# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 20:38:41 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (1~{S},2~{R},3~{S},4~{S},5~{S},6~{R})-2-(8-azidooctylamino)-3,4,5,6-tetrakis(oxidanyl)cyclohexane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@@H](O)[C@H](O)[C@H]([C@@H](NCCCCCCCCN=[N+]=[N-])[C@@H]1O)C(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
 6S6  6S6  '(1~{S},2~{R},3~{S},4~{S},5~{S},6~{R})-2-(8-azidooctylamino)-3,4,5,6-tetrakis(oxidanyl)cyclohexane-1-carboxylic acid'  ligand  53  25  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6S6
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
 6S6  C1   C  CH1    0   0.022    3.4236   1.2279  -1.1884
 6S6  C2   C  CH1    0   0.025    3.8979   1.9066   0.0924
 6S6  C3   C  CH1    0  -0.003    5.0450   1.1420   0.7408
 6S6  C4   C  CH1    0   0.069    4.6409  -0.3014   1.0332
 6S6  C5   C  CH1    0  -0.453    4.2006  -0.9685  -0.2637
 6S6  C6   C  CH1    0  -0.094    3.0139  -0.2238  -0.9109
 6S6  C8   C  C      0   0.571    3.8633  -2.4236  -0.0428
 6S6  C15  C  CH2    0  -0.444   -0.5958  -0.0656   0.1816
 6S6  C16  C  CH2    0  -0.417   -1.9299   0.0830  -0.5381
 6S6  C17  C  CH2    0  -0.413   -3.1215   0.1043   0.4111
 6S6  C18  C  CH2    0  -0.412   -4.4549   0.2522  -0.3104
 6S6  C19  C  CH2    0  -0.423   -5.6475   0.2755   0.6376
 6S6  C20  C  CH2    0  -0.435   -6.9777   0.4159  -0.0924
 6S6  C21  C  CH2    0  -0.302   -8.1490   0.4432   0.8787
 6S6  N7   N  NH1    0  -0.619    1.8374  -0.2307  -0.0598
 6S6  O9   O  OH1    0  -0.585    4.2713  -3.1905  -1.0440
 6S6  O10  O  O      0  -0.443    3.2601  -2.8530   0.9114
 6S6  O11  O  OH1    0  -0.675    5.7274  -1.0456   1.5382
 6S6  O12  O  OH1    0  -0.682    5.3882   1.8276   1.9305
 6S6  O13  O  OH1    0  -0.682    4.2812   3.2216  -0.2460
 6S6  N22  N  N      0  -0.363   -9.4437   0.6396   0.2106
 6S6  N23  N  N      1   0.352   -9.8880  -0.3120  -0.4011
 6S6  N24  N  N     -1  -0.232  -10.3845  -1.1332  -0.9893
 6S6  O1   O  OH1    0  -0.673    4.4206   1.2137  -2.1832
 6S6  H1   H  HCH1   0   0.234    2.5395   1.7740  -1.5482
 6S6  H2   H  HCH1   0   0.216    3.0489   1.9136   0.7891
 6S6  H3   H  HCH1   0   0.218    5.8994   1.1289   0.0503
 6S6  H4   H  HCH1   0   0.220    3.8091  -0.2943   1.7494
 6S6  H5   H  HCH1   0   0.288    5.0300  -0.9205  -0.9745
 6S6  H6   H  HCH1   0   0.245    2.8104  -0.7027  -1.8828
 6S6  H7   H  HCH2   0   0.194    0.4382  -0.8722  -1.5278
 6S6  H8   H  HCH2   0   0.221    0.5977   0.8636  -1.3314
 6S6  H9   H  HCH2   0   0.214   -0.5990  -0.9927   0.7666
 6S6  H10  H  HCH2   0   0.218   -0.4657   0.7524   0.8966
 6S6  H11  H  HCH2   0   0.211   -1.9231   1.0048  -1.1305
 6S6  H12  H  HCH2   0   0.211   -2.0525  -0.7370  -1.2538
 6S6  H13  H  HCH2   0   0.210   -3.1288  -0.8163   1.0053
 6S6  H14  H  HCH2   0   0.210   -3.0012   0.9259   1.1257
 6S6  H15  H  HCH2   0   0.211   -4.4474   1.1719  -0.9057
 6S6  H16  H  HCH2   0   0.211   -4.5755  -0.5704  -1.0236
 6S6  H17  H  HCH2   0   0.217   -5.6535  -0.6419   1.2363
 6S6  H18  H  HCH2   0   0.217   -5.5311   1.1019   1.3469
 6S6  H19  H  HCH2   0   0.230   -6.9820   1.3330  -0.6884
 6S6  H20  H  HCH2   0   0.225   -7.0970  -0.4167  -0.7931
 6S6  H21  H  HCH2   0   0.246   -8.1663  -0.4686   1.4837
 6S6  H22  H  HCH2   0   0.253   -8.0488   1.2834   1.5635
 6S6  H23  H  HNH1   0   0.350    1.7944  -1.0845   0.4812
 6S6  H25  H  HOH1   0   0.482    4.0006  -4.1088  -0.8904
 6S6  H26  H  HOH1   0   0.454    5.8499  -0.8213   2.4655
 6S6  H27  H  HOH1   0   0.459    6.3296   1.7222   2.0920
 6S6  H28  H  HOH1   0   0.450    4.6808   3.6232   0.5333
 6S6  H30  H  HOH1   0   0.451    4.7873   2.1018  -2.2520
 6S6  C14  C  CH2    0  -0.258    0.5835  -0.0786  -0.7771

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
 6S6  O12  C3   single  1.415  0.020  1.415
 6S6  O13  C2   single  1.411  0.020  1.411
 6S6  C3   C2   single  1.523  0.020  1.523
 6S6  C3   C4   single  1.527  0.020  1.527
 6S6  C2   C1   single  1.525  0.020  1.525
 6S6  O11  C4   single  1.410  0.020  1.410
 6S6  C4   C5   single  1.523  0.020  1.523
 6S6  C1   C6   single  1.534  0.020  1.534
 6S6  C5   C6   single  1.543  0.020  1.543
 6S6  C5   C8   single  1.510  0.020  1.510
 6S6  N7   C6   single  1.452  0.020  1.452
 6S6  N7   C14  single  1.453  0.020  1.453
 6S6  C8   O10  double  1.208  0.020  1.208
 6S6  C8   O9   single  1.325  0.020  1.325
 6S6  C14  C15  single  1.520  0.020  1.520
 6S6  C15  C16  single  1.523  0.020  1.523
 6S6  C16  C17  single  1.524  0.020  1.524
 6S6  C17  C18  single  1.523  0.020  1.523
 6S6  C18  C19  single  1.524  0.020  1.524
 6S6  C19  C20  single  1.524  0.020  1.524
 6S6  C20  C21  single  1.522  0.020  1.522
 6S6  C21  N22  single  1.470  0.020  1.470
 6S6  N22  N23  double  1.215  0.020  1.215
 6S6  N23  N24  double  1.126  0.020  1.126
 6S6  C1   O1   single  1.409  0.020  1.409
 6S6  C1   H1   single  0.970  0.020  1.090
 6S6  C2   H2   single  0.970  0.020  1.090
 6S6  C3   H3   single  0.970  0.020  1.090
 6S6  C4   H4   single  0.970  0.020  1.090
 6S6  C5   H5   single  0.970  0.020  1.090
 6S6  C6   H6   single  0.970  0.020  1.090
 6S6  C14  H7   single  0.970  0.020  1.090
 6S6  C14  H8   single  0.970  0.020  1.090
 6S6  C15  H9   single  0.970  0.020  1.090
 6S6  C15  H10  single  0.970  0.020  1.090
 6S6  C16  H11  single  0.970  0.020  1.090
 6S6  C16  H12  single  0.970  0.020  1.090
 6S6  C17  H13  single  0.970  0.020  1.090
 6S6  C17  H14  single  0.970  0.020  1.090
 6S6  C18  H15  single  0.970  0.020  1.090
 6S6  C18  H16  single  0.970  0.020  1.090
 6S6  C19  H17  single  0.970  0.020  1.090
 6S6  C19  H18  single  0.970  0.020  1.090
 6S6  C20  H19  single  0.970  0.020  1.090
 6S6  C20  H20  single  0.970  0.020  1.090
 6S6  C21  H21  single  0.970  0.020  1.090
 6S6  C21  H22  single  0.970  0.020  1.090
 6S6  N7   H23  single  0.890  0.020  1.040
 6S6  O9   H25  single  0.850  0.020  0.980
 6S6  O11  H26  single  0.850  0.020  0.980
 6S6  O12  H27  single  0.850  0.020  0.980
 6S6  O13  H28  single  0.850  0.020  0.980
 6S6  O1   H30  single  0.850  0.020  0.980

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
 6S6  H1   C1   O1   110.06  3.000
 6S6  H1   C1   C6   108.33  3.000
 6S6  O1   C1   C6   107.90  3.000
 6S6  H1   C1   C2   107.69  3.000
 6S6  O1   C1   C2   112.18  3.000
 6S6  C6   C1   C2   110.63  3.000
 6S6  H2   C2   O13  110.87  3.000
 6S6  H2   C2   C3   108.38  3.000
 6S6  O13  C2   C3   111.43  3.000
 6S6  H2   C2   C1   107.16  3.000
 6S6  C3   C2   C1   111.61  3.000
 6S6  O13  C2   C1   107.33  3.000
 6S6  H3   C3   O12  110.22  3.000
 6S6  H3   C3   C4   108.35  3.000
 6S6  O12  C3   C4   111.16  3.000
 6S6  H3   C3   C2   108.91  3.000
 6S6  C4   C3   C2   110.89  3.000
 6S6  O12  C3   C2   107.29  3.000
 6S6  H4   C4   O11  110.71  3.000
 6S6  H4   C4   C5   109.83  3.000
 6S6  O11  C4   C5   107.24  3.000
 6S6  H4   C4   C3   108.62  3.000
 6S6  C5   C4   C3   109.10  3.000
 6S6  O11  C4   C3   111.31  3.000
 6S6  H5   C5   C8   107.87  3.000
 6S6  H5   C5   C6   106.83  3.000
 6S6  C8   C5   C6   110.77  3.000
 6S6  H5   C5   C4   108.36  3.000
 6S6  C8   C5   C4   111.22  3.000
 6S6  C6   C5   C4   111.59  3.000
 6S6  H6   C6   N7   111.41  3.000
 6S6  H6   C6   C5   107.58  3.000
 6S6  N7   C6   C5   112.02  3.000
 6S6  H6   C6   C1   107.51  3.000
 6S6  N7   C6   C1   109.09  3.000
 6S6  C5   C6   C1   109.10  3.000
 6S6  O10  C8   O9   123.01  3.000
 6S6  O9   C8   C5   112.23  3.000
 6S6  O10  C8   C5   124.73  3.000
 6S6  H10  C15  H9   106.50  3.000
 6S6  H10  C15  C16  109.87  3.000
 6S6  H9   C15  C16  109.40  3.000
 6S6  H10  C15  C14  109.04  3.000
 6S6  H9   C15  C14  109.37  3.000
 6S6  C16  C15  C14  112.48  3.000
 6S6  H12  C16  H11  106.09  3.000
 6S6  H12  C16  C17  109.27  3.000
 6S6  H11  C16  C17  109.26  3.000
 6S6  H12  C16  C15  109.50  3.000
 6S6  H11  C16  C15  109.40  3.000
 6S6  C17  C16  C15  113.08  3.000
 6S6  H14  C17  H13  106.09  3.000
 6S6  H14  C17  C18  109.40  3.000
 6S6  H13  C17  C18  109.42  3.000
 6S6  H14  C17  C16  109.33  3.000
 6S6  H13  C17  C16  109.35  3.000
 6S6  C18  C17  C16  113.01  3.000
 6S6  H16  C18  H15  106.10  3.000
 6S6  H16  C18  C19  109.30  3.000
 6S6  H15  C18  C19  109.31  3.000
 6S6  H16  C18  C17  109.38  3.000
 6S6  H15  C18  C17  109.44  3.000
 6S6  C19  C18  C17  113.08  3.000
 6S6  H18  C19  H17  106.18  3.000
 6S6  H18  C19  C20  109.48  3.000
 6S6  H17  C19  C20  109.53  3.000
 6S6  H18  C19  C18  109.34  3.000
 6S6  H17  C19  C18  109.36  3.000
 6S6  C20  C19  C18  112.74  3.000
 6S6  H20  C20  H19  106.77  3.000
 6S6  H20  C20  C21  109.77  3.000
 6S6  H19  C20  C21  109.25  3.000
 6S6  H20  C20  C19  109.37  3.000
 6S6  H19  C20  C19  109.99  3.000
 6S6  C21  C20  C19  111.58  3.000
 6S6  H22  C21  H21  107.26  3.000
 6S6  H22  C21  N22  105.30  3.000
 6S6  H21  C21  N22  110.40  3.000
 6S6  H22  C21  C20  110.15  3.000
 6S6  H21  C21  C20  110.49  3.000
 6S6  N22  C21  C20  112.97  3.000
 6S6  H23  N7   C14  108.40  3.000
 6S6  H23  N7   C6   110.61  3.000
 6S6  C14  N7   C6   114.17  3.000
 6S6  H25  O9   C8   110.02  3.000
 6S6  H26  O11  C4   108.68  3.000
 6S6  H27  O12  C3   109.01  3.000
 6S6  H28  O13  C2   107.89  3.000
 6S6  N23  N22  C21  116.49  3.000
 6S6  N24  N23  N22  174.58  3.000
 6S6  H30  O1   C1   108.09  3.000
 6S6  H8   C14  H7   106.08  3.000
 6S6  H8   C14  N7   109.24  3.000
 6S6  H7   C14  N7   112.01  3.000
 6S6  H8   C14  C15  108.81  3.000
 6S6  H7   C14  C15  109.48  3.000
 6S6  N7   C14  C15  111.05  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
 6S6  CONST_01  H25  O9   C8   C5    180.00   0.0  0
 6S6  Var_01    C15  C14  N7   C6   -178.78  30.0  3
 6S6  Var_02    C17  C16  C15  C14  -179.72  30.0  3
 6S6  Var_03    C18  C17  C16  C15  -179.96  30.0  3
 6S6  Var_04    N7   C14  C15  C16  -179.61  30.0  1
 6S6  Var_05    C19  C18  C17  C16  -179.93  30.0  3
 6S6  Var_06    C20  C19  C18  C17  -179.68  30.0  3
 6S6  Var_07    C21  C20  C19  C18  -179.72  30.0  3
 6S6  Var_08    N22  C21  C20  C19   177.38  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
 6S6  chir_01  C1  C2   C6  O1  positiv
 6S6  chir_02  C2  O13  C1  C3  negativ
 6S6  chir_03  C3  O12  C2  C4  positiv
 6S6  chir_04  C4  O11  C3  C5  negativ
 6S6  chir_05  C5  C4   C6  C8  positiv
 6S6  chir_06  C6  N7   C1  C5  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
 6S6  plan-1  C5   0.020
 6S6  plan-1  C8   0.020
 6S6  plan-1  O9   0.020
 6S6  plan-1  O10  0.020
 6S6  plan-1  H25  0.020
 6S6  plan-2  C21  0.020
 6S6  plan-2  N22  0.020
 6S6  plan-2  N23  0.020
 6S6  plan-2  N24  0.020

