# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 03:30:33 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: (2S)-2-amino-4-boronobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCB(O)O)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
 XU7  XU7  "(2S)-2-amino-4-boronobutanoic acid"  ligand  19  10  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_XU7
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
 XU7  BAI  B  B      0   0.531  -22.6313  -28.8755  -10.4212
 XU7  OAK  O  OH1    0  -0.622  -21.5759  -28.0144  -10.5004
 XU7  OAL  O  OH1    0  -0.616  -22.6060  -29.8671  -11.3593
 XU7  CAH  C  CH2    0  -0.698  -23.7704  -28.7540   -9.3270
 XU7  CAG  C  CH2    0  -0.443  -24.1698  -27.3218   -8.9685
 XU7  CAD  C  CH1    0  -0.199  -25.3033  -27.2287   -7.9392
 XU7  CAB  C  C      0   0.382  -25.4733  -25.7467   -7.5145
 XU7  OAC  O  O      0  -0.604  -26.4155  -25.1143   -8.0348
 XU7  OAA  O  OC    -1  -0.616  -24.6263  -25.3016   -6.7122
 XU7  NAE  N  NH2    0  -0.787  -26.5067  -27.8545   -8.4708
 XU7  H1   H  HOH1   0   0.471  -21.6011  -27.3288   -9.8277
 XU7  H2   H  HOH1   0   0.470  -23.3669  -30.4499  -11.2927
 XU7  H3   H  HCH2   0   0.228  -24.6612  -29.3086   -9.6334
 XU7  H4   H  HCH2   0   0.233  -23.4177  -29.2592   -8.4174
 XU7  H5   H  HCH2   0   0.208  -23.3074  -26.7797   -8.5686
 XU7  H6   H  HCH2   0   0.210  -24.4757  -26.7803   -9.8718
 XU7  H11  H  HNH2   0   0.331  -27.1736  -27.9708   -7.7170
 XU7  H12  H  HNH2   0   0.321  -26.9439  -27.1814   -9.0912
 XU7  H7   H  HCH1   0   0.199  -24.9911  -27.8008   -7.0580

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
 XU7  OAL  BAI  single  1.365  0.020  1.365
 XU7  BAI  OAK  single  1.364  0.020  1.364
 XU7  BAI  CAH  single  1.584  0.020  1.584
 XU7  CAH  CAG  single  1.529  0.020  1.529
 XU7  CAG  CAD  single  1.534  0.020  1.534
 XU7  NAE  CAD  single  1.457  0.020  1.457
 XU7  OAC  CAB  deloc   1.248  0.020  1.248
 XU7  CAD  CAB  single  1.551  0.020  1.551
 XU7  CAB  OAA  deloc   1.249  0.020  1.249
 XU7  OAK  H1   single  0.850  0.020  0.980
 XU7  OAL  H2   single  0.850  0.020  0.980
 XU7  CAH  H3   single  0.970  0.020  1.090
 XU7  CAH  H4   single  0.970  0.020  1.090
 XU7  CAG  H5   single  0.970  0.020  1.090
 XU7  CAG  H6   single  0.970  0.020  1.090
 XU7  NAE  H11  single  0.890  0.020  1.040
 XU7  NAE  H12  single  0.890  0.020  1.040
 XU7  CAD  H7   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
 XU7  CAH  BAI  OAL  122.93  3.000
 XU7  CAH  BAI  OAK  123.22  3.000
 XU7  OAL  BAI  OAK  113.84  3.000
 XU7  H1   OAK  BAI  112.92  3.000
 XU7  H2   OAL  BAI  112.22  3.000
 XU7  H4   CAH  H3   105.09  3.000
 XU7  H4   CAH  CAG  108.68  3.000
 XU7  H3   CAH  CAG  109.15  3.000
 XU7  H4   CAH  BAI  107.80  3.000
 XU7  H3   CAH  BAI  110.70  3.000
 XU7  CAG  CAH  BAI  114.93  3.000
 XU7  H6   CAG  H5   106.03  3.000
 XU7  H6   CAG  CAD  108.46  3.000
 XU7  H5   CAG  CAD  107.88  3.000
 XU7  H6   CAG  CAH  110.00  3.000
 XU7  H5   CAG  CAH  110.11  3.000
 XU7  CAD  CAG  CAH  114.02  3.000
 XU7  H7   CAD  NAE  107.72  3.000
 XU7  H7   CAD  CAB  108.05  3.000
 XU7  NAE  CAD  CAB  114.82  3.000
 XU7  H7   CAD  CAG  107.30  3.000
 XU7  CAB  CAD  CAG  108.83  3.000
 XU7  NAE  CAD  CAG  109.84  3.000
 XU7  OAA  CAB  OAC  126.81  3.000
 XU7  OAA  CAB  CAD  116.24  3.000
 XU7  OAC  CAB  CAD  116.92  3.000
 XU7  H12  NAE  H11  104.33  3.000
 XU7  H12  NAE  CAD  107.11  3.000
 XU7  H11  NAE  CAD  108.76  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
 XU7  Var_01  CAD  CAG  CAH  BAI   178.23  30.0  3
 XU7  Var_02  CAG  CAH  BAI  OAK    36.94  30.0  3
 XU7  Var_03  CAG  CAH  BAI  OAL  -144.15  30.0  3
 XU7  Var_04  H5   CAG  CAH  BAI   -60.36  30.0  3
 XU7  Var_05  H6   CAG  CAH  BAI    56.15  30.0  3
 XU7  Var_06  H3   CAH  BAI  OAK   161.15  30.0  3
 XU7  Var_07  H4   CAH  BAI  OAK   -84.41  30.0  3
 XU7  Var_08  H3   CAH  BAI  OAL   -19.93  30.0  3
 XU7  Var_09  H4   CAH  BAI  OAL    94.51  30.0  3
 XU7  Var_10  H3   CAH  CAG  CAD    53.20  30.0  1
 XU7  Var_11  H4   CAH  CAG  CAD   -60.90  30.0  1

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
 XU7  chir_01  CAD  CAG  NAE  CAB  positiv

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
 XU7  plan-1  CAD  0.020
 XU7  plan-1  CAB  0.020
 XU7  plan-1  OAC  0.020
 XU7  plan-1  OAA  0.020

