# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 06:40:55 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: [(5S)-5-amino-5-carboxypentyl](trihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[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
 ABH  ABH  '[(5S)-5-amino-5-carboxypentyl](trihydroxy)borate(1-)'  ligand  27  13  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ABH
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
 ABH  N     N  NH2    0  -0.786   2.9028   1.8777   0.1376
 ABH  CA    C  CH1    0  -0.209   2.8018   0.4574   0.4418
 ABH  C     C  C      0   0.381   3.9842  -0.4118  -0.0515
 ABH  O     O  O      0  -0.611   4.7511   0.0797  -0.9041
 ABH  OT    O  OC    -1  -0.627   4.0599  -1.5605   0.4353
 ABH  CB    C  CH2    0  -0.414   1.4910  -0.1064  -0.1144
 ABH  CG    C  CH2    0  -0.389   0.2347   0.5246   0.4710
 ABH  CD    C  CH2    0  -0.429  -1.0576  -0.0651  -0.0846
 ABH  CE    C  CH2    0  -0.637  -2.3328   0.5096   0.5288
 ABH  B     B  B     -1   0.428  -3.7461  -0.1104  -0.0435
 ABH  O2    O  OB     0  -0.754  -3.8482  -1.5707   0.1691
 ABH  O1    O  OB     0  -0.747  -4.9134   0.4196   0.6985
 ABH  O3    O  OB     0  -0.751  -3.8109   0.2411  -1.4855
 ABH  HN1   H  HNH2   0   0.331   3.7315   2.2475   0.5881
 ABH  HN2   H  HNH2   0   0.320   3.0986   1.9674  -0.8535
 ABH  HCA   H  HCH1   0   0.200   2.7579   0.3588   1.5337
 ABH  HCB1  H  HCH2   0   0.195   1.4846   0.0125  -1.2061
 ABH  HCB2  H  HCH2   0   0.208   1.4690  -1.1839   0.0702
 ABH  HCG1  H  HCH2   0   0.185   0.2473   0.3988   1.5610
 ABH  HCG2  H  HCH2   0   0.198   0.2491   1.6040   0.2955
 ABH  HCD1  H  HCH2   0   0.187  -1.0732   0.0751  -1.1715
 ABH  HCD2  H  HCH2   0   0.171  -1.0288  -1.1532   0.0671
 ABH  HCE1  H  HCH2   0   0.150  -2.2764   0.3615   1.6180
 ABH  HCE2  H  HCH2   0   0.148  -2.3067   1.6032   0.3983
 ABH  HO2   H  H      0   0.417  -3.0489  -1.9863  -0.1610
 ABH  HO1   H  H      0   0.417  -4.8389   1.3755   0.7316
 ABH  HO3   H  H      0   0.417  -4.6217  -0.1201  -1.8557

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
 ABH  N   CA    single  1.456  0.020  1.456
 ABH  N   HN1   single  0.890  0.020  1.040
 ABH  N   HN2   single  0.890  0.020  1.040
 ABH  CA  C     single  1.548  0.020  1.548
 ABH  CA  CB    single  1.531  0.020  1.531
 ABH  CA  HCA   single  0.970  0.020  1.090
 ABH  C   O     deloc   1.248  0.020  1.248
 ABH  C   OT    deloc   1.250  0.020  1.250
 ABH  CB  CG    single  1.523  0.020  1.523
 ABH  CB  HCB1  single  0.970  0.020  1.090
 ABH  CB  HCB2  single  0.970  0.020  1.090
 ABH  CG  CD    single  1.525  0.020  1.525
 ABH  CG  HCG1  single  0.970  0.020  1.090
 ABH  CG  HCG2  single  0.970  0.020  1.090
 ABH  CD  CE    single  1.527  0.020  1.527
 ABH  CD  HCD1  single  0.970  0.020  1.090
 ABH  CD  HCD2  single  0.970  0.020  1.090
 ABH  CE  B     single  1.646  0.020  1.646
 ABH  CE  HCE1  single  0.970  0.020  1.090
 ABH  CE  HCE2  single  0.970  0.020  1.090
 ABH  B   O2    single  1.479  0.020  1.479
 ABH  B   O1    single  1.481  0.020  1.481
 ABH  B   O3    single  1.486  0.020  1.486
 ABH  O2  HO2   single  0.850  0.020  0.980
 ABH  O1  HO1   single  0.850  0.020  0.980
 ABH  O3  HO3   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
 ABH  HN2   N   HN1   104.14  3.000
 ABH  HN2   N   CA    107.69  3.000
 ABH  HN1   N   CA    108.66  3.000
 ABH  HCA   CA  CB    107.11  3.000
 ABH  HCA   CA  C     107.29  3.000
 ABH  CB    CA  C     109.35  3.000
 ABH  HCA   CA  N     107.36  3.000
 ABH  CB    CA  N     110.03  3.000
 ABH  C     CA  N     115.35  3.000
 ABH  OT    C   O     126.23  3.000
 ABH  OT    C   CA    115.98  3.000
 ABH  O     C   CA    117.78  3.000
 ABH  HCB2  CB  HCB1  105.92  3.000
 ABH  HCB2  CB  CG    109.07  3.000
 ABH  HCB1  CB  CG    109.42  3.000
 ABH  HCB2  CB  CA    108.59  3.000
 ABH  HCB1  CB  CA    109.04  3.000
 ABH  CG    CB  CA    114.45  3.000
 ABH  HCG2  CG  HCG1  105.81  3.000
 ABH  HCG2  CG  CD    109.53  3.000
 ABH  HCG1  CG  CD    109.11  3.000
 ABH  HCG2  CG  CB    109.66  3.000
 ABH  HCG1  CG  CB    108.95  3.000
 ABH  CD    CG  CB    113.50  3.000
 ABH  HCD2  CD  HCD1  105.30  3.000
 ABH  HCD2  CD  CE    109.81  3.000
 ABH  HCD1  CD  CE    109.77  3.000
 ABH  HCD2  CD  CG    108.08  3.000
 ABH  HCD1  CD  CG    108.90  3.000
 ABH  CE    CD  CG    114.56  3.000
 ABH  HCE2  CE  HCE1  104.46  3.000
 ABH  HCE2  CE  B     110.68  3.000
 ABH  HCE1  CE  B     109.72  3.000
 ABH  HCE2  CE  CD    107.83  3.000
 ABH  HCE1  CE  CD    107.70  3.000
 ABH  B     CE  CD    115.82  3.000
 ABH  O3    B   O1    111.54  3.000
 ABH  O3    B   O2    111.72  3.000
 ABH  O1    B   O2    103.11  3.000
 ABH  O3    B   CE    106.61  3.000
 ABH  O1    B   CE    111.57  3.000
 ABH  O2    B   CE    112.41  3.000
 ABH  HO2   O2  B     108.71  3.000
 ABH  HO1   O1  B     108.22  3.000
 ABH  HO3   O3  B     108.76  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
 ABH  Var_01  CD  CG  CB  CA  -179.26  30.0  3
 ABH  Var_02  CE  CD  CG  CB   177.57  30.0  3
 ABH  Var_03  B   CE  CD  CG  -179.72  30.0  3
 ABH  Var_04  O2  B   CE  CD    59.52  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
 ABH  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
 ABH  plan-1  CA  0.020
 ABH  plan-1  C   0.020
 ABH  plan-1  O   0.020
 ABH  plan-1  OT  0.020

