# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 02:07:37 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: [(1R)-1-amino-4-carbamimidamidobutyl]boronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(N)=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
 BOR  BOR  '[(1R)-1-amino-4-carbamimidamidobutyl]boronic acid'  peptide  27  12  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_BOR
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
 BOR  O1    O  OH1   0  -0.619   2.7941   1.9744  -0.6009
 BOR  B     B  B     0   0.519   2.8958   0.7713   0.0335
 BOR  O2    O  OH1   0  -0.627   3.3623   0.7437   1.3118
 BOR  CA    C  CH1   0  -0.274   2.4634  -0.6100  -0.6285
 BOR  N     N  NH2   0  -0.806   3.5449  -1.5842  -0.4716
 BOR  CB    C  CH2   0  -0.457   1.1145  -1.0904  -0.0675
 BOR  CG    C  CH2   0  -0.501  -0.0310  -0.1110  -0.2947
 BOR  CD    C  CH2   0  -0.202  -1.3654  -0.6718   0.1709
 BOR  NE    N  NH1   0  -0.653  -2.4174   0.2914  -0.0389
 BOR  CZ    C  C     0   0.554  -3.7242   0.0030   0.1883
 BOR  NH1   N  N     0  -0.728  -4.0586  -1.1435   0.6641
 BOR  NH2   N  NH2   0  -0.843  -4.5900   1.0494  -0.0673
 BOR  HO1   H  HOH1  0   0.478   2.4660   1.8944  -1.5008
 BOR  HO2   H  HOH1  0   0.485   3.5942   1.6089   1.6659
 BOR  HA    H  HCH1  0   0.214   2.3296  -0.4574  -1.7072
 BOR  HN1   H  HNH2  0   0.337   3.7126  -1.7538   0.5130
 BOR  HN2   H  HNH2  0   0.336   3.2507  -2.4774  -0.8511
 BOR  HB1   H  HCH2  0   0.220   0.8647  -2.0508  -0.5333
 BOR  HB2   H  HCH2  0   0.217   1.2199  -1.2879   1.0047
 BOR  HG1   H  HCH2  0   0.235   0.1644   0.8284   0.2339
 BOR  HG2   H  HCH2  0   0.227  -0.0983   0.1384  -1.3590
 BOR  HD1   H  HCH2  0   0.213  -1.5850  -1.5985  -0.3698
 BOR  HD2   H  HCH2  0   0.213  -1.3019  -0.9419   1.2302
 BOR  HNE   H  HNH1  0   0.386  -2.1745   1.1670  -0.4688
 BOR  HH1   H  H     0   0.312  -5.0636  -1.1981   0.7795
 BOR  HH21  H  HNH2  0   0.380  -4.2932   1.7258  -0.7539
 BOR  HH22  H  HNH2  0   0.383  -5.5492   0.7765  -0.2101

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
 BOR  O1   B     single  1.364  0.020  1.364
 BOR  O1   HO1   single  0.850  0.020  0.980
 BOR  B    O2    single  1.361  0.020  1.361
 BOR  B    CA    single  1.592  0.020  1.592
 BOR  O2   HO2   single  0.850  0.020  0.980
 BOR  CA   N     single  1.458  0.019  1.458
 BOR  CA   CB    single  1.530  0.020  1.530
 BOR  CA   HA    single  0.970  0.020  0.970
 BOR  N    HN1   single  0.890  0.020  1.040
 BOR  N    HN2   single  0.890  0.020  1.040
 BOR  CB   CG    single  1.524  0.020  1.524
 BOR  CB   HB1   single  0.970  0.020  1.090
 BOR  CB   HB2   single  0.970  0.020  1.090
 BOR  CG   CD    single  1.521  0.020  1.521
 BOR  CG   HG1   single  0.970  0.020  1.090
 BOR  CG   HG2   single  0.970  0.020  1.090
 BOR  CD   NE    single  1.442  0.020  1.442
 BOR  CD   HD1   single  0.970  0.020  1.090
 BOR  CD   HD2   single  0.970  0.020  1.090
 BOR  NE   CZ    single  1.357  0.020  1.357
 BOR  NE   HNE   single  0.860  0.020  1.020
 BOR  CZ   NH1   double  1.286  0.020  1.286
 BOR  CZ   NH2   single  1.382  0.020  1.382
 BOR  NH1  HH1   single  0.890  0.020  1.040
 BOR  NH2  HH21  single  0.890  0.020  1.040
 BOR  NH2  HH22  single  0.890  0.020  1.040

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
 BOR  HO1   O1   B     112.80  3.000
 BOR  CA    B    O2    117.79  3.000
 BOR  CA    B    O1    123.49  3.000
 BOR  O2    B    O1    118.71  3.000
 BOR  HO2   O2   B     114.17  3.000
 BOR  HA    CA   CB    109.00  3.000
 BOR  HA    CA   N     110.00  3.000
 BOR  CB    CA   N     110.50  1.700
 BOR  HA    CA   B     108.74  3.000
 BOR  CB    CA   B     110.96  3.000
 BOR  N     CA   B     109.40  3.000
 BOR  HN2   N    HN1   105.32  3.000
 BOR  HN2   N    CA    109.37  3.000
 BOR  HN1   N    CA    109.75  3.000
 BOR  HB2   CB   HB1   106.25  3.000
 BOR  HB2   CB   CG    109.52  3.000
 BOR  HB1   CB   CG    109.17  3.000
 BOR  HB2   CB   CA    109.21  3.000
 BOR  HB1   CB   CA    108.58  3.000
 BOR  CG    CB   CA    113.84  3.000
 BOR  HG2   CG   HG1   106.53  3.000
 BOR  HG2   CG   CD    109.13  3.000
 BOR  HG1   CG   CD    108.97  3.000
 BOR  HG2   CG   CB    109.72  3.000
 BOR  HG1   CG   CB    110.18  3.000
 BOR  CD    CG   CB    112.15  3.000
 BOR  HD2   CD   HD1   106.30  3.000
 BOR  HD2   CD   NE    110.36  3.000
 BOR  HD1   CD   NE    110.32  3.000
 BOR  HD2   CD   CG    109.65  3.000
 BOR  HD1   CD   CG    109.68  3.000
 BOR  NE    CD   CG    110.45  3.000
 BOR  HNE   NE   CZ    119.30  3.000
 BOR  HNE   NE   CD    117.90  3.000
 BOR  CZ    NE   CD    122.42  3.000
 BOR  NH2   CZ   NH1   125.50  3.000
 BOR  NH2   CZ   NE    114.29  3.000
 BOR  NH1   CZ   NE    120.12  3.000
 BOR  HH1   NH1  CZ    110.38  3.000
 BOR  HH22  NH2  HH21  111.44  3.000
 BOR  HH22  NH2  CZ    114.68  3.000
 BOR  HH21  NH2  CZ    116.70  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
 BOR  CONST_01  NH1  CZ   NE  CD     0.00   0.0  0
 BOR  CONST_02  NH2  CZ   NE  CD   180.00   0.0  0
 BOR  CONST_03  HH1  NH1  CZ  NE   180.00   0.0  0
 BOR  CONST_06  HNE  NE   CZ  NH1  180.00   0.0  0
 BOR  Var_01    CD   CG   CB  CA   175.28  30.0  3
 BOR  Var_02    NE   CD   CG  CB   178.99  30.0  3
 BOR  Var_03    CZ   NE   CD  CG   174.43  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
 BOR  chir_01  CA  B  N  CB  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
 BOR  plan-1  CD    0.020
 BOR  plan-1  NE    0.020
 BOR  plan-1  CZ    0.020
 BOR  plan-1  NH1   0.020
 BOR  plan-1  NH2   0.020
 BOR  plan-1  HNE   0.020
 BOR  plan-1  HH1   0.020
 BOR  plan-1  HH21  0.020
 BOR  plan-1  HH22  0.020

