# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 22:13:30 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: (3~{R})-3-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCN[C@@H]1CC[C@H](CC1)CC(=O)N[C@H]2Cc3cccc(C(O)=O)c3OB2O
#
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
 KJK  KJK  '(3~{R})-3-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid'  ligand  56  28  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KJK
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
 KJK  B07  B  B     0   0.531   2.2059   0.5762  -1.0670
 KJK  C10  C  CR6   0   0.405   4.3963   0.1927  -0.1876
 KJK  C11  C  CR6   0  -0.174   5.6200   0.7753   0.1552
 KJK  C12  C  C     0   0.521   5.9455   2.1691  -0.2408
 KJK  C15  C  CR16  0  -0.272   6.5253   0.0384   0.9219
 KJK  C16  C  CR16  0  -0.247   6.2088  -1.2348   1.3565
 KJK  C17  C  CR16  0  -0.314   4.9869  -1.7941   1.0097
 KJK  C18  C  CR6   0   0.040   4.0737  -1.1009   0.2293
 KJK  C19  C  CH2   0  -0.522   2.7628  -1.7032  -0.1870
 KJK  C20  C  CH1   0  -0.264   1.6643  -0.6311  -0.2107
 KJK  C23  C  CH2   0  -0.562  -1.7066  -2.3309  -0.5498
 KJK  C24  C  CH1   0  -0.229  -2.9814  -1.7689   0.0799
 KJK  C25  C  CH2   0  -0.422  -4.2120  -2.4415  -0.5234
 KJK  C26  C  CH2   0  -0.454  -5.5068  -1.8847   0.0536
 KJK  C27  C  CH1   0  -0.022  -5.6018  -0.3738  -0.1287
 KJK  C30  C  CH2   0  -0.299  -8.5318   1.8565   0.7038
 KJK  C32  C  CH2   0  -0.435  -4.3796   0.2966   0.4942
 KJK  C33  C  CH2   0  -0.425  -3.0786  -0.2530  -0.0809
 KJK  N21  N  NH1   0  -0.651   0.3960  -1.1406  -0.6699
 KJK  N28  N  NH1   0  -0.617  -6.8356   0.1132   0.4699
 KJK  N31  N  NH2   0  -0.803  -8.9445   3.1710   0.2368
 KJK  O08  O  OH1   0  -0.585   1.4132   1.2983  -1.8798
 KJK  O09  O  O2    0  -0.461   3.5429   0.8830  -0.9801
 KJK  O13  O  O     0  -0.427   5.1395   3.0475  -0.4195
 KJK  O14  O  OH1   0  -0.594   7.2563   2.3554  -0.3593
 KJK  H1   H  HCR6  0   0.272   7.4749   0.4736   1.2001
 KJK  H2   H  HCR6  0   0.265   6.9084  -1.7891   1.9664
 KJK  H3   H  HCR6  0   0.264   4.7361  -2.7923   1.3476
 KJK  H4   H  HCH2  0   0.264   2.8611  -2.1456  -1.1850
 KJK  H5   H  HCH2  0   0.268   2.4954  -2.5157   0.4899
 KJK  H6   H  HCH1  0   0.277   1.5339  -0.2644   0.8160
 KJK  H7   H  HCH2  0   0.241  -1.7002  -2.1144  -1.6221
 KJK  H8   H  HCH2  0   0.266  -1.7045  -3.4207  -0.4507
 KJK  H9   H  HCH1  0   0.223  -2.9604  -1.9984   1.1521
 KJK  H10  H  HCH2  0   0.211  -4.2055  -2.2956  -1.6101
 KJK  H11  H  HCH2  0   0.232  -4.1637  -3.5214  -0.3585
 KJK  H12  H  HCH2  0   0.229  -6.3640  -2.3691  -0.4246
 KJK  H13  H  HCH2  0   0.215  -5.5704  -2.1176   1.1226
 KJK  H14  H  HCH1  0   0.179  -5.5805  -0.1672  -1.2154
 KJK  H15  H  HCH2  0   0.184  -7.3427   1.5082  -1.0579
 KJK  H16  H  HCH2  0   0.220  -6.4535   2.1591   0.3105
 KJK  H17  H  HCH2  0   0.190  -9.2863   1.0732   0.5341
 KJK  H18  H  HCH2  0   0.218  -8.3750   1.9036   1.7839
 KJK  H19  H  HCH2  0   0.232  -4.4147   1.3787   0.3437
 KJK  H20  H  HCH2  0   0.210  -4.4061   0.1303   1.5768
 KJK  H21  H  HCH2  0   0.235  -2.2316   0.2395   0.4047
 KJK  H22  H  HCH2  0   0.210  -3.0109   0.0006  -1.1459
 KJK  H23  H  HNH1  0   0.401   0.1629  -1.0495  -1.6451
 KJK  H24  H  HNH1  0   0.336  -7.5807  -0.5292   0.2233
 KJK  H26  H  HNH2  0   0.339  -9.2406   3.1058  -0.7294
 KJK  H27  H  HNH2  0   0.349  -9.7633   3.4686   0.7509
 KJK  H29  H  HOH1  0   0.500   1.8585   2.0038  -2.3633
 KJK  H30  H  HOH1  0   0.486   7.4373   3.2862  -0.5589
 KJK  C22  C  C     0   0.543  -0.4550  -1.8150   0.1234
 KJK  C29  C  CH2   0  -0.271  -7.2300   1.4402   0.0380
 KJK  O34  O  O     0  -0.503  -0.2449  -1.9956   1.3166

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
 KJK  C33  C32  single    1.525  0.020  1.525
 KJK  C33  C24  single    1.528  0.020  1.528
 KJK  C32  C27  single    1.527  0.020  1.527
 KJK  C23  C24  single    1.529  0.020  1.529
 KJK  C23  C22  single    1.512  0.020  1.512
 KJK  C27  N28  single    1.455  0.020  1.455
 KJK  C27  C26  single    1.525  0.020  1.525
 KJK  C24  C25  single    1.527  0.020  1.527
 KJK  N28  C29  single    1.450  0.020  1.450
 KJK  C25  C26  single    1.523  0.020  1.523
 KJK  C29  C30  single    1.520  0.020  1.520
 KJK  O08  B07  single    1.346  0.020  1.346
 KJK  C22  N21  single    1.345  0.020  1.345
 KJK  C22  O34  double    1.225  0.020  1.225
 KJK  O13  C12  double    1.205  0.020  1.205
 KJK  N21  C20  single    1.442  0.020  1.442
 KJK  C30  N31  single    1.455  0.020  1.455
 KJK  B07  C20  single    1.576  0.020  1.576
 KJK  B07  O09  single    1.375  0.020  1.375
 KJK  C20  C19  single    1.535  0.020  1.535
 KJK  C12  C11  single    1.485  0.020  1.485
 KJK  C12  O14  single    1.329  0.020  1.329
 KJK  O09  C10  single    1.354  0.020  1.354
 KJK  C11  C10  aromatic  1.398  0.020  1.398
 KJK  C11  C15  aromatic  1.397  0.020  1.397
 KJK  C10  C18  aromatic  1.397  0.020  1.397
 KJK  C15  C16  aromatic  1.382  0.020  1.382
 KJK  C18  C19  single    1.501  0.020  1.501
 KJK  C18  C17  aromatic  1.387  0.020  1.387
 KJK  C16  C17  aromatic  1.388  0.020  1.388
 KJK  C15  H1   single    0.930  0.020  1.080
 KJK  C16  H2   single    0.930  0.020  1.080
 KJK  C17  H3   single    0.930  0.020  1.080
 KJK  C19  H4   single    0.970  0.020  1.090
 KJK  C19  H5   single    0.970  0.020  1.090
 KJK  C20  H6   single    0.970  0.020  1.090
 KJK  C23  H7   single    0.970  0.020  1.090
 KJK  C23  H8   single    0.970  0.020  1.090
 KJK  C24  H9   single    0.970  0.020  1.090
 KJK  C25  H10  single    0.970  0.020  1.090
 KJK  C25  H11  single    0.970  0.020  1.090
 KJK  C26  H12  single    0.970  0.020  1.090
 KJK  C26  H13  single    0.970  0.020  1.090
 KJK  C27  H14  single    0.970  0.020  1.090
 KJK  C29  H15  single    0.970  0.020  1.090
 KJK  C29  H16  single    0.970  0.020  1.090
 KJK  C30  H17  single    0.970  0.020  1.090
 KJK  C30  H18  single    0.970  0.020  1.090
 KJK  C32  H19  single    0.970  0.020  1.090
 KJK  C32  H20  single    0.970  0.020  1.090
 KJK  C33  H21  single    0.970  0.020  1.090
 KJK  C33  H22  single    0.970  0.020  1.090
 KJK  N21  H23  single    0.860  0.020  1.020
 KJK  N28  H24  single    0.890  0.020  1.040
 KJK  N31  H26  single    0.890  0.020  1.040
 KJK  N31  H27  single    0.890  0.020  1.040
 KJK  O08  H29  single    0.850  0.020  0.980
 KJK  O14  H30  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
 KJK  O09  B07  O08  119.44  3.000
 KJK  O09  B07  C20  118.09  3.000
 KJK  O08  B07  C20  122.47  3.000
 KJK  O09  C10  C18  120.09  3.000
 KJK  C18  C10  C11  120.99  3.000
 KJK  O09  C10  C11  118.87  3.000
 KJK  C15  C11  C12  119.97  3.000
 KJK  C15  C11  C10  118.83  3.000
 KJK  C12  C11  C10  121.17  3.000
 KJK  O14  C12  O13  122.95  3.000
 KJK  O14  C12  C11  111.81  3.000
 KJK  O13  C12  C11  125.23  3.000
 KJK  H1   C15  C16  119.41  3.000
 KJK  H1   C15  C11  119.89  3.000
 KJK  C16  C15  C11  120.68  3.000
 KJK  H2   C16  C17  120.27  3.000
 KJK  H2   C16  C15  120.11  3.000
 KJK  C17  C16  C15  119.62  3.000
 KJK  H3   C17  C18  118.93  3.000
 KJK  H3   C17  C16  119.81  3.000
 KJK  C18  C17  C16  121.26  3.000
 KJK  C19  C18  C17  122.03  3.000
 KJK  C17  C18  C10  118.60  3.000
 KJK  C19  C18  C10  119.36  3.000
 KJK  H5   C19  H4   106.64  3.000
 KJK  H5   C19  C20  110.75  3.000
 KJK  H4   C19  C20  109.39  3.000
 KJK  H5   C19  C18  109.92  3.000
 KJK  H4   C19  C18  109.64  3.000
 KJK  C20  C19  C18  110.42  3.000
 KJK  H6   C20  N21  108.14  3.000
 KJK  H6   C20  C19  107.68  3.000
 KJK  N21  C20  C19  112.80  3.000
 KJK  H6   C20  B07  107.04  3.000
 KJK  C19  C20  B07  107.30  3.000
 KJK  N21  C20  B07  113.57  3.000
 KJK  H8   C23  H7   106.61  3.000
 KJK  H8   C23  C24  109.29  3.000
 KJK  H7   C23  C24  109.63  3.000
 KJK  H8   C23  C22  107.33  3.000
 KJK  H7   C23  C22  111.35  3.000
 KJK  C24  C23  C22  112.42  3.000
 KJK  H9   C24  C33  108.17  3.000
 KJK  H9   C24  C25  108.03  3.000
 KJK  C33  C24  C25  110.14  3.000
 KJK  H9   C24  C23  108.05  3.000
 KJK  C25  C24  C23  110.33  3.000
 KJK  C33  C24  C23  111.99  3.000
 KJK  H11  C25  H10  106.29  3.000
 KJK  H11  C25  C26  109.97  3.000
 KJK  H10  C25  C26  109.39  3.000
 KJK  H11  C25  C24  109.87  3.000
 KJK  H10  C25  C24  109.16  3.000
 KJK  C26  C25  C24  112.00  3.000
 KJK  H13  C26  H12  106.66  3.000
 KJK  H13  C26  C27  108.88  3.000
 KJK  H12  C26  C27  109.72  3.000
 KJK  H13  C26  C25  109.95  3.000
 KJK  H12  C26  C25  109.78  3.000
 KJK  C27  C26  C25  111.71  3.000
 KJK  H14  C27  N28  110.97  3.000
 KJK  H14  C27  C32  107.66  3.000
 KJK  N28  C27  C32  111.34  3.000
 KJK  H14  C27  C26  107.53  3.000
 KJK  N28  C27  C26  109.59  3.000
 KJK  C32  C27  C26  109.66  3.000
 KJK  H18  C30  H17  106.35  3.000
 KJK  H18  C30  N31  108.61  3.000
 KJK  H17  C30  N31  113.51  3.000
 KJK  H18  C30  C29  108.78  3.000
 KJK  H17  C30  C29  108.94  3.000
 KJK  N31  C30  C29  110.47  3.000
 KJK  H20  C32  H19  106.59  3.000
 KJK  H20  C32  C33  109.79  3.000
 KJK  H19  C32  C33  109.41  3.000
 KJK  H20  C32  C27  108.49  3.000
 KJK  H19  C32  C27  110.66  3.000
 KJK  C33  C32  C27  111.77  3.000
 KJK  H22  C33  H21  106.22  3.000
 KJK  H22  C33  C32  109.60  3.000
 KJK  H21  C33  C32  109.33  3.000
 KJK  H22  C33  C24  109.13  3.000
 KJK  H21  C33  C24  110.54  3.000
 KJK  C32  C33  C24  111.85  3.000
 KJK  H23  N21  C22  118.05  3.000
 KJK  H23  N21  C20  118.70  3.000
 KJK  C22  N21  C20  123.09  3.000
 KJK  H24  N28  C29  107.90  3.000
 KJK  H24  N28  C27  108.11  3.000
 KJK  C29  N28  C27  114.48  3.000
 KJK  H27  N31  H26  105.50  3.000
 KJK  H27  N31  C30  109.41  3.000
 KJK  H26  N31  C30  109.33  3.000
 KJK  H29  O08  B07  115.05  3.000
 KJK  C10  O09  B07  122.44  3.000
 KJK  H30  O14  C12  109.71  3.000
 KJK  O34  C22  N21  122.69  3.000
 KJK  O34  C22  C23  121.70  3.000
 KJK  N21  C22  C23  115.62  3.000
 KJK  H16  C29  H15  106.24  3.000
 KJK  H16  C29  N28  109.54  3.000
 KJK  H15  C29  N28  112.33  3.000
 KJK  H16  C29  C30  108.61  3.000
 KJK  H15  C29  C30  109.30  3.000
 KJK  N28  C29  C30  110.67  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
 KJK  CONST_01  C16  C15  C11  C10     0.00   0.0  0
 KJK  CONST_02  C16  C17  C18  C10     0.00   0.0  0
 KJK  CONST_03  C17  C18  C10  C11     0.00   0.0  0
 KJK  CONST_04  C17  C16  C15  C11     0.00   0.0  0
 KJK  CONST_05  C18  C10  C11  C15     0.00   0.0  0
 KJK  CONST_06  C18  C17  C16  C15     0.00   0.0  0
 KJK  CONST_07  O09  C10  C11  C12     0.00   0.0  0
 KJK  CONST_08  C18  C10  C11  C12   180.00   0.0  0
 KJK  CONST_09  C16  C15  C11  C12   180.00   0.0  0
 KJK  CONST_10  H1   C15  C11  C10   180.00   0.0  0
 KJK  CONST_11  H3   C17  C18  C10   180.00   0.0  0
 KJK  CONST_12  H2   C16  C15  C11   180.00   0.0  0
 KJK  CONST_13  C23  C22  N21  C20   180.00   0.0  0
 KJK  CONST_14  O34  C22  N21  C20     0.00   0.0  0
 KJK  CONST_15  H30  O14  C12  C11   180.00   0.0  0
 KJK  CONST_16  H23  N21  C22  C23     0.00   0.0  0
 KJK  Var_01    C11  C10  O09  B07  -161.52  30.0  1
 KJK  Var_02    C20  B07  O09  C10    -0.29  30.0  1
 KJK  Var_03    C20  C19  C18  C10   -36.44  30.0  1
 KJK  Var_04    C27  C32  C33  C24   -56.16  30.0  1
 KJK  Var_05    C27  C26  C25  C24    56.32  30.0  1
 KJK  Var_06    O13  C12  C11  C10    28.10  30.0  2
 KJK  Var_07    N21  C22  C23  C24  -120.37  30.0  3
 KJK  Var_08    C30  C29  N28  C27   179.46  30.0  3
 KJK  Var_09    N31  C30  C29  N28  -178.28  30.0  3
 KJK  Var_10    H26  N31  C30  C29    70.10  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
 KJK  chir_01  C20  N21  B07  C19  positiv
 KJK  chir_02  C24  C33  C23  C25  positiv
 KJK  chir_03  C27  N28  C26  C32  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
 KJK  plan-1  C20  0.020
 KJK  plan-1  C23  0.020
 KJK  plan-1  N21  0.020
 KJK  plan-1  H23  0.020
 KJK  plan-1  C22  0.020
 KJK  plan-1  O34  0.020
 KJK  plan-2  C10  0.020
 KJK  plan-2  C11  0.020
 KJK  plan-2  C12  0.020
 KJK  plan-2  C15  0.020
 KJK  plan-2  C16  0.020
 KJK  plan-2  C17  0.020
 KJK  plan-2  C18  0.020
 KJK  plan-2  C19  0.020
 KJK  plan-2  O09  0.020
 KJK  plan-2  H1   0.020
 KJK  plan-2  H2   0.020
 KJK  plan-2  H3   0.020
 KJK  plan-3  C11  0.020
 KJK  plan-3  C12  0.020
 KJK  plan-3  O13  0.020
 KJK  plan-3  O14  0.020
 KJK  plan-3  H30  0.020

