# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 14:18:45 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  31  14  .  2022-03-10  2022-11-17
;
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   0.429   3.9801   0.1720  -0.0895
 5AB  C1    C  CT     0  -0.037  -2.5879  -0.4574   0.1592
 5AB  N1    N  NH2    0  -0.783  -2.6889  -1.4313  -0.9082
 5AB  C2    C  C      0   0.548  -3.6594   0.6428   0.1343
 5AB  O2    O  OB     0  -0.751   3.9901   0.7394  -1.4621
 5AB  C3    C  CH2    0  -0.413  -1.2340   0.2749   0.0477
 5AB  O3    O  OB     0  -0.747   5.1506  -0.7023   0.1470
 5AB  C4    C  CH2    0  -0.402   0.0009  -0.6145   0.1224
 5AB  O4    O  OB     0  -0.754   4.1347   1.2256   0.9387
 5AB  C5    C  CH2    0  -0.427   1.2937   0.1797  -0.0458
 5AB  O5    O  O      0  -0.453  -3.7905   1.4663   1.0084
 5AB  C6    C  CH2    0  -0.639   2.5659  -0.6559   0.0696
 5AB  C9    C  CH3    0  -0.654  -2.7270  -1.1880   1.4975
 5AB  H1N1  H  HNH2   0   0.347  -3.5872  -1.8979  -0.8905
 5AB  H2N1  H  HNH2   0   0.345  -2.6099  -0.9885  -1.8150
 5AB  HO2   H  H      0   0.418   4.8053   1.2348  -1.5842
 5AB  H13   H  HCH2   0   0.225  -1.2163   0.8240  -0.9025
 5AB  H23   H  HCH2   0   0.228  -1.1767   1.0314   0.8346
 5AB  HO3   H  H      0   0.417   5.0261  -1.5135  -0.3501
 5AB  H14   H  HCH2   0   0.203   0.0292  -1.1348   1.0852
 5AB  H24   H  HCH2   0   0.207  -0.0515  -1.3915  -0.6445
 5AB  HO4   H  H      0   0.416   3.3496   1.7767   0.9374
 5AB  H15   H  HCH2   0   0.191   1.2734   0.6915  -1.0146
 5AB  H25   H  HCH2   0   0.175   1.3033   0.9795   0.7074
 5AB  H16   H  HCH2   0   0.150   2.5075  -1.4673  -0.6730
 5AB  H26   H  HCH2   0   0.152   2.5463  -1.1692   1.0431
 5AB  H19   H  HCH3   0   0.237  -3.7120  -1.6512   1.5888
 5AB  H29   H  HCH3   0   0.244  -1.9847  -1.9809   1.5689
 5AB  H39   H  HCH3   0   0.234  -2.5929  -0.5129   2.3409
 5AB  H17   H  HOH1   0   0.478  -5.0600   1.3556  -0.9108
 5AB  O1    O  OH1    0  -0.585  -4.4263   0.6231  -0.9484

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  1.536  0.020  1.536
 5AB  C1  C3    single  1.543  0.020  1.543
 5AB  C1  C9    single  1.531  0.020  1.531
 5AB  N1  C1    single  1.448  0.020  1.448
 5AB  N1  H1N1  single  0.890  0.020  1.040
 5AB  N1  H2N1  single  0.890  0.020  1.040
 5AB  C2  O1    single  1.327  0.020  1.327
 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  1.480  0.020  1.480
 5AB  O3  HO3   single  0.850  0.020  0.980
 5AB  C4  C3    single  1.524  0.020  1.524
 5AB  C4  C5    single  1.527  0.020  1.527
 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    double  1.208  0.020  1.208
 5AB  C6  C5    single  1.526  0.020  1.526
 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
 5AB  O1  H17   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
 5AB  C6    B1  O4    112.37  3.000
 5AB  O4    B1  O3    103.11  3.000
 5AB  C6    B1  O3    111.52  3.000
 5AB  O3    B1  O2    111.59  3.000
 5AB  O4    B1  O2    111.67  3.000
 5AB  C6    B1  O2    106.69  3.000
 5AB  C9    C1  C3    111.67  3.000
 5AB  C9    C1  C2    107.01  3.000
 5AB  C3    C1  C2    105.72  3.000
 5AB  C9    C1  N1    108.48  3.000
 5AB  C3    C1  N1    109.08  3.000
 5AB  C2    C1  N1    114.90  3.000
 5AB  H2N1  N1  H1N1  106.65  3.000
 5AB  H2N1  N1  C1    111.14  3.000
 5AB  H1N1  N1  C1    111.03  3.000
 5AB  O5    C2  O1    122.53  3.000
 5AB  O5    C2  C1    123.52  3.000
 5AB  O1    C2  C1    113.94  3.000
 5AB  HO2   O2  B1    108.65  3.000
 5AB  H23   C3  H13   106.03  3.000
 5AB  H23   C3  C4    109.04  3.000
 5AB  H13   C3  C4    108.74  3.000
 5AB  C4    C3  C1    115.50  3.000
 5AB  H23   C3  C1    108.81  3.000
 5AB  H13   C3  C1    108.31  3.000
 5AB  HO3   O3  B1    108.30  3.000
 5AB  H24   C4  H14   106.29  3.000
 5AB  H24   C4  C5    109.46  3.000
 5AB  H14   C4  C5    108.80  3.000
 5AB  H24   C4  C3    109.98  3.000
 5AB  H14   C4  C3    109.96  3.000
 5AB  C5    C4  C3    112.17  3.000
 5AB  HO4   O4  B1    108.81  3.000
 5AB  H25   C5  H15   105.45  3.000
 5AB  H25   C5  C6    109.84  3.000
 5AB  H15   C5  C6    109.75  3.000
 5AB  C6    C5  C4    114.37  3.000
 5AB  H25   C5  C4    108.09  3.000
 5AB  H15   C5  C4    108.95  3.000
 5AB  H26   C6  H16   104.59  3.000
 5AB  H26   C6  C5    107.90  3.000
 5AB  H16   C6  C5    107.94  3.000
 5AB  H26   C6  B1    109.59  3.000
 5AB  H16   C6  B1    110.54  3.000
 5AB  C5    C6  B1    115.68  3.000
 5AB  H39   C9  H29   108.48  3.000
 5AB  H39   C9  H19   108.02  3.000
 5AB  H29   C9  H19   107.49  3.000
 5AB  H39   C9  C1    111.72  3.000
 5AB  H29   C9  C1    110.06  3.000
 5AB  H19   C9  C1    110.93  3.000
 5AB  H17   O1  C2    109.58  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  CONST_01  H17  O1  C2  C1   180.00   0.0  0
 5AB  Var_01    C4   C5  C6  B1  -179.32  30.0  3
 5AB  Var_02    C5   C6  B1  O2   -62.56  30.0  3
 5AB  Var_03    C6   C5  C4  C3   177.96  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  H17  0.020
 5AB  plan-1  O1   0.020

