# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 18:18:15 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: (2~{S})-2-azanyl-3-[4-(dihydroxyboranyl)phenyl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(cc1)B(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
 7N8  7N8  '(2~{S})-2-azanyl-3-[4-(dihydroxyboranyl)phenyl]propanoic acid'  L-peptide  26  15  .  2019-03-22  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_7N8
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
 7N8  O    O  O      0  -0.612  -12.1523  -28.8429   -6.7399
 7N8  C    C  C      0   0.394  -11.4704  -28.2222   -7.5847
 7N8  CA   C  CH1    0  -0.187  -12.0187  -28.2441   -9.0318
 7N8  N    N  NH2    0  -0.792  -12.4210  -29.5693   -9.4952
 7N8  CB   C  CH2    0  -0.506  -13.2362  -27.3125   -9.1396
 7N8  CG   C  CR6    0   0.112  -12.9239  -25.8863   -8.7957
 7N8  CD2  C  CR16   0  -0.286  -12.3871  -25.0275   -9.7534
 7N8  CE2  C  CR16   0  -0.308  -12.0694  -23.7160   -9.4393
 7N8  CZ   C  CR6    0  -0.114  -12.2676  -23.2035   -8.1529
 7N8  BZ   B  B      0   0.500  -11.8953  -21.7165   -7.8205
 7N8  OB1  O  OH1    0  -0.629  -11.6121  -20.8854   -8.8592
 7N8  OB2  O  OH1    0  -0.630  -11.8404  -21.2141   -6.5551
 7N8  CE1  C  CR16   0  -0.316  -12.8096  -24.0718   -7.2012
 7N8  CD1  C  CR16   0  -0.272  -13.1347  -25.3834   -7.5147
 7N8  H2   H  HCH1   0   0.204  -11.2476  -27.8724   -9.7139
 7N8  H3   H  HNH2   0   0.336  -11.5976  -30.1578   -9.5511
 7N8  H4   H  HNH2   0   0.325  -12.9871  -29.9860   -8.7634
 7N8  H6   H  HCH2   0   0.236  -13.6183  -27.3704  -10.1618
 7N8  H7   H  HCH2   0   0.230  -14.0243  -27.6905   -8.4820
 7N8  H8   H  HCR6   0   0.240  -12.2207  -25.3928  -10.7609
 7N8  H9   H  HCR6   0   0.244  -11.6579  -23.0820  -10.2151
 7N8  H10  H  HOH1   0   0.480  -11.3708  -19.9933   -8.5890
 7N8  H11  H  HOH1   0   0.482  -12.0056  -21.8523   -5.8564
 7N8  H12  H  HCR6   0   0.234  -13.0005  -23.7337   -6.1881
 7N8  H13  H  HCR6   0   0.239  -13.5544  -26.0279   -6.7512
 7N8  O1   O  OC    -1  -0.605  -10.4202  -27.5850   -7.3764

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
 7N8  CD2  CE2  aromatic  1.386  0.020  1.386
 7N8  CD2  CG   aromatic  1.394  0.020  1.394
 7N8  N    CA   single    1.458  0.019  1.458
 7N8  CE2  CZ   aromatic  1.399  0.020  1.399
 7N8  CB   CA   single    1.530  0.020  1.530
 7N8  CB   CG   single    1.500  0.020  1.500
 7N8  CA   C    single    1.525  0.021  1.525
 7N8  OB1  BZ   single    1.360  0.020  1.360
 7N8  CG   CD1  aromatic  1.392  0.020  1.392
 7N8  CZ   BZ   single    1.569  0.020  1.569
 7N8  CZ   CE1  aromatic  1.398  0.020  1.398
 7N8  BZ   OB2  single    1.363  0.020  1.363
 7N8  C    O    deloc     1.231  0.020  1.231
 7N8  CD1  CE1  aromatic  1.387  0.020  1.387
 7N8  CA   H2   single    0.970  0.020  1.090
 7N8  N    H3   single    0.890  0.020  1.040
 7N8  N    H4   single    0.890  0.020  1.040
 7N8  CB   H6   single    0.970  0.020  1.090
 7N8  CB   H7   single    0.970  0.020  1.090
 7N8  CD2  H8   single    0.930  0.020  1.080
 7N8  CE2  H9   single    0.930  0.020  1.080
 7N8  OB1  H10  single    0.850  0.020  0.980
 7N8  OB2  H11  single    0.850  0.020  0.980
 7N8  CE1  H12  single    0.930  0.020  1.080
 7N8  CD1  H13  single    0.930  0.020  1.080
 7N8  C    O1   deloc     1.246  0.020  1.246

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
 7N8  O1   C    CA   117.53  3.000
 7N8  O1   C    O    126.91  3.000
 7N8  CA   C    O    120.80  1.700
 7N8  H2   CA   CB   107.97  3.000
 7N8  H2   CA   N    107.73  3.000
 7N8  CB   CA   N    110.50  1.700
 7N8  H2   CA   C    109.16  3.000
 7N8  CB   CA   C    110.10  1.900
 7N8  N    CA   C    111.00  2.800
 7N8  H4   N    H3   104.75  3.000
 7N8  H4   N    CA   107.31  3.000
 7N8  H3   N    CA   108.70  3.000
 7N8  H7   CB   H6   106.99  3.000
 7N8  H7   CB   CG   109.92  3.000
 7N8  H6   CB   CG   109.74  3.000
 7N8  H7   CB   CA   108.61  3.000
 7N8  H6   CB   CA   108.09  3.000
 7N8  CG   CB   CA   113.29  3.000
 7N8  CD1  CG   CD2  117.91  3.000
 7N8  CD1  CG   CB   121.53  3.000
 7N8  CD2  CG   CB   120.56  3.000
 7N8  H8   CD2  CE2  119.62  3.000
 7N8  H8   CD2  CG   119.34  3.000
 7N8  CE2  CD2  CG   121.05  3.000
 7N8  H9   CE2  CZ   119.88  3.000
 7N8  H9   CE2  CD2  118.61  3.000
 7N8  CZ   CE2  CD2  121.52  3.000
 7N8  CE1  CZ   BZ   122.46  3.000
 7N8  CE1  CZ   CE2  116.97  3.000
 7N8  BZ   CZ   CE2  120.57  3.000
 7N8  OB2  BZ   OB1  118.39  3.000
 7N8  OB2  BZ   CZ   123.77  3.000
 7N8  OB1  BZ   CZ   117.83  3.000
 7N8  H10  OB1  BZ   113.83  3.000
 7N8  H11  OB2  BZ   115.06  3.000
 7N8  H12  CE1  CD1  117.67  3.000
 7N8  H12  CE1  CZ   120.70  3.000
 7N8  CD1  CE1  CZ   121.63  3.000
 7N8  H13  CD1  CE1  119.59  3.000
 7N8  H13  CD1  CG   119.48  3.000
 7N8  CE1  CD1  CG   120.93  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
 7N8  CONST_01  CZ   CE2  CD2  CG     0.00   0.0  0
 7N8  CONST_02  CZ   CE1  CD1  CG     0.00   0.0  0
 7N8  CONST_03  CE1  CZ   CE2  CD2    0.00   0.0  0
 7N8  CONST_04  CE1  CD1  CG   CD2    0.00   0.0  0
 7N8  CONST_05  CD1  CG   CD2  CE2    0.00   0.0  0
 7N8  CONST_06  CD1  CE1  CZ   CE2    0.00   0.0  0
 7N8  CONST_07  CE2  CD2  CG   CB   180.00   0.0  0
 7N8  CONST_08  CE1  CD1  CG   CB   180.00   0.0  0
 7N8  CONST_09  BZ   CZ   CE2  CD2  180.00   0.0  0
 7N8  CONST_10  CD1  CE1  CZ   BZ   180.00   0.0  0
 7N8  CONST_11  H9   CE2  CD2  CG   180.00   0.0  0
 7N8  CONST_12  H12  CE1  CD1  CG   180.00   0.0  0
 7N8  CONST_13  H13  CD1  CG   CD2  180.00   0.0  0
 7N8  CONST_14  H8   CD2  CE2  CZ   180.00   0.0  0
 7N8  Var_01    CD2  CG   CB   CA    83.88  30.0  2
 7N8  Var_02    OB1  BZ   CZ   CE2   11.77  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
 7N8  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
 7N8  plan-1  CB   0.020
 7N8  plan-1  CG   0.020
 7N8  plan-1  CD2  0.020
 7N8  plan-1  CE2  0.020
 7N8  plan-1  CZ   0.020
 7N8  plan-1  BZ   0.020
 7N8  plan-1  CE1  0.020
 7N8  plan-1  CD1  0.020
 7N8  plan-1  H8   0.020
 7N8  plan-1  H9   0.020
 7N8  plan-1  H12  0.020
 7N8  plan-1  H13  0.020
 7N8  plan-2  O    0.020
 7N8  plan-2  C    0.020
 7N8  plan-2  CA   0.020
 7N8  plan-2  O1   0.020

