# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 04:12:34 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: [(1S)-1-{[(6R)-6-amino-6-carboxyhexanoyl]amino}ethyl](trihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)CCCC[C@@H](N)C(O)=O)[B-](O)(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
 BO8  BO8  '[(1S)-1-{[(6R)-6-amino-6-carboxyhexanoyl]amino}ethyl](trihydroxy)borate(1-)'  ligand  37  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BO8
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
 BO8  O1    O  O      0  -0.534   1.4692   2.0087   0.7371
 BO8  C1    C  C      0   0.534   1.5089   1.0974  -0.0893
 BO8  N     N  NH1    0  -0.629   2.6153   0.4095  -0.3791
 BO8  CA    C  CH1    0  -0.274   3.9502   0.6556   0.1531
 BO8  B     B  B     -1   0.459   4.7686  -0.7800   0.2957
 BO8  OB1   O  OB     0  -0.753   4.7682  -1.5368  -0.9751
 BO8  OB2   O  OB     0  -0.743   6.1941  -0.5470   0.5767
 BO8  CB    C  CH3    0  -0.671   4.6684   1.6839  -0.7209
 BO8  CA1   C  CH2    0  -0.568   0.2646   0.6864  -0.8542
 BO8  CB1   C  CH2    0  -0.413  -0.9554   0.5182   0.0439
 BO8  CG1   C  CH2    0  -0.402  -2.2228   0.2107  -0.7439
 BO8  CD1   C  CH2    0  -0.420  -3.4422   0.0588   0.1546
 BO8  CE1   C  CH1    0  -0.212  -4.7505  -0.2028  -0.5941
 BO8  NZ1   N  NH2    0  -0.785  -4.6319  -1.4061  -1.4042
 BO8  CZ1   C  C      0   0.383  -5.9369  -0.1863   0.4037
 BO8  O     O  OC    -1  -0.625  -6.1188   0.8863   1.0185
 BO8  OH1   O  O      0  -0.609  -6.6097  -1.2293   0.5246
 BO8  OX0   O  OB     0  -0.748   4.0880  -1.5283   1.3732
 BO8  H     H  HNH1   0   0.367   2.5438  -0.2948  -1.0958
 BO8  HA11  H  HCH2   0   0.248   0.0632   1.4718  -1.5909
 BO8  HA12  H  HCH2   0   0.235   0.4368  -0.2298  -1.4254
 BO8  HA    H  HCH1   0   0.175   3.8115   1.1016   1.1444
 BO8  HB1C  H  HCH3   0   0.204   4.0890   2.6034  -0.8412
 BO8  HB2C  H  HCH3   0   0.199   5.6302   1.9610  -0.2867
 BO8  HB3C  H  HCH3   0   0.201   4.8671   1.2822  -1.7175
 BO8  HB1   H  H      0   0.422   3.9669  -2.0599  -1.0422
 BO8  HB2   H  H      0   0.418   6.2845   0.1780   1.1988
 BO8  HX0   H  H      0   0.423   4.5533  -2.3565   1.5227
 BO8  HB11  H  HCH2   0   0.216  -0.7714  -0.2859   0.7643
 BO8  HB12  H  HCH2   0   0.216  -1.1010   1.4286   0.6307
 BO8  HG11  H  HCH2   0   0.201  -2.4027   1.0166  -1.4652
 BO8  HG12  H  HCH2   0   0.211  -2.0828  -0.6981  -1.3345
 BO8  HD11  H  HCH2   0   0.201  -3.2683  -0.7580   0.8672
 BO8  HD12  H  HCH2   0   0.215  -3.5623   0.9630   0.7553
 BO8  HE1   H  HCH1   0   0.205  -4.9020   0.6381  -1.2841
 BO8  HZ11  H  HNH2   0   0.321  -4.5391  -2.1999  -0.7796
 BO8  HZ12  H  HNH2   0   0.332  -5.5161  -1.5649  -1.8724

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
 BO8  O1   C1    double  1.231  0.020  1.231
 BO8  C1   N     single  1.335  0.020  1.335
 BO8  C1   CA1   single  1.517  0.020  1.517
 BO8  N    CA    single  1.458  0.020  1.458
 BO8  CA   B     single  1.659  0.020  1.659
 BO8  CA   CB    single  1.529  0.020  1.529
 BO8  B    OB1   single  1.479  0.020  1.479
 BO8  B    OB2   single  1.471  0.020  1.471
 BO8  B    OX0   single  1.478  0.020  1.478
 BO8  CA1  CB1   single  1.524  0.020  1.524
 BO8  CB1  CG1   single  1.524  0.020  1.524
 BO8  CG1  CD1   single  1.522  0.020  1.522
 BO8  CD1  CE1   single  1.530  0.020  1.530
 BO8  CE1  NZ1   single  1.455  0.020  1.455
 BO8  CE1  CZ1   single  1.550  0.020  1.550
 BO8  CZ1  O     deloc   1.250  0.020  1.250
 BO8  CZ1  OH1   deloc   1.247  0.020  1.247
 BO8  N    H     single  0.860  0.020  1.020
 BO8  CA1  HA11  single  0.970  0.020  1.090
 BO8  CA1  HA12  single  0.970  0.020  1.090
 BO8  CA   HA    single  0.970  0.020  1.090
 BO8  CB   HB1C  single  0.970  0.020  1.090
 BO8  CB   HB2C  single  0.970  0.020  1.090
 BO8  CB   HB3C  single  0.970  0.020  1.090
 BO8  OB1  HB1   single  0.850  0.020  0.980
 BO8  OB2  HB2   single  0.850  0.020  0.980
 BO8  OX0  HX0   single  0.850  0.020  0.980
 BO8  CB1  HB11  single  0.970  0.020  1.090
 BO8  CB1  HB12  single  0.970  0.020  1.090
 BO8  CG1  HG11  single  0.970  0.020  1.090
 BO8  CG1  HG12  single  0.970  0.020  1.090
 BO8  CD1  HD11  single  0.970  0.020  1.090
 BO8  CD1  HD12  single  0.970  0.020  1.090
 BO8  CE1  HE1   single  0.970  0.020  1.090
 BO8  NZ1  HZ11  single  0.890  0.020  1.040
 BO8  NZ1  HZ12  single  0.890  0.020  1.040

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
 BO8  CA1   C1   N     115.51  3.000
 BO8  CA1   C1   O1    120.83  3.000
 BO8  N     C1   O1    123.65  3.000
 BO8  H     N    CA    116.28  3.000
 BO8  H     N    C1    117.13  3.000
 BO8  CA    N    C1    126.35  3.000
 BO8  HA    CA   CB    107.63  3.000
 BO8  HA    CA   B     109.69  3.000
 BO8  CB    CA   B     113.55  3.000
 BO8  HA    CA   N     106.44  3.000
 BO8  CB    CA   N     109.57  3.000
 BO8  B     CA   N     109.70  3.000
 BO8  OX0   B    OB2   112.77  3.000
 BO8  OX0   B    OB1   111.54  3.000
 BO8  OB2   B    OB1   104.21  3.000
 BO8  OX0   B    CA    105.88  3.000
 BO8  OB2   B    CA    110.94  3.000
 BO8  OB1   B    CA    111.65  3.000
 BO8  HB1   OB1  B     109.84  3.000
 BO8  HB2   OB2  B     109.56  3.000
 BO8  HB3C  CB   HB2C  107.22  3.000
 BO8  HB3C  CB   HB1C  107.77  3.000
 BO8  HB2C  CB   HB1C  107.29  3.000
 BO8  HB3C  CB   CA    111.08  3.000
 BO8  HB2C  CB   CA    110.94  3.000
 BO8  HB1C  CB   CA    112.31  3.000
 BO8  HA12  CA1  HA11  106.17  3.000
 BO8  HA12  CA1  CB1   109.97  3.000
 BO8  HA11  CA1  CB1   109.16  3.000
 BO8  HA12  CA1  C1    111.17  3.000
 BO8  HA11  CA1  C1    107.19  3.000
 BO8  CB1   CA1  C1    112.90  3.000
 BO8  HB12  CB1  HB11  106.31  3.000
 BO8  HB12  CB1  CG1   109.57  3.000
 BO8  HB11  CB1  CG1   109.37  3.000
 BO8  HB12  CB1  CA1   109.34  3.000
 BO8  HB11  CB1  CA1   109.52  3.000
 BO8  CG1   CB1  CA1   112.54  3.000
 BO8  HG12  CG1  HG11  106.07  3.000
 BO8  HG12  CG1  CD1   109.79  3.000
 BO8  HG11  CG1  CD1   109.27  3.000
 BO8  HG12  CG1  CB1   109.93  3.000
 BO8  HG11  CG1  CB1   109.17  3.000
 BO8  CD1   CG1  CB1   112.41  3.000
 BO8  HD12  CD1  HD11  106.04  3.000
 BO8  HD12  CD1  CE1   108.46  3.000
 BO8  HD11  CD1  CE1   109.02  3.000
 BO8  HD12  CD1  CG1   109.28  3.000
 BO8  HD11  CD1  CG1   109.30  3.000
 BO8  CE1   CD1  CG1   114.41  3.000
 BO8  HE1   CE1  CZ1   106.90  3.000
 BO8  HE1   CE1  NZ1   107.13  3.000
 BO8  CZ1   CE1  NZ1   115.43  3.000
 BO8  HE1   CE1  CD1   107.13  3.000
 BO8  CZ1   CE1  CD1   109.73  3.000
 BO8  NZ1   CE1  CD1   110.12  3.000
 BO8  HZ12  NZ1  HZ11  103.99  3.000
 BO8  HZ12  NZ1  CE1   108.41  3.000
 BO8  HZ11  NZ1  CE1   108.16  3.000
 BO8  OH1   CZ1  O     126.27  3.000
 BO8  OH1   CZ1  CE1   117.80  3.000
 BO8  O     CZ1  CE1   115.93  3.000
 BO8  HX0   OX0  B     109.06  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
 BO8  CONST_01  CA   N    C1   O1      0.00   0.0  0
 BO8  CONST_02  CA1  C1   N    CA    180.00   0.0  0
 BO8  CONST_03  H    N    C1   O1    180.00   0.0  0
 BO8  Var_01    CB1  CA1  C1   O1    -47.02  30.0  3
 BO8  Var_02    CG1  CB1  CA1  C1    175.59  30.0  3
 BO8  Var_03    CD1  CG1  CB1  CA1  -179.36  30.0  3
 BO8  Var_04    CE1  CD1  CG1  CB1   177.97  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
 BO8  chir_01  CA   N    B    CB   negativ
 BO8  chir_02  CE1  CD1  NZ1  CZ1  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
 BO8  plan-1  O1   0.020
 BO8  plan-1  C1   0.020
 BO8  plan-1  N    0.020
 BO8  plan-1  CA   0.020
 BO8  plan-1  CA1  0.020
 BO8  plan-1  H    0.020
 BO8  plan-2  CE1  0.020
 BO8  plan-2  CZ1  0.020
 BO8  plan-2  O    0.020
 BO8  plan-2  OH1  0.020

