# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 03:40:12 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  50  24  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.434   4.1056   2.9104  -0.4709
 GUX  C6   C  C      0   0.570   4.4400   2.2958   0.5096
 GUX  O6   O  OH1    0  -0.594   4.6514   2.8680   1.6899
 GUX  C5   C  CH1    0  -0.433   4.6113   0.7969   0.5834
 GUX  C    C  CH1    0  -0.113   3.3575   0.2043   1.1947
 GUX  N1   N  NT     0  -0.387   2.1961   0.1536   0.3489
 GUX  C1   C  CH1    0  -0.167   2.8255  -1.0929   0.7120
 GUX  C2   C  CH1    0   0.056   3.4961  -1.8594  -0.4093
 GUX  O    O  OH1    0  -0.679   3.5203  -3.2205  -0.0432
 GUX  C3   C  CH1    0   0.008   4.9016  -1.3319  -0.6706
 GUX  O3   O  OH1    0  -0.679   5.3567  -1.9444  -1.8558
 GUX  C4   C  CH1    0   0.032   4.9157   0.1948  -0.7798
 GUX  O4   O  OH1    0  -0.677   6.1913   0.6577  -1.1686
 GUX  C7   C  CH2    0  -0.278   0.9119   0.4588   0.9471
 GUX  C8   C  CH2    0  -0.431  -0.2182  -0.2182   0.1908
 GUX  C9   C  CH2    0  -0.419  -1.5908   0.2061   0.6965
 GUX  C16  C  CH2    0  -0.413  -2.7356  -0.4893  -0.0283
 GUX  C17  C  CH2    0  -0.412  -4.1083  -0.0318   0.4480
 GUX  C18  C  CH2    0  -0.423  -5.2545  -0.7325  -0.2698
 GUX  C19  C  CH2    0  -0.436  -6.6233  -0.2615   0.2058
 GUX  C21  C  CH2    0  -0.302  -7.7489  -0.9803  -0.5229
 GUX  N22  N  N      0  -0.363  -9.0839  -0.5991  -0.0395
 GUX  N25  N  N      1   0.353  -9.4728   0.5126  -0.3398
 GUX  N26  N  N     -1  -0.232  -9.9221   1.5201  -0.5636
 GUX  H1   H  HOH1   0   0.480   4.4820   3.8205   1.6331
 GUX  H2   H  HCH1   0   0.289   5.4427   0.5715   1.2607
 GUX  H3   H  HCH1   0   0.271   3.2032   0.4309   2.2481
 GUX  H5   H  HCH1   0   0.266   2.3189  -1.7101   1.4533
 GUX  H6   H  HCH1   0   0.218   2.8986  -1.7144  -1.3223
 GUX  H7   H  HOH1   0   0.451   3.9338  -3.7135  -0.7595
 GUX  H8   H  HCH1   0   0.214   5.5339  -1.6224   0.1840
 GUX  H9   H  HOH1   0   0.453   6.3086  -1.8202  -1.9200
 GUX  H10  H  HCH1   0   0.229   4.1515   0.5098  -1.4996
 GUX  H11  H  HOH1   0   0.458   6.2204   0.7146  -2.1273
 GUX  H12  H  HCH2   0   0.201   0.8741   0.1663   2.0081
 GUX  H13  H  HCH2   0   0.232   0.7812   1.5445   0.9162
 GUX  H14  H  HCH2   0   0.218  -0.1271   0.0176  -0.8736
 GUX  H15  H  HCH2   0   0.217  -0.1134  -1.3049   0.2776
 GUX  H16  H  HCH2   0   0.213  -1.6670   0.0040   1.7704
 GUX  H17  H  HCH2   0   0.212  -1.6962   1.2907   0.5847
 GUX  H18  H  HCH2   0   0.210  -2.6468  -0.3093  -1.1052
 GUX  H19  H  HCH2   0   0.212  -4.1960  -0.2045   1.5261
 GUX  H20  H  HCH2   0   0.217  -5.1647  -0.5651  -1.3484
 GUX  H21  H  HCH2   0   0.217  -5.1693  -1.8142  -0.1213
 GUX  H22  H  HCH2   0   0.231  -6.7229  -0.4322   1.2812
 GUX  H23  H  HCH2   0   0.225  -6.7102   0.8185   0.0482
 GUX  H24  H  HCH2   0   0.246  -7.6737  -0.8145  -1.6021
 GUX  H25  H  HCH2   0   0.253  -7.6796  -2.0538  -0.3559
 GUX  H4   H  HCH2   0   0.210  -2.6459  -1.5728   0.1058
 GUX  H27  H  HCH2   0   0.211  -4.1988   1.0506   0.3062

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  1.410  0.020  1.410
 GUX  O    C2   single  1.410  0.020  1.410
 GUX  C2   C3   single  1.524  0.020  1.524
 GUX  C2   C1   single  1.515  0.020  1.515
 GUX  C3   C4   single  1.531  0.020  1.531
 GUX  C1   N1   single  1.443  0.020  1.443
 GUX  C1   C    single  1.483  0.020  1.483
 GUX  C4   O4   single  1.412  0.020  1.412
 GUX  C4   C5   single  1.521  0.020  1.521
 GUX  N1   C7   single  1.449  0.020  1.449
 GUX  N1   C    single  1.438  0.020  1.438
 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  1.516  0.020  1.516
 GUX  C5   C6   single  1.511  0.020  1.511
 GUX  C16  C17  single  1.523  0.020  1.523
 GUX  N25  N26  double  1.126  0.020  1.126
 GUX  O7   C6   double  1.205  0.020  1.205
 GUX  C18  C17  single  1.523  0.020  1.523
 GUX  C6   O6   single  1.329  0.020  1.329
 GUX  O6   H1   single  0.850  0.020  0.980
 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   111.46  3.000
 GUX  O6   C6   O7   123.20  3.000
 GUX  C5   C6   O7   125.28  3.000
 GUX  H1   O6   C6   110.09  3.000
 GUX  H2   C5   C4   108.71  3.000
 GUX  H2   C5   C    107.34  3.000
 GUX  C4   C5   C    111.86  3.000
 GUX  H2   C5   C6   108.68  3.000
 GUX  C    C5   C6   108.29  3.000
 GUX  C4   C5   C6   111.82  3.000
 GUX  H3   C    C1   116.51  3.000
 GUX  H3   C    N1   117.53  3.000
 GUX  C1   C    N1    59.19  3.000
 GUX  H3   C    C5   115.23  3.000
 GUX  N1   C    C5   116.41  3.000
 GUX  C1   C    C5   120.50  3.000
 GUX  C7   N1   C1   117.69  3.000
 GUX  C7   N1   C    117.75  3.000
 GUX  C1   N1   C     61.97  3.000
 GUX  H5   C1   C2   115.01  3.000
 GUX  H5   C1   N1   117.25  3.000
 GUX  C2   C1   N1   116.36  3.000
 GUX  H5   C1   C    116.16  3.000
 GUX  N1   C1   C     58.85  3.000
 GUX  C2   C1   C    121.65  3.000
 GUX  H6   C2   C3   108.23  3.000
 GUX  H6   C2   O    110.60  3.000
 GUX  C3   C2   O    111.28  3.000
 GUX  H6   C2   C1   107.88  3.000
 GUX  C3   C2   C1   111.11  3.000
 GUX  O    C2   C1   107.70  3.000
 GUX  H7   O    C2   107.98  3.000
 GUX  H8   C3   C4   108.24  3.000
 GUX  H8   C3   O3   110.63  3.000
 GUX  C4   C3   O3   111.74  3.000
 GUX  H8   C3   C2   107.75  3.000
 GUX  C4   C3   C2   111.47  3.000
 GUX  O3   C3   C2   106.95  3.000
 GUX  H9   O3   C3   108.63  3.000
 GUX  H10  C4   O4   110.79  3.000
 GUX  H10  C4   C3   109.09  3.000
 GUX  O4   C4   C3   110.80  3.000
 GUX  H10  C4   C5   109.59  3.000
 GUX  O4   C4   C5   107.33  3.000
 GUX  C3   C4   C5   109.21  3.000
 GUX  H11  O4   C4   108.76  3.000
 GUX  H13  C7   H12  106.66  3.000
 GUX  H13  C7   C8   109.84  3.000
 GUX  H12  C7   C8   109.62  3.000
 GUX  H13  C7   N1   107.65  3.000
 GUX  H12  C7   N1   111.84  3.000
 GUX  C8   C7   N1   111.10  3.000
 GUX  H15  C8   H14  106.44  3.000
 GUX  H15  C8   C9   109.66  3.000
 GUX  H14  C8   C9   109.75  3.000
 GUX  H15  C8   C7   109.37  3.000
 GUX  H14  C8   C7   109.05  3.000
 GUX  C9   C8   C7   112.40  3.000
 GUX  H17  C9   H16  106.02  3.000
 GUX  H17  C9   C16  109.34  3.000
 GUX  H16  C9   C16  109.27  3.000
 GUX  H17  C9   C8   109.19  3.000
 GUX  H16  C9   C8   109.68  3.000
 GUX  C16  C9   C8   113.09  3.000
 GUX  H4   C16  H18  106.03  3.000
 GUX  H4   C16  C17  109.42  3.000
 GUX  H18  C16  C17  109.34  3.000
 GUX  H4   C16  C9   109.38  3.000
 GUX  H18  C16  C9   109.38  3.000
 GUX  C17  C16  C9   113.05  3.000
 GUX  H27  C17  H19  106.05  3.000
 GUX  H27  C17  C18  109.35  3.000
 GUX  H19  C17  C18  109.33  3.000
 GUX  H27  C17  C16  109.31  3.000
 GUX  H19  C17  C16  109.42  3.000
 GUX  C18  C17  C16  113.12  3.000
 GUX  H21  C18  H20  106.14  3.000
 GUX  H21  C18  C19  109.45  3.000
 GUX  H20  C18  C19  109.50  3.000
 GUX  H21  C18  C17  109.38  3.000
 GUX  H20  C18  C17  109.40  3.000
 GUX  C19  C18  C17  112.75  3.000
 GUX  H23  C19  H22  106.76  3.000
 GUX  H23  C19  C21  109.78  3.000
 GUX  H22  C19  C21  109.27  3.000
 GUX  H23  C19  C18  109.35  3.000
 GUX  H22  C19  C18  109.91  3.000
 GUX  C21  C19  C18  111.66  3.000
 GUX  H25  C21  H24  107.24  3.000
 GUX  H25  C21  N22  105.25  3.000
 GUX  H24  C21  N22  110.33  3.000
 GUX  H25  C21  C19  110.20  3.000
 GUX  H24  C21  C19  110.48  3.000
 GUX  N22  C21  C19  113.06  3.000
 GUX  N25  N22  C21  116.52  3.000
 GUX  N26  N25  N22  174.56  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  CONST_01  H1   O6   C6   C5    180.00   0.0  0
 GUX  Var_01    C2   C1   C    C5     -0.76  30.0  1
 GUX  Var_02    C8   C7   N1   C    -153.99  30.0  3
 GUX  Var_03    C9   C8   C7   N1   -173.57  30.0  3
 GUX  Var_04    C16  C9   C8   C7   -178.60  30.0  1
 GUX  Var_05    C17  C16  C9   C8   -178.19  30.0  3
 GUX  Var_06    C18  C17  C16  C9   -179.65  30.0  3
 GUX  Var_07    C19  C18  C17  C16  -179.58  30.0  1
 GUX  Var_08    C21  C19  C18  C17  -179.78  30.0  1
 GUX  Var_09    N22  C21  C19  C18   177.06  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-1  H1   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

