# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 08:11:43 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (1~{R},2~{R},3~{R},4~{S},5~{S},6~{R})-7-methyl-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: CN1[C@H]2[C@H](O)[C@@H](O)[C@H](O)[C@@H]([C@@H]12)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
 H6B  H6B  '(1~{R},2~{R},3~{R},4~{S},5~{S},6~{R})-7-methyl-3,4,5-tris(oxidanyl)-7-azabicyclo[4.1.0]heptane-2-carboxylic acid'  ligand  27  14  .  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_H6B
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
 H6B  C1   C  CH1   0  -0.404  -0.8756  -0.2978  -0.4224
 H6B  C2   C  CH1   0   0.016  -0.5214   1.1892  -0.3331
 H6B  C3   C  CH1   0  -0.054   0.9585   1.4236  -0.6630
 H6B  C4   C  CH1   0   0.044   1.9113   0.7226   0.3186
 H6B  C5   C  CH1   0  -0.128   1.4240  -0.6382   0.7519
 H6B  C6   C  CH1   0  -0.118   0.0710  -1.1375   0.4073
 H6B  N1   N  NT    0  -0.390   1.2464  -1.6377  -0.2667
 H6B  O1   O  OH1   0  -0.661   1.2525   0.9835  -1.9661
 H6B  O2   O  OH1   0  -0.674   2.0672   1.4849   1.4972
 H6B  O3   O  OH1   0  -0.662  -0.8507   1.5964   0.9717
 H6B  C7   C  C     0   0.568  -2.3195  -0.5006  -0.0203
 H6B  O4   O  O     0  -0.433  -2.7036  -1.1870   0.8933
 H6B  O5   O  OH1   0  -0.597  -3.1468   0.1663  -0.8166
 H6B  C8   C  CH3   0  -0.524   1.6658  -2.9815   0.0623
 H6B  H1   H  HCH1  0   0.304  -0.7900  -0.5994  -1.4714
 H6B  H2   H  HCH1  0   0.233  -1.1141   1.7420  -1.0766
 H6B  H3   H  HCH1  0   0.236   1.1472   2.5070  -0.5789
 H6B  H4   H  HCH1  0   0.227   2.8772   0.6012  -0.1924
 H6B  H5   H  HCH1  0   0.248   1.8396  -0.9725   1.7023
 H6B  H6   H  HCH1  0   0.257  -0.3866  -1.7959   1.1407
 H6B  H8   H  HOH1  0   0.454   0.7483   1.5188  -2.5874
 H6B  H9   H  HOH1  0   0.454   2.5527   2.2854   1.2757
 H6B  H10  H  HOH1  0   0.451  -0.4136   2.4303   1.1716
 H6B  H11  H  HOH1  0   0.481  -4.0631   0.0249  -0.5349
 H6B  H12  H  HCH3  0   0.201   1.4916  -3.2538   1.1121
 H6B  H13  H  HCH3  0   0.235   1.1307  -3.6960  -0.5640
 H6B  H14  H  HCH3  0   0.236   2.7321  -3.0902  -0.1391

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
 H6B  C8  N1   single  1.446  0.020  1.446
 H6B  N1  C5   single  1.438  0.020  1.438
 H6B  N1  C6   single  1.444  0.020  1.444
 H6B  C5  C6   single  1.483  0.020  1.483
 H6B  C5  C4   single  1.509  0.020  1.509
 H6B  C6  C1   single  1.513  0.020  1.513
 H6B  C4  O2   single  1.412  0.020  1.412
 H6B  C4  C3   single  1.537  0.020  1.537
 H6B  C1  C7   single  1.512  0.020  1.512
 H6B  C1  C2   single  1.531  0.020  1.531
 H6B  O4  C7   double  1.206  0.020  1.206
 H6B  C7  O5   single  1.328  0.020  1.328
 H6B  O1  C3   single  1.406  0.020  1.406
 H6B  C3  C2   single  1.534  0.020  1.534
 H6B  C2  O3   single  1.406  0.020  1.406
 H6B  C1  H1   single  0.970  0.020  1.090
 H6B  C2  H2   single  0.970  0.020  1.090
 H6B  C3  H3   single  0.970  0.020  1.090
 H6B  C4  H4   single  0.970  0.020  1.090
 H6B  C5  H5   single  0.970  0.020  1.090
 H6B  C6  H6   single  0.970  0.020  1.090
 H6B  O1  H8   single  0.850  0.020  0.980
 H6B  O2  H9   single  0.850  0.020  0.980
 H6B  O3  H10  single  0.850  0.020  0.980
 H6B  O5  H11  single  0.850  0.020  0.980
 H6B  C8  H12  single  0.970  0.020  1.090
 H6B  C8  H13  single  0.970  0.020  1.090
 H6B  C8  H14  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
 H6B  H1   C1  C7   107.00  3.000
 H6B  H1   C1  C6   108.88  3.000
 H6B  C7   C1  C6   112.15  3.000
 H6B  H1   C1  C2   107.78  3.000
 H6B  C7   C1  C2   109.61  3.000
 H6B  C6   C1  C2   111.24  3.000
 H6B  H2   C2  O3   110.83  3.000
 H6B  H2   C2  C3   107.31  3.000
 H6B  O3   C2  C3   112.41  3.000
 H6B  H2   C2  C1   108.90  3.000
 H6B  O3   C2  C1   106.34  3.000
 H6B  C3   C2  C1   111.04  3.000
 H6B  H3   C3  O1   110.02  3.000
 H6B  H3   C3  C4   107.05  3.000
 H6B  O1   C3  C4   108.63  3.000
 H6B  H3   C3  C2   107.38  3.000
 H6B  O1   C3  C2   110.67  3.000
 H6B  C4   C3  C2   113.01  3.000
 H6B  H4   C4  O2   110.52  3.000
 H6B  H4   C4  C5   108.52  3.000
 H6B  O2   C4  C5   106.42  3.000
 H6B  H4   C4  C3   107.34  3.000
 H6B  O2   C4  C3   110.81  3.000
 H6B  C5   C4  C3   113.23  3.000
 H6B  H5   C5  N1   116.85  3.000
 H6B  H5   C5  C6   116.58  3.000
 H6B  N1   C5  C6    59.25  3.000
 H6B  H5   C5  C4   113.82  3.000
 H6B  C6   C5  C4   122.11  3.000
 H6B  N1   C5  C4   117.59  3.000
 H6B  H6   C6  N1   116.61  3.000
 H6B  H6   C6  C5   115.56  3.000
 H6B  N1   C6  C5    58.84  3.000
 H6B  H6   C6  C1   116.29  3.000
 H6B  C5   C6  C1   120.76  3.000
 H6B  N1   C6  C1   116.44  3.000
 H6B  C8   N1  C6   116.86  3.000
 H6B  C6   N1  C5    61.91  3.000
 H6B  C8   N1  C5   116.68  3.000
 H6B  H8   O1  C3   108.33  3.000
 H6B  H9   O2  C4   108.22  3.000
 H6B  H10  O3  C2   109.72  3.000
 H6B  O5   C7  O4   122.81  3.000
 H6B  O5   C7  C1   111.59  3.000
 H6B  O4   C7  C1   125.59  3.000
 H6B  H11  O5  C7   109.97  3.000
 H6B  H14  C8  H13  107.97  3.000
 H6B  H14  C8  H12  107.87  3.000
 H6B  H13  C8  H12  107.98  3.000
 H6B  H14  C8  N1   109.53  3.000
 H6B  H13  C8  N1   109.62  3.000
 H6B  H12  C8  N1   113.70  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
 H6B  CONST_01  H11  O5  C7  C1   180.00   0.0  0
 H6B  Var_01    C5   N1  C6  C1   111.51  30.0  1
 H6B  Var_02    C6   N1  C5  C4  -112.77  30.0  1
 H6B  Var_03    H12  C8  N1  C5    35.57  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
 H6B  chir_01  C1  C6  C7  C2  negativ
 H6B  chir_02  C2  O3  C1  C3  positiv
 H6B  chir_03  C3  O1  C2  C4  negativ
 H6B  chir_04  C4  O2  C3  C5  positiv
 H6B  chir_05  C5  N1  C6  C4  both
 H6B  chir_06  C6  N1  C5  C1  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
 H6B  plan-1  C1   0.020
 H6B  plan-1  C7   0.020
 H6B  plan-1  O4   0.020
 H6B  plan-1  O5   0.020
 H6B  plan-1  H11  0.020

