# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 07:18:43 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: [(1R)-1-amino-2-phenylethyl]boronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1)B(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
 B2F  B2F  '[(1R)-1-amino-2-phenylethyl]boronic acid'  peptide  24  12  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_B2F
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
 B2F  N    N  NH2   0  -0.816   2.8746   1.5572   0.0105
 B2F  CA   C  CH1   0  -0.242   1.6012   0.8809   0.3113
 B2F  CB   C  CH2   0  -0.523   0.5814   1.2485  -0.7770
 B2F  CG   C  CR6   0   0.107  -0.7670   0.6423  -0.5073
 B2F  CD1  C  CR16  0  -0.306  -1.6311   1.2296   0.4161
 B2F  CD2  C  CR16  0  -0.299  -1.1719  -0.5343  -1.1340
 B2F  CE1  C  CR16  0  -0.243  -2.8619   0.6590   0.7073
 B2F  CE2  C  CR16  0  -0.246  -2.4031  -1.1106  -0.8460
 B2F  CZ   C  CR16  0  -0.272  -3.2528  -0.5161   0.0766
 B2F  B    B  B     0   0.516   1.7302  -0.6994   0.4624
 B2F  O1   O  OH1   0  -0.620   1.3610  -1.2782   1.6403
 B2F  O2   O  OH1   0  -0.632   2.2394  -1.3812  -0.6045
 B2F  HN1  H  HNH2  0   0.346   3.5181   1.4245   0.7815
 B2F  HN2  H  HNH2  0   0.340   3.3165   1.1108  -0.7853
 B2F  HA   H  HCH1  0   0.215   1.2347   1.3070   1.2521
 B2F  HB1  H  HCH2  0   0.238   0.5027   2.3380  -0.8289
 B2F  HB2  H  HCH2  0   0.234   0.9499   0.9129  -1.7512
 B2F  HD1  H  HCR6  0   0.245  -1.3377   2.1490   0.9105
 B2F  HD2  H  HCR6  0   0.246  -0.5178  -1.0055  -1.8581
 B2F  HE1  H  HCR6  0   0.252  -3.5186   1.1337   1.4254
 B2F  HE2  H  HCR6  0   0.252  -2.6989  -2.0245  -1.3457
 B2F  HZ   H  HCR6  0   0.252  -4.2139  -0.9612   0.3005
 B2F  HO1  H  HOH1  0   0.479   1.4624  -2.2348   1.6876
 B2F  HO2  H  HOH1  0   0.479   2.3194  -2.3345  -0.5013

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
 B2F  N    CA   single    1.458  0.019  1.458
 B2F  N    HN1  single    0.890  0.020  1.040
 B2F  N    HN2  single    0.890  0.020  1.040
 B2F  CA   CB   single    1.530  0.020  1.530
 B2F  CA   B    single    1.593  0.020  1.593
 B2F  CA   HA   single    0.970  0.020  0.970
 B2F  CB   CG   single    1.503  0.020  1.503
 B2F  CB   HB1  single    0.970  0.020  1.090
 B2F  CB   HB2  single    0.970  0.020  1.090
 B2F  CG   CD1  aromatic  1.394  0.020  1.394
 B2F  CG   CD2  aromatic  1.393  0.020  1.393
 B2F  CD1  CE1  aromatic  1.388  0.020  1.388
 B2F  CD1  HD1  single    0.930  0.020  1.080
 B2F  CD2  CE2  aromatic  1.390  0.020  1.390
 B2F  CD2  HD2  single    0.930  0.020  1.080
 B2F  CE1  CZ   aromatic  1.390  0.020  1.390
 B2F  CE1  HE1  single    0.930  0.020  1.080
 B2F  CE2  CZ   aromatic  1.388  0.020  1.388
 B2F  CE2  HE2  single    0.930  0.020  1.080
 B2F  CZ   HZ   single    0.930  0.020  1.080
 B2F  B    O1   single    1.363  0.020  1.363
 B2F  B    O2   single    1.365  0.020  1.365
 B2F  O1   HO1  single    0.850  0.020  0.980
 B2F  O2   HO2  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
 B2F  HN2  N    HN1  105.24  3.000
 B2F  HN2  N    CA   109.57  3.000
 B2F  HN1  N    CA   109.49  3.000
 B2F  HA   CA   B    109.35  3.000
 B2F  HA   CA   CB   109.00  3.000
 B2F  B    CA   CB   111.01  3.000
 B2F  HA   CA   N    110.00  3.000
 B2F  B    CA   N    113.89  3.000
 B2F  CB   CA   N    110.50  1.700
 B2F  HB2  CB   HB1  106.71  3.000
 B2F  HB2  CB   CG   109.76  3.000
 B2F  HB1  CB   CG   110.23  3.000
 B2F  HB2  CB   CA   109.50  3.000
 B2F  HB1  CB   CA   108.65  3.000
 B2F  CG   CB   CA   111.84  3.000
 B2F  CD2  CG   CD1  118.26  3.000
 B2F  CD2  CG   CB   121.38  3.000
 B2F  CD1  CG   CB   120.33  3.000
 B2F  HD1  CD1  CE1  119.53  3.000
 B2F  HD1  CD1  CG   119.43  3.000
 B2F  CE1  CD1  CG   121.03  3.000
 B2F  HD2  CD2  CE2  119.53  3.000
 B2F  HD2  CD2  CG   119.50  3.000
 B2F  CE2  CD2  CG   120.97  3.000
 B2F  HE1  CE1  CZ   120.07  3.000
 B2F  HE1  CE1  CD1  119.80  3.000
 B2F  CZ   CE1  CD1  120.13  3.000
 B2F  HE2  CE2  CZ   120.07  3.000
 B2F  HE2  CE2  CD2  119.77  3.000
 B2F  CZ   CE2  CD2  120.16  3.000
 B2F  HZ   CZ   CE2  120.32  3.000
 B2F  HZ   CZ   CE1  120.23  3.000
 B2F  CE2  CZ   CE1  119.45  3.000
 B2F  O2   B    O1   124.36  3.000
 B2F  O2   B    CA   116.86  3.000
 B2F  O1   B    CA   118.77  3.000
 B2F  HO1  O1   B    115.82  3.000
 B2F  HO2  O2   B    116.24  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
 B2F  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 B2F  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 B2F  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 B2F  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 B2F  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 B2F  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 B2F  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 B2F  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 B2F  CONST_09  HE1  CE1  CD1  CG   180.00   0.0  0
 B2F  CONST_10  HE2  CE2  CD2  CG   180.00   0.0  0
 B2F  CONST_11  HD2  CD2  CG   CD1  180.00   0.0  0
 B2F  CONST_12  HZ   CZ   CE1  CD1  180.00   0.0  0
 B2F  CONST_13  HD1  CD1  CG   CD2  180.00   0.0  0
 B2F  Var_01    CD1  CG   CB   CA    79.58  30.0  2

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
 B2F  chir_01  CA  N  CB  B  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
 B2F  plan-1  CB   0.020
 B2F  plan-1  CG   0.020
 B2F  plan-1  CD1  0.020
 B2F  plan-1  CD2  0.020
 B2F  plan-1  CE1  0.020
 B2F  plan-1  CE2  0.020
 B2F  plan-1  CZ   0.020
 B2F  plan-1  HD1  0.020
 B2F  plan-1  HD2  0.020
 B2F  plan-1  HE1  0.020
 B2F  plan-1  HE2  0.020
 B2F  plan-1  HZ   0.020

