# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 22:14:55 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  52  22  .  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_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  OH1    0  -0.581  -0.2036  -2.7477   1.1667
 X8A  C7   C  C      0   0.557  -0.3046  -1.9360   0.1252
 X8A  O8   O  O      0  -0.449  -0.3389  -2.3392  -1.0128
 X8A  C1   C  CT     0  -0.032  -0.3465  -0.4491   0.4796
 X8A  N6   N  NH1    0  -0.602  -0.4123  -0.2855   1.9244
 X8A  C18  C  CH3    0  -0.533  -0.5640   1.0743   2.4053
 X8A  C2   C  CH2    0  -0.405   0.8988   0.1967  -0.1746
 X8A  C3   C  CH2    0  -0.425   2.2419  -0.3163   0.3301
 X8A  C4   C  CH2    0  -0.427   3.4296   0.3752  -0.3337
 X8A  C5   C  CH2    0  -0.638   4.7893  -0.1369   0.1339
 X8A  B19  B  B     -1   0.429   6.1037   0.6027  -0.5255
 X8A  O22  O  OB     0  -0.748   7.3598  -0.0577  -0.1038
 X8A  O21  O  OB     0  -0.753   6.1434   0.4871  -2.0000
 X8A  O20  O  OB     0  -0.750   6.0562   2.0206  -0.0857
 X8A  C10  C  CH2    0  -0.448  -1.6054   0.1458  -0.1738
 X8A  C11  C  CH2    0  -0.263  -2.9175  -0.4354   0.3401
 X8A  N12  N  NT     0  -0.421  -4.0705   0.1818  -0.2930
 X8A  C17  C  CH2    0  -0.279  -5.2285  -0.6962  -0.2787
 X8A  C16  C  CH2    0  -0.437  -6.3903  -0.0898  -1.0509
 X8A  C15  C  CH2    0  -0.440  -6.7567   1.2796  -0.4942
 X8A  C14  C  CH2    0  -0.434  -5.5186   2.1655  -0.4446
 X8A  C13  C  CH2    0  -0.286  -4.3879   1.4705   0.2998
 X8A  H1   H  HOH1   0   0.480  -0.1510  -3.6648   0.8566
 X8A  H2   H  HNH1   0   0.352   0.4057  -0.6919   2.3577
 X8A  H4   H  HCH3   0   0.241  -0.4208   1.0741   3.4851
 X8A  H5   H  HCH3   0   0.204   0.1396   1.8013   1.9817
 X8A  H6   H  HCH3   0   0.223  -1.5729   1.4455   2.2179
 X8A  H7   H  HCH2   0   0.227   0.8377   0.0563  -1.2572
 X8A  H8   H  HCH2   0   0.229   0.8431   1.2779  -0.0158
 X8A  H9   H  HCH2   0   0.201   2.3215  -0.1745   1.4137
 X8A  H10  H  HCH2   0   0.208   2.3278  -1.3960   0.1592
 X8A  H11  H  HCH2   0   0.179   3.3358   0.2486  -1.4204
 X8A  H12  H  HCH2   0   0.195   3.3534   1.4535  -0.1550
 X8A  H13  H  HCH2   0   0.151   4.8195  -0.0596   1.2324
 X8A  H14  H  HCH2   0   0.153   4.8287  -1.2178  -0.0679
 X8A  H15  H  H      0   0.417   7.3203  -0.2018   0.8439
 X8A  H16  H  H      0   0.417   5.3197   0.8212  -2.3613
 X8A  H17  H  H      0   0.417   6.8197   2.4807  -0.4466
 X8A  H18  H  HCH2   0   0.244  -1.5775   1.2291  -0.0305
 X8A  H19  H  HCH2   0   0.245  -1.5457  -0.0106  -1.2520
 X8A  H20  H  HCH2   0   0.229  -2.9449  -1.5043   0.1089
 X8A  H21  H  HCH2   0   0.205  -2.9704  -0.3629   1.4375
 X8A  H23  H  HCH2   0   0.232  -4.9454  -1.6501  -0.7304
 X8A  H24  H  HCH2   0   0.180  -5.5556  -0.9208   0.7531
 X8A  H25  H  HCH2   0   0.213  -6.1057   0.0047  -2.1033
 X8A  H26  H  HCH2   0   0.228  -7.2446  -0.7690  -1.0107
 X8A  H27  H  HCH2   0   0.230  -7.5422   1.7441  -1.0944
 X8A  H28  H  HCH2   0   0.209  -7.1601   1.1641   0.5180
 X8A  H29  H  HCH2   0   0.214  -5.1888   2.3991  -1.4613
 X8A  H30  H  HCH2   0   0.228  -5.7406   3.1168   0.0443
 X8A  H31  H  HCH2   0   0.182  -4.6696   1.3561   1.3631
 X8A  H32  H  HCH2   0   0.233  -3.4995   2.1050   0.2807

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  1.450  0.020  1.450
 X8A  O22  B19  single  1.480  0.020  1.480
 X8A  N6   C1   single  1.456  0.020  1.456
 X8A  O21  B19  single  1.480  0.020  1.480
 X8A  O8   C7   double  1.208  0.020  1.208
 X8A  B19  C5   single  1.646  0.020  1.646
 X8A  B19  O20  single  1.485  0.020  1.485
 X8A  C5   C4   single  1.526  0.020  1.526
 X8A  C3   C4   single  1.526  0.020  1.526
 X8A  C3   C2   single  1.524  0.020  1.524
 X8A  C1   C7   single  1.529  0.020  1.529
 X8A  C1   C2   single  1.548  0.020  1.548
 X8A  C1   C10  single  1.538  0.020  1.538
 X8A  C7   O9   single  1.324  0.020  1.324
 X8A  C11  C10  single  1.524  0.020  1.524
 X8A  C11  N12  single  1.453  0.020  1.453
 X8A  C13  N12  single  1.454  0.020  1.454
 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  1.521  0.020  1.521
 X8A  C15  C16  single  1.523  0.020  1.523
 X8A  O9   H1   single  0.850  0.020  0.980
 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  H1   O9   C7   109.42  3.000
 X8A  C1   C7   O8   122.83  3.000
 X8A  C1   C7   O9   114.57  3.000
 X8A  O8   C7   O9   122.59  3.000
 X8A  C10  C1   C2   108.52  3.000
 X8A  C10  C1   N6   109.95  3.000
 X8A  C2   C1   N6   114.14  3.000
 X8A  C10  C1   C7   107.47  3.000
 X8A  C2   C1   C7   106.60  3.000
 X8A  N6   C1   C7   109.91  3.000
 X8A  H2   N6   C18  108.63  3.000
 X8A  H2   N6   C1   110.10  3.000
 X8A  C18  N6   C1   116.06  3.000
 X8A  H6   C18  H5   107.53  3.000
 X8A  H6   C18  H4   106.97  3.000
 X8A  H5   C18  H4   107.38  3.000
 X8A  H6   C18  N6   111.02  3.000
 X8A  H5   C18  N6   115.23  3.000
 X8A  H4   C18  N6   108.35  3.000
 X8A  H8   C2   H7   105.53  3.000
 X8A  H8   C2   C3   109.23  3.000
 X8A  H7   C2   C3   109.51  3.000
 X8A  H8   C2   C1   108.06  3.000
 X8A  H7   C2   C1   108.66  3.000
 X8A  C3   C2   C1   115.39  3.000
 X8A  H10  C3   H9   106.01  3.000
 X8A  H10  C3   C4   108.51  3.000
 X8A  H9   C3   C4   108.35  3.000
 X8A  H10  C3   C2   110.42  3.000
 X8A  H9   C3   C2   110.37  3.000
 X8A  C4   C3   C2   112.92  3.000
 X8A  H12  C4   H11  105.61  3.000
 X8A  H12  C4   C5   110.01  3.000
 X8A  H11  C4   C5   109.91  3.000
 X8A  H12  C4   C3   108.71  3.000
 X8A  H11  C4   C3   108.16  3.000
 X8A  C5   C4   C3   114.08  3.000
 X8A  H14  C5   H13  104.52  3.000
 X8A  H14  C5   B19  109.84  3.000
 X8A  H13  C5   B19  110.24  3.000
 X8A  H14  C5   C4   107.78  3.000
 X8A  H13  C5   C4   107.84  3.000
 X8A  B19  C5   C4   115.97  3.000
 X8A  O20  B19  O21  111.75  3.000
 X8A  O20  B19  O22  111.63  3.000
 X8A  O21  B19  O22  103.08  3.000
 X8A  O20  B19  C5   106.55  3.000
 X8A  O21  B19  C5   112.67  3.000
 X8A  O22  B19  C5   111.28  3.000
 X8A  H15  O22  B19  108.26  3.000
 X8A  H16  O21  B19  108.97  3.000
 X8A  H17  O20  B19  108.68  3.000
 X8A  H19  C10  H18  105.67  3.000
 X8A  H19  C10  C11  109.00  3.000
 X8A  H18  C10  C11  110.83  3.000
 X8A  H19  C10  C1   108.64  3.000
 X8A  H18  C10  C1   107.86  3.000
 X8A  C11  C10  C1   114.45  3.000
 X8A  H21  C11  H20  105.89  3.000
 X8A  H21  C11  N12  111.60  3.000
 X8A  H20  C11  N12  107.64  3.000
 X8A  H21  C11  C10  110.63  3.000
 X8A  H20  C11  C10  108.84  3.000
 X8A  N12  C11  C10  111.98  3.000
 X8A  C13  N12  C17  110.95  3.000
 X8A  C17  N12  C11  111.80  3.000
 X8A  C13  N12  C11  111.85  3.000
 X8A  H24  C17  H23  106.57  3.000
 X8A  H24  C17  C16  109.20  3.000
 X8A  H23  C17  C16  109.63  3.000
 X8A  H24  C17  N12  111.57  3.000
 X8A  H23  C17  N12  108.47  3.000
 X8A  C16  C17  N12  111.27  3.000
 X8A  H26  C16  H25  107.01  3.000
 X8A  H26  C16  C15  110.95  3.000
 X8A  H25  C16  C15  109.66  3.000
 X8A  H26  C16  C17  109.32  3.000
 X8A  H25  C16  C17  108.91  3.000
 X8A  C15  C16  C17  110.90  3.000
 X8A  H28  C15  H27  106.72  3.000
 X8A  H28  C15  C14  109.29  3.000
 X8A  H27  C15  C14  110.80  3.000
 X8A  H28  C15  C16  109.36  3.000
 X8A  H27  C15  C16  110.77  3.000
 X8A  C14  C15  C16  109.83  3.000
 X8A  H30  C14  H29  106.93  3.000
 X8A  H30  C14  C13  109.26  3.000
 X8A  H29  C14  C13  109.16  3.000
 X8A  H30  C14  C15  110.85  3.000
 X8A  H29  C14  C15  109.81  3.000
 X8A  C13  C14  C15  110.75  3.000
 X8A  H32  C13  H31  106.51  3.000
 X8A  H32  C13  C14  109.30  3.000
 X8A  H31  C13  C14  109.16  3.000
 X8A  H32  C13  N12  109.29  3.000
 X8A  H31  C13  N12  110.86  3.000
 X8A  C14  C13  N12  111.57  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  CONST_01  H1   O9   C7   O8      0.00   0.0  0
 X8A  Var_01    C15  C14  C13  N12    56.37  30.0  1
 X8A  Var_02    C15  C16  C17  N12   -56.76  30.0  1
 X8A  Var_03    C14  C13  N12  C17   -59.35  30.0  1
 X8A  Var_04    C14  C15  C16  C17    53.20  30.0  1
 X8A  Var_05    C13  N12  C17  C16    59.41  30.0  1
 X8A  Var_06    C13  C14  C15  C16   -52.88  30.0  1
 X8A  Var_07    N12  C11  C10  C1    178.88  30.0  2
 X8A  Var_08    C4   C3   C2   C1   -178.97  30.0  1
 X8A  Var_09    C5   C4   C3   C2   -178.93  30.0  3
 X8A  Var_10    B19  C5   C4   C3   -178.56  30.0  1
 X8A  Var_11    O22  B19  C5   C4   -174.47  30.0  3
 X8A  Var_12    H4   C18  N6   C1   -170.02  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
 X8A  plan-1  H1  0.020

