# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun 10 14:36:32 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 1-{(2R)-2-(dihydroxyboranyl)-2-[(thiophen-2-ylacetyl)amino]ethyl}-1H-1,2,3-triazole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OB(O)[C@H](Cn1cc(nn1)C(O)=O)NC(=O)Cc2sccc2
#
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
 ZXM  ZXM  '1-{(2R)-2-(dihydroxyboranyl)-2-[(thiophen-2-ylacetyl)amino]ethyl}-1H-1,2,3-triazole-4-carboxylic acid'  ligand  34  22  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZXM
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
 ZXM  B1   B  B      0   0.578   0.9546  -2.3757  -0.3869
 ZXM  O1   O  OH1    0  -0.541   1.3288  -2.6882  -1.6554
 ZXM  O2   O  OH1    0  -0.715   0.9352  -3.3365   0.5732
 ZXM  N4   N  NR5    0  -0.340   2.4935  -0.0500   0.7686
 ZXM  N5   N  N      0  -0.086   3.2268  -1.0567   0.3200
 ZXM  N6   N  N      0  -0.321   4.3786  -0.5921  -0.0197
 ZXM  C7   C  CH1    0  -0.263   0.3467  -0.9500   0.0279
 ZXM  C8   C  CH2    0  -0.284   1.1249  -0.2907   1.1743
 ZXM  N10  N  NH1    0  -0.715  -1.0406  -1.1315   0.4133
 ZXM  C11  C  C      0   0.614  -1.9492  -0.1424   0.3687
 ZXM  C12  C  CH2    0  -0.654  -3.3208  -0.5032   0.9062
 ZXM  C13  C  CR5    0  -0.116  -4.4470   0.1033   0.1376
 ZXM  C14  C  CR15   0  -0.200  -5.5917  -0.5233  -0.2588
 ZXM  C15  C  CR15   0  -0.198  -6.5156   0.3474  -0.8995
 ZXM  C16  C  CR15   0  -0.536  -6.0545   1.6251  -0.9734
 ZXM  O18  O  O      0  -0.423  -1.7018   0.9803  -0.0419
 ZXM  C19  C  CR5    0  -0.110   4.4074   0.7401   0.2086
 ZXM  C20  C  CR15   0  -0.036   3.1826   1.0969   0.7221
 ZXM  C21  C  C      0   0.296   5.5820   1.6372  -0.0752
 ZXM  O22  O  O      0  -0.342   5.4077   2.8383   0.2112
 ZXM  O23  O  OC    -1  -0.582   6.5908   1.1048  -0.5699
 ZXM  S24  S  S2     0   0.342  -4.4882   1.7735  -0.2904
 ZXM  H1   H  HOH1   0   0.461   1.2896  -1.9440  -2.2628
 ZXM  H2   H  HOH1   0   0.446   1.2510  -4.1977   0.2789
 ZXM  H3   H  HCH1   0   0.270   0.3701  -0.2649  -0.8244
 ZXM  H4   H  HCH2   0   0.263   1.1199  -0.9185   2.0662
 ZXM  H5   H  HCH2   0   0.260   0.6904   0.6718   1.4371
 ZXM  H6   H  HNH1   0   0.363  -1.3260  -2.0214   0.7908
 ZXM  H7   H  HCH2   0   0.312  -3.4637  -1.5841   0.9430
 ZXM  H8   H  HCH2   0   0.232  -3.3449  -0.1571   1.9460
 ZXM  H9   H  HCR5   0   0.224  -5.7728  -1.5756  -0.0864
 ZXM  H10  H  HCR5   0   0.252  -7.4734   0.0319  -1.2877
 ZXM  H11  H  HCR5   0   0.254  -6.5372   2.4807  -1.4206
 ZXM  H12  H  HCR5   0   0.296   2.7690   2.0395   1.0355

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
 ZXM  C14  C13  aromatic  1.364  0.020  1.364
 ZXM  C14  C15  aromatic  1.422  0.020  1.422
 ZXM  C12  C13  single    1.492  0.020  1.492
 ZXM  C12  C11  single    1.517  0.020  1.517
 ZXM  O18  C11  double    1.221  0.020  1.221
 ZXM  C13  S24  aromatic  1.725  0.020  1.725
 ZXM  C15  C16  aromatic  1.360  0.020  1.360
 ZXM  C11  N10  single    1.344  0.020  1.344
 ZXM  N10  C7   single    1.451  0.020  1.451
 ZXM  C16  S24  aromatic  1.715  0.020  1.715
 ZXM  C7   C8   single    1.534  0.020  1.534
 ZXM  C7   B1   single    1.604  0.020  1.604
 ZXM  C8   N4   single    1.448  0.020  1.448
 ZXM  B1   O2   single    1.358  0.020  1.358
 ZXM  B1   O1   single    1.359  0.020  1.359
 ZXM  C20  N4   aromatic  1.339  0.020  1.339
 ZXM  C20  C19  aromatic  1.375  0.020  1.375
 ZXM  N4   N5   aromatic  1.324  0.020  1.324
 ZXM  O22  C21  deloc     1.247  0.020  1.247
 ZXM  C19  C21  single    1.505  0.020  1.505
 ZXM  C19  N6   aromatic  1.352  0.020  1.352
 ZXM  N5   N6   aromatic  1.288  0.020  1.288
 ZXM  C21  O23  deloc     1.243  0.020  1.243
 ZXM  O1   H1   single    0.850  0.020  0.980
 ZXM  O2   H2   single    0.850  0.020  0.980
 ZXM  C7   H3   single    0.970  0.020  1.090
 ZXM  C8   H4   single    0.970  0.020  1.090
 ZXM  C8   H5   single    0.970  0.020  1.090
 ZXM  N10  H6   single    0.860  0.020  1.020
 ZXM  C12  H7   single    0.970  0.020  1.090
 ZXM  C12  H8   single    0.970  0.020  1.090
 ZXM  C14  H9   single    0.930  0.020  1.080
 ZXM  C15  H10  single    0.930  0.020  1.080
 ZXM  C16  H11  single    0.930  0.020  1.080
 ZXM  C20  H12  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
 ZXM  C7   B1   O2   116.12  3.000
 ZXM  O2   B1   O1   120.07  3.000
 ZXM  C7   B1   O1   123.37  3.000
 ZXM  H1   O1   B1   113.61  3.000
 ZXM  H2   O2   B1   114.31  3.000
 ZXM  C20  N4   C8   129.70  3.000
 ZXM  C20  N4   N5   110.77  3.000
 ZXM  C8   N4   N5   119.48  3.000
 ZXM  N6   N5   N4   108.09  3.000
 ZXM  C19  N6   N5   109.28  3.000
 ZXM  H3   C7   N10  107.80  3.000
 ZXM  H3   C7   C8   107.59  3.000
 ZXM  N10  C7   C8   109.89  3.000
 ZXM  H3   C7   B1   110.30  3.000
 ZXM  C8   C7   B1   112.51  3.000
 ZXM  N10  C7   B1   108.65  3.000
 ZXM  H5   C8   H4   108.04  3.000
 ZXM  H5   C8   C7   110.97  3.000
 ZXM  H4   C8   C7   111.18  3.000
 ZXM  H5   C8   N4   107.34  3.000
 ZXM  H4   C8   N4   109.23  3.000
 ZXM  C7   C8   N4   109.97  3.000
 ZXM  H6   N10  C11  118.09  3.000
 ZXM  H6   N10  C7   118.72  3.000
 ZXM  C11  N10  C7   123.06  3.000
 ZXM  O18  C11  C12  121.42  3.000
 ZXM  O18  C11  N10  123.44  3.000
 ZXM  C12  C11  N10  115.13  3.000
 ZXM  H8   C12  H7   106.13  3.000
 ZXM  H8   C12  C13  110.10  3.000
 ZXM  H7   C12  C13  108.74  3.000
 ZXM  H8   C12  C11  106.32  3.000
 ZXM  H7   C12  C11  111.48  3.000
 ZXM  C13  C12  C11  113.78  3.000
 ZXM  S24  C13  C14  110.66  3.000
 ZXM  S24  C13  C12  122.65  3.000
 ZXM  C14  C13  C12  126.61  3.000
 ZXM  H9   C14  C15  123.97  3.000
 ZXM  H9   C14  C13  122.77  3.000
 ZXM  C15  C14  C13  113.26  3.000
 ZXM  H10  C15  C16  123.72  3.000
 ZXM  H10  C15  C14  123.98  3.000
 ZXM  C16  C15  C14  112.29  3.000
 ZXM  H11  C16  S24  120.31  3.000
 ZXM  H11  C16  C15  127.99  3.000
 ZXM  S24  C16  C15  111.66  3.000
 ZXM  C21  C19  C20  127.65  3.000
 ZXM  C21  C19  N6   124.90  3.000
 ZXM  C20  C19  N6   107.44  3.000
 ZXM  H12  C20  C19  132.71  3.000
 ZXM  H12  C20  N4   122.86  3.000
 ZXM  C19  C20  N4   104.42  3.000
 ZXM  O23  C21  O22  128.12  3.000
 ZXM  O23  C21  C19  116.94  3.000
 ZXM  O22  C21  C19  114.94  3.000
 ZXM  C16  S24  C13   92.11  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
 ZXM  CONST_01  N6   C19  C20  N4      0.00   0.0  0
 ZXM  CONST_02  C19  N6   N5   N4      0.00   0.0  0
 ZXM  CONST_03  C19  C20  N4   N5      0.00   0.0  0
 ZXM  CONST_04  C20  C19  N6   N5      0.00   0.0  0
 ZXM  CONST_05  C20  N4   N5   N6      0.00   0.0  0
 ZXM  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 ZXM  CONST_07  C15  C16  S24  C13     0.00   0.0  0
 ZXM  CONST_08  C16  S24  C13  C14     0.00   0.0  0
 ZXM  CONST_09  S24  C16  C15  C14     0.00   0.0  0
 ZXM  CONST_10  S24  C13  C14  C15     0.00   0.0  0
 ZXM  CONST_11  C21  C19  C20  N4    180.00   0.0  0
 ZXM  CONST_12  C21  C19  N6   N5    180.00   0.0  0
 ZXM  CONST_13  C8   N4   N5   N6    180.00   0.0  0
 ZXM  CONST_14  C19  C20  N4   C8    180.00   0.0  0
 ZXM  CONST_15  C15  C14  C13  C12   180.00   0.0  0
 ZXM  CONST_16  C16  S24  C13  C12   180.00   0.0  0
 ZXM  CONST_17  H12  C20  N4   N5    180.00   0.0  0
 ZXM  CONST_18  H10  C15  C14  C13   180.00   0.0  0
 ZXM  CONST_19  H11  C16  S24  C13   180.00   0.0  0
 ZXM  CONST_20  H9   C14  C15  C16   180.00   0.0  0
 ZXM  CONST_21  C12  C11  N10  C7    180.00   0.0  0
 ZXM  CONST_22  O18  C11  N10  C7      0.00   0.0  0
 ZXM  CONST_23  H6   N10  C11  C12     0.00   0.0  0
 ZXM  Var_01    C7   C8   N4   N5    -55.19  30.0  2
 ZXM  Var_02    O22  C21  C19  N6   -179.78  30.0  2
 ZXM  Var_03    C14  C13  C12  C11   135.60  30.0  2
 ZXM  Var_04    C13  C12  C11  N10  -142.28  30.0  1

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
 ZXM  chir_01  C7  N10  C8  B1  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
 ZXM  plan-1  C12  0.020
 ZXM  plan-1  C13  0.020
 ZXM  plan-1  C14  0.020
 ZXM  plan-1  C15  0.020
 ZXM  plan-1  C16  0.020
 ZXM  plan-1  S24  0.020
 ZXM  plan-1  H9   0.020
 ZXM  plan-1  H10  0.020
 ZXM  plan-1  H11  0.020
 ZXM  plan-2  N4   0.020
 ZXM  plan-2  N5   0.020
 ZXM  plan-2  N6   0.020
 ZXM  plan-2  C8   0.020
 ZXM  plan-2  C19  0.020
 ZXM  plan-2  C20  0.020
 ZXM  plan-2  C21  0.020
 ZXM  plan-2  H12  0.020
 ZXM  plan-3  C7   0.020
 ZXM  plan-3  N10  0.020
 ZXM  plan-3  C11  0.020
 ZXM  plan-3  C12  0.020
 ZXM  plan-3  O18  0.020
 ZXM  plan-3  H6   0.020
 ZXM  plan-4  C19  0.020
 ZXM  plan-4  C21  0.020
 ZXM  plan-4  O22  0.020
 ZXM  plan-4  O23  0.020

