# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 19:05:54 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: [(5R)-5-amino-5-carboxy-7-(piperidin-1-yl)heptyl](trihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[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
 X7A  X7A  '[(5R)-5-amino-5-carboxy-7-(piperidin-1-yl)heptyl](trihydroxy)borate(1-)'  ligand  49  21  .  2021-08-24  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_X7A
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
 X7A  O20  O  OH1    0  -0.580  -0.3021  -2.9781  -0.1162
 X7A  C18  C  C      0   0.560  -0.3563  -1.7616  -0.6363
 X7A  O21  O  O      0  -0.452  -0.4146  -1.5610  -1.8260
 X7A  C1   C  CT     0  -0.058  -0.3518  -0.6367   0.3922
 X7A  N2   N  NH2    0  -0.788  -0.2286  -1.1650   1.7407
 X7A  C3   C  CH2    0  -0.399   0.8798   0.2452   0.1076
 X7A  C4   C  CH2    0  -0.406   2.2273  -0.4593   0.2115
 X7A  C5   C  CH2    0  -0.428   3.4104   0.4886   0.0365
 X7A  C6   C  CH2    0  -0.639   4.7738  -0.1883   0.1604
 X7A  B7   B  B     -1   0.428   6.0842   0.7953   0.0006
 X7A  O8   O  OB     0  -0.753   6.1148   1.8654   1.0207
 X7A  O9   O  OB     0  -0.747   7.3442   0.0586   0.2478
 X7A  O19  O  OB     0  -0.751   6.0357   1.3486  -1.3770
 X7A  C10  C  CH2    0  -0.421  -1.6240   0.2127   0.1697
 X7A  C11  C  CH2    0  -0.262  -2.9323  -0.5397   0.3880
 X7A  N12  N  NT     0  -0.420  -4.0932   0.3279   0.3147
 X7A  C13  C  CH2    0  -0.279  -5.2534  -0.2777   0.9483
 X7A  C14  C  CH2    0  -0.438  -6.4239   0.6930   0.9968
 X7A  C15  C  CH2    0  -0.440  -6.7801   1.1814  -0.4016
 X7A  C16  C  CH2    0  -0.435  -5.5379   1.7407  -1.0829
 X7A  C17  C  CH2    0  -0.286  -4.4032   0.7271  -1.0485
 X7A  H1   H  HOH1   0   0.478  -0.3284  -3.6352  -0.8285
 X7A  H2   H  HNH2   0   0.348  -0.1946  -0.3850   2.3868
 X7A  H3   H  HNH2   0   0.350  -1.0391  -1.7104   2.0057
 X7A  H5   H  HCH2   0   0.227   0.7746   0.6936  -0.8837
 X7A  H6   H  HCH2   0   0.226   0.8510   1.0782   0.8196
 X7A  H7   H  HCH2   0   0.208   2.3050  -0.9584   1.1804
 X7A  H8   H  HCH2   0   0.202   2.2991  -1.2496  -0.5448
 X7A  H9   H  HCH2   0   0.191   3.3309   0.9889  -0.9350
 X7A  H10  H  HCH2   0   0.176   3.3209   1.2861   0.7864
 X7A  H11  H  HCH2   0   0.152   4.8083  -0.6948   1.1371
 X7A  H12  H  HCH2   0   0.151   4.8132  -1.0063  -0.5763
 X7A  H13  H  H      0   0.417   5.2666   2.3138   1.0271
 X7A  H14  H  H      0   0.417   7.3307  -0.7444  -0.2772
 X7A  H15  H  H      0   0.418   6.7919   1.9290  -1.5037
 X7A  H16  H  HCH2   0   0.234  -1.5862   1.0506   0.8724
 X7A  H17  H  HCH2   0   0.232  -1.5921   0.6430  -0.8330
 X7A  H18  H  HCH2   0   0.194  -3.0162  -1.3820  -0.3216
 X7A  H19  H  HCH2   0   0.216  -2.9229  -0.9812   1.3879
 X7A  H21  H  HCH2   0   0.181  -5.5652  -1.1975   0.4208
 X7A  H22  H  HCH2   0   0.232  -4.9778  -0.5766   1.9628
 X7A  H23  H  HCH2   0   0.229  -7.2787   0.2048   1.4701
 X7A  H24  H  HCH2   0   0.214  -6.1528   1.5452   1.6274
 X7A  H25  H  HCH2   0   0.209  -7.1702   0.3443  -0.9906
 X7A  H26  H  HCH2   0   0.230  -7.5719   1.9324  -0.3596
 X7A  H27  H  HCH2   0   0.229  -5.7503   2.0097  -2.1199
 X7A  H28  H  HCH2   0   0.214  -5.2176   2.6547  -0.5739
 X7A  H29  H  HCH2   0   0.237  -3.5157   1.1614  -1.5114
 X7A  H30  H  HCH2   0   0.182  -4.6821  -0.1496  -1.6621

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
 X7A  O19  B7   single  1.485  0.020  1.485
 X7A  N2   C1   single  1.453  0.020  1.453
 X7A  O21  C18  double  1.208  0.020  1.208
 X7A  O9   B7   single  1.480  0.020  1.480
 X7A  B7   C6   single  1.646  0.020  1.646
 X7A  B7   O8   single  1.479  0.020  1.479
 X7A  C6   C5   single  1.527  0.020  1.527
 X7A  C4   C5   single  1.526  0.020  1.526
 X7A  C4   C3   single  1.524  0.020  1.524
 X7A  C1   C18  single  1.524  0.020  1.524
 X7A  C1   C3   single  1.541  0.020  1.541
 X7A  C1   C10  single  1.546  0.020  1.546
 X7A  C18  O20  single  1.324  0.020  1.324
 X7A  C17  C16  single  1.522  0.020  1.522
 X7A  C17  N12  single  1.454  0.020  1.454
 X7A  C11  C10  single  1.525  0.020  1.525
 X7A  C11  N12  single  1.451  0.020  1.451
 X7A  C16  C15  single  1.523  0.020  1.523
 X7A  N12  C13  single  1.454  0.020  1.454
 X7A  C13  C14  single  1.521  0.020  1.521
 X7A  C15  C14  single  1.523  0.020  1.523
 X7A  O20  H1   single  0.850  0.020  0.980
 X7A  N2   H2   single  0.890  0.020  1.040
 X7A  N2   H3   single  0.890  0.020  1.040
 X7A  C3   H5   single  0.970  0.020  1.090
 X7A  C3   H6   single  0.970  0.020  1.090
 X7A  C4   H7   single  0.970  0.020  1.090
 X7A  C4   H8   single  0.970  0.020  1.090
 X7A  C5   H9   single  0.970  0.020  1.090
 X7A  C5   H10  single  0.970  0.020  1.090
 X7A  C6   H11  single  0.970  0.020  1.090
 X7A  C6   H12  single  0.970  0.020  1.090
 X7A  O8   H13  single  0.850  0.020  0.980
 X7A  O9   H14  single  0.850  0.020  0.980
 X7A  O19  H15  single  0.850  0.020  0.980
 X7A  C10  H16  single  0.970  0.020  1.090
 X7A  C10  H17  single  0.970  0.020  1.090
 X7A  C11  H18  single  0.970  0.020  1.090
 X7A  C11  H19  single  0.970  0.020  1.090
 X7A  C13  H21  single  0.970  0.020  1.090
 X7A  C13  H22  single  0.970  0.020  1.090
 X7A  C14  H23  single  0.970  0.020  1.090
 X7A  C14  H24  single  0.970  0.020  1.090
 X7A  C15  H25  single  0.970  0.020  1.090
 X7A  C15  H26  single  0.970  0.020  1.090
 X7A  C16  H27  single  0.970  0.020  1.090
 X7A  C16  H28  single  0.970  0.020  1.090
 X7A  C17  H29  single  0.970  0.020  1.090
 X7A  C17  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
 X7A  H1   O20  C18  109.45  3.000
 X7A  C1   C18  O21  122.84  3.000
 X7A  C1   C18  O20  114.38  3.000
 X7A  O21  C18  O20  122.78  3.000
 X7A  C10  C1   C3   108.46  3.000
 X7A  C10  C1   N2   113.77  3.000
 X7A  C3   C1   N2   108.16  3.000
 X7A  C10  C1   C18  107.81  3.000
 X7A  C3   C1   C18  107.46  3.000
 X7A  N2   C1   C18  110.98  3.000
 X7A  H3   N2   H2   105.94  3.000
 X7A  H3   N2   C1   111.77  3.000
 X7A  H2   N2   C1   108.34  3.000
 X7A  H6   C3   H5   105.95  3.000
 X7A  H6   C3   C4   109.28  3.000
 X7A  H5   C3   C4   109.67  3.000
 X7A  H6   C3   C1   107.09  3.000
 X7A  H5   C3   C1   108.98  3.000
 X7A  C4   C3   C1   115.43  3.000
 X7A  H8   C4   H7   106.13  3.000
 X7A  H8   C4   C5   108.53  3.000
 X7A  H7   C4   C5   109.28  3.000
 X7A  H8   C4   C3   110.13  3.000
 X7A  H7   C4   C3   109.54  3.000
 X7A  C5   C4   C3   112.98  3.000
 X7A  H10  C5   H9   105.54  3.000
 X7A  H10  C5   C6   109.82  3.000
 X7A  H9   C5   C6   109.82  3.000
 X7A  H10  C5   C4   108.03  3.000
 X7A  H9   C5   C4   109.21  3.000
 X7A  C6   C5   C4   114.04  3.000
 X7A  H12  C6   H11  104.51  3.000
 X7A  H12  C6   B7   110.50  3.000
 X7A  H11  C6   B7   109.64  3.000
 X7A  H12  C6   C5   107.87  3.000
 X7A  H11  C6   C5   107.69  3.000
 X7A  B7   C6   C5   115.97  3.000
 X7A  O19  B7   O9   111.60  3.000
 X7A  O9   B7   O8   103.14  3.000
 X7A  O19  B7   O8   111.77  3.000
 X7A  O8   B7   C6   112.45  3.000
 X7A  O9   B7   C6   111.35  3.000
 X7A  O19  B7   C6   106.65  3.000
 X7A  H13  O8   B7   108.94  3.000
 X7A  H14  O9   B7   108.25  3.000
 X7A  H15  O19  B7   108.75  3.000
 X7A  H17  C10  H16  106.68  3.000
 X7A  H17  C10  C11  110.56  3.000
 X7A  H16  C10  C11  108.40  3.000
 X7A  H17  C10  C1   108.95  3.000
 X7A  H16  C10  C1   107.45  3.000
 X7A  C11  C10  C1   114.48  3.000
 X7A  H19  C11  H18  106.28  3.000
 X7A  H19  C11  N12  107.13  3.000
 X7A  H18  C11  N12  111.27  3.000
 X7A  H19  C11  C10  108.84  3.000
 X7A  H18  C11  C10  110.45  3.000
 X7A  N12  C11  C10  112.59  3.000
 X7A  C17  N12  C13  110.66  3.000
 X7A  C13  N12  C11  111.55  3.000
 X7A  C17  N12  C11  112.46  3.000
 X7A  H22  C13  H21  106.65  3.000
 X7A  H22  C13  C14  109.81  3.000
 X7A  H21  C13  C14  109.21  3.000
 X7A  H22  C13  N12  108.49  3.000
 X7A  H21  C13  N12  111.33  3.000
 X7A  C14  C13  N12  111.23  3.000
 X7A  H24  C14  H23  107.00  3.000
 X7A  H24  C14  C15  109.70  3.000
 X7A  H23  C14  C15  110.98  3.000
 X7A  H24  C14  C13  108.94  3.000
 X7A  H23  C14  C13  109.32  3.000
 X7A  C15  C14  C13  110.80  3.000
 X7A  H26  C15  H25  106.73  3.000
 X7A  H26  C15  C16  110.85  3.000
 X7A  H25  C15  C16  109.30  3.000
 X7A  H26  C15  C14  110.78  3.000
 X7A  H25  C15  C14  109.38  3.000
 X7A  C16  C15  C14  109.74  3.000
 X7A  H28  C16  H27  107.03  3.000
 X7A  H28  C16  C17  109.12  3.000
 X7A  H27  C16  C17  109.30  3.000
 X7A  H28  C16  C15  109.72  3.000
 X7A  H27  C16  C15  110.89  3.000
 X7A  C17  C16  C15  110.70  3.000
 X7A  H30  C17  H29  106.58  3.000
 X7A  H30  C17  C16  109.11  3.000
 X7A  H29  C17  C16  109.37  3.000
 X7A  H30  C17  N12  110.88  3.000
 X7A  H29  C17  N12  109.49  3.000
 X7A  C16  C17  N12  111.29  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
 X7A  CONST_01  H1   O20  C18  O21     0.00   0.0  0
 X7A  Var_01    C15  C16  C17  N12   -57.01  30.0  1
 X7A  Var_02    C15  C14  C13  N12    56.92  30.0  1
 X7A  Var_03    C16  C17  N12  C13    60.01  30.0  1
 X7A  Var_04    C16  C15  C14  C13   -53.18  30.0  1
 X7A  Var_05    C17  N12  C13  C14   -59.93  30.0  1
 X7A  Var_06    C17  C16  C15  C14    53.16  30.0  1
 X7A  Var_07    N12  C11  C10  C1    173.58  30.0  1
 X7A  Var_08    C5   C4   C3   C1   -175.11  30.0  1
 X7A  Var_09    C6   C5   C4   C3    178.99  30.0  3
 X7A  Var_10    B7   C6   C5   C4   -179.17  30.0  1
 X7A  Var_11    O19  B7   C6   C5    -62.70  30.0  2

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
 X7A  chir_01  C1  C18  C3  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
 X7A  plan-1  O20  0.020
 X7A  plan-1  C18  0.020
 X7A  plan-1  O21  0.020
 X7A  plan-1  C1   0.020
 X7A  plan-1  H1   0.020

