# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 06:23:46 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: [(5S)-5-ammonio-5-carboxypentyl](trihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+][C@@H](CCCC[B-](O)(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
 AB5  AB5  '[(5S)-5-ammonio-5-carboxypentyl](trihydroxy)borate(1-)'  ligand  28  13  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AB5
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
 AB5  N    N  NT3    1  -0.776  -2.9592   1.7914  -0.1965
 AB5  CA   C  CH1    0  -0.263  -2.7644   0.3376  -0.4709
 AB5  C    C  C      0   0.449  -3.9857  -0.4402   0.0774
 AB5  O    O  OC    -1  -0.586  -4.0014  -1.6477  -0.1996
 AB5  OT   O  O      0  -0.592  -4.8062   0.2165   0.7426
 AB5  CB   C  CH2    0  -0.433  -1.4515  -0.1438   0.1303
 AB5  CG   C  CH2    0  -0.421  -0.2020   0.5008  -0.4609
 AB5  CD   C  CH2    0  -0.426   1.0900  -0.1002   0.0841
 AB5  CE   C  CH2    0  -0.641   2.3602   0.5042  -0.5079
 AB5  B    B  B     -1   0.431   3.7750  -0.1492   0.0247
 AB5  O2   O  OB     0  -0.753   3.8903  -1.5843  -0.3146
 AB5  O1   O  OB     0  -0.746   4.9399   0.4532  -0.6595
 AB5  O3   O  OB     0  -0.751   3.8218   0.0751   1.4918
 AB5  H0A  H  HNT3   0   0.466  -3.7229   2.1769  -0.7491
 AB5  H0B  H  HNT3   0   0.462  -2.1305   2.3467  -0.4050
 AB5  H0C  H  HNT3   0   0.451  -3.2106   1.9414   0.7808
 AB5  HA   H  HCH1   0   0.292  -2.7253   0.2425  -1.5580
 AB5  HB1  H  HCH2   0   0.235  -1.4707  -0.0060   1.2170
 AB5  HB2  H  HCH2   0   0.251  -1.4099  -1.2209  -0.0405
 AB5  HG1  H  HCH2   0   0.214  -0.2227   0.3909  -1.5509
 AB5  HG2  H  HCH2   0   0.201  -0.1844   1.5805  -0.2666
 AB5  HD1  H  HCH2   0   0.197   1.0994   0.0077   1.1740
 AB5  HD2  H  HCH2   0   0.182   1.0645  -1.1820  -0.1032
 AB5  HE1  H  HCH2   0   0.154   2.3007   0.4067  -1.6022
 AB5  HE2  H  HCH2   0   0.153   2.3350   1.5896  -0.3242
 AB5  H2   H  H      0   0.416   3.1087  -2.0405   0.0036
 AB5  H1   H  H      0   0.417   4.8603   1.4079  -0.6066
 AB5  H3   H  H      0   0.418   4.6444  -0.2870   1.8343

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
 AB5  N   CA   single  1.492  0.020  1.492
 AB5  N   H0A  single  0.890  0.020  1.040
 AB5  N   H0B  single  0.890  0.020  1.040
 AB5  N   H0C  single  0.890  0.020  1.040
 AB5  CA  C    single  1.548  0.020  1.548
 AB5  CA  CB   single  1.522  0.020  1.522
 AB5  CA  HA   single  0.970  0.020  1.090
 AB5  C   O    deloc   1.239  0.020  1.239
 AB5  C   OT   deloc   1.244  0.020  1.244
 AB5  CB  CG   single  1.525  0.020  1.525
 AB5  CB  HB1  single  0.970  0.020  1.090
 AB5  CB  HB2  single  0.970  0.020  1.090
 AB5  CG  CD   single  1.526  0.020  1.526
 AB5  CG  HG1  single  0.970  0.020  1.090
 AB5  CG  HG2  single  0.970  0.020  1.090
 AB5  CD  CE   single  1.526  0.020  1.526
 AB5  CD  HD1  single  0.970  0.020  1.090
 AB5  CD  HD2  single  0.970  0.020  1.090
 AB5  CE  B    single  1.647  0.020  1.647
 AB5  CE  HE1  single  0.970  0.020  1.090
 AB5  CE  HE2  single  0.970  0.020  1.090
 AB5  B   O2   single  1.479  0.020  1.479
 AB5  B   O1   single  1.479  0.020  1.479
 AB5  B   O3   single  1.485  0.020  1.485
 AB5  O2  H2   single  0.850  0.020  0.980
 AB5  O1  H1   single  0.850  0.020  0.980
 AB5  O3  H3   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
 AB5  H0C  N   H0B  108.44  3.000
 AB5  H0C  N   H0A  106.22  3.000
 AB5  H0B  N   H0A  107.02  3.000
 AB5  H0C  N   CA   110.58  3.000
 AB5  H0B  N   CA   112.77  3.000
 AB5  H0A  N   CA   111.52  3.000
 AB5  HA   CA  CB   109.56  3.000
 AB5  HA   CA  C    109.70  3.000
 AB5  CB   CA  C    112.43  3.000
 AB5  HA   CA  N    105.82  3.000
 AB5  CB   CA  N    110.37  3.000
 AB5  C    CA  N    108.75  3.000
 AB5  OT   C   O    128.75  3.000
 AB5  OT   C   CA   116.39  3.000
 AB5  O    C   CA   114.86  3.000
 AB5  HB2  CB  HB1  106.27  3.000
 AB5  HB2  CB  CG   108.98  3.000
 AB5  HB1  CB  CG   110.23  3.000
 AB5  HB2  CB  CA   106.45  3.000
 AB5  HB1  CB  CA   109.68  3.000
 AB5  CG   CB  CA   114.82  3.000
 AB5  HG2  CG  HG1  105.97  3.000
 AB5  HG2  CG  CD   108.11  3.000
 AB5  HG1  CG  CD   109.38  3.000
 AB5  HG2  CG  CB   111.13  3.000
 AB5  HG1  CG  CB   109.13  3.000
 AB5  CD   CG  CB   112.88  3.000
 AB5  HD2  CD  HD1  105.49  3.000
 AB5  HD2  CD  CE   110.08  3.000
 AB5  HD1  CD  CE   109.87  3.000
 AB5  HD2  CD  CG   107.91  3.000
 AB5  HD1  CD  CG   108.90  3.000
 AB5  CE   CD  CG   114.22  3.000
 AB5  HE2  CE  HE1  104.60  3.000
 AB5  HE2  CE  B    110.90  3.000
 AB5  HE1  CE  B    109.45  3.000
 AB5  HE2  CE  CD   107.86  3.000
 AB5  HE1  CE  CD   107.80  3.000
 AB5  B    CE  CD   115.62  3.000
 AB5  O3   B   O1   111.75  3.000
 AB5  O3   B   O2   111.77  3.000
 AB5  O1   B   O2   103.16  3.000
 AB5  O3   B   CE   106.66  3.000
 AB5  O1   B   CE   111.43  3.000
 AB5  O2   B   CE   112.19  3.000
 AB5  H2   O2  B    108.76  3.000
 AB5  H1   O1  B    108.33  3.000
 AB5  H3   O3  B    108.78  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
 AB5  Var_01  CD  CG  CB  CA  -174.93  30.0  3
 AB5  Var_02  CE  CD  CG  CB   178.86  30.0  3
 AB5  Var_03  B   CE  CD  CG  -178.32  30.0  3
 AB5  Var_04  O2  B   CE  CD    61.87  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
 AB5  chir_01  CA  N  C  CB  positiv

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
 AB5  plan-1  CA  0.020
 AB5  plan-1  C   0.020
 AB5  plan-1  O   0.020
 AB5  plan-1  OT  0.020

