# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  2 01:28:01 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: {(5R)-5-amino-5-carboxy-5-[1-(4-chlorobenzyl)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)cc2)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
 XA1  XA1  {(5R)-5-amino-5-carboxy-5-[1-(4-chlorobenzyl)piperidin-4-yl]pentyl}(trihydroxy)borate(1-)  ligand  56  27  .  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_XA1
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
 XA1  CL1  CL  CL     0  -0.136   7.5357  -2.8386  -0.0607
 XA1  C23  C   CR6    0  -0.056   6.3330  -1.5983   0.1048
 XA1  C22  C   CR16   0  -0.200   6.3764  -0.4912  -0.7313
 XA1  C21  C   CR16   0  -0.288   5.4141   0.4957  -0.5936
 XA1  C24  C   CR16   0  -0.196   5.3454  -1.7291   1.0656
 XA1  C25  C   CR16   0  -0.318   4.3893  -0.7284   1.1868
 XA1  C20  C   CR6    0   0.108   4.4116   0.3947   0.3692
 XA1  C19  C   CH2    0  -0.339   3.3898   1.4877   0.5288
 XA1  N16  N   NT     0  -0.398   2.7535   1.8350  -0.7292
 XA1  C15  C   CH2    0  -0.324   1.9432   3.0377  -0.6234
 XA1  C14  C   CH2    0  -0.451   0.6538   2.8495   0.1762
 XA1  C17  C   CH2    0  -0.316   1.9612   0.7582  -1.3026
 XA1  C18  C   CH2    0  -0.462   0.6713   0.4565  -0.5385
 XA1  C13  C   CH1    0  -0.186  -0.1943   1.7134  -0.4050
 XA1  C4   C   CT     0  -0.039  -1.5012   1.4644   0.3997
 XA1  C1   C   C      0   0.559  -2.2532   2.7912   0.4310
 XA1  O3   O   OH1    0  -0.583  -2.4781   3.2643   1.6475
 XA1  O2   O   O      0  -0.450  -2.6251   3.3583  -0.5686
 XA1  N5   N   NH2    0  -0.800  -1.1575   1.0371   1.7476
 XA1  C6   C   CH2    0  -0.410  -2.4094   0.4580  -0.3463
 XA1  C7   C   CH2    0  -0.418  -3.7648   0.2049   0.3053
 XA1  C8   C   CH2    0  -0.424  -4.5651  -0.8966  -0.3853
 XA1  C9   C   CH2    0  -0.639  -5.9171  -1.1824   0.2631
 XA1  B10  B   B     -1   0.429  -6.7989  -2.3958  -0.4146
 XA1  O27  O   OB     0  -0.747  -8.0437  -2.6461   0.3459
 XA1  O12  O   OB     0  -0.751  -7.0836  -1.9887  -1.8141
 XA1  O11  O   OB     0  -0.753  -6.1013  -3.6993  -0.3545
 XA1  H1   H   HCR6   0   0.277   7.1516  -0.3986  -1.4802
 XA1  H2   H   HCR6   0   0.255   5.4394   1.3562  -1.2503
 XA1  H3   H   HCR6   0   0.277   5.3135  -2.5977   1.7094
 XA1  H4   H   HCR6   0   0.258   3.6140  -0.8343   1.9361
 XA1  H5   H   HCH2   0   0.218   2.6809   1.2008   1.3194
 XA1  H6   H   HCH2   0   0.254   3.8922   2.3877   0.8978
 XA1  H8   H   HCH2   0   0.237   2.5472   3.8334  -0.1796
 XA1  H9   H   HCH2   0   0.228   1.6912   3.3645  -1.6385
 XA1  H10  H   HCH2   0   0.231   0.8807   2.6368   1.2237
 XA1  H11  H   HCH2   0   0.236   0.1066   3.7965   0.1631
 XA1  H12  H   HCH2   0   0.229   1.7107   1.0406  -2.3306
 XA1  H13  H   HCH2   0   0.243   2.5724  -0.1442  -1.3691
 XA1  H14  H   HCH2   0   0.245   0.1368  -0.3353  -1.0667
 XA1  H15  H   HCH2   0   0.217   0.9257   0.0572   0.4484
 XA1  H16  H   HCH1   0   0.224  -0.5013   2.0053  -1.4165
 XA1  H17  H   HOH1   0   0.479  -2.9785   4.0927   1.5875
 XA1  H18  H   HNH2   0   0.351  -1.9865   0.9475   2.3213
 XA1  H19  H   HNH2   0   0.350  -0.7683   0.1034   1.6981
 XA1  H21  H   HCH2   0   0.220  -2.5570   0.7915  -1.3775
 XA1  H22  H   HCH2   0   0.231  -1.8709  -0.4921  -0.4068
 XA1  H23  H   HCH2   0   0.195  -3.6287  -0.0756   1.3551
 XA1  H24  H   HCH2   0   0.208  -4.3671   1.1206   0.3094
 XA1  H25  H   HCH2   0   0.193  -4.7065  -0.6301  -1.4383
 XA1  H26  H   HCH2   0   0.177  -3.9518  -1.8078  -0.3912
 XA1  H27  H   HCH2   0   0.152  -5.7396  -1.4103   1.3248
 XA1  H28  H   HCH2   0   0.151  -6.4937  -0.2441   0.2732
 XA1  H29  H   H      0   0.417  -8.4744  -1.8035   0.5047
 XA1  H30  H   H      0   0.418  -7.6092  -2.6758  -2.2339
 XA1  H31  H   H      0   0.416  -5.2246  -3.5977  -0.7305

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
 XA1  O27  B10  single    1.480  0.020  1.480
 XA1  O12  B10  single    1.485  0.020  1.485
 XA1  B10  O11  single    1.480  0.020  1.480
 XA1  B10  C9   single    1.646  0.020  1.646
 XA1  C9   C8   single    1.526  0.020  1.526
 XA1  C8   C7   single    1.527  0.020  1.527
 XA1  C7   C6   single    1.525  0.020  1.525
 XA1  C6   C4   single    1.547  0.020  1.547
 XA1  N5   C4   single    1.455  0.020  1.455
 XA1  O2   C1   double    1.208  0.020  1.208
 XA1  C4   C1   single    1.525  0.020  1.525
 XA1  C4   C13  single    1.555  0.020  1.555
 XA1  C1   O3   single    1.325  0.020  1.325
 XA1  C13  C18  single    1.532  0.020  1.532
 XA1  C13  C14  single    1.532  0.020  1.532
 XA1  C18  C17  single    1.529  0.020  1.529
 XA1  C14  C15  single    1.529  0.020  1.529
 XA1  C17  N16  single    1.455  0.020  1.455
 XA1  C15  N16  single    1.454  0.020  1.454
 XA1  N16  C19  single    1.452  0.020  1.452
 XA1  C19  C20  single    1.505  0.020  1.505
 XA1  C20  C21  aromatic  1.394  0.020  1.394
 XA1  C20  C25  aromatic  1.389  0.020  1.389
 XA1  C21  C22  aromatic  1.385  0.020  1.385
 XA1  C25  C24  aromatic  1.389  0.020  1.389
 XA1  C22  C23  aromatic  1.388  0.020  1.388
 XA1  C24  C23  aromatic  1.384  0.020  1.384
 XA1  C23  CL1  single    1.736  0.020  1.736
 XA1  C22  H1   single    0.930  0.020  1.080
 XA1  C21  H2   single    0.930  0.020  1.080
 XA1  C24  H3   single    0.930  0.020  1.080
 XA1  C25  H4   single    0.930  0.020  1.080
 XA1  C19  H5   single    0.970  0.020  1.090
 XA1  C19  H6   single    0.970  0.020  1.090
 XA1  C15  H8   single    0.970  0.020  1.090
 XA1  C15  H9   single    0.970  0.020  1.090
 XA1  C14  H10  single    0.970  0.020  1.090
 XA1  C14  H11  single    0.970  0.020  1.090
 XA1  C17  H12  single    0.970  0.020  1.090
 XA1  C17  H13  single    0.970  0.020  1.090
 XA1  C18  H14  single    0.970  0.020  1.090
 XA1  C18  H15  single    0.970  0.020  1.090
 XA1  C13  H16  single    0.970  0.020  1.090
 XA1  O3   H17  single    0.850  0.020  0.980
 XA1  N5   H18  single    0.890  0.020  1.040
 XA1  N5   H19  single    0.890  0.020  1.040
 XA1  C6   H21  single    0.970  0.020  1.090
 XA1  C6   H22  single    0.970  0.020  1.090
 XA1  C7   H23  single    0.970  0.020  1.090
 XA1  C7   H24  single    0.970  0.020  1.090
 XA1  C8   H25  single    0.970  0.020  1.090
 XA1  C8   H26  single    0.970  0.020  1.090
 XA1  C9   H27  single    0.970  0.020  1.090
 XA1  C9   H28  single    0.970  0.020  1.090
 XA1  O27  H29  single    0.850  0.020  0.980
 XA1  O12  H30  single    0.850  0.020  0.980
 XA1  O11  H31  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
 XA1  C24  C23  C22  121.06  3.000
 XA1  C24  C23  CL1  119.55  3.000
 XA1  C22  C23  CL1  119.40  3.000
 XA1  H1   C22  C21  120.38  3.000
 XA1  H1   C22  C23  120.51  3.000
 XA1  C21  C22  C23  119.11  3.000
 XA1  H2   C21  C20  119.57  3.000
 XA1  H2   C21  C22  119.32  3.000
 XA1  C20  C21  C22  121.12  3.000
 XA1  H3   C24  C25  120.41  3.000
 XA1  H3   C24  C23  120.67  3.000
 XA1  C25  C24  C23  118.92  3.000
 XA1  H4   C25  C20  119.84  3.000
 XA1  H4   C25  C24  118.84  3.000
 XA1  C20  C25  C24  121.32  3.000
 XA1  C19  C20  C25  120.92  3.000
 XA1  C25  C20  C21  118.47  3.000
 XA1  C19  C20  C21  120.61  3.000
 XA1  H6   C19  H5   105.55  3.000
 XA1  H6   C19  N16  107.25  3.000
 XA1  H5   C19  N16  113.75  3.000
 XA1  H6   C19  C20  108.73  3.000
 XA1  H5   C19  C20  108.93  3.000
 XA1  N16  C19  C20  112.29  3.000
 XA1  C17  N16  C15  109.72  3.000
 XA1  C15  N16  C19  112.27  3.000
 XA1  C17  N16  C19  113.78  3.000
 XA1  H9   C15  H8   106.63  3.000
 XA1  H9   C15  C14  109.10  3.000
 XA1  H8   C15  C14  110.08  3.000
 XA1  H9   C15  N16  107.90  3.000
 XA1  H8   C15  N16  108.88  3.000
 XA1  C14  C15  N16  113.97  3.000
 XA1  H11  C14  H10  106.49  3.000
 XA1  H11  C14  C13  111.13  3.000
 XA1  H10  C14  C13  109.52  3.000
 XA1  H11  C14  C15  108.00  3.000
 XA1  H10  C14  C15  110.50  3.000
 XA1  C13  C14  C15  111.08  3.000
 XA1  H13  C17  H12  106.49  3.000
 XA1  H13  C17  C18  109.85  3.000
 XA1  H12  C17  C18  109.09  3.000
 XA1  H13  C17  N16  109.32  3.000
 XA1  H12  C17  N16  107.68  3.000
 XA1  C18  C17  N16  114.11  3.000
 XA1  H15  C18  H14  106.59  3.000
 XA1  H15  C18  C13  110.61  3.000
 XA1  H14  C18  C13  111.14  3.000
 XA1  H15  C18  C17  109.05  3.000
 XA1  H14  C18  C17  108.32  3.000
 XA1  C13  C18  C17  110.99  3.000
 XA1  H16  C13  C4   106.54  3.000
 XA1  H16  C13  C18  107.23  3.000
 XA1  C4   C13  C18  112.87  3.000
 XA1  H16  C13  C14  107.91  3.000
 XA1  C18  C13  C14  109.19  3.000
 XA1  C4   C13  C14  112.80  3.000
 XA1  C6   C4   N5   113.22  3.000
 XA1  N5   C4   C1   110.66  3.000
 XA1  C6   C4   C1   106.63  3.000
 XA1  C1   C4   C13  106.60  3.000
 XA1  N5   C4   C13  109.14  3.000
 XA1  C6   C4   C13  110.36  3.000
 XA1  O2   C1   O3   122.69  3.000
 XA1  O3   C1   C4   114.40  3.000
 XA1  O2   C1   C4   122.90  3.000
 XA1  H17  O3   C1   109.63  3.000
 XA1  H19  N5   H18  105.12  3.000
 XA1  H19  N5   C4   108.43  3.000
 XA1  H18  N5   C4   110.95  3.000
 XA1  H22  C6   H21  106.21  3.000
 XA1  H22  C6   C7   108.48  3.000
 XA1  H21  C6   C7   109.48  3.000
 XA1  H22  C6   C4   107.62  3.000
 XA1  H21  C6   C4   109.60  3.000
 XA1  C7   C6   C4   115.06  3.000
 XA1  H24  C7   H23  106.18  3.000
 XA1  H24  C7   C8   108.45  3.000
 XA1  H23  C7   C8   108.30  3.000
 XA1  H24  C7   C6   110.57  3.000
 XA1  H23  C7   C6   109.97  3.000
 XA1  C8   C7   C6   113.10  3.000
 XA1  H26  C8   H25  105.59  3.000
 XA1  H26  C8   C9   109.97  3.000
 XA1  H25  C8   C9   109.85  3.000
 XA1  H26  C8   C7   107.96  3.000
 XA1  H25  C8   C7   109.08  3.000
 XA1  C9   C8   C7   114.04  3.000
 XA1  H28  C9   H27  104.60  3.000
 XA1  H28  C9   B10  110.57  3.000
 XA1  H27  C9   B10  109.33  3.000
 XA1  H28  C9   C8   107.94  3.000
 XA1  H27  C9   C8   107.80  3.000
 XA1  B10  C9   C8   115.96  3.000
 XA1  O11  B10  O12  111.72  3.000
 XA1  O11  B10  O27  103.10  3.000
 XA1  O12  B10  O27  111.68  3.000
 XA1  O11  B10  C9   112.34  3.000
 XA1  O12  B10  C9   106.77  3.000
 XA1  O27  B10  C9   111.33  3.000
 XA1  H29  O27  B10  108.30  3.000
 XA1  H30  O12  B10  108.68  3.000
 XA1  H31  O11  B10  108.76  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
 XA1  CONST_01  C20  C21  C22  C23     0.00   0.0  0
 XA1  CONST_02  C20  C25  C24  C23     0.00   0.0  0
 XA1  CONST_03  C25  C20  C21  C22     0.00   0.0  0
 XA1  CONST_04  C25  C24  C23  C22     0.00   0.0  0
 XA1  CONST_05  C24  C25  C20  C21     0.00   0.0  0
 XA1  CONST_06  C24  C23  C22  C21     0.00   0.0  0
 XA1  CONST_07  C21  C22  C23  CL1   180.00   0.0  0
 XA1  CONST_08  C25  C24  C23  CL1   180.00   0.0  0
 XA1  CONST_09  C19  C20  C21  C22   180.00   0.0  0
 XA1  CONST_10  C19  C20  C25  C24   180.00   0.0  0
 XA1  CONST_11  H2   C21  C22  C23   180.00   0.0  0
 XA1  CONST_12  H4   C25  C24  C23   180.00   0.0  0
 XA1  CONST_13  H3   C24  C23  C22   180.00   0.0  0
 XA1  CONST_14  H1   C22  C23  C24   180.00   0.0  0
 XA1  CONST_15  H17  O3   C1   C4    180.00   0.0  0
 XA1  Var_01    C13  C18  C17  N16    55.70  30.0  1
 XA1  Var_02    C13  C14  C15  N16   -55.86  30.0  1
 XA1  Var_03    C18  C17  N16  C15   -55.96  30.0  1
 XA1  Var_04    C17  N16  C15  C14    55.97  30.0  1
 XA1  Var_05    N16  C19  C20  C21    51.67  30.0  2
 XA1  Var_06    C8   C7   C6   C4   -174.14  30.0  1
 XA1  Var_07    C9   C8   C7   C6    179.11  30.0  1
 XA1  Var_08    B10  C9   C8   C7   -178.10  30.0  1
 XA1  Var_09    O27  B10  C9   C8    176.17  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
 XA1  chir_01  C13  C4  C18  C14  positiv
 XA1  chir_02  C4   C6  C1   C13  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
 XA1  plan-1  CL1  0.020
 XA1  plan-1  C23  0.020
 XA1  plan-1  C22  0.020
 XA1  plan-1  C21  0.020
 XA1  plan-1  C24  0.020
 XA1  plan-1  C25  0.020
 XA1  plan-1  C20  0.020
 XA1  plan-1  C19  0.020
 XA1  plan-1  H1   0.020
 XA1  plan-1  H2   0.020
 XA1  plan-1  H3   0.020
 XA1  plan-1  H4   0.020
 XA1  plan-2  C4   0.020
 XA1  plan-2  C1   0.020
 XA1  plan-2  O3   0.020
 XA1  plan-2  O2   0.020
 XA1  plan-2  H17  0.020

