# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 23:24:16 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  48  21  .  2021-08-24  2022-09-22
;
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  OC    -1  -0.607  -0.5760  -2.9569  -0.0068
 X7A  C18  C  C      0   0.426  -0.3823  -1.8412  -0.5304
 X7A  O21  O  O      0  -0.616  -0.2438  -1.6157  -1.7498
 X7A  C1   C  CT     0  -0.035  -0.3544  -0.5996   0.4004
 X7A  N2   N  NH2    0  -0.807  -0.2725  -1.0245   1.7942
 X7A  C3   C  CH2    0  -0.362   0.8680   0.2760   0.0907
 X7A  C4   C  CH2    0  -0.402   2.2127  -0.4278   0.2136
 X7A  C5   C  CH2    0  -0.427   3.4095   0.5057   0.0533
 X7A  C6   C  CH2    0  -0.636   4.7664  -0.1839   0.1847
 X7A  B7   B  B     -1   0.427   6.0881   0.7843   0.0323
 X7A  O8   O  OB     0  -0.754   6.1254   1.8534   1.0540
 X7A  O9   O  OB     0  -0.747   7.3406   0.0351   0.2839
 X7A  O19  O  OB     0  -0.751   6.0539   1.3410  -1.3449
 X7A  C10  C  CH2    0  -0.432  -1.6250   0.2314   0.1142
 X7A  C11  C  CH2    0  -0.255  -2.9341  -0.5072   0.3675
 X7A  N12  N  NT     0  -0.419  -4.0979   0.3631   0.3211
 X7A  C13  C  CH2    0  -0.275  -5.2512  -0.2627   0.9446
 X7A  C14  C  CH2    0  -0.437  -6.4318   0.6947   1.0147
 X7A  C15  C  CH2    0  -0.439  -6.7959   1.2054  -0.3736
 X7A  C16  C  CH2    0  -0.434  -5.5609   1.7897  -1.0467
 X7A  C17  C  CH2    0  -0.282  -4.4139   0.7895  -1.0314
 X7A  H2   H  HNH2   0   0.323  -0.6127  -0.2856   2.3983
 X7A  H3   H  HNH2   0   0.333  -0.8698  -1.8274   1.9351
 X7A  H5   H  HCH2   0   0.196   0.7693   0.6950  -0.9144
 X7A  H6   H  HCH2   0   0.187   0.8513   1.1327   0.7778
 X7A  H7   H  HCH2   0   0.191   2.2686  -0.9250   1.1860
 X7A  H8   H  HCH2   0   0.191   2.2818  -1.2202  -0.5395
 X7A  H9   H  HCH2   0   0.184   3.3447   1.0115  -0.9168
 X7A  H10  H  HCH2   0   0.169   3.3236   1.3032   0.8045
 X7A  H11  H  HCH2   0   0.149   4.7903  -0.6922   1.1610
 X7A  H12  H  HCH2   0   0.148   4.8010  -1.0024  -0.5520
 X7A  H13  H  H      0   0.416   5.2766   2.3004   1.0648
 X7A  H14  H  H      0   0.417   7.3203  -0.7677  -0.2415
 X7A  H15  H  H      0   0.417   6.8174   1.9133  -1.4654
 X7A  H16  H  HCH2   0   0.203  -1.6074   1.1209   0.7554
 X7A  H17  H  HCH2   0   0.214  -1.5831   0.5897  -0.9163
 X7A  H18  H  HCH2   0   0.188  -3.0383  -1.3491  -0.3375
 X7A  H19  H  HCH2   0   0.205  -2.8987  -0.9464   1.3681
 X7A  H21  H  HCH2   0   0.176  -5.5580  -1.1760   0.4017
 X7A  H22  H  HCH2   0   0.228  -4.9701  -0.5795   1.9523
 X7A  H23  H  HCH2   0   0.227  -7.2810   0.1891   1.4801
 X7A  H24  H  HCH2   0   0.212  -6.1686   1.5378   1.6608
 X7A  H25  H  HCH2   0   0.208  -7.1781   0.3746  -0.9768
 X7A  H26  H  HCH2   0   0.229  -7.5958   1.9468  -0.3169
 X7A  H27  H  HCH2   0   0.227  -5.7781   2.0745  -2.0786
 X7A  H28  H  HCH2   0   0.212  -5.2507   2.6987  -0.5227
 X7A  H29  H  HCH2   0   0.235  -3.5309   1.2443  -1.4832
 X7A  H30  H  HCH2   0   0.177  -4.6812  -0.0763  -1.6665

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  1.486  0.020  1.486
 X7A  N2   C1   single  1.459  0.020  1.459
 X7A  O21  C18  deloc   1.248  0.020  1.248
 X7A  O9   B7   single  1.481  0.020  1.481
 X7A  B7   C6   single  1.645  0.020  1.645
 X7A  B7   O8   single  1.479  0.020  1.479
 X7A  C6   C5   single  1.528  0.020  1.528
 X7A  C4   C5   single  1.526  0.020  1.526
 X7A  C4   C3   single  1.523  0.020  1.523
 X7A  C1   C18  single  1.552  0.020  1.552
 X7A  C1   C3   single  1.535  0.020  1.535
 X7A  C1   C10  single  1.545  0.020  1.545
 X7A  C18  O20  deloc   1.248  0.020  1.248
 X7A  C17  C16  single  1.522  0.020  1.522
 X7A  C17  N12  single  1.453  0.020  1.453
 X7A  C11  C10  single  1.524  0.020  1.524
 X7A  C11  N12  single  1.454  0.020  1.454
 X7A  C16  C15  single  1.523  0.020  1.523
 X7A  N12  C13  single  1.453  0.020  1.453
 X7A  C13  C14  single  1.522  0.020  1.522
 X7A  C15  C14  single  1.523  0.020  1.523
 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  C1   C18  O21  116.08  3.000
 X7A  C1   C18  O20  117.81  3.000
 X7A  O21  C18  O20  126.09  3.000
 X7A  C10  C1   C3   108.10  3.000
 X7A  C10  C1   N2   112.31  3.000
 X7A  C3   C1   N2   108.31  3.000
 X7A  C10  C1   C18  107.72  3.000
 X7A  C3   C1   C18  110.46  3.000
 X7A  N2   C1   C18  109.93  3.000
 X7A  H3   N2   H2   107.32  3.000
 X7A  H3   N2   C1   109.35  3.000
 X7A  H2   N2   C1   109.77  3.000
 X7A  H6   C3   H5   105.95  3.000
 X7A  H6   C3   C4   108.87  3.000
 X7A  H5   C3   C4   109.33  3.000
 X7A  H6   C3   C1   107.85  3.000
 X7A  H5   C3   C1   109.40  3.000
 X7A  C4   C3   C1   115.04  3.000
 X7A  H8   C4   H7   106.21  3.000
 X7A  H8   C4   C5   108.71  3.000
 X7A  H7   C4   C5   109.36  3.000
 X7A  H8   C4   C3   109.54  3.000
 X7A  H7   C4   C3   109.09  3.000
 X7A  C5   C4   C3   113.66  3.000
 X7A  H10  C5   H9   105.39  3.000
 X7A  H10  C5   C6   109.77  3.000
 X7A  H9   C5   C6   109.69  3.000
 X7A  H10  C5   C4   108.11  3.000
 X7A  H9   C5   C4   109.20  3.000
 X7A  C6   C5   C4   114.29  3.000
 X7A  H12  C6   H11  104.43  3.000
 X7A  H12  C6   B7   110.49  3.000
 X7A  H11  C6   B7   109.66  3.000
 X7A  H12  C6   C5   107.80  3.000
 X7A  H11  C6   C5   107.69  3.000
 X7A  B7   C6   C5   116.10  3.000
 X7A  O19  B7   O9   111.50  3.000
 X7A  O9   B7   O8   103.11  3.000
 X7A  O19  B7   O8   111.71  3.000
 X7A  O8   B7   C6   112.43  3.000
 X7A  O9   B7   C6   111.46  3.000
 X7A  O19  B7   C6   106.73  3.000
 X7A  H13  O8   B7   108.79  3.000
 X7A  H14  O9   B7   108.20  3.000
 X7A  H15  O19  B7   108.71  3.000
 X7A  H17  C10  H16  106.56  3.000
 X7A  H17  C10  C11  110.41  3.000
 X7A  H16  C10  C11  108.04  3.000
 X7A  H17  C10  C1   108.65  3.000
 X7A  H16  C10  C1   108.35  3.000
 X7A  C11  C10  C1   114.52  3.000
 X7A  H19  C11  H18  106.34  3.000
 X7A  H19  C11  N12  107.19  3.000
 X7A  H18  C11  N12  111.15  3.000
 X7A  H19  C11  C10  108.60  3.000
 X7A  H18  C11  C10  110.17  3.000
 X7A  N12  C11  C10  113.09  3.000
 X7A  C17  N12  C13  110.69  3.000
 X7A  C13  N12  C11  111.34  3.000
 X7A  C17  N12  C11  112.30  3.000
 X7A  H22  C13  H21  106.53  3.000
 X7A  H22  C13  C14  109.84  3.000
 X7A  H21  C13  C14  109.09  3.000
 X7A  H22  C13  N12  108.44  3.000
 X7A  H21  C13  N12  111.43  3.000
 X7A  C14  C13  N12  111.39  3.000
 X7A  H24  C14  H23  106.98  3.000
 X7A  H24  C14  C15  109.71  3.000
 X7A  H23  C14  C15  110.95  3.000
 X7A  H24  C14  C13  108.99  3.000
 X7A  H23  C14  C13  109.37  3.000
 X7A  C15  C14  C13  110.75  3.000
 X7A  H26  C15  H25  106.73  3.000
 X7A  H26  C15  C16  110.88  3.000
 X7A  H25  C15  C16  109.30  3.000
 X7A  H26  C15  C14  110.81  3.000
 X7A  H25  C15  C14  109.33  3.000
 X7A  C16  C15  C14  109.73  3.000
 X7A  H28  C16  H27  106.99  3.000
 X7A  H28  C16  C17  109.12  3.000
 X7A  H27  C16  C17  109.31  3.000
 X7A  H28  C16  C15  109.70  3.000
 X7A  H27  C16  C15  110.87  3.000
 X7A  C17  C16  C15  110.76  3.000
 X7A  H30  C17  H29  106.49  3.000
 X7A  H30  C17  C16  109.05  3.000
 X7A  H29  C17  C16  109.38  3.000
 X7A  H30  C17  N12  110.93  3.000
 X7A  H29  C17  N12  109.37  3.000
 X7A  C16  C17  N12  111.48  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  Var_01  C15  C16  C17  N12   -56.72  30.0  1
 X7A  Var_02  C15  C14  C13  N12    56.94  30.0  1
 X7A  Var_03  C16  C17  N12  C13    59.62  30.0  1
 X7A  Var_04  C16  C15  C14  C13   -53.16  30.0  1
 X7A  Var_05  C17  N12  C13  C14   -59.71  30.0  1
 X7A  Var_06  C17  C16  C15  C14    53.03  30.0  1
 X7A  Var_07  N12  C11  C10  C1    169.68  30.0  2
 X7A  Var_08  C5   C4   C3   C1   -173.51  30.0  1
 X7A  Var_09  C6   C5   C4   C3    179.56  30.0  3
 X7A  Var_10  B7   C6   C5   C4   -179.49  30.0  1
 X7A  Var_11  O19  B7   C6   C5    -62.59  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

