# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 23:48:41 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: [(1R)-1-aminopentyl]boronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@H](N)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
 BNO  BNO  '[(1R)-1-aminopentyl]boronic acid'  peptide  23  9  .  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_BNO
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
 BNO  N    N  NH2   0  -0.817   2.0189  -1.7876  -0.2415
 BNO  CA   C  CH1   0  -0.245   1.0448  -0.7227  -0.5511
 BNO  CB   C  CH2   0  -0.439  -0.2930  -1.0750   0.1038
 BNO  CG   C  CH2   0  -0.431  -1.3985  -0.0624  -0.1702
 BNO  CD   C  CH2   0  -0.416  -2.7540  -0.4973   0.3752
 BNO  CE   C  CH3   0  -0.662  -3.8452   0.5384   0.1418
 BNO  B    B  B     0   0.500   1.5373   0.7298  -0.1290
 BNO  O1   O  OH1   0  -0.625   1.5749   1.7113  -1.0769
 BNO  O2   O  OH1   0  -0.631   1.9103   0.9083   1.1719
 BNO  HN1  H  HNH2  0   0.343   2.8946  -1.5916  -0.7121
 BNO  HN2  H  HNH2  0   0.336   2.2411  -1.7581   0.7472
 BNO  HA   H  HCH1  0   0.205   0.8891  -0.7494  -1.6361
 BNO  HB1  H  HCH2  0   0.212  -0.6066  -2.0639  -0.2481
 BNO  HB2  H  HCH2  0   0.206  -0.1544  -1.1669   1.1872
 BNO  HG1  H  HCH2  0   0.217  -1.1386   0.9066   0.2714
 BNO  HG2  H  HCH2  0   0.208  -1.4825   0.1096  -1.2489
 BNO  HD1  H  HCH2  0   0.212  -3.0420  -1.4463  -0.0872
 BNO  HD2  H  HCH2  0   0.210  -2.6640  -0.6978   1.4473
 BNO  HE1  H  HCH3  0   0.216  -3.5849   1.4934   0.6024
 BNO  HE2  H  HCH3  0   0.216  -3.9985   0.7188  -0.9238
 BNO  HE3  H  HCH3  0   0.226  -4.7993   0.2182   0.5619
 BNO  HO1  H  HOH1  0   0.478   1.8868   2.5722  -0.7782
 BNO  HO2  H  HOH1  0   0.480   2.2140   1.7900   1.4093

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
 BNO  N   CA   single  1.458  0.019  1.458
 BNO  N   HN1  single  0.890  0.020  1.040
 BNO  N   HN2  single  0.890  0.020  1.040
 BNO  CA  CB   single  1.521  0.033  1.521
 BNO  CA  B    single  1.591  0.020  1.591
 BNO  CA  HA   single  0.970  0.020  0.970
 BNO  CB  CG   single  1.524  0.020  1.524
 BNO  CB  HB1  single  0.970  0.020  1.090
 BNO  CB  HB2  single  0.970  0.020  1.090
 BNO  CG  CD   single  1.524  0.020  1.524
 BNO  CG  HG1  single  0.970  0.020  1.090
 BNO  CG  HG2  single  0.970  0.020  1.090
 BNO  CD  CE   single  1.522  0.020  1.522
 BNO  CD  HD1  single  0.970  0.020  1.090
 BNO  CD  HD2  single  0.970  0.020  1.090
 BNO  CE  HE1  single  0.970  0.020  1.090
 BNO  CE  HE2  single  0.970  0.020  1.090
 BNO  CE  HE3  single  0.970  0.020  1.090
 BNO  B   O1   single  1.365  0.020  1.365
 BNO  B   O2   single  1.365  0.020  1.365
 BNO  O1  HO1  single  0.850  0.020  0.980
 BNO  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
 BNO  HN2  N   HN1  104.95  3.000
 BNO  HN2  N   CA   109.16  3.000
 BNO  HN1  N   CA   109.48  3.000
 BNO  HA   CA  B    109.19  3.000
 BNO  HA   CA  CB   109.00  3.000
 BNO  B    CA  CB   111.54  3.000
 BNO  HA   CA  N    110.00  3.000
 BNO  B    CA  N    113.50  3.000
 BNO  CB   CA  N    110.40  1.500
 BNO  HB2  CB  HB1  106.14  3.000
 BNO  HB2  CB  CG   108.97  3.000
 BNO  HB1  CB  CG   109.53  3.000
 BNO  HB2  CB  CA   109.38  3.000
 BNO  HB1  CB  CA   108.70  3.000
 BNO  CG   CB  CA   113.84  3.000
 BNO  HG2  CG  HG1  106.03  3.000
 BNO  HG2  CG  CD   109.20  3.000
 BNO  HG1  CG  CD   108.59  3.000
 BNO  HG2  CG  CB   109.69  3.000
 BNO  HG1  CG  CB   110.05  3.000
 BNO  CD   CG  CB   113.03  3.000
 BNO  HD2  CD  HD1  106.06  3.000
 BNO  HD2  CD  CE   109.50  3.000
 BNO  HD1  CD  CE   109.67  3.000
 BNO  HD2  CD  CG   109.24  3.000
 BNO  HD1  CD  CG   109.28  3.000
 BNO  CE   CD  CG   112.85  3.000
 BNO  HE3  CE  HE2  107.56  3.000
 BNO  HE3  CE  HE1  107.63  3.000
 BNO  HE2  CE  HE1  107.51  3.000
 BNO  HE3  CE  CD   111.61  3.000
 BNO  HE2  CE  CD   111.27  3.000
 BNO  HE1  CE  CD   111.07  3.000
 BNO  O2   B   O1   124.07  3.000
 BNO  O2   B   CA   117.18  3.000
 BNO  O1   B   CA   118.74  3.000
 BNO  HO1  O1  B    115.87  3.000
 BNO  HO2  O2  B    116.18  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
 BNO  Var_01  CD   CG  CB  CA  174.42  30.0  3
 BNO  Var_02  CE   CD  CG  CB  178.01  30.0  3
 BNO  Var_03  HE1  CE  CD  CG  -58.43  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
 BNO  chir_01  CA  N  CB  B  negativ

