# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 15:57:48 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: [(5R)-5-amino-5-carboxy-7-(4-hydroxypiperidin-1-yl)heptyl](trihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@](CCCC[B-](O)(O)O)(CCN1CC[C@@H](O)CC1)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
 1EE  1EE  '[(5R)-5-amino-5-carboxy-7-(4-hydroxypiperidin-1-yl)heptyl](trihydroxy)borate(1-)'  ligand  50  22  .  2021-08-03  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1EE
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
 1EE  O3   O  OH1    0  -0.584   0.4206  -3.0764   0.7520
 1EE  C1   C  C      0   0.564   0.1008  -2.1293  -0.1175
 1EE  O2   O  O      0  -0.450  -0.0851  -2.3559  -1.2893
 1EE  C4   C  CT     0  -0.055   0.0422  -0.7285   0.4819
 1EE  N5   N  NH2    0  -0.792   0.0246  -0.7918   1.9345
 1EE  C6   C  CH2    0  -0.398   1.2441   0.0577  -0.0966
 1EE  C7   C  CH2    0  -0.421   2.6274  -0.4652   0.2698
 1EE  C8   C  CH2    0  -0.422   3.7459   0.4544  -0.2141
 1EE  C9   C  CH2    0  -0.642   5.1514  -0.0049   0.1643
 1EE  B10  B  B     -1   0.429   6.3704   1.0182  -0.2566
 1EE  O22  O  OB     0  -0.746   7.6872   0.5061   0.1822
 1EE  O12  O  OB     0  -0.751   6.3083   1.1714  -1.7325
 1EE  O11  O  OB     0  -0.753   6.2693   2.3225   0.4354
 1EE  C13  C  CH2    0  -0.431  -1.2469  -0.0405   0.0073
 1EE  C14  C  CH2    0  -0.257  -2.5361  -0.6802   0.5095
 1EE  N15  N  NT     0  -0.422  -3.7161  -0.0205  -0.0259
 1EE  C20  C  CH2    0  -0.297  -3.9867   1.2402   0.6430
 1EE  C19  C  CH2    0  -0.457  -5.1537   1.9756  -0.0000
 1EE  C18  C  CH1    0   0.066  -6.3967   1.1047   0.0012
 1EE  O21  O  OH1    0  -0.675  -7.4339   1.8026  -0.6570
 1EE  C17  C  CH2    0  -0.475  -6.0763  -0.2307  -0.6556
 1EE  C16  C  CH2    0  -0.288  -4.8809  -0.8863   0.0196
 1EE  H1   H  HOH1   0   0.479   0.4848  -3.9280   0.2931
 1EE  H2   H  HNH2   0   0.351   0.9195  -1.0920   2.3007
 1EE  H3   H  HNH2   0   0.348  -0.1215   0.1434   2.2960
 1EE  H5   H  HCH2   0   0.223   1.1502   0.1074  -1.1854
 1EE  H6   H  HCH2   0   0.226   1.1423   1.0879   0.2617
 1EE  H7   H  HCH2   0   0.197   2.7190  -0.5700   1.3561
 1EE  H8   H  HCH2   0   0.209   2.7850  -1.4663  -0.1477
 1EE  H9   H  HCH2   0   0.194   3.6711   0.5669  -1.3009
 1EE  H10  H  HCH2   0   0.177   3.5553   1.4554   0.1965
 1EE  H11  H  HCH2   0   0.153   5.1734  -0.1696   1.2520
 1EE  H12  H  HCH2   0   0.152   5.3135  -1.0037  -0.2702
 1EE  H13  H  H      0   0.417   7.7576  -0.4135  -0.0830
 1EE  H14  H  H      0   0.418   7.0135   1.7644  -2.0081
 1EE  H15  H  H      0   0.416   5.3757   2.6564   0.3365
 1EE  H16  H  HCH2   0   0.237  -1.1824   1.0035   0.3287
 1EE  H17  H  HCH2   0   0.238  -1.2631  -0.0208  -1.0833
 1EE  H18  H  HCH2   0   0.226  -2.5654  -1.7235   0.1820
 1EE  H19  H  HCH2   0   0.202  -2.5514  -0.7049   1.6090
 1EE  H21  H  HCH2   0   0.188  -4.1992   1.0832   1.7165
 1EE  H22  H  HCH2   0   0.241  -3.1008   1.8750   0.5949
 1EE  H23  H  HCH2   0   0.236  -5.3375   2.9062   0.5429
 1EE  H24  H  HCH2   0   0.220  -4.8932   2.2408  -1.0293
 1EE  H25  H  HCH1   0   0.185  -6.6734   0.9081   1.0495
 1EE  H26  H  HOH1   0   0.446  -8.2270   1.2586  -0.6273
 1EE  H27  H  HCH2   0   0.233  -6.9368  -0.9037  -0.5985
 1EE  H28  H  HCH2   0   0.219  -5.8538  -0.0710  -1.7153
 1EE  H29  H  HCH2   0   0.238  -4.6417  -1.8213  -0.4921
 1EE  H30  H  HCH2   0   0.186  -5.1491  -1.1559   1.0570

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
 1EE  O22  B10  single  1.480  0.020  1.480
 1EE  O12  B10  single  1.485  0.020  1.485
 1EE  B10  O11  single  1.480  0.020  1.480
 1EE  B10  C9   single  1.646  0.020  1.646
 1EE  C9   C8   single  1.526  0.020  1.526
 1EE  C8   C7   single  1.527  0.020  1.527
 1EE  C6   C7   single  1.523  0.020  1.523
 1EE  C6   C4   single  1.548  0.020  1.548
 1EE  N5   C4   single  1.454  0.020  1.454
 1EE  C4   C1   single  1.525  0.020  1.525
 1EE  C4   C13  single  1.536  0.020  1.536
 1EE  O2   C1   double  1.208  0.020  1.208
 1EE  C1   O3   single  1.325  0.020  1.325
 1EE  C13  C14  single  1.524  0.020  1.524
 1EE  C14  N15  single  1.454  0.020  1.454
 1EE  N15  C16  single  1.452  0.020  1.452
 1EE  N15  C20  single  1.453  0.020  1.453
 1EE  C16  C17  single  1.521  0.020  1.521
 1EE  C20  C19  single  1.522  0.020  1.522
 1EE  C17  C18  single  1.522  0.020  1.522
 1EE  C19  C18  single  1.518  0.020  1.518
 1EE  C18  O21  single  1.413  0.020  1.413
 1EE  O3   H1   single  0.850  0.020  0.980
 1EE  N5   H2   single  0.890  0.020  1.040
 1EE  N5   H3   single  0.890  0.020  1.040
 1EE  C6   H5   single  0.970  0.020  1.090
 1EE  C6   H6   single  0.970  0.020  1.090
 1EE  C7   H7   single  0.970  0.020  1.090
 1EE  C7   H8   single  0.970  0.020  1.090
 1EE  C8   H9   single  0.970  0.020  1.090
 1EE  C8   H10  single  0.970  0.020  1.090
 1EE  C9   H11  single  0.970  0.020  1.090
 1EE  C9   H12  single  0.970  0.020  1.090
 1EE  O22  H13  single  0.850  0.020  0.980
 1EE  O12  H14  single  0.850  0.020  0.980
 1EE  O11  H15  single  0.850  0.020  0.980
 1EE  C13  H16  single  0.970  0.020  1.090
 1EE  C13  H17  single  0.970  0.020  1.090
 1EE  C14  H18  single  0.970  0.020  1.090
 1EE  C14  H19  single  0.970  0.020  1.090
 1EE  C20  H21  single  0.970  0.020  1.090
 1EE  C20  H22  single  0.970  0.020  1.090
 1EE  C19  H23  single  0.970  0.020  1.090
 1EE  C19  H24  single  0.970  0.020  1.090
 1EE  C18  H25  single  0.970  0.020  1.090
 1EE  O21  H26  single  0.850  0.020  0.980
 1EE  C17  H27  single  0.970  0.020  1.090
 1EE  C17  H28  single  0.970  0.020  1.090
 1EE  C16  H29  single  0.970  0.020  1.090
 1EE  C16  H30  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
 1EE  H1   O3   C1   109.47  3.000
 1EE  C4   C1   O2   123.21  3.000
 1EE  O2   C1   O3   122.67  3.000
 1EE  C4   C1   O3   114.08  3.000
 1EE  C13  C4   C6   107.97  3.000
 1EE  C13  C4   N5   108.54  3.000
 1EE  C6   C4   N5   113.87  3.000
 1EE  C13  C4   C1   108.80  3.000
 1EE  N5   C4   C1   110.68  3.000
 1EE  C6   C4   C1   106.84  3.000
 1EE  H3   N5   H2   105.78  3.000
 1EE  H3   N5   C4   108.54  3.000
 1EE  H2   N5   C4   111.32  3.000
 1EE  H6   C6   H5   105.95  3.000
 1EE  H6   C6   C7   109.18  3.000
 1EE  H5   C6   C7   109.45  3.000
 1EE  H6   C6   C4   106.45  3.000
 1EE  H5   C6   C4   109.16  3.000
 1EE  C7   C6   C4   116.15  3.000
 1EE  H8   C7   H7   106.17  3.000
 1EE  H8   C7   C8   108.91  3.000
 1EE  H7   C7   C8   108.11  3.000
 1EE  H8   C7   C6   110.64  3.000
 1EE  H7   C7   C6   110.32  3.000
 1EE  C8   C7   C6   112.47  3.000
 1EE  H10  C8   H9   105.40  3.000
 1EE  H10  C8   C9   109.96  3.000
 1EE  H9   C8   C9   109.87  3.000
 1EE  H10  C8   C7   107.65  3.000
 1EE  H9   C8   C7   109.04  3.000
 1EE  C9   C8   C7   114.50  3.000
 1EE  H12  C9   H11  104.56  3.000
 1EE  H12  C9   B10  110.72  3.000
 1EE  H11  C9   B10  109.33  3.000
 1EE  H12  C9   C8   108.09  3.000
 1EE  H11  C9   C8   107.97  3.000
 1EE  B10  C9   C8   115.56  3.000
 1EE  O11  B10  O12  111.77  3.000
 1EE  O11  B10  O22  103.13  3.000
 1EE  O12  B10  O22  111.57  3.000
 1EE  O11  B10  C9   112.19  3.000
 1EE  O12  B10  C9   106.70  3.000
 1EE  O22  B10  C9   111.60  3.000
 1EE  H13  O22  B10  108.36  3.000
 1EE  H14  O12  B10  108.52  3.000
 1EE  H15  O11  B10  108.80  3.000
 1EE  H17  C13  H16  106.10  3.000
 1EE  H17  C13  C14  108.94  3.000
 1EE  H16  C13  C14  110.70  3.000
 1EE  H17  C13  C4   109.23  3.000
 1EE  H16  C13  C4   106.68  3.000
 1EE  C14  C13  C4   114.83  3.000
 1EE  H19  C14  H18  106.11  3.000
 1EE  H19  C14  N15  111.53  3.000
 1EE  H18  C14  N15  107.50  3.000
 1EE  H19  C14  C13  110.52  3.000
 1EE  H18  C14  C13  108.92  3.000
 1EE  N15  C14  C13  112.00  3.000
 1EE  C16  N15  C20  110.71  3.000
 1EE  C20  N15  C14  112.05  3.000
 1EE  C16  N15  C14  111.65  3.000
 1EE  H22  C20  H21  106.35  3.000
 1EE  H22  C20  C19  108.84  3.000
 1EE  H21  C20  C19  109.36  3.000
 1EE  H22  C20  N15  109.48  3.000
 1EE  H21  C20  N15  111.08  3.000
 1EE  C19  C20  N15  111.57  3.000
 1EE  H24  C19  H23  107.51  3.000
 1EE  H24  C19  C18  109.56  3.000
 1EE  H23  C19  C18  110.52  3.000
 1EE  H24  C19  C20  109.38  3.000
 1EE  H23  C19  C20  109.30  3.000
 1EE  C18  C19  C20  110.51  3.000
 1EE  H25  C18  C17  107.86  3.000
 1EE  H25  C18  O21  110.31  3.000
 1EE  C17  C18  O21  112.76  3.000
 1EE  H25  C18  C19  107.99  3.000
 1EE  O21  C18  C19  108.51  3.000
 1EE  C17  C18  C19  109.31  3.000
 1EE  H26  O21  C18  108.15  3.000
 1EE  H28  C17  H27  107.47  3.000
 1EE  H28  C17  C16  109.44  3.000
 1EE  H27  C17  C16  109.26  3.000
 1EE  H28  C17  C18  109.42  3.000
 1EE  H27  C17  C18  110.58  3.000
 1EE  C16  C17  C18  110.61  3.000
 1EE  H30  C16  H29  106.51  3.000
 1EE  H30  C16  C17  109.33  3.000
 1EE  H29  C16  C17  109.45  3.000
 1EE  H30  C16  N15  111.69  3.000
 1EE  H29  C16  N15  108.67  3.000
 1EE  C17  C16  N15  111.07  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
 1EE  CONST_01  H1   O3   C1   O2      0.00   0.0  0
 1EE  Var_01    C18  C17  C16  N15   -57.66  30.0  1
 1EE  Var_02    C18  C19  C20  N15    57.04  30.0  1
 1EE  Var_03    C17  C16  N15  C20    59.49  30.0  1
 1EE  Var_04    C16  N15  C20  C19   -59.33  30.0  1
 1EE  Var_05    N15  C14  C13  C4   -177.30  30.0  3
 1EE  Var_06    C8   C7   C6   C4   -173.73  30.0  3
 1EE  Var_07    C9   C8   C7   C6    178.29  30.0  1
 1EE  Var_08    B10  C9   C8   C7   -176.08  30.0  1
 1EE  Var_09    O22  B10  C9   C8    178.49  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
 1EE  chir_01  C4   N5   C1   C13  negativ
 1EE  chir_02  C18  O21  C17  C19  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
 1EE  plan-1  O3  0.020
 1EE  plan-1  C1  0.020
 1EE  plan-1  O2  0.020
 1EE  plan-1  C4  0.020
 1EE  plan-1  H1  0.020

