# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 22:40:14 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: [(1~{R})-1-[[(2~{S})-2-methyl-3-sulfanyl-propanoyl]amino]-2-phenyl-ethyl]boronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CS)C(=O)N[C@@H](Cc1ccccc1)B(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
 BX6  BX6  '[(1~{R})-1-[[(2~{S})-2-methyl-3-sulfanyl-propanoyl]amino]-2-phenyl-ethyl]boronic acid'  ligand  36  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BX6
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
 BX6  C1   C  CR16  0  -0.321  -1.7303  -1.7810   1.1746
 BX6  C2   C  CR6   0   0.142  -1.9910  -0.8249   0.1972
 BX6  C3   C  CR16  0  -0.286  -1.7951  -1.1722  -1.1386
 BX6  C4   C  CR16  0  -0.240  -1.3546  -2.4408  -1.4856
 BX6  C5   C  CR16  0  -0.269  -1.1026  -3.3891  -0.5010
 BX6  C6   C  CR16  0  -0.244  -1.2921  -3.0552   0.8323
 BX6  C7   C  CH2   0  -0.564  -2.4541   0.5542   0.5826
 BX6  C8   C  CH1   0  -0.298  -1.4764   1.6624   0.1488
 BX6  N9   N  NH1   0  -0.659  -0.1173   1.3210   0.5300
 BX6  C10  C  C     0   0.576   0.8576   1.0167  -0.3505
 BX6  O11  O  O     0  -0.486   0.7674   1.2196  -1.5509
 BX6  C12  C  CH1   0  -0.383   2.0862   0.3599   0.2611
 BX6  C13  C  CH2   0  -0.544   1.9413  -1.1416  -0.0061
 BX6  S14  S  S2    0  -0.252   3.2364  -2.0619   0.8909
 BX6  C15  C  CH3   0  -0.650   3.3680   0.9458  -0.3155
 BX6  B16  B  B     0   0.538  -1.8924   3.1072   0.6840
 BX6  O17  O  OH1   0  -0.609  -0.9738   3.9772   1.1742
 BX6  O18  O  OH1   0  -0.616  -3.1748   3.5572   0.6601
 BX6  H1   H  HCR6  0   0.248  -1.8706  -1.5250   2.2184
 BX6  H2   H  HCR6  0   0.246  -1.9851  -0.4431  -1.9179
 BX6  H3   H  HCR6  0   0.253  -1.2062  -2.6910  -2.5284
 BX6  H4   H  HCR6  0   0.253  -0.7566  -4.3779  -0.7732
 BX6  H5   H  HCR6  0   0.253  -1.0962  -3.7832   1.6091
 BX6  H6   H  HCH2  0   0.255  -3.4313   0.7520   0.1310
 BX6  H7   H  HCH2  0   0.259  -2.6047   0.5899   1.6649
 BX6  H8   H  HCH1  0   0.276  -1.4880   1.7196  -0.9443
 BX6  H9   H  HNH1  0   0.401   0.0349   1.0624   1.4934
 BX6  H10  H  HCH1  0   0.264   2.0767   0.5179   1.3445
 BX6  H11  H  HCH2  0   0.295   0.9670  -1.4930   0.3337
 BX6  H12  H  HCH2  0   0.270   2.0210  -1.3427  -1.0745
 BX6  H13  H  HSH1  0   0.224   2.8202  -3.2899   0.5644
 BX6  H14  H  HCH3  0   0.242   3.4221   2.0199  -0.1370
 BX6  H15  H  HCH3  0   0.239   4.2458   0.4939   0.1452
 BX6  H16  H  HCH3  0   0.231   3.4298   0.7769  -1.3903
 BX6  H17  H  HOH1  0   0.477  -0.0859   3.6029   1.1741
 BX6  H18  H  HOH1  0   0.478  -3.8030   2.9262   0.2992

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
 BX6  C6   C5   aromatic  1.387  0.020  1.387
 BX6  C6   C1   aromatic  1.390  0.020  1.390
 BX6  C5   C4   aromatic  1.390  0.020  1.390
 BX6  C1   C2   aromatic  1.392  0.020  1.392
 BX6  C4   C3   aromatic  1.387  0.020  1.387
 BX6  C2   C3   aromatic  1.394  0.020  1.394
 BX6  C2   C7   single    1.505  0.020  1.505
 BX6  C7   C8   single    1.540  0.020  1.540
 BX6  C8   B16  single    1.596  0.020  1.596
 BX6  C8   N9   single    1.452  0.020  1.452
 BX6  O18  B16  single    1.359  0.020  1.359
 BX6  B16  O17  single    1.357  0.020  1.357
 BX6  N9   C10  single    1.348  0.020  1.348
 BX6  C13  S14  single    1.825  0.020  1.825
 BX6  C13  C12  single    1.532  0.020  1.532
 BX6  C10  O11  double    1.221  0.020  1.221
 BX6  C10  C12  single    1.521  0.020  1.521
 BX6  C12  C15  single    1.523  0.020  1.523
 BX6  C1   H1   single    0.930  0.020  1.080
 BX6  C3   H2   single    0.930  0.020  1.080
 BX6  C4   H3   single    0.930  0.020  1.080
 BX6  C5   H4   single    0.930  0.020  1.080
 BX6  C6   H5   single    0.930  0.020  1.080
 BX6  C7   H6   single    0.970  0.020  1.090
 BX6  C7   H7   single    0.970  0.020  1.090
 BX6  C8   H8   single    0.970  0.020  1.090
 BX6  N9   H9   single    0.860  0.020  1.020
 BX6  C12  H10  single    0.970  0.020  1.090
 BX6  C13  H11  single    0.970  0.020  1.090
 BX6  C13  H12  single    0.970  0.020  1.090
 BX6  S14  H13  single    1.200  0.020  1.300
 BX6  C15  H14  single    0.970  0.020  1.090
 BX6  C15  H15  single    0.970  0.020  1.090
 BX6  C15  H16  single    0.970  0.020  1.090
 BX6  O17  H17  single    0.850  0.020  0.980
 BX6  O18  H18  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
 BX6  H1   C1   C6   119.63  3.000
 BX6  H1   C1   C2   119.33  3.000
 BX6  C6   C1   C2   121.05  3.000
 BX6  C7   C2   C3   121.13  3.000
 BX6  C7   C2   C1   120.48  3.000
 BX6  C3   C2   C1   118.39  3.000
 BX6  H2   C3   C4   119.41  3.000
 BX6  H2   C3   C2   119.78  3.000
 BX6  C4   C3   C2   120.81  3.000
 BX6  H3   C4   C5   119.99  3.000
 BX6  H3   C4   C3   119.73  3.000
 BX6  C5   C4   C3   120.29  3.000
 BX6  H4   C5   C6   120.35  3.000
 BX6  H4   C5   C4   120.20  3.000
 BX6  C6   C5   C4   119.45  3.000
 BX6  H5   C6   C5   120.20  3.000
 BX6  H5   C6   C1   119.78  3.000
 BX6  C5   C6   C1   120.02  3.000
 BX6  H7   C7   H6   106.23  3.000
 BX6  H7   C7   C8   110.05  3.000
 BX6  H6   C7   C8   108.70  3.000
 BX6  H7   C7   C2   109.02  3.000
 BX6  H6   C7   C2   109.55  3.000
 BX6  C8   C7   C2   113.07  3.000
 BX6  H8   C8   B16  106.55  3.000
 BX6  H8   C8   N9   106.52  3.000
 BX6  B16  C8   N9   111.64  3.000
 BX6  H8   C8   C7   108.19  3.000
 BX6  N9   C8   C7   110.55  3.000
 BX6  B16  C8   C7   113.04  3.000
 BX6  H9   N9   C10  117.16  3.000
 BX6  H9   N9   C8   116.88  3.000
 BX6  C10  N9   C8   123.93  3.000
 BX6  C12  C10  O11  121.78  3.000
 BX6  C12  C10  N9   114.75  3.000
 BX6  O11  C10  N9   123.45  3.000
 BX6  H10  C12  C15  109.06  3.000
 BX6  H10  C12  C13  108.25  3.000
 BX6  C15  C12  C13  112.99  3.000
 BX6  H10  C12  C10  109.18  3.000
 BX6  C15  C12  C10  111.19  3.000
 BX6  C13  C12  C10  106.06  3.000
 BX6  H12  C13  H11  108.15  3.000
 BX6  H12  C13  S14  109.69  3.000
 BX6  H11  C13  S14  108.57  3.000
 BX6  H12  C13  C12  110.18  3.000
 BX6  H11  C13  C12  110.25  3.000
 BX6  S14  C13  C12  109.97  3.000
 BX6  H13  S14  C13   97.02  3.000
 BX6  H16  C15  H15  107.88  3.000
 BX6  H16  C15  H14  108.14  3.000
 BX6  H15  C15  H14  107.43  3.000
 BX6  H16  C15  C12  111.20  3.000
 BX6  H15  C15  C12  111.01  3.000
 BX6  H14  C15  C12  111.03  3.000
 BX6  O18  B16  O17  115.64  3.000
 BX6  O17  B16  C8   121.68  3.000
 BX6  O18  B16  C8   122.67  3.000
 BX6  H17  O17  B16  112.01  3.000
 BX6  H18  O18  B16  113.95  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
 BX6  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 BX6  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 BX6  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 BX6  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 BX6  CONST_05  C6   C5   C4   C3     0.00   0.0  0
 BX6  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 BX6  CONST_07  C7   C2   C3   C4   180.00   0.0  0
 BX6  CONST_08  C7   C2   C1   C6   180.00   0.0  0
 BX6  CONST_09  H4   C5   C6   C1   180.00   0.0  0
 BX6  CONST_10  H2   C3   C2   C1   180.00   0.0  0
 BX6  CONST_11  H5   C6   C1   C2   180.00   0.0  0
 BX6  CONST_12  H3   C4   C3   C2   180.00   0.0  0
 BX6  CONST_13  H1   C1   C2   C3   180.00   0.0  0
 BX6  CONST_14  O11  C10  N9   C8     0.00   0.0  0
 BX6  CONST_15  C12  C10  N9   C8   180.00   0.0  0
 BX6  CONST_16  H9   N9   C10  O11  180.00   0.0  0
 BX6  Var_01    C8   C7   C2   C1   118.17  30.0  2

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
 BX6  chir_01  C8   C7   B16  N9   negativ
 BX6  chir_02  C12  C13  C10  C15  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
 BX6  plan-1  C1   0.020
 BX6  plan-1  C2   0.020
 BX6  plan-1  C3   0.020
 BX6  plan-1  C4   0.020
 BX6  plan-1  C5   0.020
 BX6  plan-1  C6   0.020
 BX6  plan-1  C7   0.020
 BX6  plan-1  H1   0.020
 BX6  plan-1  H2   0.020
 BX6  plan-1  H3   0.020
 BX6  plan-1  H4   0.020
 BX6  plan-1  H5   0.020
 BX6  plan-2  C8   0.020
 BX6  plan-2  N9   0.020
 BX6  plan-2  C10  0.020
 BX6  plan-2  O11  0.020
 BX6  plan-2  C12  0.020
 BX6  plan-2  H9   0.020

