# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  2 03:39:42 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: {(5R)-5-amino-5-carboxy-5-[1-(3,4-dichlorobenzyl)piperidin-4-yl]pentyl}(trihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@](CCCC[B-](O)(O)O)(C1CCN(CC1)Cc2ccc(Cl)c(Cl)c2)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
 XA2  XA2  {(5R)-5-amino-5-carboxy-5-[1-(3,4-dichlorobenzyl)piperidin-4-yl]pentyl}(trihydroxy)borate(1-)  ligand  56  28  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XA2
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
 XA2  O01  O   OB     0  -0.754   7.9080  -2.1107   1.4046
 XA2  B02  B   B     -1   0.427   7.5893  -2.3694  -0.0171
 XA2  O03  O   OB     0  -0.747   8.9210  -2.3741  -0.6639
 XA2  O04  O   OB     0  -0.750   6.8897  -3.6668  -0.1961
 XA2  C05  C   CH2    0  -0.637   6.6125  -1.2134  -0.6645
 XA2  C06  C   CH2    0  -0.429   5.2601  -1.0193   0.0160
 XA2  C07  C   CH2    0  -0.403   4.3970   0.0691  -0.6165
 XA2  C08  C   CH2    0  -0.419   3.0649   0.2582   0.0997
 XA2  C09  C   CT     0  -0.030   2.1617   1.3685  -0.4701
 XA2  N10  N   NH2    0  -0.800   1.8742   1.0602  -1.8590
 XA2  C11  C   CH1    0  -0.216   0.8976   1.5493   0.4267
 XA2  C12  C   CH2    0  -0.447   0.0462   2.7528   0.0181
 XA2  C13  C   CH2    0  -0.273  -1.1863   2.8867   0.8993
 XA2  N14  N   NT     0  -0.416  -1.9889   1.6817   0.8392
 XA2  C15  C   CH2    0  -0.308  -3.2562   1.8153   1.5171
 XA2  C16  C   CR6    0   0.081  -4.2461   0.7620   1.0864
 XA2  C17  C   CR16   0  -0.312  -5.1667   0.2319   1.9822
 XA2  C18  C   CR16   0  -0.202  -6.1035  -0.7033   1.5709
 XA2  C19  C   CR6    0  -0.020  -6.1264  -1.1268   0.2517
 XA2  CL1  CL  CL     0  -0.103  -7.2872  -2.2986  -0.2502
 XA2  C21  C   CR6    0   0.022  -5.2054  -0.6052  -0.6509
 XA2  CL2  CL  CL     0  -0.104  -5.2078  -1.1190  -2.2977
 XA2  C23  C   CR16   0  -0.246  -4.2745   0.3319  -0.2353
 XA2  C24  C   CH2    0  -0.277  -1.2342   0.5331   1.3023
 XA2  C25  C   CH2    0  -0.436   0.0047   0.3090   0.4502
 XA2  C26  C   C      0   0.561   2.9500   2.6729  -0.3643
 XA2  O27  O   O      0  -0.452   3.3738   3.1009   0.6835
 XA2  O28  O   OH1    0  -0.581   3.1183   3.3074  -1.5141
 XA2  H1   H   H      0   0.417   7.0918  -1.9440   1.8802
 XA2  H2   H   H      0   0.417   8.7928  -2.3780  -1.6149
 XA2  H3   H   H      0   0.418   7.4492  -4.3680   0.1504
 XA2  H4   H   HCH2   0   0.152   7.1356  -0.2451  -0.6570
 XA2  H5   H   HCH2   0   0.150   6.4303  -1.4206  -1.7307
 XA2  H6   H   HCH2   0   0.192   4.7011  -1.9617   0.0164
 XA2  H7   H   HCH2   0   0.176   5.4094  -0.7650   1.0739
 XA2  H8   H   HCH2   0   0.203   4.9713   1.0027  -0.6157
 XA2  H9   H   HCH2   0   0.208   4.2193  -0.1751  -1.6670
 XA2  H10  H   HCH2   0   0.233   2.5094  -0.6839   0.0631
 XA2  H11  H   HCH2   0   0.227   3.2401   0.4627   1.1591
 XA2  H12  H   HNH2   0   0.352   1.5056   0.1201  -1.9231
 XA2  H13  H   HNH2   0   0.349   1.1618   1.6711  -2.2389
 XA2  H15  H   HCH1   0   0.223   1.2540   1.7252   1.4487
 XA2  H16  H   HCH2   0   0.241   0.6130   3.6853   0.0806
 XA2  H17  H   HCH2   0   0.216  -0.2873   2.6487  -1.0193
 XA2  H18  H   HCH2   0   0.189  -0.8731   3.1191   1.9323
 XA2  H19  H   HCH2   0   0.238  -1.7899   3.7293   0.5541
 XA2  H21  H   HCH2   0   0.218  -3.1582   1.7941   2.6149
 XA2  H22  H   HCH2   0   0.260  -3.6725   2.7967   1.2693
 XA2  H23  H   HCR6   0   0.264  -5.1553   0.5448   3.0188
 XA2  H24  H   HCR6   0   0.286  -6.8136  -1.1118   2.2770
 XA2  H25  H   HCR6   0   0.276  -3.5527   0.7254  -0.9389
 XA2  H26  H   HCH2   0   0.194  -0.9401   0.6514   2.3608
 XA2  H27  H   HCH2   0   0.241  -1.8691  -0.3545   1.2522
 XA2  H28  H   HCH2   0   0.213  -0.3140   0.0547  -0.5650
 XA2  H29  H   HCH2   0   0.241   0.5402  -0.5544   0.8479
 XA2  H30  H   HOH1   0   0.477   3.6082   4.1294  -1.3581

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
 XA2  CL2  C21  single    1.725  0.020  1.725
 XA2  CL1  C19  single    1.724  0.020  1.724
 XA2  C21  C19  aromatic  1.391  0.020  1.391
 XA2  C21  C23  aromatic  1.385  0.020  1.385
 XA2  C19  C18  aromatic  1.386  0.020  1.386
 XA2  C23  C16  aromatic  1.390  0.020  1.390
 XA2  C18  C17  aromatic  1.386  0.020  1.386
 XA2  C16  C17  aromatic  1.390  0.020  1.390
 XA2  C16  C15  single    1.508  0.020  1.508
 XA2  C15  N14  single    1.443  0.020  1.443
 XA2  C13  N14  single    1.449  0.020  1.449
 XA2  C13  C12  single    1.521  0.020  1.521
 XA2  N14  C24  single    1.450  0.020  1.450
 XA2  C12  C11  single    1.530  0.020  1.530
 XA2  C24  C25  single    1.520  0.020  1.520
 XA2  O27  C26  double    1.209  0.020  1.209
 XA2  C11  C25  single    1.528  0.020  1.528
 XA2  C11  C09  single    1.560  0.020  1.560
 XA2  C26  O28  single    1.324  0.020  1.324
 XA2  C26  C09  single    1.528  0.020  1.528
 XA2  C09  N10  single    1.451  0.020  1.451
 XA2  C09  C08  single    1.540  0.020  1.540
 XA2  C08  C07  single    1.524  0.020  1.524
 XA2  C07  C06  single    1.526  0.020  1.526
 XA2  C06  C05  single    1.526  0.020  1.526
 XA2  C05  B02  single    1.646  0.020  1.646
 XA2  O04  B02  single    1.485  0.020  1.485
 XA2  B02  O01  single    1.480  0.020  1.480
 XA2  B02  O03  single    1.480  0.020  1.480
 XA2  O01  H1   single    0.850  0.020  0.980
 XA2  O03  H2   single    0.850  0.020  0.980
 XA2  O04  H3   single    0.850  0.020  0.980
 XA2  C05  H4   single    0.970  0.020  1.090
 XA2  C05  H5   single    0.970  0.020  1.090
 XA2  C06  H6   single    0.970  0.020  1.090
 XA2  C06  H7   single    0.970  0.020  1.090
 XA2  C07  H8   single    0.970  0.020  1.090
 XA2  C07  H9   single    0.970  0.020  1.090
 XA2  C08  H10  single    0.970  0.020  1.090
 XA2  C08  H11  single    0.970  0.020  1.090
 XA2  N10  H12  single    0.890  0.020  1.040
 XA2  N10  H13  single    0.890  0.020  1.040
 XA2  C11  H15  single    0.970  0.020  1.090
 XA2  C12  H16  single    0.970  0.020  1.090
 XA2  C12  H17  single    0.970  0.020  1.090
 XA2  C13  H18  single    0.970  0.020  1.090
 XA2  C13  H19  single    0.970  0.020  1.090
 XA2  C15  H21  single    0.970  0.020  1.090
 XA2  C15  H22  single    0.970  0.020  1.090
 XA2  C17  H23  single    0.930  0.020  1.080
 XA2  C18  H24  single    0.930  0.020  1.080
 XA2  C23  H25  single    0.930  0.020  1.080
 XA2  C24  H26  single    0.970  0.020  1.090
 XA2  C24  H27  single    0.970  0.020  1.090
 XA2  C25  H28  single    0.970  0.020  1.090
 XA2  C25  H29  single    0.970  0.020  1.090
 XA2  O28  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
 XA2  H1   O01  B02  108.87  3.000
 XA2  C05  B02  O04  106.66  3.000
 XA2  O04  B02  O03  111.61  3.000
 XA2  C05  B02  O03  111.35  3.000
 XA2  O03  B02  O01  103.10  3.000
 XA2  O04  B02  O01  111.72  3.000
 XA2  C05  B02  O01  112.51  3.000
 XA2  H2   O03  B02  108.23  3.000
 XA2  H3   O04  B02  108.63  3.000
 XA2  H5   C05  H4   104.53  3.000
 XA2  H5   C05  C06  108.00  3.000
 XA2  H4   C05  C06  107.83  3.000
 XA2  H5   C05  B02  110.29  3.000
 XA2  H4   C05  B02  109.46  3.000
 XA2  C06  C05  B02  116.09  3.000
 XA2  H7   C06  H6   105.55  3.000
 XA2  H7   C06  C07  108.11  3.000
 XA2  H6   C06  C07  108.97  3.000
 XA2  H7   C06  C05  109.78  3.000
 XA2  H6   C06  C05  110.05  3.000
 XA2  C07  C06  C05  114.02  3.000
 XA2  H9   C07  H8   106.03  3.000
 XA2  H9   C07  C08  109.71  3.000
 XA2  H8   C07  C08  110.61  3.000
 XA2  H9   C07  C06  109.32  3.000
 XA2  H8   C07  C06  108.11  3.000
 XA2  C08  C07  C06  112.83  3.000
 XA2  H11  C08  H10  105.96  3.000
 XA2  H11  C08  C09  108.52  3.000
 XA2  H10  C08  C09  108.09  3.000
 XA2  H11  C08  C07  109.78  3.000
 XA2  H10  C08  C07  108.73  3.000
 XA2  C09  C08  C07  115.34  3.000
 XA2  C26  C09  C11  106.22  3.000
 XA2  C26  C09  N10  110.47  3.000
 XA2  C11  C09  N10  114.46  3.000
 XA2  N10  C09  C08  108.48  3.000
 XA2  C26  C09  C08  106.69  3.000
 XA2  C11  C09  C08  110.24  3.000
 XA2  H13  N10  H12  106.29  3.000
 XA2  H13  N10  C09  111.73  3.000
 XA2  H12  N10  C09  109.27  3.000
 XA2  H15  C11  C25  107.80  3.000
 XA2  H15  C11  C12  107.68  3.000
 XA2  C25  C11  C12  108.50  3.000
 XA2  H15  C11  C09  106.91  3.000
 XA2  C25  C11  C09  112.83  3.000
 XA2  C12  C11  C09  112.86  3.000
 XA2  H17  C12  H16  107.05  3.000
 XA2  H17  C12  C13  108.09  3.000
 XA2  H16  C12  C13  108.18  3.000
 XA2  H17  C12  C11  110.36  3.000
 XA2  H16  C12  C11  111.55  3.000
 XA2  C13  C12  C11  111.44  3.000
 XA2  H19  C13  H18  106.86  3.000
 XA2  H19  C13  N14  108.80  3.000
 XA2  H18  C13  N14  111.77  3.000
 XA2  H19  C13  C12  109.43  3.000
 XA2  H18  C13  C12  109.31  3.000
 XA2  N14  C13  C12  110.58  3.000
 XA2  C24  N14  C15  112.35  3.000
 XA2  C24  N14  C13  110.93  3.000
 XA2  C15  N14  C13  112.95  3.000
 XA2  H22  C15  H21  106.05  3.000
 XA2  H22  C15  C16  108.17  3.000
 XA2  H21  C15  C16  109.23  3.000
 XA2  H22  C15  N14  108.10  3.000
 XA2  H21  C15  N14  112.82  3.000
 XA2  C16  C15  N14  112.18  3.000
 XA2  C23  C16  C17  118.77  3.000
 XA2  C17  C16  C15  121.14  3.000
 XA2  C23  C16  C15  120.07  3.000
 XA2  H23  C17  C18  119.09  3.000
 XA2  H23  C17  C16  119.99  3.000
 XA2  C18  C17  C16  120.92  3.000
 XA2  H24  C18  C19  119.69  3.000
 XA2  H24  C18  C17  120.32  3.000
 XA2  C19  C18  C17  119.99  3.000
 XA2  C21  C19  CL1  120.78  3.000
 XA2  C21  C19  C18  119.48  3.000
 XA2  CL1  C19  C18  119.73  3.000
 XA2  C23  C21  CL2  119.28  3.000
 XA2  C23  C21  C19  120.27  3.000
 XA2  CL2  C21  C19  120.45  3.000
 XA2  H25  C23  C21  119.96  3.000
 XA2  H25  C23  C16  119.47  3.000
 XA2  C21  C23  C16  120.57  3.000
 XA2  H27  C24  H26  106.59  3.000
 XA2  H27  C24  C25  109.16  3.000
 XA2  H26  C24  C25  109.62  3.000
 XA2  H27  C24  N14  109.05  3.000
 XA2  H26  C24  N14  111.08  3.000
 XA2  C25  C24  N14  111.22  3.000
 XA2  H29  C25  H28  107.29  3.000
 XA2  H29  C25  C24  108.20  3.000
 XA2  H28  C25  C24  108.48  3.000
 XA2  H29  C25  C11  111.17  3.000
 XA2  H28  C25  C11  110.15  3.000
 XA2  C24  C25  C11  111.41  3.000
 XA2  O28  C26  O27  122.59  3.000
 XA2  O28  C26  C09  114.49  3.000
 XA2  O27  C26  C09  122.91  3.000
 XA2  H30  O28  C26  109.32  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
 XA2  CONST_01  C19  C21  C23  C16     0.00   0.0  0
 XA2  CONST_02  C19  C18  C17  C16     0.00   0.0  0
 XA2  CONST_03  C21  C19  C18  C17     0.00   0.0  0
 XA2  CONST_04  C21  C23  C16  C17     0.00   0.0  0
 XA2  CONST_05  C23  C21  C19  C18     0.00   0.0  0
 XA2  CONST_06  C23  C16  C17  C18     0.00   0.0  0
 XA2  CONST_07  C21  C23  C16  C15   180.00   0.0  0
 XA2  CONST_08  C18  C17  C16  C15   180.00   0.0  0
 XA2  CONST_09  CL2  C21  C23  C16   180.00   0.0  0
 XA2  CONST_10  CL1  C19  C18  C17   180.00   0.0  0
 XA2  CONST_11  CL2  C21  C19  C18   180.00   0.0  0
 XA2  CONST_12  C23  C21  C19  CL1   180.00   0.0  0
 XA2  CONST_13  H24  C18  C17  C16   180.00   0.0  0
 XA2  CONST_14  H25  C23  C16  C17   180.00   0.0  0
 XA2  CONST_15  H23  C17  C18  C19   180.00   0.0  0
 XA2  CONST_16  H30  O28  C26  C09   180.00   0.0  0
 XA2  Var_01    N14  C13  C12  C11   -57.87  30.0  1
 XA2  Var_02    N14  C24  C25  C11    56.76  30.0  1
 XA2  Var_03    C24  N14  C13  C12    60.39  30.0  1
 XA2  Var_04    C25  C24  N14  C13   -60.04  30.0  1
 XA2  Var_05    C16  C15  N14  C13   161.55  30.0  1
 XA2  Var_06    C23  C16  C15  N14   -36.25  30.0  2
 XA2  Var_07    C06  C05  B02  O01   -58.94  30.0  3
 XA2  Var_08    C07  C06  C05  B02   179.63  30.0  1
 XA2  Var_09    C08  C07  C06  C05  -178.91  30.0  1
 XA2  Var_10    C09  C08  C07  C06   178.53  30.0  1

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
 XA2  chir_01  C09  C11  N10  C08  positiv
 XA2  chir_02  C11  C12  C25  C09  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
 XA2  plan-1  C15  0.020
 XA2  plan-1  C16  0.020
 XA2  plan-1  C17  0.020
 XA2  plan-1  C18  0.020
 XA2  plan-1  C19  0.020
 XA2  plan-1  CL1  0.020
 XA2  plan-1  C21  0.020
 XA2  plan-1  CL2  0.020
 XA2  plan-1  C23  0.020
 XA2  plan-1  H23  0.020
 XA2  plan-1  H24  0.020
 XA2  plan-1  H25  0.020
 XA2  plan-2  C09  0.020
 XA2  plan-2  C26  0.020
 XA2  plan-2  O27  0.020
 XA2  plan-2  O28  0.020
 XA2  plan-2  H30  0.020

