# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 10:38:07 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  38  18  .  2021-08-06  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.532   1.5015   2.1795   0.2171
 BO8  C1    C  C      0   0.532   1.5124   1.0903  -0.3545
 BO8  N     N  NH1    0  -0.634   2.5892   0.3035  -0.4222
 BO8  CA    C  CH1    0  -0.281   3.8874   0.5911   0.1835
 BO8  B     B  B     -1   0.448   4.7835  -0.7926   0.3643
 BO8  OB1   O  OB     0  -0.746   5.3026  -1.3090  -0.9150
 BO8  OB2   O  OB     0  -0.738   6.0007  -0.5200   1.1451
 BO8  CB    C  CH3    0  -0.668   4.6271   1.6594  -0.6182
 BO8  CA1   C  CH2    0  -0.563   0.2615   0.5614  -1.0320
 BO8  CB1   C  CH2    0  -0.419  -0.9336   0.5272  -0.0831
 BO8  CG1   C  CH2    0  -0.407  -2.2326   0.1720  -0.7955
 BO8  CD1   C  CH2    0  -0.434  -3.4128   0.1220   0.1660
 BO8  CE1   C  CH1    0  -0.203  -4.7519  -0.1422  -0.5366
 BO8  NZ1   N  NH2    0  -0.777  -4.7155  -1.3902  -1.2601
 BO8  CZ1   C  C      0   0.519  -5.8726  -0.0711   0.4924
 BO8  O     O  OH1    0  -0.594  -6.1122   1.1741   0.8897
 BO8  OH1   O  O      0  -0.442  -6.4726  -1.0264   0.9188
 BO8  OX0   O  OB     0  -0.748   3.8892  -1.7670   1.0318
 BO8  H     H  HNH1   0   0.379   2.4598  -0.6032  -0.8402
 BO8  HA11  H  HCH2   0   0.248   0.0352   1.2281  -1.8701
 BO8  HA12  H  HCH2   0   0.237   0.4270  -0.4301  -1.4610
 BO8  HA    H  HCH1   0   0.170   3.6821   1.0097   1.1788
 BO8  HB1C  H  HCH3   0   0.206   4.0567   2.5854  -0.7185
 BO8  HB2C  H  HCH3   0   0.202   5.5716   1.9052  -0.1299
 BO8  HB3C  H  HCH3   0   0.195   4.8649   1.3014  -1.6221
 BO8  HB1   H  H      0   0.417   4.5937  -1.3976  -1.5552
 BO8  HB2   H  H      0   0.420   5.7566  -0.0648   1.9538
 BO8  HX0   H  H      0   0.425   4.3602  -2.5999   1.1259
 BO8  HB11  H  HCH2   0   0.222  -0.7438  -0.1974   0.7152
 BO8  HB12  H  HCH2   0   0.222  -1.0370   1.5021   0.3995
 BO8  HG11  H  HCH2   0   0.213  -2.4305   0.9166  -1.5740
 BO8  HG12  H  HCH2   0   0.223  -2.1314  -0.7884  -1.3050
 BO8  HD11  H  HCH2   0   0.229  -3.2438  -0.6576   0.9171
 BO8  HD12  H  HCH2   0   0.239  -3.4713   1.0676   0.7104
 BO8  HE1   H  HCH1   0   0.264  -4.9179   0.6662  -1.2567
 BO8  HZ11  H  HNH2   0   0.342  -4.6033  -2.1646  -0.6170
 BO8  HZ12  H  HNH2   0   0.353  -5.5925  -1.5456  -1.7404
 BO8  HB    H  HOH1   0   0.480  -6.8073   1.1807   1.5648

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  1.230  0.020  1.230
 BO8  C1   N     single  1.335  0.020  1.335
 BO8  C1   CA1   single  1.518  0.020  1.518
 BO8  N    CA    single  1.461  0.020  1.461
 BO8  CA   B     single  1.658  0.020  1.658
 BO8  CA   CB    single  1.527  0.020  1.527
 BO8  B    OB1   single  1.474  0.020  1.474
 BO8  B    OB2   single  1.472  0.020  1.472
 BO8  B    OX0   single  1.481  0.020  1.481
 BO8  CA1  CB1   single  1.526  0.020  1.526
 BO8  CB1  CG1   single  1.523  0.020  1.523
 BO8  CG1  CD1   single  1.523  0.020  1.523
 BO8  CD1  CE1   single  1.535  0.020  1.535
 BO8  CE1  NZ1   single  1.443  0.020  1.443
 BO8  CE1  CZ1   single  1.523  0.020  1.523
 BO8  CZ1  O     single  1.329  0.020  1.329
 BO8  CZ1  OH1   double  1.206  0.020  1.206
 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
 BO8  O    HB    single  0.850  0.020  0.980

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     115.89  3.000
 BO8  CA1   C1   O1    120.58  3.000
 BO8  N     C1   O1    123.53  3.000
 BO8  H     N    CA    117.62  3.000
 BO8  H     N    C1    116.62  3.000
 BO8  CA    N    C1    125.41  3.000
 BO8  HA    CA   CB    107.42  3.000
 BO8  HA    CA   B     108.66  3.000
 BO8  CB    CA   B     112.29  3.000
 BO8  HA    CA   N     106.53  3.000
 BO8  CB    CA   N     110.52  3.000
 BO8  B     CA   N     111.16  3.000
 BO8  OX0   B    OB2   112.47  3.000
 BO8  OX0   B    OB1   111.91  3.000
 BO8  OB2   B    OB1   103.53  3.000
 BO8  OX0   B    CA    105.77  3.000
 BO8  OB2   B    CA    110.50  3.000
 BO8  OB1   B    CA    112.83  3.000
 BO8  HB1   OB1  B     110.56  3.000
 BO8  HB2   OB2  B     108.94  3.000
 BO8  HB3C  CB   HB2C  107.26  3.000
 BO8  HB3C  CB   HB1C  107.89  3.000
 BO8  HB2C  CB   HB1C  107.58  3.000
 BO8  HB3C  CB   CA    111.03  3.000
 BO8  HB2C  CB   CA    109.99  3.000
 BO8  HB1C  CB   CA    112.86  3.000
 BO8  HA12  CA1  HA11  106.46  3.000
 BO8  HA12  CA1  CB1   110.01  3.000
 BO8  HA11  CA1  CB1   109.13  3.000
 BO8  HA12  CA1  C1    111.51  3.000
 BO8  HA11  CA1  C1    107.46  3.000
 BO8  CB1   CA1  C1    112.06  3.000
 BO8  HB12  CB1  HB11  106.55  3.000
 BO8  HB12  CB1  CG1   109.50  3.000
 BO8  HB11  CB1  CG1   109.55  3.000
 BO8  HB12  CB1  CA1   109.18  3.000
 BO8  HB11  CB1  CA1   109.42  3.000
 BO8  CG1   CB1  CA1   112.47  3.000
 BO8  HG12  CG1  HG11  106.44  3.000
 BO8  HG12  CG1  CD1   109.72  3.000
 BO8  HG11  CG1  CD1   109.33  3.000
 BO8  HG12  CG1  CB1   110.13  3.000
 BO8  HG11  CG1  CB1   109.15  3.000
 BO8  CD1   CG1  CB1   111.91  3.000
 BO8  HD12  CD1  HD11  106.41  3.000
 BO8  HD12  CD1  CE1   109.28  3.000
 BO8  HD11  CD1  CE1   109.02  3.000
 BO8  HD12  CD1  CG1   109.13  3.000
 BO8  HD11  CD1  CG1   109.67  3.000
 BO8  CE1   CD1  CG1   113.12  3.000
 BO8  HE1   CE1  CZ1   107.35  3.000
 BO8  HE1   CE1  NZ1   108.21  3.000
 BO8  CZ1   CE1  NZ1   113.43  3.000
 BO8  HE1   CE1  CD1   107.82  3.000
 BO8  CZ1   CE1  CD1   108.94  3.000
 BO8  NZ1   CE1  CD1   110.87  3.000
 BO8  HZ12  NZ1  HZ11  106.25  3.000
 BO8  HZ12  NZ1  CE1   110.42  3.000
 BO8  HZ11  NZ1  CE1   110.23  3.000
 BO8  OH1   CZ1  O     123.15  3.000
 BO8  OH1   CZ1  CE1   124.61  3.000
 BO8  O     CZ1  CE1   112.23  3.000
 BO8  HB    O    CZ1   110.12  3.000
 BO8  HX0   OX0  B     108.55  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  CONST_04  HB   O    CZ1  CE1  180.00   0.0  0
 BO8  Var_01    CB1  CA1  C1   O1   -54.17  30.0  3
 BO8  Var_02    CG1  CB1  CA1  C1   172.54  30.0  3
 BO8  Var_03    CD1  CG1  CB1  CA1  179.19  30.0  3
 BO8  Var_04    CE1  CD1  CG1  CB1  176.19  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
 BO8  plan-2  HB   0.020

