# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 15:09:30 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: {(5R)-5-amino-5-carboxy-5-[(3-endo)-8-(3,4-dichlorobenzyl)-8-azabicyclo[3.2.1]oct-3-yl]pentyl}(trihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@](CCCC[B-](O)(O)O)(C1C[C@H]2CC[C@@H](C1)N2Cc3ccc(Cl)c(Cl)c3)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
 38I  38I  {(5R)-5-amino-5-carboxy-5-[(3-endo)-8-(3,4-dichlorobenzyl)-8-azabicyclo[3.2.1]oct-3-yl]pentyl}(trihydroxy)borate(1-)  ligand  59  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_38I
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
 38I  CL2  CL  CL     0  -0.102  29.3025  87.2897  78.3970
 38I  C26  C   CR6    0   0.024  30.3610  85.9843  78.0119
 38I  C25  C   CR6    0  -0.023  31.1247  85.3784  78.9996
 38I  CL1  CL  CL     0  -0.104  31.0366  85.9101  80.6369
 38I  C24  C   CR16   0  -0.204  31.9741  84.3326  78.6626
 38I  C23  C   CR16   0  -0.281  32.0551  83.8995  77.3520
 38I  C27  C   CR16   0  -0.284  30.4500  85.5473  76.6968
 38I  C22  C   CR6    0   0.110  31.2913  84.4993  76.3533
 38I  C21  C   CH2    0  -0.336  31.3709  84.0139  74.9301
 38I  N16  N   NT     0  -0.415  32.7420  83.8493  74.5140
 38I  C17  C   CH1    0  -0.101  32.9341  83.2650  73.1904
 38I  C19  C   CH2    0  -0.448  34.4604  83.2885  73.0733
 38I  C20  C   CH2    0  -0.450  34.8687  84.5344  73.8786
 38I  C15  C   CH1    0  -0.093  33.5449  85.0679  74.4399
 38I  C14  C   CH2    0  -0.477  32.9044  86.1342  73.5468
 38I  C18  C   CH2    0  -0.458  32.2350  84.0657  72.0828
 38I  C7   C   CH1    0  -0.204  32.2449  85.6108  72.2428
 38I  C4   C   CT     0  -0.052  32.7352  86.3531  70.9655
 38I  C1   C   C      0   0.429  32.4545  87.8724  71.2031
 38I  O3   O   OC    -1  -0.600  33.4061  88.6197  71.5088
 38I  O2   O   O      0  -0.616  31.2605  88.2286  71.0932
 38I  N6   N   NH2    0  -0.805  31.9324  85.8379  69.8525
 38I  C5   C   CH2    0  -0.381  34.2113  86.0760  70.6757
 38I  C8   C   CH2    0  -0.413  34.7606  86.6371  69.3663
 38I  C9   C   CH2    0  -0.421  36.2619  86.4058  69.2161
 38I  C10  C   CH2    0  -0.684  36.8590  86.9052  67.9020
 38I  B11  B   B     -1   0.454  38.4889  86.6847  67.7267
 38I  O30  O   OB     0  -0.742  38.9403  87.1802  66.4073
 38I  O13  O   OB     0  -0.746  39.2436  87.4128  68.7687
 38I  O12  O   OB     0  -0.748  38.8620  85.2547  67.8115
 38I  H1   H   HCR6   0   0.285  32.5723  83.8617  79.4307
 38I  H2   H   HCR6   0   0.261  32.7282  83.0907  77.1000
 38I  H3   H   HCR6   0   0.278  29.8539  86.0360  75.9364
 38I  H4   H   HCH2   0   0.222  30.7828  84.6877  74.2886
 38I  H5   H   HCH2   0   0.258  30.8811  83.0363  74.8644
 38I  H7   H   HCH1   0   0.224  32.5518  82.2394  73.1772
 38I  H8   H   HCH2   0   0.233  34.8841  82.3858  73.5159
 38I  H9   H   HCH2   0   0.227  34.7898  83.3236  72.0350
 38I  H10  H   HCH2   0   0.234  35.5472  84.2696  74.6906
 38I  H11  H   HCH2   0   0.230  35.3735  85.2839  73.2702
 38I  H12  H   HCH1   0   0.228  33.6853  85.4897  75.4392
 38I  H13  H   HCH2   0   0.239  33.6590  86.8910  73.3296
 38I  H14  H   HCH2   0   0.223  32.1444  86.6604  74.1330
 38I  H15  H   HCH2   0   0.221  31.1940  83.7372  72.0298
 38I  H16  H   HCH2   0   0.233  32.6650  83.7805  71.1219
 38I  H17  H   HCH1   0   0.220  31.1914  85.8979  72.3207
 38I  H19  H   HNH2   0   0.324  30.9794  86.1526  69.9969
 38I  H20  H   HNH2   0   0.334  32.2208  86.2947  68.9952
 38I  H22  H   HCH2   0   0.203  34.3742  84.9938  70.6716
 38I  H23  H   HCH2   0   0.205  34.8161  86.4695  71.4941
 38I  H24  H   HCH2   0   0.201  34.5557  87.7096  69.3043
 38I  H25  H   HCH2   0   0.186  34.2569  86.1750  68.5098
 38I  H26  H   HCH2   0   0.172  36.4530  85.3296  69.3286
 38I  H27  H   HCH2   0   0.184  36.7771  86.8827  70.0583
 38I  H28  H   HCH2   0   0.153  36.6065  87.9731  67.8018
 38I  H29  H   HCH2   0   0.152  36.3149  86.4170  67.0778
 38I  H30  H   H      0   0.414  38.2932  86.9231  65.7465
 38I  H31  H   H      0   0.413  38.7870  88.2330  68.9663
 38I  H32  H   H      0   0.414  38.4314  84.8638  68.5752

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
 38I  O30  B11  single    1.480  0.020  1.480
 38I  O12  B11  single    1.480  0.020  1.480
 38I  B11  O13  single    1.478  0.020  1.478
 38I  B11  C10  single    1.654  0.020  1.654
 38I  C10  C9   single    1.527  0.020  1.527
 38I  C9   C8   single    1.527  0.020  1.527
 38I  C8   C5   single    1.527  0.020  1.527
 38I  C5   C4   single    1.530  0.020  1.530
 38I  N6   C4   single    1.466  0.020  1.466
 38I  O2   C1   deloc     1.251  0.020  1.251
 38I  C4   C1   single    1.563  0.020  1.563
 38I  C4   C7   single    1.557  0.020  1.557
 38I  C1   O3   deloc     1.248  0.020  1.248
 38I  C18  C7   single    1.553  0.020  1.553
 38I  C18  C17  single    1.535  0.020  1.535
 38I  C7   C14  single    1.552  0.020  1.552
 38I  C17  C19  single    1.531  0.020  1.531
 38I  C17  N16  single    1.459  0.020  1.459
 38I  C14  C15  single    1.531  0.020  1.531
 38I  C19  C20  single    1.539  0.020  1.539
 38I  C21  N16  single    1.442  0.020  1.442
 38I  C21  C22  single    1.506  0.020  1.506
 38I  N16  C15  single    1.461  0.020  1.461
 38I  C15  C20  single    1.534  0.020  1.534
 38I  C22  C27  aromatic  1.387  0.020  1.387
 38I  C22  C23  aromatic  1.393  0.020  1.393
 38I  C27  C26  aromatic  1.389  0.020  1.389
 38I  CL2  C26  single    1.724  0.020  1.724
 38I  C23  C24  aromatic  1.383  0.020  1.383
 38I  C26  C25  aromatic  1.388  0.020  1.388
 38I  C24  C25  aromatic  1.389  0.020  1.389
 38I  C25  CL1  single    1.724  0.020  1.724
 38I  C24  H1   single    0.930  0.020  1.080
 38I  C23  H2   single    0.930  0.020  1.080
 38I  C27  H3   single    0.930  0.020  1.080
 38I  C21  H4   single    0.970  0.020  1.090
 38I  C21  H5   single    0.970  0.020  1.090
 38I  C17  H7   single    0.970  0.020  1.090
 38I  C19  H8   single    0.970  0.020  1.090
 38I  C19  H9   single    0.970  0.020  1.090
 38I  C20  H10  single    0.970  0.020  1.090
 38I  C20  H11  single    0.970  0.020  1.090
 38I  C15  H12  single    0.970  0.020  1.090
 38I  C14  H13  single    0.970  0.020  1.090
 38I  C14  H14  single    0.970  0.020  1.090
 38I  C18  H15  single    0.970  0.020  1.090
 38I  C18  H16  single    0.970  0.020  1.090
 38I  C7   H17  single    0.970  0.020  1.090
 38I  N6   H19  single    0.890  0.020  1.040
 38I  N6   H20  single    0.890  0.020  1.040
 38I  C5   H22  single    0.970  0.020  1.090
 38I  C5   H23  single    0.970  0.020  1.090
 38I  C8   H24  single    0.970  0.020  1.090
 38I  C8   H25  single    0.970  0.020  1.090
 38I  C9   H26  single    0.970  0.020  1.090
 38I  C9   H27  single    0.970  0.020  1.090
 38I  C10  H28  single    0.970  0.020  1.090
 38I  C10  H29  single    0.970  0.020  1.090
 38I  O30  H30  single    0.850  0.020  0.980
 38I  O13  H31  single    0.850  0.020  0.980
 38I  O12  H32  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
 38I  C27  C26  C25  120.09  3.000
 38I  C25  C26  CL2  120.63  3.000
 38I  C27  C26  CL2  119.29  3.000
 38I  C24  C25  CL1  119.61  3.000
 38I  CL1  C25  C26  120.88  3.000
 38I  C24  C25  C26  119.51  3.000
 38I  H1   C24  C23  120.30  3.000
 38I  H1   C24  C25  119.59  3.000
 38I  C23  C24  C25  120.11  3.000
 38I  H2   C23  C22  119.73  3.000
 38I  H2   C23  C24  119.43  3.000
 38I  C22  C23  C24  120.83  3.000
 38I  H3   C27  C22  120.07  3.000
 38I  H3   C27  C26  119.19  3.000
 38I  C22  C27  C26  120.74  3.000
 38I  C21  C22  C27  120.64  3.000
 38I  C27  C22  C23  118.71  3.000
 38I  C21  C22  C23  120.65  3.000
 38I  H5   C21  H4   105.81  3.000
 38I  H5   C21  N16  107.81  3.000
 38I  H4   C21  N16  114.18  3.000
 38I  H5   C21  C22  108.71  3.000
 38I  H4   C21  C22  108.98  3.000
 38I  N16  C21  C22  111.08  3.000
 38I  C15  N16  C17  102.45  3.000
 38I  C15  N16  C21  116.22  3.000
 38I  C17  N16  C21  115.62  3.000
 38I  H7   C17  C18  108.72  3.000
 38I  H7   C17  C19  111.20  3.000
 38I  C18  C17  C19  113.01  3.000
 38I  H7   C17  N16  109.88  3.000
 38I  C19  C17  N16  101.21  3.000
 38I  C18  C17  N16  112.68  3.000
 38I  H9   C19  H8   107.20  3.000
 38I  H9   C19  C20  113.10  3.000
 38I  H8   C19  C20  110.77  3.000
 38I  H9   C19  C17  112.01  3.000
 38I  H8   C19  C17  110.09  3.000
 38I  C20  C19  C17  103.70  3.000
 38I  H11  C20  H10  107.13  3.000
 38I  H11  C20  C15  111.41  3.000
 38I  H10  C20  C15  110.42  3.000
 38I  H11  C20  C19  112.82  3.000
 38I  H10  C20  C19  110.98  3.000
 38I  C15  C20  C19  104.13  3.000
 38I  H12  C15  C14  108.54  3.000
 38I  H12  C15  C20  110.96  3.000
 38I  C14  C15  C20  112.94  3.000
 38I  H12  C15  N16  110.24  3.000
 38I  C20  C15  N16  101.70  3.000
 38I  C14  C15  N16  112.37  3.000
 38I  H14  C14  H13  104.69  3.000
 38I  H14  C14  C7   108.48  3.000
 38I  H13  C14  C7   111.14  3.000
 38I  H14  C14  C15  108.22  3.000
 38I  H13  C14  C15  108.06  3.000
 38I  C7   C14  C15  115.65  3.000
 38I  H16  C18  H15  104.73  3.000
 38I  H16  C18  C7   110.39  3.000
 38I  H15  C18  C7   108.06  3.000
 38I  H16  C18  C17  108.65  3.000
 38I  H15  C18  C17  108.18  3.000
 38I  C7   C18  C17  116.20  3.000
 38I  H17  C7   C4   103.68  3.000
 38I  H17  C7   C18  105.19  3.000
 38I  C4   C7   C18  113.07  3.000
 38I  H17  C7   C14  105.11  3.000
 38I  C18  C7   C14  115.13  3.000
 38I  C4   C7   C14  113.25  3.000
 38I  C5   C4   N6   108.72  3.000
 38I  N6   C4   C1   111.02  3.000
 38I  C5   C4   C1   112.22  3.000
 38I  C1   C4   C7   106.39  3.000
 38I  N6   C4   C7   106.43  3.000
 38I  C5   C4   C7   111.90  3.000
 38I  O2   C1   O3   125.37  3.000
 38I  O3   C1   C4   118.83  3.000
 38I  O2   C1   C4   115.78  3.000
 38I  H20  N6   H19  104.36  3.000
 38I  H20  N6   C4   109.15  3.000
 38I  H19  N6   C4   107.31  3.000
 38I  H23  C5   H22  106.08  3.000
 38I  H23  C5   C8   108.14  3.000
 38I  H22  C5   C8   107.86  3.000
 38I  H23  C5   C4   109.11  3.000
 38I  H22  C5   C4   108.88  3.000
 38I  C8   C5   C4   116.30  3.000
 38I  H25  C8   H24  106.44  3.000
 38I  H25  C8   C9   108.13  3.000
 38I  H24  C8   C9   109.10  3.000
 38I  H25  C8   C5   110.49  3.000
 38I  H24  C8   C5   109.98  3.000
 38I  C9   C8   C5   112.49  3.000
 38I  H27  C9   H26  105.41  3.000
 38I  H27  C9   C10  109.57  3.000
 38I  H26  C9   C10  109.90  3.000
 38I  H27  C9   C8   108.70  3.000
 38I  H26  C9   C8   108.02  3.000
 38I  C10  C9   C8   114.81  3.000
 38I  H29  C10  H28  104.38  3.000
 38I  H29  C10  B11  110.38  3.000
 38I  H28  C10  B11  110.20  3.000
 38I  H29  C10  C9   107.80  3.000
 38I  H28  C10  C9   107.79  3.000
 38I  B11  C10  C9   115.64  3.000
 38I  O12  B11  O13  107.86  3.000
 38I  O13  B11  O30  107.93  3.000
 38I  O12  B11  O30  107.32  3.000
 38I  O13  B11  C10  111.27  3.000
 38I  O12  B11  C10  111.78  3.000
 38I  O30  B11  C10  110.51  3.000
 38I  H30  O30  B11  108.57  3.000
 38I  H31  O13  B11  108.86  3.000
 38I  H32  O12  B11  109.02  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
 38I  CONST_01  C23  C22  C27  C26    0.00   0.0  0
 38I  CONST_02  C23  C24  C25  C26    0.00   0.0  0
 38I  CONST_03  C22  C27  C26  C25    0.00   0.0  0
 38I  CONST_04  C22  C23  C24  C25    0.00   0.0  0
 38I  CONST_05  C27  C22  C23  C24    0.00   0.0  0
 38I  CONST_06  C27  C26  C25  C24    0.00   0.0  0
 38I  CONST_07  C22  C27  C26  CL2  180.00   0.0  0
 38I  CONST_08  C24  C25  C26  CL2  180.00   0.0  0
 38I  CONST_09  C21  C22  C27  C26  180.00   0.0  0
 38I  CONST_10  C27  C26  C25  CL1  180.00   0.0  0
 38I  CONST_11  C23  C24  C25  CL1  180.00   0.0  0
 38I  CONST_12  C21  C22  C23  C24  180.00   0.0  0
 38I  CONST_13  H1   C24  C25  C26  180.00   0.0  0
 38I  CONST_14  H3   C27  C26  C25  180.00   0.0  0
 38I  CONST_15  H2   C23  C24  C25  180.00   0.0  0
 38I  Var_01    C15  C20  C19  C17    2.74  30.0  3
 38I  Var_02    N16  C21  C22  C23  -47.04  30.0  2
 38I  Var_03    C17  N16  C21  C22  174.60  30.0  3
 38I  Var_04    C9   C8   C5   C4   175.51  30.0  2
 38I  Var_05    C10  C9   C8   C5   178.04  30.0  1
 38I  Var_06    B11  C10  C9   C8   179.15  30.0  1
 38I  Var_07    O30  B11  C10  C9   178.77  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
 38I  chir_01  C17  C18  C19  N16  negativ
 38I  chir_02  C15  N16  C20  C14  negativ
 38I  chir_03  C7   C14  C18  C4   positiv
 38I  chir_04  C4   C5   C1   C7   positiv

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
 38I  plan-1  CL2  0.020
 38I  plan-1  C26  0.020
 38I  plan-1  C25  0.020
 38I  plan-1  CL1  0.020
 38I  plan-1  C24  0.020
 38I  plan-1  C23  0.020
 38I  plan-1  C27  0.020
 38I  plan-1  C22  0.020
 38I  plan-1  C21  0.020
 38I  plan-1  H1   0.020
 38I  plan-1  H2   0.020
 38I  plan-1  H3   0.020
 38I  plan-2  C4   0.020
 38I  plan-2  C1   0.020
 38I  plan-2  O3   0.020
 38I  plan-2  O2   0.020

