HCH2  0   0.228   6.9985   0.5285   1.0789
 78D  H41  H  HCH2  0   0.277   7.6069  -1.1997  -1.3774
 78D  H42  H  HCH2  0   0.276   7.1910  -1.8210   0.1949
 78D  OXT  O  OH1   0  -0.598   9.7216  -2.1119  -0.2034
 78D  HXT  H  HOH1  0   0.478  10.6549  -2.0687   0.0523
 78D  H5   H  HNR6  0   0.349  -8.1192  -1.5212  -1.5541

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
 78D  C30  C29  single  1.519  0.020  1.519
 78D  C30  C15  single  1.503  0.020  1.503
 78D  C29  C23  single  1.523  0.020  1.523
 78D  C23  C22  single  1.530  0.020  1.530
 78D  C22  C21  single  1.492  0.020  1.492
 78D  C15  O5   double  1.206  0.020  1.206
 78D  C21  C20  double  1.336  0.020  1.336
 78D  C20  C19  single  1.453  0.020  1.453
 78D  C19  C18  double  1.336  0.020  1.336
 78D  C18  C17  single  1.495  0.020  1.495
 78D  C17  C16  single  1.519  0.020  1.519
 78D  O2   C5   double  1.206  0.020  1.206
 78D  N2   N1   single  1.408  0.020  1.408
 78D  N2   C4   single  1.456  0.020  1.456
 78D  C16  O1   single  1.434  0.020  1.434
 78D  C5   O1   single  1.324  0.020  1.324
 78D  C5   C4   single  1.511  0.020  1.511
 78D  N1   C3   single  1.457  0.020  1.457
 78D  C4   C1   single  1.536  0.020  1.536
 78D  C3   C2   single  1.522  0.020  1.522
 78D  C1   C2   single  1.523  0.020  1.523
 78D  N2   H1   single  0.890  0.020  1.040
 78D  C2   H2   single  0.970  0.020  1.090
 78D  C2   H3   single  0.970  0.020  1.090
 78D  C4   H4   single  0.970  0.020  1.090
 78D  C16  H6   single  0.970  0.020  1.090
 78D  C16  H7   single  0.970  0.020  1.090
 78D  C18  H9   single  0.930  0.020  1.080
 78D  C17  H12  single  0.970  0.020  1.090
 78D  C17  H13  single  0.970  0.020  1.090
 78D  C19  H18  single  0.930  0.020  1.080
 78D  C1   H19  single  0.970  0.020  1.090
 78D  C1   H20  single  0.970  0.020  1.090
 78D  C3   H21  single  0.970  0.020  1.090
 78D  C3   H22  single  0.970  0.020  1.090
 78D  C20  H26  single  0.930  0.020  1.080
 78D  C21  H27  single  0.930  0.020  1.080
 78D  C22  H31  single  0.970  0.020  1.090
 78D  C22  H32  single  0.970  0.020  1.090
 78D  C23  H33  single  0.970  0.020  1.090
 78D  C23  H34  single  0.970  0.020  1.090
 78D  C29  H39  single  0.970  0.020  1.090
 78D  C29  H40  single  0.970  0.020  1.090
 78D  C30  H41  single  0.970  0.020  1.090
 78D  C30  H42  single  0.970  0.020  1.090
 78D  C15  OXT  single  1.331  0.020  1.331
 78D  OXT  HXT  single  0.850  0.020  0.980
 78D  N1   H5   single  0.890  0.020  1.040

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
 78D  H1   N2   C4   110.47  3.000
 78D  H1   N2   N1   107.69  3.000
 78D  C4   N2   N1   114.60  3.000
 78D  H3   C2   H2   106.90  3.000
 78D  H3   C2   C3   109.66  3.000
 78D  H2   C2   C3   110.31  3.000
 78D  H3   C2   C1   109.69  3.000
 78D  H2   C2   C1   110.34  3.000
 78D  C3   C2   C1   109.89  3.000
 78D  H5   N1   C3   110.21  3.000
 78D  H5   N1   N2   107.50  3.000
 78D  C3   N1   N2   114.71  3.000
 78D  H4   C4   C1   107.88  3.000
 78D  H4   C4   C5   107.77  3.000
 78D  C1   C4   C5   110.38  3.000
 78D  H4   C4   N2   107.56  3.000
 78D  C1   C4   N2   113.98  3.000
 78D  C5   C4   N2   109.05  3.000
 78D  O2   C5   O1   123.93  3.000
 78D  O1   C5   C4   111.26  3.000
 78D  O2   C5   C4   124.79  3.000
 78D  H7   C16  H6   108.10  3.000
 78D  H7   C16  O1   110.02  3.000
 78D  H6   C16  O1   109.80  3.000
 78D  H7   C16  C17  110.69  3.000
 78D  H6   C16  C17  110.69  3.000
 78D  O1   C16  C17  107.55  3.000
 78D  H9   C18  C19  118.98  3.000
 78D  H9   C18  C17  116.54  3.000
 78D  C19  C18  C17  124.47  3.000
 78D  OXT  C15  C30  111.85  3.000
 78D  OXT  C15  O5   122.83  3.000
 78D  C30  C15  O5   125.32  3.000
 78D  H13  C17  H12  107.50  3.000
 78D  H13  C17  C18  109.59  3.000
 78D  H12  C17  C18  110.32  3.000
 78D  H13  C17  C16  108.79  3.000
 78D  H12  C17  C16  110.00  3.000
 78D  C18  C17  C16  110.57  3.000
 78D  H18  C19  C20  116.71  3.000
 78D  H18  C19  C18  119.15  3.000
 78D  C20  C19  C18  124.15  3.000
 78D  H20  C1   H19  107.29  3.000
 78D  H20  C1   C4   109.40  3.000
 78D  H19  C1   C4   110.40  3.000
 78D  H20  C1   C2   109.88  3.000
 78D  H19  C1   C2   110.75  3.000
 78D  C4   C1   C2   109.10  3.000
 78D  H22  C3   H21  106.77  3.000
 78D  H22  C3   N1   107.54  3.000
 78D  H21  C3   N1   107.99  3.000
 78D  H22  C3   C2   110.99  3.000
 78D  H21  C3   C2   109.49  3.000
 78D  N1   C3   C2   113.78  3.000
 78D  H26  C20  C21  119.36  3.000
 78D  H26  C20  C19  116.92  3.000
 78D  C21  C20  C19  123.71  3.000
 78D  C16  O1   C5   118.33  3.000
 78D  H27  C21  C22  116.18  3.000
 78D  H27  C21  C20  118.65  3.000
 78D  C22  C21  C20  125.15  3.000
 78D  H32  C22  H31  106.72  3.000
 78D  H32  C22  C23  109.63  3.000
 78D  H31  C22  C23  108.56  3.000
 78D  H32  C22  C21  110.19  3.000
 78D  H31  C22  C21  109.25  3.000
 78D  C23  C22  C21  112.32  3.000
 78D  H34  C23  H33  106.20  3.000
 78D  H34  C23  C29  109.54  3.000
 78D  H33  C23  C29  109.89  3.000
 78D  H34  C23  C22  109.46  3.000
 78D  H33  C23  C22  109.15  3.000
 78D  C29  C23  C22  112.40  3.000
 78D  H40  C29  H39  106.46  3.000
 78D  H40  C29  C30  109.83  3.000
 78D  H39  C29  C30  109.98  3.000
 78D  H40  C29  C23  109.49  3.000
 78D  H39  C29  C23  109.32  3.000
 78D  C30  C29  C23  111.62  3.000
 78D  H42  C30  H41  105.33  3.000
 78D  H42  C30  C29  110.51  3.000
 78D  H41  C30  C29  110.53  3.000
 78D  H42  C30  C15  108.10  3.000
 78D  H41  C30  C15  108.05  3.000
 78D  C29  C30  C15  113.92  3.000
 78D  HXT  OXT  C15  109.88  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
 78D  CONST_01  HXT  OXT  C15  O5      0.00   0.0  0
 78D  Var_01    C2   C3   N1   N2     50.54  30.0  1
 78D  Var_02    C1   C2   C3   N1    -52.73  30.0  1
 78D  Var_03    C3   N1   N2   C4    -48.64  30.0  1
 78D  Var_04    C3   C2   C1   C4     52.08  30.0  1
 78D  Var_05    C20  C19  C18  C17  -179.84   0.0  2
 78D  Var_06    C22  C21  C20  C19  -179.08   0.0  2
 78D  Var_07    C17  C16  O1   C5   -174.71  30.0  1
 78D  Var_08    C19  C18  C17  C16   115.74  30.0  1
 78D  Var_09    O2   C5   O1   C16    -1.82  30.0  1
 78D  Var_10    C21  C20  C19  C18  -179.88  30.0  2
 78D  Var_11    O1   C16  C17  C18   176.78  30.0  3
 78D  Var_12    C23  C29  C30  C15   179.97  30.0  3
 78D  Var_13    C23  C22  C21  C20   115.18  30.0  2
 78D  Var_14    C29  C23  C22  C21   175.25  30.0  1
 78D  Var_15    C29  C30  C15  O5     -0.51  30.0  2
 78D  Var_16    C30  C29  C23  C22   178.93  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
 78D  chir_01  C4  N2  C5  C1  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
 78D  plan-1  C15  0.020
 78D  plan-1  O5   0.020
 78D  plan-1  C30  0.020
 78D  plan-1  OXT  0.020
 78D  plan-1  HXT  0.020
 78D  plan-2  C19  0.020
 78D  plan-2  C20  0.020
 78D  plan-2  C21  0.020
 78D  plan-2  C22  0.020
 78D  plan-2  H26  0.020
 78D  plan-2  H27  0.020
 78D  plan-3  C18  0.020
 78D  plan-3  C17  0.020
 78D  plan-3  C19  0.020
 78D  plan-3  C20  0.020
 78D  plan-3  H9   0.020
 78D  plan-3  H18  0.020
 78D  plan-4  C4   0.020
 78D  plan-4  C5   0.020
 78D  plan-4  O1   0.020
 78D  plan-4  O2   0.020

