# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 08:44:56 2020
#   Inital geometry file: a 180 line input string
#   Ligand name: (5~{S},6~{R},7~{E},9~{E},11~{Z},14~{Z})-6-[(2~{R})-2-azanyl-3-(2-hydroxy-2-oxoethylamino)-3-oxidanylidene-propyl]sulfanyl-5-oxidanyl-icosa-7,9,11,14-tetraenoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC\C=C/C\C=C/C=C/C=C/[C@@H](SC[C@H](N)C(=O)NCC(O)=O)[C@@H](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
 LTD  LTD  '(5~{S},6~{R},7~{E},9~{E},11~{Z},14~{Z})-6-[(2~{R})-2-azanyl-3-(2-hydroxy-2-oxoethylamino)-3-oxidanylidene-propyl]sulfanyl-5-oxidanyl-icosa-7,9,11,14-tetraenoic acid'  ligand  72  34  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LTD
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
 LTD  O2   O  OC    -1  -0.634  -9.5984   1.8542  -2.5666
 LTD  C1   C  C      0   0.410  -8.8132   2.2928  -1.6989
 LTD  O1   O  O      0  -0.610  -8.9855   3.3120  -1.0006
 LTD  C2   C  CH2    0  -0.582  -7.5302   1.4748  -1.4731
 LTD  C3   C  CH2    0  -0.402  -6.4827   2.1148  -0.5761
 LTD  C4   C  CH2    0  -0.450  -5.2536   1.2271  -0.4147
 LTD  C5   C  CH1    0   0.073  -4.2154   1.7821   0.5540
 LTD  O3   O  OH1    0  -0.657  -3.7862   3.0745   0.1859
 LTD  C6   C  CH1    0  -0.498  -2.9967   0.8523   0.6971
 LTD  C7   C  C1     0  -0.135  -1.9084   1.4637   1.5062
 LTD  C8   C  C1     0  -0.254  -0.6285   1.5147   1.1185
 LTD  C9   C  C1     0  -0.245   0.4436   2.0461   1.9296
 LTD  C10  C  C1     0  -0.273   1.7276   2.0872   1.5305
 LTD  C11  C  C1     0  -0.253   2.8039   2.5933   2.3551
 LTD  C12  C  C1     0  -0.208   4.1013   2.6570   2.0231
 LTD  C13  C  CH2    0  -0.575   4.7249   2.2596   0.7190
 LTD  C14  C  C1     0  -0.206   5.3690   3.4467   0.0592
 LTD  C15  C  C1     0  -0.212   6.6513   3.5863  -0.2737
 LTD  C16  C  CH2    0  -0.491   7.7508   2.5827  -0.1233
 LTD  C17  C  CH2    0  -0.412   8.2602   2.0971  -1.4818
 LTD  C18  C  CH2    0  -0.407   9.3974   1.0896  -1.3717
 LTD  C19  C  CH2    0  -0.420   9.9045   0.6150  -2.7278
 LTD  C20  C  CH3    0  -0.661  11.0208  -0.4145  -2.6207
 LTD  O32  O  O      0  -0.599  -0.0465  -4.4508  -2.4917
 LTD  C21  C  C      0   0.399   0.8715  -4.8961  -1.7761
 LTD  O31  O  OC    -1  -0.609   1.9505  -5.3902  -2.1432
 LTD  CA3  C  CH2    0  -0.410   0.6589  -4.8393  -0.2484
 LTD  C22  C  C      0   0.524  -1.0140  -3.9303   1.3020
 LTD  O33  O  O      0  -0.507  -0.3832  -4.2136   2.3148
 LTD  CA2  C  CH1    0  -0.215  -2.3387  -3.1593   1.3816
 LTD  SG2  S  S2     0   0.002  -3.5329  -0.7058   1.5065
 LTD  N2   N  NH2    0  -0.773  -3.1029  -3.4308   2.5766
 LTD  H2   H  HCH2   0   0.220  -7.8207   0.5024  -1.0560
 LTD  H3   H  HCH2   0   0.213  -7.0899   1.2400  -2.4487
 LTD  H4   H  HCH2   0   0.208  -6.1910   3.0847  -0.9845
 LTD  H5   H  HCH2   0   0.204  -6.9148   2.3163   0.4082
 LTD  H6   H  HCH2   0   0.224  -5.5664   0.2380  -0.0688
 LTD  H7   H  HCH2   0   0.214  -4.7778   1.0633  -1.3909
 LTD  H8   H  HCH1   0   0.226  -4.6751   1.9024   1.5422
 LTD  H9   H  HOH1   0   0.442  -3.4232   3.0305  -0.7058
 LTD  H10  H  HCH1   0   0.280  -2.6251   0.5949  -0.3020
 LTD  H11  H  H      0   0.250  -2.1912   1.8444   2.4849
 LTD  H12  H  H      0   0.244  -0.3566   1.1229   0.1413
 LTD  H13  H  H      0   0.246   0.1795   2.4198   2.9160
 LTD  H14  H  H      0   0.248   1.9705   1.7096   0.5420
 LTD  H15  H  H      0   0.242   2.5182   2.9443   3.3425
 LTD  H16  H  H      0   0.246   4.7906   3.0581   2.7598
 LTD  H17  H  HCH2   0   0.256   5.4632   1.4736   0.8964
 LTD  H18  H  HCH2   0   0.255   3.9798   1.8323   0.0444
 LTD  H19  H  H      0   0.237   4.6955   4.2728  -0.1501
 LTD  H20  H  H      0   0.232   6.9443   4.5210  -0.7451
 LTD  H21  H  HCH2   0   0.230   8.5830   3.0385   0.4238
 LTD  H22  H  HCH2   0   0.230   7.4264   1.7247   0.4706
 LTD  H23  H  HCH2   0   0.216   7.4286   1.6490  -2.0347
 LTD  H24  H  HCH2   0   0.213   8.5908   2.9574  -2.0739
 LTD  H25  H  HCH2   0   0.209  10.2257   1.5324  -0.8077
 LTD  H26  H  HCH2   0   0.208   9.0608   0.2258  -0.7872
 LTD  H27  H  HCH2   0   0.211   9.0707   0.1920  -3.2965
 LTD  H28  H  HCH2   0   0.211  10.2558   1.4770  -3.3037
 LTD  H29  H  HCH3   0   0.226  11.3667  -0.7337  -3.6045
 LTD  H30  H  HCH3   0   0.216  11.8813  -0.0117  -2.0834
 LTD  H31  H  HCH3   0   0.216  10.6874  -1.3044  -2.0836
 LTD  H33  H  HCH2   0   0.241   0.7033  -5.8577   0.1509
 LTD  H34  H  HCH2   0   0.241   1.4886  -4.2923   0.2087
 LTD  H35  H  HNH1   0   0.388  -1.1577  -3.9647  -0.7367
 LTD  H36  H  HCH1   0   0.261  -2.9582  -3.4160   0.5177
 LTD  H37  H  HCH2   0   0.267  -1.2876  -1.3994   2.0788
 LTD  H38  H  HCH2   0   0.275  -1.5661  -1.4262   0.3375
 LTD  H39  H  HNH2   0   0.356  -3.4246  -4.3905   2.5728
 LTD  H40  H  HNH2   0   0.344  -2.5053  -3.3369   3.3899
 LTD  CB2  C  CH2    0  -0.533  -2.0086  -1.6706   1.3048
 LTD  N3   N  NH1    0  -0.624  -0.5999  -4.2154   0.0687

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
 LTD  O32  C21  deloc   1.246  0.020  1.246
 LTD  C20  C19  single  1.522  0.020  1.522
 LTD  C21  O31  deloc   1.242  0.020  1.242
 LTD  C21  CA3  single  1.543  0.020  1.543
 LTD  C19  C18  single  1.524  0.020  1.524
 LTD  CA3  N3   single  1.440  0.020  1.440
 LTD  C18  C17  single  1.523  0.020  1.523
 LTD  C17  C16  single  1.530  0.020  1.530
 LTD  N3   C22  single  1.332  0.020  1.332
 LTD  C11  C12  double  1.341  0.020  1.341
 LTD  C11  C10  single  1.447  0.020  1.447
 LTD  O3   C5   single  1.411  0.020  1.411
 LTD  O1   C1   deloc   1.247  0.020  1.247
 LTD  C12  C13  single  1.499  0.020  1.499
 LTD  O33  C22  double  1.226  0.020  1.226
 LTD  C9   C10  double  1.345  0.020  1.345
 LTD  C9   C8   single  1.446  0.020  1.446
 LTD  C22  CA2  single  1.535  0.020  1.535
 LTD  C16  C15  single  1.496  0.020  1.496
 LTD  C7   C8   double  1.338  0.020  1.338
 LTD  C7   C6   single  1.488  0.020  1.488
 LTD  C1   C2   single  1.538  0.020  1.538
 LTD  C1   O2   deloc   1.250  0.020  1.250
 LTD  C5   C4   single  1.525  0.020  1.525
 LTD  C5   C6   single  1.539  0.020  1.539
 LTD  SG2  C6   single  1.836  0.020  1.836
 LTD  SG2  CB2  single  1.815  0.020  1.815
 LTD  C3   C4   single  1.525  0.020  1.525
 LTD  C3   C2   single  1.520  0.020  1.520
 LTD  C13  C14  single  1.503  0.020  1.503
 LTD  C15  C14  double  1.332  0.020  1.332
 LTD  CA2  N2   single  1.444  0.020  1.444
 LTD  CA2  CB2  single  1.527  0.020  1.527
 LTD  C2   H2   single  0.970  0.020  1.090
 LTD  C2   H3   single  0.970  0.020  1.090
 LTD  C3   H4   single  0.970  0.020  1.090
 LTD  C3   H5   single  0.970  0.020  1.090
 LTD  C4   H6   single  0.970  0.020  1.090
 LTD  C4   H7   single  0.970  0.020  1.090
 LTD  C5   H8   single  0.970  0.020  1.090
 LTD  O3   H9   single  0.850  0.020  0.980
 LTD  C6   H10  single  0.970  0.020  1.090
 LTD  C7   H11  single  0.930  0.020  1.080
 LTD  C8   H12  single  0.930  0.020  1.080
 LTD  C9   H13  single  0.930  0.020  1.080
 LTD  C10  H14  single  0.930  0.020  1.080
 LTD  C11  H15  single  0.930  0.020  1.080
 LTD  C12  H16  single  0.930  0.020  1.080
 LTD  C13  H17  single  0.970  0.020  1.090
 LTD  C13  H18  single  0.970  0.020  1.090
 LTD  C14  H19  single  0.930  0.020  1.080
 LTD  C15  H20  single  0.930  0.020  1.080
 LTD  C16  H21  single  0.970  0.020  1.090
 LTD  C16  H22  single  0.970  0.020  1.090
 LTD  C17  H23  single  0.970  0.020  1.090
 LTD  C17  H24  single  0.970  0.020  1.090
 LTD  C18  H25  single  0.970  0.020  1.090
 LTD  C18  H26  single  0.970  0.020  1.090
 LTD  C19  H27  single  0.970  0.020  1.090
 LTD  C19  H28  single  0.970  0.020  1.090
 LTD  C20  H29  single  0.970  0.020  1.090
 LTD  C20  H30  single  0.970  0.020  1.090
 LTD  C20  H31  single  0.970  0.020  1.090
 LTD  CA3  H33  single  0.970  0.020  1.090
 LTD  CA3  H34  single  0.970  0.020  1.090
 LTD  N3   H35  single  0.860  0.020  1.020
 LTD  CA2  H36  single  0.970  0.020  1.090
 LTD  CB2  H37  single  0.970  0.020  1.090
 LTD  CB2  H38  single  0.970  0.020  1.090
 LTD  N2   H39  single  0.890  0.020  1.040
 LTD  N2   H40  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
 LTD  C2   C1   O1   117.87  3.000
 LTD  C2   C1   O2   116.07  3.000
 LTD  O1   C1   O2   126.06  3.000
 LTD  H3   C2   H2   104.77  3.000
 LTD  H3   C2   C3   109.80  3.000
 LTD  H2   C2   C3   109.34  3.000
 LTD  H3   C2   C1   108.56  3.000
 LTD  H2   C2   C1   107.83  3.000
 LTD  C3   C2   C1   115.94  3.000
 LTD  H5   C3   H4   106.17  3.000
 LTD  H5   C3   C4   109.30  3.000
 LTD  H4   C3   C4   109.96  3.000
 LTD  H5   C3   C2   109.66  3.000
 LTD  H4   C3   C2   109.71  3.000
 LTD  C4   C3   C2   111.89  3.000
 LTD  H7   C4   H6   105.68  3.000
 LTD  H7   C4   C5   108.91  3.000
 LTD  H6   C4   C5   108.84  3.000
 LTD  H7   C4   C3   110.00  3.000
 LTD  H6   C4   C3   109.24  3.000
 LTD  C5   C4   C3   113.85  3.000
 LTD  H8   C5   C6   108.32  3.000
 LTD  H8   C5   O3   105.20  3.000
 LTD  C6   C5   O3   109.68  3.000
 LTD  H8   C5   C4   109.09  3.000
 LTD  C6   C5   C4   112.23  3.000
 LTD  O3   C5   C4   112.01  3.000
 LTD  H9   O3   C5   108.31  3.000
 LTD  H10  C6   SG2  107.54  3.000
 LTD  H10  C6   C7   110.13  3.000
 LTD  SG2  C6   C7   108.83  3.000
 LTD  H10  C6   C5   108.98  3.000
 LTD  SG2  C6   C5   108.81  3.000
 LTD  C7   C6   C5   112.42  3.000
 LTD  H11  C7   C8   119.73  3.000
 LTD  H11  C7   C6   116.30  3.000
 LTD  C8   C7   C6   123.91  3.000
 LTD  H12  C8   C9   116.83  3.000
 LTD  H12  C8   C7   119.06  3.000
 LTD  C9   C8   C7   124.11  3.000
 LTD  H13  C9   C10  119.37  3.000
 LTD  H13  C9   C8   117.08  3.000
 LTD  C10  C9   C8   123.55  3.000
 LTD  H14  C10  C11  118.29  3.000
 LTD  H14  C10  C9   118.24  3.000
 LTD  C11  C10  C9   123.47  3.000
 LTD  H15  C11  C12  117.67  3.000
 LTD  H15  C11  C10  115.81  3.000
 LTD  C12  C11  C10  126.53  3.000
 LTD  H16  C12  C13  115.10  3.000
 LTD  H16  C12  C11  117.63  3.000
 LTD  C13  C12  C11  127.25  3.000
 LTD  H18  C13  H17  106.24  3.000
 LTD  H18  C13  C14  109.28  3.000
 LTD  H17  C13  C14  110.47  3.000
 LTD  H18  C13  C12  110.93  3.000
 LTD  H17  C13  C12  109.30  3.000
 LTD  C14  C13  C12  110.54  3.000
 LTD  H19  C14  C15  117.96  3.000
 LTD  H19  C14  C13  114.81  3.000
 LTD  C15  C14  C13  127.22  3.000
 LTD  H20  C15  C16  114.98  3.000
 LTD  H20  C15  C14  117.26  3.000
 LTD  C16  C15  C14  127.73  3.000
 LTD  H22  C16  H21  106.31  3.000
 LTD  H22  C16  C17  109.40  3.000
 LTD  H21  C16  C17  108.82  3.000
 LTD  H22  C16  C15  111.30  3.000
 LTD  H21  C16  C15  109.23  3.000
 LTD  C17  C16  C15  111.61  3.000
 LTD  H24  C17  H23  106.13  3.000
 LTD  H24  C17  C18  109.47  3.000
 LTD  H23  C17  C18  109.45  3.000
 LTD  H24  C17  C16  109.34  3.000
 LTD  H23  C17  C16  109.00  3.000
 LTD  C18  C17  C16  113.22  3.000
 LTD  H26  C18  H25  106.04  3.000
 LTD  H26  C18  C19  109.35  3.000
 LTD  H25  C18  C19  109.41  3.000
 LTD  H26  C18  C17  109.31  3.000
 LTD  H25  C18  C17  109.53  3.000
 LTD  C19  C18  C17  112.96  3.000
 LTD  H28  C19  H27  106.00  3.000
 LTD  H28  C19  C20  109.53  3.000
 LTD  H27  C19  C20  109.51  3.000
 LTD  H28  C19  C18  109.26  3.000
 LTD  H27  C19  C18  109.22  3.000
 LTD  C20  C19  C18  113.08  3.000
 LTD  H31  C20  H30  107.42  3.000
 LTD  H31  C20  H29  107.58  3.000
 LTD  H30  C20  H29  107.58  3.000
 LTD  H31  C20  C19  111.23  3.000
 LTD  H30  C20  C19  111.29  3.000
 LTD  H29  C20  C19  111.53  3.000
 LTD  CA3  C21  O31  115.26  3.000
 LTD  CA3  C21  O32  116.98  3.000
 LTD  O31  C21  O32  127.76  3.000
 LTD  H34  CA3  H33  106.37  3.000
 LTD  H34  CA3  N3   110.75  3.000
 LTD  H33  CA3  N3   110.98  3.000
 LTD  H34  CA3  C21  109.12  3.000
 LTD  H33  CA3  C21  108.73  3.000
 LTD  N3   CA3  C21  110.75  3.000
 LTD  CA2  C22  O33  121.14  3.000
 LTD  CA2  C22  N3   115.08  3.000
 LTD  O33  C22  N3   123.73  3.000
 LTD  H36  CA2  N2   108.05  3.000
 LTD  H36  CA2  CB2  108.15  3.000
 LTD  N2   CA2  CB2  109.84  3.000
 LTD  H36  CA2  C22  109.27  3.000
 LTD  CB2  CA2  C22  107.49  3.000
 LTD  N2   CA2  C22  113.90  3.000
 LTD  CB2  SG2  C6    99.02  3.000
 LTD  H40  N2   H39  106.15  3.000
 LTD  H40  N2   CA2  109.54  3.000
 LTD  H39  N2   CA2  110.08  3.000
 LTD  H38  CB2  H37  107.75  3.000
 LTD  H38  CB2  SG2  108.66  3.000
 LTD  H37  CB2  SG2  110.10  3.000
 LTD  H38  CB2  CA2  110.53  3.000
 LTD  H37  CB2  CA2  110.44  3.000
 LTD  SG2  CB2  CA2  109.33  3.000
 LTD  H35  N3   C22  120.86  3.000
 LTD  H35  N3   CA3  114.46  3.000
 LTD  C22  N3   CA3  124.64  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
 LTD  CONST_01  O33  C22  N3   CA3     0.00   0.0  0
 LTD  CONST_02  CA2  C22  N3   CA3   180.00   0.0  0
 LTD  CONST_03  H35  N3   C22  O33   180.00   0.0  0
 LTD  Var_01    C9   C8   C7   C6   -176.71   0.0  2
 LTD  Var_02    C11  C10  C9   C8   -178.63   0.0  2
 LTD  Var_03    C13  C12  C11  C10     1.92   0.0  2
 LTD  Var_04    C16  C15  C14  C13     2.60   0.0  2
 LTD  Var_05    C3   C2   C1   O2    171.10  30.0  3
 LTD  Var_06    C4   C3   C2   C1    179.94  30.0  1
 LTD  Var_07    C5   C4   C3   C2   -175.97  30.0  3
 LTD  Var_08    CA2  CB2  SG2  C6   -157.50  30.0  3
 LTD  Var_09    C10  C9   C8   C7    179.74  30.0  1
 LTD  Var_10    C12  C11  C10  C9    179.67  30.0  1
 LTD  Var_11    C14  C13  C12  C11   117.88  30.0  3
 LTD  Var_12    C15  C14  C13  C12   120.44  30.0  3
 LTD  Var_13    C17  C16  C15  C14   112.70  30.0  1
 LTD  Var_14    C18  C17  C16  C15   179.06  30.0  2
 LTD  Var_15    C19  C18  C17  C16  -179.73  30.0  1
 LTD  Var_16    C20  C19  C18  C17  -178.76  30.0  1
 LTD  Var_17    N3   CA3  C21  O32    -1.88  30.0  3
 LTD  Var_18    C22  N3   CA3  C21  -174.53  30.0  3
 LTD  Var_19    H29  C20  C19  C18  -179.80  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
 LTD  chir_01  C5   O3   C4   C6   negativ
 LTD  chir_02  C6   SG2  C7   C5   positiv
 LTD  chir_03  CA2  N2   CB2  C22  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
 LTD  plan-1  CA3  0.020
 LTD  plan-1  C22  0.020
 LTD  plan-1  O33  0.020
 LTD  plan-1  CA2  0.020
 LTD  plan-1  H35  0.020
 LTD  plan-1  N3   0.020
 LTD  plan-2  C6   0.020
 LTD  plan-2  C7   0.020
 LTD  plan-2  C8   0.020
 LTD  plan-2  C9   0.020
 LTD  plan-2  H11  0.020
 LTD  plan-2  H12  0.020
 LTD  plan-3  C13  0.020
 LTD  plan-3  C14  0.020
 LTD  plan-3  C15  0.020
 LTD  plan-3  C16  0.020
 LTD  plan-3  H19  0.020
 LTD  plan-3  H20  0.020
 LTD  plan-4  O2   0.020
 LTD  plan-4  C1   0.020
 LTD  plan-4  O1   0.020
 LTD  plan-4  C2   0.020
 LTD  plan-5  O32  0.020
 LTD  plan-5  C21  0.020
 LTD  plan-5  O31  0.020
 LTD  plan-5  CA3  0.020
 LTD  plan-6  C10  0.020
 LTD  plan-6  C11  0.020
 LTD  plan-6  C12  0.020
 LTD  plan-6  C13  0.020
 LTD  plan-6  H15  0.020
 LTD  plan-6  H16  0.020
 LTD  plan-7  C8   0.020
 LTD  plan-7  C9   0.020
 LTD  plan-7  C10  0.020
 LTD  plan-7  C11  0.020
 LTD  plan-7  H13  0.020
 LTD  plan-7  H14  0.020

