# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 23:50:41 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: [(5R)-5-carboxy-5-(methylamino)-7-(piperidin-1-yl)heptyl](trihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@](CCCC[B-](O)(O)O)(CCN1CCCCC1)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
 X8A  X8A  '[(5R)-5-carboxy-5-(methylamino)-7-(piperidin-1-yl)heptyl](trihydroxy)borate(1-)'  ligand  51  22  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X8A
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
 X8A  O9   O  OC    -1  -0.606  -0.0173  -2.8773   0.8674
 X8A  C7   C  C      0   0.428  -0.3657  -2.0436   0.0067
 X8A  O8   O  O      0  -0.611  -0.6384  -2.2947  -1.1846
 X8A  C1   C  CT     0  -0.014  -0.4122  -0.5466   0.4300
 X8A  N6   N  NH1    0  -0.605  -0.4592  -0.4796   1.8853
 X8A  C18  C  CH3    0  -0.524  -0.2717   0.8186   2.4891
 X8A  C2   C  CH2    0  -0.418   0.8322   0.1330  -0.1902
 X8A  C3   C  CH2    0  -0.410   2.1808  -0.3667   0.3119
 X8A  C4   C  CH2    0  -0.425   3.3657   0.3667  -0.3101
 X8A  C5   C  CH2    0  -0.637   4.7288  -0.1168   0.1798
 X8A  B19  B  B     -1   0.428   6.0418   0.6442  -0.4551
 X8A  O22  O  OB     0  -0.748   7.3021   0.0273   0.0183
 X8A  O21  O  OB     0  -0.753   6.1298   0.4982  -1.9253
 X8A  O20  O  OB     0  -0.751   5.9458   2.0703  -0.0501
 X8A  C10  C  CH2    0  -0.425  -1.6541   0.1386  -0.1543
 X8A  C11  C  CH2    0  -0.254  -2.9729  -0.4121   0.3688
 X8A  N12  N  NT     0  -0.421  -4.1379   0.1336  -0.3133
 X8A  C17  C  CH2    0  -0.273  -5.3211  -0.6637  -0.0399
 X8A  C16  C  CH2    0  -0.437  -6.5230  -0.1743  -0.8341
 X8A  C15  C  CH2    0  -0.438  -6.7995   1.2952  -0.5466
 X8A  C14  C  CH2    0  -0.434  -5.5322   2.1101  -0.7663
 X8A  C13  C  CH2    0  -0.280  -4.3707   1.5269   0.0252
 X8A  H2   H  HNH1   0   0.334   0.1995  -1.1467   2.2609
 X8A  H4   H  HCH3   0   0.223  -0.2821   0.7105   3.5749
 X8A  H5   H  HCH3   0   0.189   0.6624   1.3332   2.2236
 X8A  H6   H  HCH3   0   0.212  -1.0952   1.4887   2.2318
 X8A  H7   H  HCH2   0   0.209   0.7808   0.0046  -1.2758
 X8A  H8   H  HCH2   0   0.200   0.7700   1.2153  -0.0237
 X8A  H9   H  HCH2   0   0.191   2.2374  -0.2586   1.4011
 X8A  H10  H  HCH2   0   0.202   2.2836  -1.4388   0.1149
 X8A  H11  H  HCH2   0   0.172   3.3008   0.2593  -1.4016
 X8A  H12  H  HCH2   0   0.186   3.2604   1.4401  -0.1155
 X8A  H13  H  HCH2   0   0.148   4.7373  -0.0393   1.2790
 X8A  H14  H  HCH2   0   0.151   4.7932  -1.1974  -0.0193
 X8A  H15  H  H      0   0.416   7.2381  -0.0927   0.9680
 X8A  H16  H  H      0   0.416   5.3059   0.7978  -2.3153
 X8A  H17  H  H      0   0.417   6.7098   2.5397  -0.3977
 X8A  H18  H  HCH2   0   0.208  -1.5830   1.2131   0.0443
 X8A  H19  H  HCH2   0   0.214  -1.6307   0.0303  -1.2396
 X8A  H20  H  HCH2   0   0.216  -2.9833  -1.4944   0.2103
 X8A  H21  H  HCH2   0   0.186  -3.0366  -0.2607   1.4585
 X8A  H23  H  HCH2   0   0.228  -5.1080  -1.7040  -0.2999
 X8A  H24  H  HCH2   0   0.174  -5.5732  -0.6547   1.0373
 X8A  H25  H  HCH2   0   0.212  -6.3252  -0.3099  -1.9019
 X8A  H26  H  HCH2   0   0.226  -7.3922  -0.7895  -0.5895
 X8A  H27  H  HCH2   0   0.228  -7.6151   1.6671  -1.1709
 X8A  H28  H  HCH2   0   0.208  -7.1248   1.4058   0.4938
 X8A  H29  H  HCH2   0   0.212  -5.2747   2.1131  -1.8299
 X8A  H30  H  HCH2   0   0.226  -5.6825   3.1513  -0.4716
 X8A  H31  H  HCH2   0   0.174  -4.5759   1.6424   1.1068
 X8A  H32  H  HCH2   0   0.233  -3.4677   2.1034  -0.1807

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
 X8A  C18  N6   single  1.444  0.020  1.444
 X8A  O22  B19  single  1.481  0.020  1.481
 X8A  N6   C1   single  1.458  0.020  1.458
 X8A  O21  B19  single  1.480  0.020  1.480
 X8A  O8   C7   deloc   1.248  0.020  1.248
 X8A  B19  C5   single  1.645  0.020  1.645
 X8A  B19  O20  single  1.486  0.020  1.486
 X8A  C5   C4   single  1.527  0.020  1.527
 X8A  C3   C4   single  1.526  0.020  1.526
 X8A  C3   C2   single  1.523  0.020  1.523
 X8A  C1   C7   single  1.556  0.020  1.556
 X8A  C1   C2   single  1.548  0.020  1.548
 X8A  C1   C10  single  1.534  0.020  1.534
 X8A  C7   O9   deloc   1.248  0.020  1.248
 X8A  C11  C10  single  1.522  0.020  1.522
 X8A  C11  N12  single  1.456  0.020  1.456
 X8A  C13  N12  single  1.453  0.020  1.453
 X8A  C13  C14  single  1.522  0.020  1.522
 X8A  N12  C17  single  1.453  0.020  1.453
 X8A  C14  C15  single  1.523  0.020  1.523
 X8A  C17  C16  single  1.522  0.020  1.522
 X8A  C15  C16  single  1.523  0.020  1.523
 X8A  N6   H2   single  0.890  0.020  1.040
 X8A  C18  H4   single  0.970  0.020  1.090
 X8A  C18  H5   single  0.970  0.020  1.090
 X8A  C18  H6   single  0.970  0.020  1.090
 X8A  C2   H7   single  0.970  0.020  1.090
 X8A  C2   H8   single  0.970  0.020  1.090
 X8A  C3   H9   single  0.970  0.020  1.090
 X8A  C3   H10  single  0.970  0.020  1.090
 X8A  C4   H11  single  0.970  0.020  1.090
 X8A  C4   H12  single  0.970  0.020  1.090
 X8A  C5   H13  single  0.970  0.020  1.090
 X8A  C5   H14  single  0.970  0.020  1.090
 X8A  O22  H15  single  0.850  0.020  0.980
 X8A  O21  H16  single  0.850  0.020  0.980
 X8A  O20  H17  single  0.850  0.020  0.980
 X8A  C10  H18  single  0.970  0.020  1.090
 X8A  C10  H19  single  0.970  0.020  1.090
 X8A  C11  H20  single  0.970  0.020  1.090
 X8A  C11  H21  single  0.970  0.020  1.090
 X8A  C17  H23  single  0.970  0.020  1.090
 X8A  C17  H24  single  0.970  0.020  1.090
 X8A  C16  H25  single  0.970  0.020  1.090
 X8A  C16  H26  single  0.970  0.020  1.090
 X8A  C15  H27  single  0.970  0.020  1.090
 X8A  C15  H28  single  0.970  0.020  1.090
 X8A  C14  H29  single  0.970  0.020  1.090
 X8A  C14  H30  single  0.970  0.020  1.090
 X8A  C13  H31  single  0.970  0.020  1.090
 X8A  C13  H32  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
 X8A  C1   C7   O8   116.54  3.000
 X8A  C1   C7   O9   117.60  3.000
 X8A  O8   C7   O9   125.81  3.000
 X8A  C10  C1   C2   107.59  3.000
 X8A  C10  C1   N6   109.49  3.000
 X8A  C2   C1   N6   113.95  3.000
 X8A  C10  C1   C7   110.50  3.000
 X8A  C2   C1   C7   106.82  3.000
 X8A  N6   C1   C7   108.47  3.000
 X8A  H2   N6   C18  110.71  3.000
 X8A  H2   N6   C1   108.66  3.000
 X8A  C18  N6   C1   117.04  3.000
 X8A  H6   C18  H5   107.25  3.000
 X8A  H6   C18  H4   106.74  3.000
 X8A  H5   C18  H4   107.15  3.000
 X8A  H6   C18  N6   110.80  3.000
 X8A  H5   C18  N6   115.49  3.000
 X8A  H4   C18  N6   109.01  3.000
 X8A  H8   C2   H7   105.29  3.000
 X8A  H8   C2   C3   108.90  3.000
 X8A  H7   C2   C3   109.27  3.000
 X8A  H8   C2   C1   109.08  3.000
 X8A  H7   C2   C1   107.95  3.000
 X8A  C3   C2   C1   115.83  3.000
 X8A  H10  C3   H9   105.70  3.000
 X8A  H10  C3   C4   108.93  3.000
 X8A  H9   C3   C4   108.51  3.000
 X8A  H10  C3   C2   110.19  3.000
 X8A  H9   C3   C2   109.93  3.000
 X8A  C4   C3   C2   113.29  3.000
 X8A  H12  C4   H11  105.45  3.000
 X8A  H12  C4   C5   109.81  3.000
 X8A  H11  C4   C5   109.91  3.000
 X8A  H12  C4   C3   108.89  3.000
 X8A  H11  C4   C3   108.18  3.000
 X8A  C5   C4   C3   114.22  3.000
 X8A  H14  C5   H13  104.42  3.000
 X8A  H14  C5   B19  109.74  3.000
 X8A  H13  C5   B19  110.26  3.000
 X8A  H14  C5   C4   107.76  3.000
 X8A  H13  C5   C4   107.74  3.000
 X8A  B19  C5   C4   116.24  3.000
 X8A  O20  B19  O21  111.68  3.000
 X8A  O20  B19  O22  111.58  3.000
 X8A  O21  B19  O22  103.05  3.000
 X8A  O20  B19  C5   106.70  3.000
 X8A  O21  B19  C5   112.65  3.000
 X8A  O22  B19  C5   111.29  3.000
 X8A  H15  O22  B19  108.17  3.000
 X8A  H16  O21  B19  108.78  3.000
 X8A  H17  O20  B19  108.58  3.000
 X8A  H19  C10  H18  106.05  3.000
 X8A  H19  C10  C11  108.94  3.000
 X8A  H18  C10  C11  110.42  3.000
 X8A  H19  C10  C1   108.50  3.000
 X8A  H18  C10  C1   108.46  3.000
 X8A  C11  C10  C1   114.14  3.000
 X8A  H21  C11  H20  106.18  3.000
 X8A  H21  C11  N12  111.44  3.000
 X8A  H20  C11  N12  107.18  3.000
 X8A  H21  C11  C10  109.90  3.000
 X8A  H20  C11  C10  108.44  3.000
 X8A  N12  C11  C10  113.37  3.000
 X8A  C13  N12  C17  110.62  3.000
 X8A  C17  N12  C11  110.96  3.000
 X8A  C13  N12  C11  112.24  3.000
 X8A  H24  C17  H23  106.48  3.000
 X8A  H24  C17  C16  109.01  3.000
 X8A  H23  C17  C16  109.62  3.000
 X8A  H24  C17  N12  111.37  3.000
 X8A  H23  C17  N12  108.59  3.000
 X8A  C16  C17  N12  111.63  3.000
 X8A  H26  C16  H25  107.01  3.000
 X8A  H26  C16  C15  110.89  3.000
 X8A  H25  C16  C15  109.67  3.000
 X8A  H26  C16  C17  109.29  3.000
 X8A  H25  C16  C17  109.07  3.000
 X8A  C15  C16  C17  110.81  3.000
 X8A  H28  C15  H27  106.65  3.000
 X8A  H28  C15  C14  109.27  3.000
 X8A  H27  C15  C14  110.90  3.000
 X8A  H28  C15  C16  109.31  3.000
 X8A  H27  C15  C16  110.87  3.000
 X8A  C14  C15  C16  109.76  3.000
 X8A  H30  C14  H29  106.97  3.000
 X8A  H30  C14  C13  109.27  3.000
 X8A  H29  C14  C13  109.09  3.000
 X8A  H30  C14  C15  110.89  3.000
 X8A  H29  C14  C15  109.73  3.000
 X8A  C13  C14  C15  110.80  3.000
 X8A  H32  C13  H31  106.43  3.000
 X8A  H32  C13  C14  109.33  3.000
 X8A  H31  C13  C14  109.07  3.000
 X8A  H32  C13  N12  109.28  3.000
 X8A  H31  C13  N12  110.94  3.000
 X8A  C14  C13  N12  111.63  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
 X8A  Var_01  C15  C14  C13  N12    56.69  30.0  1
 X8A  Var_02  C15  C16  C17  N12   -56.69  30.0  1
 X8A  Var_03  C14  C13  N12  C17   -59.37  30.0  1
 X8A  Var_04  C14  C15  C16  C17    52.94  30.0  1
 X8A  Var_05  C13  N12  C17  C16    59.37  30.0  1
 X8A  Var_06  C13  C14  C15  C16   -52.94  30.0  1
 X8A  Var_07  N12  C11  C10  C1   -172.93  30.0  2
 X8A  Var_08  C4   C3   C2   C1   -178.50  30.0  1
 X8A  Var_09  C5   C4   C3   C2    179.94  30.0  3
 X8A  Var_10  B19  C5   C4   C3   -179.79  30.0  1
 X8A  Var_11  O22  B19  C5   C4   -175.90  30.0  2
 X8A  Var_12  H4   C18  N6   C1   -177.24  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
 X8A  chir_01  C1  C7  C2  C10  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
 X8A  plan-1  O9  0.020
 X8A  plan-1  C7  0.020
 X8A  plan-1  O8  0.020
 X8A  plan-1  C1  0.020

