# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 08:26:33 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 2-[(~{E})-[(~{E})-16-azido-2-oxidanylidene-hexadec-3-enylidene]amino]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CN=CC(=O)/C=C/CCCCCCCCCCCCN=[N+]=[N-]
#
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
 8XO  8XO  '2-[(~{E})-[(~{E})-16-azido-2-oxidanylidene-hexadec-3-enylidene]amino]ethanoic acid'  ligand  55  25  .  2021-08-06  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8XO
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
 8XO  C15  C  C1     0  -0.106   -7.6777  -0.5580   0.1294
 8XO  C14  C  C      0   0.316   -6.6361   0.3934  -0.3956
 8XO  C13  C  C1     0  -0.383   -5.3816   0.4085   0.3633
 8XO  C12  C  C1     0  -0.115   -4.3503   1.1963   0.0395
 8XO  C16  C  CH2    0  -0.438   -9.7074  -1.6503   0.0294
 8XO  C11  C  CH2    0  -0.497   -3.0578   1.2398   0.7714
 8XO  O2   O  O      0  -0.431  -11.3044   0.1518  -0.0650
 8XO  C17  C  C      0   0.538  -11.0680  -1.0062   0.1541
 8XO  O1   O  OH1    0  -0.592  -11.9739  -1.8921   0.5446
 8XO  N    N  N      0  -0.291   -8.7562  -0.7151  -0.5000
 8XO  O    O  O      0  -0.392   -6.8549   1.0772  -1.3738
 8XO  C10  C  CH2    0  -0.423   -1.8636   0.9393  -0.1387
 8XO  C9   C  CH2    0  -0.415   -0.5436   0.9721   0.6209
 8XO  C8   C  CH2    0  -0.414    0.6694   0.7355  -0.2695
 8XO  C7   C  CH2    0  -0.412    1.9784   0.6911   0.5098
 8XO  C    C  CH2    0  -0.412    3.2048   0.5169  -0.3767
 8XO  C1   C  CH2    0  -0.412    4.5058   0.4224   0.4107
 8XO  C2   C  CH2    0  -0.412    5.7383   0.2918  -0.4752
 8XO  C3   C  CH2    0  -0.412    7.0354   0.1726   0.3148
 8XO  C4   C  CH2    0  -0.426    8.2686   0.0707  -0.5740
 8XO  C5   C  CH2    0  -0.426    9.5621  -0.0500   0.2221
 8XO  C6   C  CH2    0  -0.307   10.7753  -0.1554  -0.6893
 8XO  N1   N  N      0  -0.356   12.0281  -0.1724   0.0810
 8XO  N2   N  N      1   0.349   12.5379  -1.2555   0.2794
 8XO  N3   N  N     -1  -0.235   13.0897  -2.2101   0.5079
 8XO  H1   H  H      0   0.252   -7.4436  -1.0850   1.0601
 8XO  H2   H  H      0   0.266   -5.3069  -0.2563   1.2173
 8XO  H3   H  H      0   0.270   -4.4404   1.8550  -0.8207
 8XO  H4   H  HCH2   0   0.269   -9.4258  -2.0743   1.0025
 8XO  H5   H  HCH2   0   0.304   -9.7922  -2.4903  -0.6676
 8XO  H6   H  HCH2   0   0.252   -2.9321   2.2460   1.1873
 8XO  H7   H  HCH2   0   0.244   -3.0757   0.5456   1.6153
 8XO  H8   H  HOH1   0   0.486  -12.8404  -1.4670   0.6323
 8XO  H9   H  HCH2   0   0.226   -1.9955  -0.0431  -0.6020
 8XO  H10  H  HCH2   0   0.224   -1.8387   1.6664  -0.9567
 8XO  H11  H  HCH2   0   0.213   -0.4396   1.9387   1.1257
 8XO  H12  H  HCH2   0   0.213   -0.5666   0.2169   1.4142
 8XO  H13  H  HCH2   0   0.209    0.5437  -0.2046  -0.8181
 8XO  H14  H  HCH2   0   0.209    0.7226   1.5241  -1.0282
 8XO  H15  H  HCH2   0   0.207    2.0840   1.6108   1.0963
 8XO  H16  H  HCH2   0   0.208    1.9353  -0.1268   1.2378
 8XO  H17  H  HCH2   0   0.207    3.0869  -0.3835  -0.9902
 8XO  H18  H  HCH2   0   0.207    3.2659   1.3549  -1.0803
 8XO  H19  H  HCH2   0   0.207    4.6106   1.3075   1.0484
 8XO  H20  H  HCH2   0   0.207    4.4553  -0.4349   1.0914
 8XO  H21  H  HCH2   0   0.208    5.6276  -0.5834  -1.1253
 8XO  H22  H  HCH2   0   0.208    5.7983   1.1581  -1.1437
 8XO  H23  H  HCH2   0   0.210    7.1385   1.0381   0.9788
 8XO  H24  H  HCH2   0   0.211    6.9835  -0.7053   0.9681
 8XO  H25  H  HCH2   0   0.216    8.1648  -0.7931  -1.2398
 8XO  H26  H  HCH2   0   0.216    8.3212   0.9508  -1.2241
 8XO  H27  H  HCH2   0   0.229    9.6773   0.8184   0.8772
 8XO  H28  H  HCH2   0   0.227    9.5179  -0.9303   0.8704
 8XO  H29  H  HCH2   0   0.247   10.6941  -1.0383  -1.3293
 8XO  H30  H  HCH2   0   0.252   10.8315   0.7152  -1.3431

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
 8XO  C3   C2   single  1.523  0.020  1.523
 8XO  C3   C4   single  1.524  0.020  1.524
 8XO  C1   C2   single  1.523  0.020  1.523
 8XO  C1   C    single  1.524  0.020  1.524
 8XO  C7   C    single  1.523  0.020  1.523
 8XO  C7   C8   single  1.524  0.020  1.524
 8XO  C4   C5   single  1.524  0.020  1.524
 8XO  C5   C6   single  1.521  0.020  1.521
 8XO  C8   C9   single  1.523  0.020  1.523
 8XO  C9   C10  single  1.523  0.020  1.523
 8XO  C6   N1   single  1.471  0.020  1.471
 8XO  N1   N2   double  1.213  0.020  1.213
 8XO  C10  C11  single  1.531  0.020  1.531
 8XO  N2   N3   double  1.126  0.020  1.126
 8XO  C11  C12  single  1.486  0.020  1.486
 8XO  C12  C13  double  1.338  0.020  1.338
 8XO  C13  C14  single  1.466  0.020  1.466
 8XO  C14  C15  single  1.505  0.020  1.505
 8XO  C14  O    double  1.213  0.020  1.213
 8XO  C15  N    double  1.259  0.020  1.259
 8XO  N    C16  single  1.435  0.020  1.435
 8XO  C16  C17  single  1.511  0.020  1.511
 8XO  C17  O2   double  1.202  0.020  1.202
 8XO  C17  O1   single  1.326  0.020  1.326
 8XO  C15  H1   single  0.930  0.020  1.080
 8XO  C13  H2   single  0.930  0.020  1.080
 8XO  C12  H3   single  0.930  0.020  1.080
 8XO  C16  H4   single  0.970  0.020  1.090
 8XO  C16  H5   single  0.970  0.020  1.090
 8XO  C11  H6   single  0.970  0.020  1.090
 8XO  C11  H7   single  0.970  0.020  1.090
 8XO  O1   H8   single  0.850  0.020  0.980
 8XO  C10  H9   single  0.970  0.020  1.090
 8XO  C10  H10  single  0.970  0.020  1.090
 8XO  C9   H11  single  0.970  0.020  1.090
 8XO  C9   H12  single  0.970  0.020  1.090
 8XO  C8   H13  single  0.970  0.020  1.090
 8XO  C8   H14  single  0.970  0.020  1.090
 8XO  C7   H15  single  0.970  0.020  1.090
 8XO  C7   H16  single  0.970  0.020  1.090
 8XO  C    H17  single  0.970  0.020  1.090
 8XO  C    H18  single  0.970  0.020  1.090
 8XO  C1   H19  single  0.970  0.020  1.090
 8XO  C1   H20  single  0.970  0.020  1.090
 8XO  C2   H21  single  0.970  0.020  1.090
 8XO  C2   H22  single  0.970  0.020  1.090
 8XO  C3   H23  single  0.970  0.020  1.090
 8XO  C3   H24  single  0.970  0.020  1.090
 8XO  C4   H25  single  0.970  0.020  1.090
 8XO  C4   H26  single  0.970  0.020  1.090
 8XO  C5   H27  single  0.970  0.020  1.090
 8XO  C5   H28  single  0.970  0.020  1.090
 8XO  C6   H29  single  0.970  0.020  1.090
 8XO  C6   H30  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
 8XO  H1   C15  N    123.25  3.000
 8XO  H1   C15  C14  116.92  3.000
 8XO  N    C15  C14  119.83  3.000
 8XO  O    C14  C13  124.45  3.000
 8XO  O    C14  C15  120.84  3.000
 8XO  C13  C14  C15  114.71  3.000
 8XO  H2   C13  C12  119.90  3.000
 8XO  H2   C13  C14  117.39  3.000
 8XO  C12  C13  C14  122.72  3.000
 8XO  H3   C12  C11  116.36  3.000
 8XO  H3   C12  C13  118.98  3.000
 8XO  C11  C12  C13  124.66  3.000
 8XO  H5   C16  H4   106.73  3.000
 8XO  H5   C16  N    108.45  3.000
 8XO  H4   C16  N    114.11  3.000
 8XO  H5   C16  C17  108.06  3.000
 8XO  H4   C16  C17  108.82  3.000
 8XO  N    C16  C17  110.46  3.000
 8XO  H7   C11  H6   106.98  3.000
 8XO  H7   C11  C10  110.30  3.000
 8XO  H6   C11  C10  108.44  3.000
 8XO  H7   C11  C12  110.33  3.000
 8XO  H6   C11  C12  108.28  3.000
 8XO  C10  C11  C12  112.33  3.000
 8XO  O1   C17  O2   124.26  3.000
 8XO  O1   C17  C16  110.78  3.000
 8XO  O2   C17  C16  124.96  3.000
 8XO  H8   O1   C17  110.14  3.000
 8XO  C16  N    C15  117.70  3.000
 8XO  H10  C10  H9   106.42  3.000
 8XO  H10  C10  C9   109.79  3.000
 8XO  H9   C10  C9   109.56  3.000
 8XO  H10  C10  C11  109.36  3.000
 8XO  H9   C10  C11  109.51  3.000
 8XO  C9   C10  C11  112.04  3.000
 8XO  H12  C9   H11  106.05  3.000
 8XO  H12  C9   C8   109.45  3.000
 8XO  H11  C9   C8   109.32  3.000
 8XO  H12  C9   C10  109.15  3.000
 8XO  H11  C9   C10  109.33  3.000
 8XO  C8   C9   C10  113.28  3.000
 8XO  H14  C8   H13  106.05  3.000
 8XO  H14  C8   C7   109.47  3.000
 8XO  H13  C8   C7   109.24  3.000
 8XO  H14  C8   C9   109.37  3.000
 8XO  H13  C8   C9   109.55  3.000
 8XO  C7   C8   C9   112.93  3.000
 8XO  H16  C7   H15  105.94  3.000
 8XO  H16  C7   C    109.45  3.000
 8XO  H15  C7   C    109.26  3.000
 8XO  H16  C7   C8   109.13  3.000
 8XO  H15  C7   C8   109.39  3.000
 8XO  C    C7   C8   113.41  3.000
 8XO  H18  C    H17  105.96  3.000
 8XO  H18  C    C1   109.37  3.000
 8XO  H17  C    C1   109.28  3.000
 8XO  H18  C    C7   109.33  3.000
 8XO  H17  C    C7   109.46  3.000
 8XO  C1   C    C7   113.19  3.000
 8XO  H20  C1   H19  105.94  3.000
 8XO  H20  C1   C2   109.36  3.000
 8XO  H19  C1   C2   109.28  3.000
 8XO  H20  C1   C    109.28  3.000
 8XO  H19  C1   C    109.40  3.000
 8XO  C2   C1   C    113.31  3.000
 8XO  H22  C2   H21  105.96  3.000
 8XO  H22  C2   C3   109.37  3.000
 8XO  H21  C2   C3   109.34  3.000
 8XO  H22  C2   C1   109.34  3.000
 8XO  H21  C2   C1   109.37  3.000
 8XO  C3   C2   C1   113.20  3.000
 8XO  H24  C3   H23  106.02  3.000
 8XO  H24  C3   C4   109.43  3.000
 8XO  H23  C3   C4   109.28  3.000
 8XO  H24  C3   C2   109.37  3.000
 8XO  H23  C3   C2   109.43  3.000
 8XO  C4   C3   C2   113.07  3.000
 8XO  H26  C4   H25  106.10  3.000
 8XO  H26  C4   C5   109.45  3.000
 8XO  H25  C4   C5   109.61  3.000
 8XO  H26  C4   C3   109.35  3.000
 8XO  H25  C4   C3   109.31  3.000
 8XO  C5   C4   C3   112.81  3.000
 8XO  H28  C5   H27  106.74  3.000
 8XO  H28  C5   C6   109.36  3.000
 8XO  H27  C5   C6   109.27  3.000
 8XO  H28  C5   C4   109.81  3.000
 8XO  H27  C5   C4   109.84  3.000
 8XO  C6   C5   C4   111.69  3.000
 8XO  H30  C6   H29  107.32  3.000
 8XO  H30  C6   N1   106.23  3.000
 8XO  H29  C6   N1   111.13  3.000
 8XO  H30  C6   C5   110.19  3.000
 8XO  H29  C6   C5   110.33  3.000
 8XO  N1   C6   C5   111.49  3.000
 8XO  N2   N1   C6   116.99  3.000
 8XO  N3   N2   N1   174.73  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
 8XO  CONST_01  H8   O1   C17  C16   180.00   0.0  0
 8XO  Var_01    C11  C12  C13  C14  -179.56   0.0  2
 8XO  Var_02    C12  C13  C14  C15  -179.81  30.0  2
 8XO  Var_03    C17  C16  N    C15   128.37  30.0  3
 8XO  Var_04    C10  C11  C12  C13   122.93  30.0  2
 8XO  Var_05    N    C15  C14  C13  -175.24  30.0  2
 8XO  Var_06    C9   C10  C11  C12  -179.43  30.0  1
 8XO  Var_07    C8   C9   C10  C11  -177.54  30.0  3
 8XO  Var_08    N    C16  C17  O2     -5.04  30.0  1
 8XO  Var_09    C7   C8   C9   C10  -176.73  30.0  3
 8XO  Var_10    C    C7   C8   C9   -177.44  30.0  1
 8XO  Var_11    C1   C    C7   C8   -177.91  30.0  3
 8XO  Var_12    C2   C1   C    C7   -178.20  30.0  2
 8XO  Var_13    C3   C2   C1   C    -178.98  30.0  3
 8XO  Var_14    C4   C3   C2   C1   -178.83  30.0  1
 8XO  Var_15    C5   C4   C3   C2   -179.93  30.0  3
 8XO  Var_16    C6   C5   C4   C3    179.78  30.0  3
 8XO  Var_17    N1   C6   C5   C4    175.83  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
 8XO  plan-1  C15  0.020
 8XO  plan-1  C14  0.020
 8XO  plan-1  C13  0.020
 8XO  plan-1  O    0.020
 8XO  plan-2  C16  0.020
 8XO  plan-2  O2   0.020
 8XO  plan-2  C17  0.020
 8XO  plan-2  O1   0.020
 8XO  plan-2  H8   0.020
 8XO  plan-3  C6   0.020
 8XO  plan-3  N1   0.020
 8XO  plan-3  N2   0.020
 8XO  plan-3  N3   0.020
 8XO  plan-4  C14  0.020
 8XO  plan-4  C13  0.020
 8XO  plan-4  C12  0.020
 8XO  plan-4  C11  0.020
 8XO  plan-4  H2   0.020
 8XO  plan-4  H3   0.020
 8XO  plan-5  C15  0.020
 8XO  plan-5  C14  0.020
 8XO  plan-5  C16  0.020
 8XO  plan-5  N    0.020
 8XO  plan-5  H1   0.020

