# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 18:56:58 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (5R)-5-amino-5-(dihydroxyboranyl)pentan-1-aminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCC[NH3+])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
 BLY  BLY  (5R)-5-amino-5-(dihydroxyboranyl)pentan-1-aminium  peptide  26  10  .  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_BLY
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
 BLY  N    N  NH2   0  -0.809   2.6907   1.6969   0.2384
 BLY  CA   C  CH1   0  -0.249   1.6452   0.7126   0.5367
 BLY  CB   C  CH2   0  -0.456   0.2798   1.0621  -0.0736
 BLY  CG   C  CH2   0  -0.445  -0.8213   0.0734   0.2915
 BLY  CD   C  CH2   0  -0.444  -2.1866   0.4982  -0.2372
 BLY  CE   C  CH2   0  -0.302  -3.2548  -0.5033   0.1508
 BLY  NZ   N  NT3   1  -0.777  -4.5885  -0.0966  -0.3672
 BLY  B    B  B     0   0.522   2.1577  -0.7205   0.0767
 BLY  O    O  OH1   0  -0.624   2.2288  -1.7185   1.0024
 BLY  OXT  O  OH1   0  -0.631   2.4965  -0.8634  -1.2364
 BLY  HN1  H  HNH2  0   0.336   2.8218   1.7622  -0.7641
 BLY  HN2  H  HNH2  0   0.336   2.3807   2.6177   0.5286
 BLY  HA   H  HCH1  0   0.208   1.5229   0.7014   1.6259
 BLY  HB1  H  HCH2  0   0.217  -0.0113   2.0635   0.2651
 BLY  HB2  H  HCH2  0   0.213   0.3707   1.1214  -1.1637
 BLY  HG1  H  HCH2  0   0.233  -0.5831  -0.9203  -0.1020
 BLY  HG2  H  HCH2  0   0.225  -0.8712  -0.0320   1.3799
 BLY  HD1  H  HCH2  0   0.246  -2.4454   1.4840   0.1600
 BLY  HD2  H  HCH2  0   0.245  -2.1481   0.5916  -1.3263
 BLY  HE1  H  HCH2  0   0.290  -3.0493  -1.4915  -0.2556
 BLY  HE2  H  HCH2  0   0.290  -3.3541  -0.5876   1.2310
 BLY  HZ1  H  HNT3  0   0.468  -4.8728   0.8139  -0.0077
 BLY  HZ2  H  HNT3  0   0.468  -4.5995  -0.0365  -1.3848
 BLY  HZ3  H  HNT3  0   0.478  -5.3138  -0.7612  -0.1004
 BLY  HO   H  HOH1  0   0.481   2.5536  -2.5664   0.6809
 BLY  HXT  H  HOH1  0   0.481   2.8146  -1.7317  -1.5029

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
 BLY  N    CA   single  1.458  0.019  1.458
 BLY  N    HN1  single  0.890  0.020  1.040
 BLY  N    HN2  single  0.890  0.020  1.040
 BLY  CA   CB   single  1.530  0.020  1.530
 BLY  CA   B    single  1.590  0.020  1.590
 BLY  CA   HA   single  0.970  0.020  0.970
 BLY  CB   CG   single  1.524  0.020  1.524
 BLY  CB   HB1  single  0.970  0.020  1.090
 BLY  CB   HB2  single  0.970  0.020  1.090
 BLY  CG   CD   single  1.524  0.020  1.524
 BLY  CG   HG1  single  0.970  0.020  1.090
 BLY  CG   HG2  single  0.970  0.020  1.090
 BLY  CD   CE   single  1.515  0.020  1.515
 BLY  CD   HD1  single  0.970  0.020  1.090
 BLY  CD   HD2  single  0.970  0.020  1.090
 BLY  CE   NZ   single  1.487  0.020  1.487
 BLY  CE   HE1  single  0.970  0.020  1.090
 BLY  CE   HE2  single  0.970  0.020  1.090
 BLY  NZ   HZ1  single  0.890  0.020  1.040
 BLY  NZ   HZ2  single  0.890  0.020  1.040
 BLY  NZ   HZ3  single  0.890  0.020  1.040
 BLY  B    O    single  1.363  0.020  1.363
 BLY  B    OXT  single  1.364  0.020  1.364
 BLY  O    HO   single  0.850  0.020  0.980
 BLY  OXT  HXT  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
 BLY  HN2  N    HN1  105.32  3.000
 BLY  HN2  N    CA   109.47  3.000
 BLY  HN1  N    CA   109.68  3.000
 BLY  HA   CA   B    108.31  3.000
 BLY  HA   CA   CB   109.00  3.000
 BLY  B    CA   CB   112.13  3.000
 BLY  HA   CA   N    110.00  3.000
 BLY  B    CA   N    108.44  3.000
 BLY  CB   CA   N    110.50  1.700
 BLY  HB2  CB   HB1  106.26  3.000
 BLY  HB2  CB   CG   109.47  3.000
 BLY  HB1  CB   CG   109.07  3.000
 BLY  HB2  CB   CA   109.51  3.000
 BLY  HB1  CB   CA   108.73  3.000
 BLY  CG   CB   CA   113.54  3.000
 BLY  HG2  CG   HG1  106.25  3.000
 BLY  HG2  CG   CD   109.32  3.000
 BLY  HG1  CG   CD   108.85  3.000
 BLY  HG2  CG   CB   109.48  3.000
 BLY  HG1  CG   CB   110.21  3.000
 BLY  CD   CG   CB   112.53  3.000
 BLY  HD2  CD   HD1  107.03  3.000
 BLY  HD2  CD   CE   109.65  3.000
 BLY  HD1  CD   CE   109.64  3.000
 BLY  HD2  CD   CG   109.73  3.000
 BLY  HD1  CD   CG   109.70  3.000
 BLY  CE   CD   CG   111.01  3.000
 BLY  HE2  CE   HE1  108.53  3.000
 BLY  HE2  CE   NZ   106.56  3.000
 BLY  HE1  CE   NZ   106.71  3.000
 BLY  HE2  CE   CD   111.71  3.000
 BLY  HE1  CE   CD   111.81  3.000
 BLY  NZ   CE   CD   111.24  3.000
 BLY  HZ3  NZ   HZ2  106.98  3.000
 BLY  HZ3  NZ   HZ1  106.95  3.000
 BLY  HZ2  NZ   HZ1  107.24  3.000
 BLY  HZ3  NZ   CE   111.63  3.000
 BLY  HZ2  NZ   CE   111.93  3.000
 BLY  HZ1  NZ   CE   111.80  3.000
 BLY  OXT  B    O    124.35  3.000
 BLY  OXT  B    CA   116.94  3.000
 BLY  O    B    CA   118.71  3.000
 BLY  HO   O    B    115.81  3.000
 BLY  HXT  OXT  B    116.31  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
 BLY  Var_01  CD   CG  CB  CA   175.64  30.0  3
 BLY  Var_02  CE   CD  CG  CB  -179.70  30.0  3
 BLY  Var_03  NZ   CE  CD  CG  -179.77  30.0  3
 BLY  Var_04  HZ1  NZ  CE  CD   -59.59  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
 BLY  chir_01  CA  N  CB  B  negativ

