# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 04:32:23 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: [(5S)-5-amino-5-carboxyhexyl](trihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@](N)(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
 5AB  5AB  '[(5S)-5-amino-5-carboxyhexyl](trihydroxy)borate(1-)'  L-peptide  30  14  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5AB
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
 5AB  B1    B  B     -1   0.427   3.9913   0.1694  -0.0887
 5AB  C1    C  CT     0  -0.031  -2.5952  -0.4157   0.1004
 5AB  N1    N  NH2    0  -0.789  -2.6860  -1.4200  -0.9561
 5AB  C2    C  C      0   0.400  -3.7011   0.6807   0.0174
 5AB  O2    O  OB     0  -0.751   4.0275   0.6888  -1.4799
 5AB  C3    C  CH2    0  -0.402  -1.2325   0.2886  -0.0126
 5AB  O3    O  OB     0  -0.747   5.1571  -0.6974   0.1982
 5AB  C4    C  CH2    0  -0.397   0.0030  -0.5967   0.0978
 5AB  O4    O  OB     0  -0.754   4.1313   1.2580   0.9044
 5AB  C5    C  CH2    0  -0.425   1.3028   0.1844  -0.0763
 5AB  O5    O  O      0  -0.619  -3.6956   1.5446   0.9202
 5AB  C6    C  CH2    0  -0.636   2.5730  -0.6492   0.0752
 5AB  C9    C  CH3    0  -0.656  -2.7368  -1.1336   1.4439
 5AB  H1N1  H  HNH2   0   0.323  -3.6105  -1.8357  -0.9233
 5AB  H2N1  H  HNH2   0   0.322  -2.6667  -0.9426  -1.8506
 5AB  HO2   H  H      0   0.417   4.8452   1.1796  -1.6032
 5AB  H13   H  HCH2   0   0.197  -1.1983   0.8150  -0.9768
 5AB  H23   H  HCH2   0   0.206  -1.1834   1.0675   0.7524
 5AB  HO3   H  H      0   0.417   5.0559  -1.5115  -0.2995
 5AB  H14   H  HCH2   0   0.193   0.0214  -1.0933   1.0740
 5AB  H24   H  HCH2   0   0.195  -0.0432  -1.3967  -0.6468
 5AB  HO4   H  H      0   0.416   3.3366   1.7951   0.8875
 5AB  H15   H  HCH2   0   0.186   1.2957   0.6723  -1.0579
 5AB  H25   H  HCH2   0   0.170   1.3055   1.0041   0.6558
 5AB  H16   H  HCH2   0   0.148   2.5217  -1.4793  -0.6473
 5AB  H26   H  HCH2   0   0.149   2.5415  -1.1382   1.0609
 5AB  H19   H  HCH3   0   0.214  -3.7258  -1.5914   1.5382
 5AB  H29   H  HCH3   0   0.217  -2.0002  -1.9310   1.5483
 5AB  H39   H  HCH3   0   0.217  -2.6136  -0.4411   2.2749
 5AB  O1    O  OC    -1  -0.607  -4.5068   0.6252  -0.9342

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
 5AB  B1  C6    single  1.646  0.020  1.646
 5AB  B1  O4    single  1.480  0.020  1.480
 5AB  C1  C2    single  1.560  0.020  1.560
 5AB  C1  C3    single  1.538  0.020  1.538
 5AB  C1  C9    single  1.530  0.020  1.530
 5AB  N1  C1    single  1.461  0.020  1.461
 5AB  N1  H1N1  single  0.890  0.020  1.040
 5AB  N1  H2N1  single  0.890  0.020  1.040
 5AB  C2  O1    deloc   1.248  0.020  1.248
 5AB  O2  B1    single  1.485  0.020  1.485
 5AB  O2  HO2   single  0.850  0.020  0.980
 5AB  C3  H13   single  0.970  0.020  1.090
 5AB  C3  H23   single  0.970  0.020  1.090
 5AB  O3  B1    single  1.481  0.020  1.481
 5AB  O3  HO3   single  0.850  0.020  0.980
 5AB  C4  C3    single  1.524  0.020  1.524
 5AB  C4  C5    single  1.526  0.020  1.526
 5AB  C4  H14   single  0.970  0.020  1.090
 5AB  C4  H24   single  0.970  0.020  1.090
 5AB  O4  HO4   single  0.850  0.020  0.980
 5AB  C5  H15   single  0.970  0.020  1.090
 5AB  C5  H25   single  0.970  0.020  1.090
 5AB  O5  C2    deloc   1.250  0.020  1.250
 5AB  C6  C5    single  1.527  0.020  1.527
 5AB  C6  H16   single  0.970  0.020  1.090
 5AB  C6  H26   single  0.970  0.020  1.090
 5AB  C9  H19   single  0.970  0.020  1.090
 5AB  C9  H29   single  0.970  0.020  1.090
 5AB  C9  H39   single  0.970  0.020  1.090

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
 5AB  C6    B1  O4    112.36  3.000
 5AB  O4    B1  O3    103.07  3.000
 5AB  C6    B1  O3    111.59  3.000
 5AB  O3    B1  O2    111.53  3.000
 5AB  O4    B1  O2    111.65  3.000
 5AB  C6    B1  O2    106.75  3.000
 5AB  C9    C1  C3    111.19  3.000
 5AB  C9    C1  C2    108.12  3.000
 5AB  C3    C1  C2    107.60  3.000
 5AB  C9    C1  N1    107.87  3.000
 5AB  C3    C1  N1    108.47  3.000
 5AB  C2    C1  N1    113.63  3.000
 5AB  H2N1  N1  H1N1  103.82  3.000
 5AB  H2N1  N1  C1    108.25  3.000
 5AB  H1N1  N1  C1    108.37  3.000
 5AB  O5    C2  O1    125.76  3.000
 5AB  O5    C2  C1    116.39  3.000
 5AB  O1    C2  C1    117.85  3.000
 5AB  HO2   O2  B1    108.62  3.000
 5AB  H23   C3  H13   105.74  3.000
 5AB  H23   C3  C4    109.08  3.000
 5AB  H13   C3  C4    108.46  3.000
 5AB  C4    C3  C1    116.55  3.000
 5AB  H23   C3  C1    108.34  3.000
 5AB  H13   C3  C1    108.14  3.000
 5AB  HO3   O3  B1    108.25  3.000
 5AB  H24   C4  H14   106.01  3.000
 5AB  H24   C4  C5    109.42  3.000
 5AB  H14   C4  C5    108.62  3.000
 5AB  H24   C4  C3    109.96  3.000
 5AB  H14   C4  C3    109.97  3.000
 5AB  C5    C4  C3    112.63  3.000
 5AB  HO4   O4  B1    108.77  3.000
 5AB  H25   C5  H15   105.34  3.000
 5AB  H25   C5  C6    109.81  3.000
 5AB  H15   C5  C6    109.71  3.000
 5AB  C6    C5  C4    114.69  3.000
 5AB  H25   C5  C4    107.93  3.000
 5AB  H15   C5  C4    108.93  3.000
 5AB  H26   C6  H16   104.55  3.000
 5AB  H26   C6  C5    107.91  3.000
 5AB  H16   C6  C5    107.91  3.000
 5AB  H26   C6  B1    109.56  3.000
 5AB  H16   C6  B1    110.46  3.000
 5AB  C5    C6  B1    115.82  3.000
 5AB  H39   C9  H29   108.40  3.000
 5AB  H39   C9  H19   107.62  3.000
 5AB  H29   C9  H19   107.25  3.000
 5AB  H39   C9  C1    111.18  3.000
 5AB  H29   C9  C1    111.39  3.000
 5AB  H19   C9  C1    110.84  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
 5AB  Var_01  C4  C5  C6  B1  -179.27  30.0  3
 5AB  Var_02  C5  C6  B1  O2   -63.17  30.0  3
 5AB  Var_03  C6  C5  C4  C3   177.92  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
 5AB  chir_01  C1  C3  C9  N1  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
 5AB  plan-1  C1  0.020
 5AB  plan-1  C2  0.020
 5AB  plan-1  O5  0.020
 5AB  plan-1  O1  0.020

