# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 15:14:19 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: [(5S)-5-amino-5-carboxy-6,6-difluorohexyl](trihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@](CCCC[B-](O)(O)O)(C(F)F)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
 4U7  4U7  '[(5S)-5-amino-5-carboxy-6,6-difluorohexyl](trihydroxy)borate(1-)'  L-peptide  30  16  .  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_4U7
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
 4U7  B1    B  B     -1   0.429   4.4966   0.0815   0.0691
 4U7  C1    C  CT     0  -0.160  -2.1060   0.1512  -0.3712
 4U7  N1    N  NH2    0  -0.829  -2.2728   0.1925  -1.8153
 4U7  C2    C  C      0   0.428  -3.1546   1.0874   0.3099
 4U7  O2    O  OB     0  -0.747   5.5862  -0.8069  -0.3953
 4U7  C3    C  CH2    0  -0.428  -0.7090   0.5998   0.1025
 4U7  O3    O  OB     0  -0.754   4.6186   0.0236   1.5428
 4U7  C4    C  CH2    0  -0.424   0.4765  -0.1842  -0.4549
 4U7  O4    O  OB     0  -0.750   4.6638   1.4663  -0.4413
 4U7  C5    C  CH2    0  -0.424   1.8172   0.3244   0.0679
 4U7  O5    O  O      0  -0.594  -3.2875   0.9598   1.5384
 4U7  C6    C  CH2    0  -0.640   3.0282  -0.4398  -0.4619
 4U7  C9    C  CH1    0   0.564  -2.3652  -1.3008   0.0104
 4U7  H1N1  H  HNH2   0   0.344  -2.6200   1.1093  -2.0636
 4U7  H2N1  H  HNH2   0   0.339  -1.3916   0.0526  -2.2915
 4U7  HO2   H  H      0   0.417   5.4689  -0.9634  -1.3346
 4U7  H13   H  HCH2   0   0.220  -0.5928   1.6520  -0.1816
 4U7  H23   H  HCH2   0   0.220  -0.6705   0.5773   1.1933
 4U7  HO3   H  H      0   0.417   3.8430   0.4311   1.9338
 4U7  H14   H  HCH2   0   0.206   0.3846  -1.2476  -0.2102
 4U7  H24   H  HCH2   0   0.196   0.4933  -0.1282  -1.5498
 4U7  HO4   H  H      0   0.417   5.5159   1.8025  -0.1484
 4U7  H15   H  HCH2   0   0.193   1.9112   1.3889  -0.1738
 4U7  H25   H  HCH2   0   0.177   1.7934   0.2740   1.1648
 4U7  H16   H  HCH2   0   0.151   2.9864  -0.4153  -1.5623
 4U7  H26   H  HCH2   0   0.153   2.8951  -1.5011  -0.2036
 4U7  H9    H  HCH1   0   0.179  -1.8269  -1.9936  -0.6417
 4U7  F1    F  F      0  -0.348  -2.0167  -1.5989   1.2947
 4U7  O1    O  OC    -1  -0.594  -3.7356   1.9088  -0.4248
 4U7  F2    F  F      0  -0.356  -3.6971  -1.5914  -0.0999

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
 4U7  B1  O3    single  1.480  0.020  1.480
 4U7  B1  O2    single  1.481  0.020  1.481
 4U7  C1  C3    single  1.542  0.020  1.542
 4U7  C1  N1    single  1.454  0.020  1.454
 4U7  F1  C9    single  1.364  0.020  1.364
 4U7  N1  H1N1  single  0.890  0.020  1.040
 4U7  N1  H2N1  single  0.890  0.020  1.040
 4U7  O1  C2    deloc   1.246  0.020  1.246
 4U7  C2  C1    single  1.562  0.020  1.562
 4U7  C2  O5    deloc   1.242  0.020  1.242
 4U7  O2  HO2   single  0.850  0.020  0.980
 4U7  C3  H13   single  0.970  0.020  1.090
 4U7  C3  H23   single  0.970  0.020  1.090
 4U7  O3  HO3   single  0.850  0.020  0.980
 4U7  C4  C5    single  1.526  0.020  1.526
 4U7  C4  C3    single  1.527  0.020  1.527
 4U7  C4  H14   single  0.970  0.020  1.090
 4U7  C4  H24   single  0.970  0.020  1.090
 4U7  O4  B1    single  1.485  0.020  1.485
 4U7  O4  HO4   single  0.850  0.020  0.980
 4U7  C5  C6    single  1.527  0.020  1.527
 4U7  C5  H15   single  0.970  0.020  1.090
 4U7  C5  H25   single  0.970  0.020  1.090
 4U7  C6  B1    single  1.646  0.020  1.646
 4U7  C6  H16   single  0.970  0.020  1.090
 4U7  C6  H26   single  0.970  0.020  1.090
 4U7  C9  F2    single  1.368  0.020  1.368
 4U7  C9  C1    single  1.524  0.020  1.524
 4U7  C9  H9    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
 4U7  C6    B1  O4    106.55  3.000
 4U7  C6    B1  O3    112.48  3.000
 4U7  O4    B1  O3    111.68  3.000
 4U7  C6    B1  O2    111.42  3.000
 4U7  O4    B1  O2    111.64  3.000
 4U7  O3    B1  O2    103.19  3.000
 4U7  C9    C1  C3    110.76  3.000
 4U7  C9    C1  C2    110.35  3.000
 4U7  C3    C1  C2    107.45  3.000
 4U7  C9    C1  N1    104.85  3.000
 4U7  C2    C1  N1    109.82  3.000
 4U7  C3    C1  N1    113.62  3.000
 4U7  H2N1  N1  H1N1  107.99  3.000
 4U7  H2N1  N1  C1    111.33  3.000
 4U7  H1N1  N1  C1    108.00  3.000
 4U7  O5    C2  O1    126.94  3.000
 4U7  O5    C2  C1    116.20  3.000
 4U7  O1    C2  C1    116.81  3.000
 4U7  HO2   O2  B1    108.36  3.000
 4U7  H23   C3  H13   105.97  3.000
 4U7  H23   C3  C4    109.07  3.000
 4U7  H13   C3  C4    108.43  3.000
 4U7  C4    C3  C1    116.23  3.000
 4U7  H23   C3  C1    109.44  3.000
 4U7  H13   C3  C1    107.20  3.000
 4U7  HO3   O3  B1    108.81  3.000
 4U7  H24   C4  H14   105.90  3.000
 4U7  H24   C4  C5    108.16  3.000
 4U7  H14   C4  C5    108.71  3.000
 4U7  H24   C4  C3    110.50  3.000
 4U7  H14   C4  C3    110.61  3.000
 4U7  C5    C4  C3    112.70  3.000
 4U7  HO4   O4  B1    108.72  3.000
 4U7  H25   C5  H15   105.48  3.000
 4U7  H25   C5  C6    109.93  3.000
 4U7  H15   C5  C6    109.98  3.000
 4U7  H25   C5  C4    107.92  3.000
 4U7  H15   C5  C4    108.88  3.000
 4U7  C6    C5  C4    114.27  3.000
 4U7  H26   C6  H16   104.56  3.000
 4U7  H26   C6  C5    107.78  3.000
 4U7  H16   C6  C5    107.78  3.000
 4U7  H26   C6  B1    109.73  3.000
 4U7  H16   C6  B1    110.43  3.000
 4U7  C5    C6  B1    115.91  3.000
 4U7  H9    C9  F2    107.26  3.000
 4U7  H9    C9  F1    107.30  3.000
 4U7  F2    C9  F1    106.16  3.000
 4U7  H9    C9  C1    111.76  3.000
 4U7  F2    C9  C1    110.36  3.000
 4U7  F1    C9  C1    113.63  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
 4U7  Var_01  C4  C5  C6  B1  179.63  30.0  1
 4U7  Var_02  C5  C6  B1  O2  174.35  30.0  2
 4U7  Var_03  C6  C5  C4  C3  179.71  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
 4U7  chir_01  C1  N1  C2  C9  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
 4U7  plan-1  C1  0.020
 4U7  plan-1  C2  0.020
 4U7  plan-1  O5  0.020
 4U7  plan-1  O1  0.020

