# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:41:42 2022
#   Inital geometry file: a 89 line input string
#   Ligand name: {(3R,6S)-2-hydroxy-3-[(thiophen-2-ylacetyl)amino]-1,2-oxaborinan-6-yl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OB1O[C@@H](CC[C@@H]1NC(=O)Cc2sccc2)CC(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
 4D6  4D6  '{(3R,6S)-2-hydroxy-3-[(thiophen-2-ylacetyl)amino]-1,2-oxaborinan-6-yl}acetic acid'  ligand  35  20  .  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_4D6
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
 4D6  C1   C  CR15   0  -0.478   6.2007  -0.4418   0.1860
 4D6  C3   C  CR5    0  -0.133   3.8814  -0.1667  -0.6400
 4D6  C5   C  CR15   0  -0.187   5.9216  -1.2645  -0.8607
 4D6  C7   C  C      0   0.567   1.6254   0.4517   0.3024
 4D6  C11  C  CH2    0  -0.451  -1.2622   1.6686   1.1140
 4D6  C12  C  CH2    0  -0.486  -2.3046   1.7467   0.0085
 4D6  C14  C  CH1    0   0.073  -3.4856   0.8314   0.2929
 4D6  C17  C  CH2    0  -0.581  -4.4428   0.7299  -0.8760
 4D6  O20  O  O      0  -0.615  -6.2519   0.0925   0.5256
 4D6  C18  C  C      0   0.408  -5.7039  -0.1019  -0.5783
 4D6  O19  O  OC    -1  -0.618  -6.0938  -0.8783  -1.4728
 4D6  O16  O  O2     0  -0.453  -3.0668  -0.4968   0.6314
 4D6  B15  B  B      0   0.523  -1.8155  -0.8289   1.0186
 4D6  O27  O  OH1    0  -0.615  -1.5119  -2.1306   1.2695
 4D6  C34  C  CH1    0  -0.287  -0.6644   0.2608   1.1804
 4D6  N9   N  NH1    0  -0.652   0.3548   0.0480   0.1622
 4D6  O8   O  O      0  -0.489   2.0733   0.9402   1.3299
 4D6  C6   C  CH2    0  -0.644   2.4940   0.2981  -0.9324
 4D6  S2   S  S2     0   0.216   4.8459   0.5197   0.6144
 4D6  C4   C  CR15   0  -0.238   4.5913  -1.1006  -1.3359
 4D6  H1   H  HCR5   0   0.289   7.1202  -0.3680   0.7463
 4D6  H2   H  HCR5   0   0.262   6.6302  -1.9646  -1.2795
 4D6  H3   H  HCH2   0   0.244  -0.4781   2.4150   0.9697
 4D6  H4   H  HCH2   0   0.230  -1.7330   1.8992   2.0751
 4D6  H5   H  HCH2   0   0.248  -2.6882   2.7645  -0.0921
 4D6  H6   H  HCH2   0   0.221  -1.8531   1.4921  -0.9575
 4D6  H7   H  HCH1   0   0.216  -4.0287   1.2234   1.1585
 4D6  H8   H  HCH2   0   0.232  -4.7599   1.7460  -1.1370
 4D6  H9   H  HCH2   0   0.210  -3.9154   0.3365  -1.7498
 4D6  H11  H  HOH1   0   0.487  -2.2453  -2.7376   1.1206
 4D6  H12  H  HCH1   0   0.258  -0.1855   0.1136   2.1524
 4D6  H13  H  HNH1   0   0.405   0.0800  -0.3164  -0.7353
 4D6  H14  H  HCH2   0   0.298   2.5223   1.2851  -1.4088
 4D6  H15  H  HCH2   0   0.279   2.0428  -0.3775  -1.6603
 4D6  H16  H  HCR5   0   0.259   4.1760  -1.6500  -2.1700

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
 4D6  O20  C18  deloc     1.248  0.020  1.248
 4D6  C18  C17  single    1.540  0.020  1.540
 4D6  C18  O19  deloc     1.247  0.020  1.247
 4D6  C17  C14  single    1.514  0.020  1.514
 4D6  C14  C12  single    1.521  0.020  1.521
 4D6  C14  O16  single    1.433  0.020  1.433
 4D6  C12  C11  single    1.521  0.020  1.521
 4D6  O16  B15  single    1.351  0.020  1.351
 4D6  C11  C34  single    1.531  0.020  1.531
 4D6  B15  O27  single    1.360  0.020  1.360
 4D6  B15  C34  single    1.593  0.020  1.593
 4D6  C34  N9   single    1.456  0.020  1.456
 4D6  N9   C7   single    1.341  0.020  1.341
 4D6  O8   C7   double    1.223  0.020  1.223
 4D6  S2   C1   aromatic  1.716  0.020  1.716
 4D6  S2   C3   aromatic  1.725  0.020  1.725
 4D6  C7   C6   single    1.517  0.020  1.517
 4D6  C1   C5   aromatic  1.360  0.020  1.360
 4D6  C6   C3   single    1.492  0.020  1.492
 4D6  C3   C4   aromatic  1.364  0.020  1.364
 4D6  C5   C4   aromatic  1.422  0.020  1.422
 4D6  C1   H1   single    0.930  0.020  1.080
 4D6  C5   H2   single    0.930  0.020  1.080
 4D6  C11  H3   single    0.970  0.020  1.090
 4D6  C11  H4   single    0.970  0.020  1.090
 4D6  C12  H5   single    0.970  0.020  1.090
 4D6  C12  H6   single    0.970  0.020  1.090
 4D6  C14  H7   single    0.970  0.020  1.090
 4D6  C17  H8   single    0.970  0.020  1.090
 4D6  C17  H9   single    0.970  0.020  1.090
 4D6  O27  H11  single    0.850  0.020  0.980
 4D6  C34  H12  single    0.970  0.020  1.090
 4D6  N9   H13  single    0.860  0.020  1.020
 4D6  C6   H14  single    0.970  0.020  1.090
 4D6  C6   H15  single    0.970  0.020  1.090
 4D6  C4   H16  single    0.930  0.020  1.080

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
 4D6  H1   C1   S2   120.32  3.000
 4D6  H1   C1   C5   128.00  3.000
 4D6  S2   C1   C5   111.66  3.000
 4D6  C4   C3   S2   110.64  3.000
 4D6  C4   C3   C6   126.67  3.000
 4D6  S2   C3   C6   122.58  3.000
 4D6  H2   C5   C4   123.96  3.000
 4D6  H2   C5   C1   123.75  3.000
 4D6  C4   C5   C1   112.29  3.000
 4D6  C6   C7   O8   120.97  3.000
 4D6  C6   C7   N9   115.27  3.000
 4D6  O8   C7   N9   123.74  3.000
 4D6  H4   C11  H3   106.30  3.000
 4D6  H4   C11  C34  108.88  3.000
 4D6  H3   C11  C34  110.73  3.000
 4D6  H4   C11  C12  109.42  3.000
 4D6  H3   C11  C12  111.15  3.000
 4D6  C34  C11  C12  110.26  3.000
 4D6  H6   C12  H5   106.26  3.000
 4D6  H6   C12  C14  110.17  3.000
 4D6  H5   C12  C14  107.77  3.000
 4D6  H6   C12  C11  110.25  3.000
 4D6  H5   C12  C11  110.82  3.000
 4D6  C14  C12  C11  111.42  3.000
 4D6  H7   C14  O16  106.86  3.000
 4D6  H7   C14  C17  108.72  3.000
 4D6  O16  C14  C17  107.75  3.000
 4D6  H7   C14  C12  108.52  3.000
 4D6  O16  C14  C12  112.02  3.000
 4D6  C17  C14  C12  112.76  3.000
 4D6  H9   C17  H8   106.42  3.000
 4D6  H9   C17  C18  110.80  3.000
 4D6  H8   C17  C18  108.05  3.000
 4D6  H9   C17  C14  109.64  3.000
 4D6  H8   C17  C14  107.74  3.000
 4D6  C18  C17  C14  113.87  3.000
 4D6  O19  C18  O20  126.46  3.000
 4D6  O19  C18  C17  116.99  3.000
 4D6  O20  C18  C17  116.53  3.000
 4D6  B15  O16  C14  124.48  3.000
 4D6  C34  B15  O27  118.33  3.000
 4D6  C34  B15  O16  122.01  3.000
 4D6  O27  B15  O16  119.66  3.000
 4D6  H11  O27  B15  113.86  3.000
 4D6  H12  C34  N9   107.17  3.000
 4D6  H12  C34  B15  108.34  3.000
 4D6  N9   C34  B15  109.55  3.000
 4D6  H12  C34  C11  109.47  3.000
 4D6  N9   C34  C11  112.17  3.000
 4D6  B15  C34  C11  110.02  3.000
 4D6  H13  N9   C34  119.02  3.000
 4D6  H13  N9   C7   117.45  3.000
 4D6  C34  N9   C7   123.10  3.000
 4D6  H15  C6   H14  106.16  3.000
 4D6  H15  C6   C7   111.65  3.000
 4D6  H14  C6   C7   106.10  3.000
 4D6  H15  C6   C3   108.81  3.000
 4D6  H14  C6   C3   109.97  3.000
 4D6  C7   C6   C3   113.85  3.000
 4D6  C3   S2   C1    92.12  3.000
 4D6  H16  C4   C5   123.94  3.000
 4D6  H16  C4   C3   122.78  3.000
 4D6  C5   C4   C3   113.28  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
 4D6  CONST_01  C4   C3   S2   C1      0.00   0.0  0
 4D6  CONST_02  C3   C4   C5   C1      0.00   0.0  0
 4D6  CONST_03  C5   C1   S2   C3      0.00   0.0  0
 4D6  CONST_04  S2   C3   C4   C5      0.00   0.0  0
 4D6  CONST_05  C4   C5   C1   S2      0.00   0.0  0
 4D6  CONST_06  C6   C3   S2   C1    180.00   0.0  0
 4D6  CONST_07  C6   C3   C4   C5    180.00   0.0  0
 4D6  CONST_08  H16  C4   C5   C1    180.00   0.0  0
 4D6  CONST_09  H1   C1   S2   C3    180.00   0.0  0
 4D6  CONST_10  H2   C5   C4   C3    180.00   0.0  0
 4D6  CONST_11  O8   C7   N9   C34     0.00   0.0  0
 4D6  CONST_12  C6   C7   N9   C34   180.00   0.0  0
 4D6  CONST_13  H13  N9   C7   O8    180.00   0.0  0
 4D6  Var_01    C34  C11  C12  C14    63.86  30.0  1
 4D6  Var_02    C34  B15  O16  C14     1.83  30.0  1
 4D6  Var_03    S2   C3   C6   C7    -46.58  30.0  2
 4D6  Var_04    N9   C7   C6   C3   -140.20  30.0  1
 4D6  Var_05    O20  C18  C17  C14    43.19  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
 4D6  chir_01  C14  C17  C12  O16  positiv
 4D6  chir_02  C34  N9   C11  B15  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
 4D6  plan-1  C1   0.020
 4D6  plan-1  C3   0.020
 4D6  plan-1  C5   0.020
 4D6  plan-1  C6   0.020
 4D6  plan-1  S2   0.020
 4D6  plan-1  C4   0.020
 4D6  plan-1  H1   0.020
 4D6  plan-1  H2   0.020
 4D6  plan-1  H16  0.020
 4D6  plan-2  C7   0.020
 4D6  plan-2  C34  0.020
 4D6  plan-2  N9   0.020
 4D6  plan-2  O8   0.020
 4D6  plan-2  C6   0.020
 4D6  plan-2  H13  0.020
 4D6  plan-3  C17  0.020
 4D6  plan-3  O20  0.020
 4D6  plan-3  C18  0.020
 4D6  plan-3  O19  0.020

