# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 18:45:55 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: (9~{Z},12~{Z},15~{Z},18~{Z},21~{Z})-5-oxidanylidenetetracosa-9,12,15,18,21-pentaen-6-ynoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC\C=C/C/C=C\C\C=C/C/C=C\C\C=C/CC#CC(=O)CCCC(O)=O
#
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
 EJL  EJL  '(9~{Z},12~{Z},15~{Z},18~{Z},21~{Z})-5-oxidanylidenetetracosa-9,12,15,18,21-pentaen-6-ynoic acid'  ligand  58  27  .  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_EJL
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
 EJL  C24  C  CH3    0  -0.657  -12.9500  -1.4755   0.7349
 EJL  C23  C  CH2    0  -0.491  -11.7673  -1.8411  -0.1604
 EJL  C22  C  C1     0  -0.210  -11.1399  -0.6311  -0.7789
 EJL  C21  C  C1     0  -0.206   -9.9124  -0.1567  -0.5726
 EJL  C20  C  CH2    0  -0.579   -8.8460  -0.7489   0.3051
 EJL  C19  C  C1     0  -0.203   -7.7609  -1.3645  -0.5314
 EJL  C18  C  C1     0  -0.203   -6.5170  -0.9182  -0.6953
 EJL  C17  C  CH2    0  -0.581   -5.8897   0.2854  -0.0519
 EJL  C16  C  C1     0  -0.203   -4.8701  -0.1357   0.9675
 EJL  C15  C  C1     0  -0.204   -3.5449  -0.0499   0.8691
 EJL  C14  C  CH2    0  -0.579   -2.7515   0.5196  -0.2717
 EJL  C13  C  C1     0  -0.198   -2.1075   1.8163   0.1265
 EJL  C12  C  C1     0  -0.207   -0.8066   2.0652   0.2627
 EJL  C11  C  CH2    0  -0.589    0.3320   1.1165   0.0145
 EJL  C10  C  C1     0  -0.186    1.0622   1.5025  -1.2386
 EJL  C9   C  C1     0  -0.228    2.2830   2.0186  -1.3474
 EJL  C8   C  CH2    0  -0.683    3.2303   2.3216  -0.2193
 EJL  C7   C  CSP    0   0.136    4.4854   1.5980  -0.3590
 EJL  C6   C  CSP    0   0.027    5.5176   0.9923  -0.5037
 EJL  C5   C  C      0   0.228    6.7708   0.2855  -0.6717
 EJL  O2   O  O      0  -0.388    6.9951  -0.3364  -1.6874
 EJL  C4   C  CH2    0  -0.574    7.7265   0.3896   0.4816
 EJL  C3   C  CH2    0  -0.414    9.0710  -0.2863   0.2664
 EJL  C2   C  CH2    0  -0.586    9.9699  -0.1183   1.4808
 EJL  C1   C  C      0   0.413   11.3701  -0.7484   1.3718
 EJL  O1'  O  O      0  -0.608   11.6629  -1.3411   0.3151
 EJL  O1   O  OC    -1  -0.632   12.1067  -0.6098   2.3712
 EJL  H1   H  HCH3   0   0.223  -12.6278  -0.8629   1.5779
 EJL  H2   H  HCH3   0   0.222  -13.7033  -0.9097   0.1844
 EJL  H3   H  HCH3   0   0.229  -13.4314  -2.3692   1.1333
 EJL  H4   H  HCH2   0   0.232  -11.0367  -2.4153   0.4115
 EJL  H5   H  HCH2   0   0.233  -12.1193  -2.5019  -0.9585
 EJL  H6   H  H      0   0.231  -11.7836  -0.0772  -1.4575
 EJL  H7   H  H      0   0.235   -9.6171   0.7420  -1.1068
 EJL  H8   H  HCH2   0   0.251   -8.4376   0.0294   0.9533
 EJL  H9   H  HCH2   0   0.253   -9.2687  -1.5107   0.9638
 EJL  H10  H  H      0   0.239   -8.0537  -2.2592  -1.0735
 EJL  H11  H  H      0   0.239   -5.8549  -1.4848  -1.3435
 EJL  H12  H  HCH2   0   0.253   -5.4327   0.9070  -0.8247
 EJL  H13  H  HCH2   0   0.255   -6.6470   0.9032   0.4352
 EJL  H14  H  H      0   0.239   -5.2826  -0.5811   1.8681
 EJL  H15  H  H      0   0.240   -2.9514  -0.4089   1.7052
 EJL  H16  H  HCH2   0   0.255   -1.9976  -0.2078  -0.5807
 EJL  H17  H  HCH2   0   0.253   -3.3894   0.6889  -1.1424
 EJL  H18  H  H      0   0.241   -2.8017   2.6238   0.3408
 EJL  H19  H  H      0   0.243   -0.5093   3.0665   0.5596
 EJL  H20  H  HCH2   0   0.258    0.9998   1.1230   0.8787
 EJL  H21  H  HCH2   0   0.260   -0.0310   0.0919  -0.0887
 EJL  H22  H  H      0   0.250    0.4992   1.3603  -2.1562
 EJL  H23  H  H      0   0.256    2.6578   2.2561  -2.3370
 EJL  H24  H  HCH2   0   0.300    3.4601   3.3924  -0.2053
 EJL  H25  H  HCH2   0   0.293    2.7966   2.0952   0.7564
 EJL  H26  H  HCH2   0   0.270    7.8518   1.4546   0.7087
 EJL  H27  H  HCH2   0   0.273    7.2146  -0.0201   1.3612
 EJL  H28  H  HCH2   0   0.220    8.9229  -1.3474   0.0569
 EJL  H29  H  HCH2   0   0.219    9.5569   0.1354  -0.6160
 EJL  H30  H  HCH2   0   0.221   10.0923   0.9478   1.7050
 EJL  H31  H  HCH2   0   0.221    9.4771  -0.5366   2.3662

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
 EJL  C21  C22  double  1.332  0.020  1.332
 EJL  C21  C20  single  1.503  0.020  1.503
 EJL  C16  C15  double  1.332  0.020  1.332
 EJL  C16  C17  single  1.502  0.020  1.502
 EJL  C22  C23  single  1.497  0.020  1.497
 EJL  C19  C18  double  1.332  0.020  1.332
 EJL  C19  C20  single  1.502  0.020  1.502
 EJL  C24  C23  single  1.528  0.020  1.528
 EJL  C18  C17  single  1.502  0.020  1.502
 EJL  C15  C14  single  1.502  0.020  1.502
 EJL  C14  C13  single  1.502  0.020  1.502
 EJL  O2   C5   double  1.212  0.020  1.212
 EJL  C13  C12  double  1.332  0.020  1.332
 EJL  C5   C6   single  1.449  0.020  1.449
 EJL  C5   C4   single  1.501  0.020  1.501
 EJL  C11  C12  single  1.503  0.020  1.503
 EJL  C11  C10  single  1.501  0.020  1.501
 EJL  C6   C7   triple  1.206  0.020  1.206
 EJL  C7   C8   single  1.455  0.020  1.455
 EJL  C4   C3   single  1.520  0.020  1.520
 EJL  C8   C9   single  1.504  0.020  1.504
 EJL  C10  C9   double  1.330  0.020  1.330
 EJL  C3   C2   single  1.520  0.020  1.520
 EJL  C2   C1   single  1.539  0.020  1.539
 EJL  C1   O1'  deloc   1.246  0.020  1.246
 EJL  C1   O1   deloc   1.249  0.020  1.249
 EJL  C24  H1   single  0.970  0.020  1.090
 EJL  C24  H2   single  0.970  0.020  1.090
 EJL  C24  H3   single  0.970  0.020  1.090
 EJL  C23  H4   single  0.970  0.020  1.090
 EJL  C23  H5   single  0.970  0.020  1.090
 EJL  C22  H6   single  0.930  0.020  1.080
 EJL  C21  H7   single  0.930  0.020  1.080
 EJL  C20  H8   single  0.970  0.020  1.090
 EJL  C20  H9   single  0.970  0.020  1.090
 EJL  C19  H10  single  0.930  0.020  1.080
 EJL  C18  H11  single  0.930  0.020  1.080
 EJL  C17  H12  single  0.970  0.020  1.090
 EJL  C17  H13  single  0.970  0.020  1.090
 EJL  C16  H14  single  0.930  0.020  1.080
 EJL  C15  H15  single  0.930  0.020  1.080
 EJL  C14  H16  single  0.970  0.020  1.090
 EJL  C14  H17  single  0.970  0.020  1.090
 EJL  C13  H18  single  0.930  0.020  1.080
 EJL  C12  H19  single  0.930  0.020  1.080
 EJL  C11  H20  single  0.970  0.020  1.090
 EJL  C11  H21  single  0.970  0.020  1.090
 EJL  C10  H22  single  0.930  0.020  1.080
 EJL  C9   H23  single  0.930  0.020  1.080
 EJL  C8   H24  single  0.970  0.020  1.090
 EJL  C8   H25  single  0.970  0.020  1.090
 EJL  C4   H26  single  0.970  0.020  1.090
 EJL  C4   H27  single  0.970  0.020  1.090
 EJL  C3   H28  single  0.970  0.020  1.090
 EJL  C3   H29  single  0.970  0.020  1.090
 EJL  C2   H30  single  0.970  0.020  1.090
 EJL  C2   H31  single  0.970  0.020  1.090

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
 EJL  H3   C24  H2   107.73  3.000
 EJL  H3   C24  H1   107.96  3.000
 EJL  H2   C24  H1   107.62  3.000
 EJL  H3   C24  C23  111.08  3.000
 EJL  H2   C24  C23  111.27  3.000
 EJL  H1   C24  C23  111.02  3.000
 EJL  H5   C23  H4   106.26  3.000
 EJL  H5   C23  C22  108.76  3.000
 EJL  H4   C23  C22  111.19  3.000
 EJL  H5   C23  C24  108.84  3.000
 EJL  H4   C23  C24  109.70  3.000
 EJL  C22  C23  C24  111.91  3.000
 EJL  H6   C22  C21  117.44  3.000
 EJL  H6   C22  C23  114.95  3.000
 EJL  C21  C22  C23  127.60  3.000
 EJL  H7   C21  C20  114.85  3.000
 EJL  H7   C21  C22  117.97  3.000
 EJL  C20  C21  C22  127.16  3.000
 EJL  H9   C20  H8   106.48  3.000
 EJL  H9   C20  C19  109.24  3.000
 EJL  H8   C20  C19  110.64  3.000
 EJL  H9   C20  C21  110.64  3.000
 EJL  H8   C20  C21  109.34  3.000
 EJL  C19  C20  C21  110.42  3.000
 EJL  H10  C19  C18  117.80  3.000
 EJL  H10  C19  C20  114.88  3.000
 EJL  C18  C19  C20  127.29  3.000
 EJL  H11  C18  C17  114.78  3.000
 EJL  H11  C18  C19  117.91  3.000
 EJL  C17  C18  C19  127.30  3.000
 EJL  H13  C17  H12  106.49  3.000
 EJL  H13  C17  C16  109.06  3.000
 EJL  H12  C17  C16  110.84  3.000
 EJL  H13  C17  C18  110.78  3.000
 EJL  H12  C17  C18  109.13  3.000
 EJL  C16  C17  C18  110.46  3.000
 EJL  H14  C16  C15  117.75  3.000
 EJL  H14  C16  C17  114.83  3.000
 EJL  C15  C16  C17  127.40  3.000
 EJL  H15  C15  C14  114.92  3.000
 EJL  H15  C15  C16  117.75  3.000
 EJL  C14  C15  C16  127.32  3.000
 EJL  H17  C14  H16  106.30  3.000
 EJL  H17  C14  C13  109.15  3.000
 EJL  H16  C14  C13  110.74  3.000
 EJL  H17  C14  C15  110.84  3.000
 EJL  H16  C14  C15  109.09  3.000
 EJL  C13  C14  C15  110.65  3.000
 EJL  H18  C13  C12  117.73  3.000
 EJL  H18  C13  C14  114.85  3.000
 EJL  C12  C13  C14  127.41  3.000
 EJL  H19  C12  C11  114.83  3.000
 EJL  H19  C12  C13  117.89  3.000
 EJL  C11  C12  C13  127.26  3.000
 EJL  H21  C11  H20  106.48  3.000
 EJL  H21  C11  C10  108.92  3.000
 EJL  H20  C11  C10  111.20  3.000
 EJL  H21  C11  C12  110.86  3.000
 EJL  H20  C11  C12  109.20  3.000
 EJL  C10  C11  C12  110.13  3.000
 EJL  H22  C10  C9   117.24  3.000
 EJL  H22  C10  C11  114.80  3.000
 EJL  C9   C10  C11  127.93  3.000
 EJL  H23  C9   C8   115.00  3.000
 EJL  H23  C9   C10  118.48  3.000
 EJL  C8   C9   C10  126.52  3.000
 EJL  H25  C8   H24  105.95  3.000
 EJL  H25  C8   C7   108.98  3.000
 EJL  H24  C8   C7   107.84  3.000
 EJL  H25  C8   C9   112.24  3.000
 EJL  H24  C8   C9   109.80  3.000
 EJL  C7   C8   C9   111.78  3.000
 EJL  C6   C7   C8   180.00  3.000
 EJL  C5   C6   C7   180.00  3.000
 EJL  C4   C5   O2   124.17  3.000
 EJL  C4   C5   C6   115.33  3.000
 EJL  O2   C5   C6   120.51  3.000
 EJL  H27  C4   H26  104.48  3.000
 EJL  H27  C4   C3   111.11  3.000
 EJL  H26  C4   C3   111.12  3.000
 EJL  H27  C4   C5   107.03  3.000
 EJL  H26  C4   C5   107.41  3.000
 EJL  C3   C4   C5   115.05  3.000
 EJL  H29  C3   H28  106.30  3.000
 EJL  H29  C3   C2   109.86  3.000
 EJL  H28  C3   C2   109.93  3.000
 EJL  H29  C3   C4   109.65  3.000
 EJL  H28  C3   C4   109.84  3.000
 EJL  C2   C3   C4   111.14  3.000
 EJL  H31  C2   H30  104.84  3.000
 EJL  H31  C2   C1   108.05  3.000
 EJL  H30  C2   C1   108.12  3.000
 EJL  H31  C2   C3   109.71  3.000
 EJL  H30  C2   C3   109.68  3.000
 EJL  C1   C2   C3   115.85  3.000
 EJL  O1   C1   O1'  126.33  3.000
 EJL  O1   C1   C2   115.74  3.000
 EJL  O1'  C1   C2   117.93  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
 EJL  Var_01  C20  C21  C22  C23     1.90   0.0  2
 EJL  Var_02  C17  C18  C19  C20     1.92   0.0  2
 EJL  Var_03  C14  C15  C16  C17     1.62   0.0  2
 EJL  Var_04  C11  C12  C13  C14     1.78   0.0  2
 EJL  Var_05  C8   C9   C10  C11     0.80   0.0  2
 EJL  Var_06  C21  C22  C23  C24   114.92  30.0  1
 EJL  Var_07  C19  C20  C21  C22   107.35  30.0  3
 EJL  Var_08  C18  C19  C20  C21   109.39  30.0  1
 EJL  Var_09  C16  C17  C18  C19   109.17  30.0  3
 EJL  Var_10  C15  C16  C17  C18   107.46  30.0  1
 EJL  Var_11  C13  C14  C15  C16   109.55  30.0  3
 EJL  Var_12  C12  C13  C14  C15   113.39  30.0  3
 EJL  Var_13  C10  C11  C12  C13   107.90  30.0  2
 EJL  Var_14  C9   C10  C11  C12   109.94  30.0  3
 EJL  Var_15  C7   C8   C9   C10   121.12  30.0  2
 EJL  Var_16  O2   C5   C6   C7   -128.00  30.0  1
 EJL  Var_17  C3   C4   C5   C6   -176.60  30.0  3
 EJL  Var_18  C2   C3   C4   C5    179.59  30.0  3
 EJL  Var_19  C1   C2   C3   C4   -179.26  30.0  3
 EJL  Var_20  O1'  C1   C2   C3     -0.00  30.0  3
 EJL  Var_21  H1   C24  C23  C22   -63.06  30.0  3

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
 EJL  plan-1  C6   0.020
 EJL  plan-1  C5   0.020
 EJL  plan-1  O2   0.020
 EJL  plan-1  C4   0.020
 EJL  plan-2  C2   0.020
 EJL  plan-2  C1   0.020
 EJL  plan-2  O1'  0.020
 EJL  plan-2  O1   0.020
 EJL  plan-3  C23  0.020
 EJL  plan-3  C22  0.020
 EJL  plan-3  C21  0.020
 EJL  plan-3  C20  0.020
 EJL  plan-3  H6   0.020
 EJL  plan-3  H7   0.020
 EJL  plan-4  C17  0.020
 EJL  plan-4  C16  0.020
 EJL  plan-4  C15  0.020
 EJL  plan-4  C14  0.020
 EJL  plan-4  H14  0.020
 EJL  plan-4  H15  0.020
 EJL  plan-5  C20  0.020
 EJL  plan-5  C19  0.020
 EJL  plan-5  C18  0.020
 EJL  plan-5  C17  0.020
 EJL  plan-5  H10  0.020
 EJL  plan-5  H11  0.020
 EJL  plan-6  C14  0.020
 EJL  plan-6  C13  0.020
 EJL  plan-6  C12  0.020
 EJL  plan-6  C11  0.020
 EJL  plan-6  H18  0.020
 EJL  plan-6  H19  0.020
 EJL  plan-7  C11  0.020
 EJL  plan-7  C10  0.020
 EJL  plan-7  C9   0.020
 EJL  plan-7  C8   0.020
 EJL  plan-7  H22  0.020
 EJL  plan-7  H23  0.020

