# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 21:46:58 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (1~{R},2~{S},3~{R},4~{S},5~{S},6~{R})-7-(8-azidooctyl)-3,4,5-tris(oxidanyl)-7-azabicyclo[4.1.0]heptane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@@H](O)[C@H]2[C@@H]([C@@H]([C@H]1O)C(O)=O)N2CCCCCCCCN=[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
 GUX  GUX  '(1~{R},2~{S},3~{R},4~{S},5~{S},6~{R})-7-(8-azidooctyl)-3,4,5-tris(oxidanyl)-7-azabicyclo[4.1.0]heptane-2-carboxylic acid'  ligand  49  24  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_GUX
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
 GUX  O7   O  O      0  -0.563   3.7448   2.8673   1.4389
 GUX  C6   C  C      0   0.484   4.5937   2.2760   0.7616
 GUX  O6   O  OC    -1  -0.623   5.5045   2.8232   0.0788
 GUX  C5   C  CH1    0  -0.487   4.5867   0.7356   0.7468
 GUX  C    C  CH1    0  -0.074   3.3056   0.1524   1.2690
 GUX  N1   N  NT     0  -0.394   2.1710   0.1495   0.3845
 GUX  C1   C  CH1    0  -0.175   2.7735  -1.1210   0.7211
 GUX  C2   C  CH1    0   0.055   3.4640  -1.8494  -0.4146
 GUX  O    O  OH1    0  -0.682   3.4594  -3.2280  -0.1089
 GUX  C3   C  CH1    0   0.020   4.8832  -1.3340  -0.6242
 GUX  O3   O  OH1    0  -0.686   5.3547  -1.8963  -1.8291
 GUX  C4   C  CH1    0   0.040   4.9277   0.1881  -0.6456
 GUX  O4   O  OH1    0  -0.721   6.2169   0.5917  -1.0413
 GUX  C7   C  CH2    0  -0.271   0.8792   0.4459   0.9642
 GUX  C8   C  CH2    0  -0.430  -0.2457  -0.1998   0.1727
 GUX  C9   C  CH2    0  -0.418  -1.6229   0.2111   0.6766
 GUX  C16  C  CH2    0  -0.412  -2.7620  -0.4740  -0.0669
 GUX  C17  C  CH2    0  -0.412  -4.1385  -0.0286   0.4097
 GUX  C18  C  CH2    0  -0.423  -5.2796  -0.7253  -0.3202
 GUX  C19  C  CH2    0  -0.436  -6.6515  -0.2652   0.1572
 GUX  C21  C  CH2    0  -0.302  -7.7731  -0.9823  -0.5794
 GUX  N22  N  N      0  -0.363  -9.1099  -0.6120  -0.0926
 GUX  N25  N  N      1   0.353  -9.5054   0.4997  -0.3839
 GUX  N26  N  N     -1  -0.232  -9.9626   1.5055  -0.5994
 GUX  H2   H  HCH1   0   0.245   5.3917   0.4065   1.4208
 GUX  H3   H  HCH1   0   0.237   3.1032   0.3393   2.3217
 GUX  H5   H  HCH1   0   0.250   2.2258  -1.7630   1.4106
 GUX  H6   H  HCH1   0   0.207   2.8924  -1.6571  -1.3357
 GUX  H7   H  HOH1   0   0.449   3.8719  -3.6972  -0.8412
 GUX  H8   H  HCH1   0   0.195   5.4938  -1.6771   0.2287
 GUX  H9   H  HOH1   0   0.450   6.2482  -1.5699  -1.9785
 GUX  H10  H  HCH1   0   0.184   4.1732   0.5520  -1.3623
 GUX  H11  H  HOH1   0   0.439   6.2351   1.5381  -0.7596
 GUX  H12  H  HCH2   0   0.190   0.8170   0.1238   2.0165
 GUX  H13  H  HCH2   0   0.225   0.7590   1.5331   0.9654
 GUX  H14  H  HCH2   0   0.215  -0.1423   0.0699  -0.8827
 GUX  H15  H  HCH2   0   0.214  -0.1462  -1.2894   0.2243
 GUX  H16  H  HCH2   0   0.211  -1.7049  -0.0118   1.7461
 GUX  H17  H  HCH2   0   0.211  -1.7309   1.2975   0.5856
 GUX  H18  H  HCH2   0   0.209  -2.6680  -0.2753  -1.1401
 GUX  H19  H  HCH2   0   0.211  -4.2292  -0.2152   1.4853
 GUX  H20  H  HCH2   0   0.217  -5.1872  -0.5451  -1.3965
 GUX  H21  H  HCH2   0   0.217  -5.1903  -1.8083  -0.1839
 GUX  H22  H  HCH2   0   0.230  -6.7519  -0.4464   1.2308
 GUX  H23  H  HCH2   0   0.225  -6.7426   0.8158   0.0098
 GUX  H24  H  HCH2   0   0.246  -7.6983  -0.8057  -1.6570
 GUX  H25  H  HCH2   0   0.253  -7.6986  -2.0570  -0.4225
 GUX  H4   H  HCH2   0   0.209  -2.6701  -1.5595   0.0491
 GUX  H27  H  HCH2   0   0.211  -4.2332   1.0552   0.2814

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
 GUX  O3   C3   single  1.411  0.020  1.411
 GUX  O    C2   single  1.412  0.020  1.412
 GUX  C2   C3   single  1.524  0.020  1.524
 GUX  C2   C1   single  1.516  0.020  1.516
 GUX  C3   C4   single  1.523  0.020  1.523
 GUX  C1   N1   single  1.446  0.020  1.446
 GUX  C1   C    single  1.485  0.020  1.485
 GUX  C4   O4   single  1.408  0.020  1.408
 GUX  C4   C5   single  1.534  0.020  1.534
 GUX  N1   C7   single  1.447  0.020  1.447
 GUX  N1   C    single  1.439  0.020  1.439
 GUX  C7   C8   single  1.519  0.020  1.519
 GUX  C19  C21  single  1.521  0.020  1.521
 GUX  C19  C18  single  1.524  0.020  1.524
 GUX  N22  C21  single  1.470  0.020  1.470
 GUX  N22  N25  double  1.215  0.020  1.215
 GUX  C9   C8   single  1.523  0.020  1.523
 GUX  C9   C16  single  1.523  0.020  1.523
 GUX  C    C5   single  1.501  0.020  1.501
 GUX  C5   C6   single  1.540  0.020  1.540
 GUX  C16  C17  single  1.523  0.020  1.523
 GUX  N25  N26  double  1.126  0.020  1.126
 GUX  O7   C6   deloc   1.237  0.020  1.237
 GUX  C18  C17  single  1.523  0.020  1.523
 GUX  C6   O6   deloc   1.263  0.020  1.263
 GUX  C5   H2   single  0.970  0.020  1.090
 GUX  C    H3   single  0.970  0.020  1.090
 GUX  C1   H5   single  0.970  0.020  1.090
 GUX  C2   H6   single  0.970  0.020  1.090
 GUX  O    H7   single  0.850  0.020  0.980
 GUX  C3   H8   single  0.970  0.020  1.090
 GUX  O3   H9   single  0.850  0.020  0.980
 GUX  C4   H10  single  0.970  0.020  1.090
 GUX  O4   H11  single  0.850  0.020  0.980
 GUX  C7   H12  single  0.970  0.020  1.090
 GUX  C7   H13  single  0.970  0.020  1.090
 GUX  C8   H14  single  0.970  0.020  1.090
 GUX  C8   H15  single  0.970  0.020  1.090
 GUX  C9   H16  single  0.970  0.020  1.090
 GUX  C9   H17  single  0.970  0.020  1.090
 GUX  C16  H18  single  0.970  0.020  1.090
 GUX  C17  H19  single  0.970  0.020  1.090
 GUX  C18  H20  single  0.970  0.020  1.090
 GUX  C18  H21  single  0.970  0.020  1.090
 GUX  C19  H22  single  0.970  0.020  1.090
 GUX  C19  H23  single  0.970  0.020  1.090
 GUX  C21  H24  single  0.970  0.020  1.090
 GUX  C21  H25  single  0.970  0.020  1.090
 GUX  C16  H4   single  0.970  0.020  1.090
 GUX  C17  H27  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
 GUX  C5   C6   O6   115.55  3.000
 GUX  O6   C6   O7   125.74  3.000
 GUX  C5   C6   O7   118.71  3.000
 GUX  H2   C5   C4   106.65  3.000
 GUX  H2   C5   C    107.16  3.000
 GUX  C4   C5   C    111.51  3.000
 GUX  H2   C5   C6   106.85  3.000
 GUX  C    C5   C6   112.89  3.000
 GUX  C4   C5   C6   111.37  3.000
 GUX  H3   C    C1   115.95  3.000
 GUX  H3   C    N1   116.64  3.000
 GUX  C1   C    N1    59.26  3.000
 GUX  H3   C    C5   115.37  3.000
 GUX  N1   C    C5   117.38  3.000
 GUX  C1   C    C5   120.70  3.000
 GUX  C7   N1   C1   117.32  3.000
 GUX  C7   N1   C    117.23  3.000
 GUX  C1   N1   C     61.97  3.000
 GUX  H5   C1   C2   114.84  3.000
 GUX  H5   C1   N1   117.10  3.000
 GUX  C2   C1   N1   115.95  3.000
 GUX  H5   C1   C    116.87  3.000
 GUX  N1   C1   C     58.78  3.000
 GUX  C2   C1   C    121.69  3.000
 GUX  H6   C2   C3   108.02  3.000
 GUX  H6   C2   O    110.49  3.000
 GUX  C3   C2   O    111.28  3.000
 GUX  H6   C2   C1   107.84  3.000
 GUX  C3   C2   C1   111.39  3.000
 GUX  O    C2   C1   107.78  3.000
 GUX  H7   O    C2   108.05  3.000
 GUX  H8   C3   C4   107.78  3.000
 GUX  H8   C3   O3   110.56  3.000
 GUX  C4   C3   O3   112.13  3.000
 GUX  H8   C3   C2   107.68  3.000
 GUX  C4   C3   C2   111.53  3.000
 GUX  O3   C3   C2   107.08  3.000
 GUX  H9   O3   C3   107.90  3.000
 GUX  H10  C4   O4   110.45  3.000
 GUX  H10  C4   C3   108.60  3.000
 GUX  O4   C4   C3   108.49  3.000
 GUX  H10  C4   C5   108.67  3.000
 GUX  O4   C4   C5   110.87  3.000
 GUX  C3   C4   C5   109.72  3.000
 GUX  H11  O4   C4   102.20  3.000
 GUX  H13  C7   H12  106.45  3.000
 GUX  H13  C7   C8   109.98  3.000
 GUX  H12  C7   C8   109.35  3.000
 GUX  H13  C7   N1   107.59  3.000
 GUX  H12  C7   N1   111.90  3.000
 GUX  C8   C7   N1   111.43  3.000
 GUX  H15  C8   H14  106.38  3.000
 GUX  H15  C8   C9   109.57  3.000
 GUX  H14  C8   C9   109.76  3.000
 GUX  H15  C8   C7   109.33  3.000
 GUX  H14  C8   C7   109.13  3.000
 GUX  C9   C8   C7   112.49  3.000
 GUX  H17  C9   H16  105.99  3.000
 GUX  H17  C9   C16  109.38  3.000
 GUX  H16  C9   C16  109.21  3.000
 GUX  H17  C9   C8   109.22  3.000
 GUX  H16  C9   C8   109.62  3.000
 GUX  C16  C9   C8   113.17  3.000
 GUX  H4   C16  H18  106.03  3.000
 GUX  H4   C16  C17  109.41  3.000
 GUX  H18  C16  C17  109.33  3.000
 GUX  H4   C16  C9   109.35  3.000
 GUX  H18  C16  C9   109.42  3.000
 GUX  C17  C16  C9   113.05  3.000
 GUX  H27  C17  H19  106.04  3.000
 GUX  H27  C17  C18  109.37  3.000
 GUX  H19  C17  C18  109.31  3.000
 GUX  H27  C17  C16  109.31  3.000
 GUX  H19  C17  C16  109.40  3.000
 GUX  C18  C17  C16  113.16  3.000
 GUX  H21  C18  H20  106.15  3.000
 GUX  H21  C18  C19  109.45  3.000
 GUX  H20  C18  C19  109.52  3.000
 GUX  H21  C18  C17  109.37  3.000
 GUX  H20  C18  C17  109.42  3.000
 GUX  C19  C18  C17  112.72  3.000
 GUX  H23  C19  H22  106.75  3.000
 GUX  H23  C19  C21  109.81  3.000
 GUX  H22  C19  C21  109.25  3.000
 GUX  H23  C19  C18  109.32  3.000
 GUX  H22  C19  C18  109.89  3.000
 GUX  C21  C19  C18  111.70  3.000
 GUX  H25  C21  H24  107.25  3.000
 GUX  H25  C21  N22  105.25  3.000
 GUX  H24  C21  N22  110.34  3.000
 GUX  H25  C21  C19  110.19  3.000
 GUX  H24  C21  C19  110.50  3.000
 GUX  N22  C21  C19  113.03  3.000
 GUX  N25  N22  C21  116.54  3.000
 GUX  N26  N25  N22  174.47  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
 GUX  Var_01  C2   C1   C    C5     -2.49  30.0  1
 GUX  Var_02  C8   C7   N1   C    -153.05  30.0  3
 GUX  Var_03  C9   C8   C7   N1   -174.18  30.0  3
 GUX  Var_04  C16  C9   C8   C7   -177.51  30.0  1
 GUX  Var_05  C17  C16  C9   C8   -178.21  30.0  3
 GUX  Var_06  C18  C17  C16  C9   -179.27  30.0  3
 GUX  Var_07  C19  C18  C17  C16  -179.59  30.0  1
 GUX  Var_08  C21  C19  C18  C17  -179.59  30.0  1
 GUX  Var_09  N22  C21  C19  C18   176.99  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
 GUX  chir_01  C5  C4  C   C6  positiv
 GUX  chir_04  C2  O   C3  C1  positiv
 GUX  chir_05  C3  O3  C2  C4  positiv
 GUX  chir_06  C4  O4  C3  C5  negativ
 GUX  chir_07  C   C1  N1  C5  both
 GUX  chir_08  C1  N1  C2  C   both

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
 GUX  plan-1  O7   0.020
 GUX  plan-1  C6   0.020
 GUX  plan-1  O6   0.020
 GUX  plan-1  C5   0.020
 GUX  plan-2  C21  0.020
 GUX  plan-2  N22  0.020
 GUX  plan-2  N25  0.020
 GUX  plan-2  N26  0.020

