# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 15:34:10 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: trihydroxy(L-serinato-kappaO~3~)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CO[B-](O)(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
 SEE  SEE  trihydroxy(L-serinato-kappaO~3~)borate(1-)  L-peptide  19  11  .  2016-05-13  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_SEE
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
 SEE  N    N  NH2    0  -0.767  5.8563  -12.5043  -18.8328
 SEE  CA   C  CH1    0  -0.230  4.5263  -11.9037  -18.8160
 SEE  CB   C  CH2    0  -0.075  3.6723  -12.5359  -17.7115
 SEE  OG   O  OC2    0  -0.599  3.3874  -13.8680  -17.9752
 SEE  B    B  B     -1   0.387  3.1230  -14.7642  -16.8304
 SEE  O1B  O  OB     0  -0.688  4.3650  -15.0295  -16.0699
 SEE  O2B  O  OB     0  -0.686  2.5632  -15.9602  -17.4657
 SEE  O3B  O  OB     0  -0.717  2.1395  -14.2253  -15.8766
 SEE  C    C  C      0   0.345  4.5044  -10.3642  -18.6373
 SEE  O    O  O      0  -0.430  3.4706   -9.7784  -19.0246
 SEE  H    H  HNH2   0   0.295  6.3339  -12.2060  -19.6755
 SEE  H2   H  HNH2   0   0.301  6.3875  -12.0746  -18.0825
 SEE  HA   H  HCH1   0   0.193  4.0447  -12.1342  -19.7733
 SEE  HB2  H  HCH2   0   0.061  4.2190  -12.3980  -16.7619
 SEE  HB3  H  HCH2   0   0.135  2.7527  -11.9377  -17.6170
 SEE  OXT  O  OC    -1  -0.754  5.4945   -9.8378  -18.0879
 SEE  H6   H  H      0   0.429  5.0795  -15.1666  -16.6965
 SEE  H7   H  H      0   0.416  2.4074  -16.6207  -16.7876
 SEE  H8   H  H      0   0.383  2.5686  -13.5949  -15.2941

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
 SEE  N    CA   single  1.458  0.019  1.458
 SEE  N    H    single  0.860  0.020  0.860
 SEE  N    H2   single  0.890  0.020  1.040
 SEE  CA   CB   single  1.530  0.020  1.530
 SEE  CA   C    single  1.525  0.021  1.525
 SEE  CA   HA   single  0.970  0.020  0.970
 SEE  CB   OG   single  1.388  0.020  1.388
 SEE  CB   HB2  single  0.970  0.020  1.090
 SEE  CB   HB3  single  0.970  0.020  1.090
 SEE  OG   B    single  1.478  0.020  1.478
 SEE  B    O1B  single  1.480  0.020  1.480
 SEE  B    O2B  single  1.465  0.020  1.465
 SEE  B    O3B  single  1.472  0.020  1.472
 SEE  C    O    deloc   1.231  0.020  1.231
 SEE  C    OXT  deloc   1.249  0.020  1.249
 SEE  O1B  H6   single  0.850  0.020  0.980
 SEE  O2B  H7   single  0.850  0.020  0.980
 SEE  O3B  H8   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
 SEE  H2   N    H    104.09  3.000
 SEE  H2   N    CA   107.11  3.000
 SEE  H    N    CA   114.00  3.000
 SEE  HA   CA   C    109.00  3.000
 SEE  HA   CA   CB   109.00  3.000
 SEE  C    CA   CB   110.10  1.900
 SEE  HA   CA   N    110.00  3.000
 SEE  C    CA   N    111.00  2.800
 SEE  CB   CA   N    110.50  1.700
 SEE  HB3  CB   HB2  105.77  3.000
 SEE  HB3  CB   OG   111.50  3.000
 SEE  HB2  CB   OG   112.64  3.000
 SEE  HB3  CB   CA   107.64  3.000
 SEE  HB2  CB   CA   106.99  3.000
 SEE  OG   CB   CA   111.93  3.000
 SEE  B    OG   CB   118.15  3.000
 SEE  O3B  B    O2B  108.93  3.000
 SEE  O3B  B    O1B  107.06  3.000
 SEE  O2B  B    O1B  113.39  3.000
 SEE  O3B  B    OG   113.54  3.000
 SEE  O2B  B    OG   103.14  3.000
 SEE  O1B  B    OG   110.89  3.000
 SEE  H6   O1B  B    108.35  3.000
 SEE  H7   O2B  B    108.51  3.000
 SEE  H8   O3B  B    109.57  3.000
 SEE  OXT  C    O    126.49  3.000
 SEE  OXT  C    CA   117.27  3.000
 SEE  O    C    CA   120.80  1.700

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
 SEE  Var_01  O1B  B   OG  CB  -71.16  30.0  3
 SEE  Var_02  HB2  CB  OG  B    32.88  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
 SEE  chir_01  CA  N  CB  C  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
 SEE  plan-1  CA   0.020
 SEE  plan-1  C    0.020
 SEE  plan-1  O    0.020
 SEE  plan-1  OXT  0.020

