# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 00:45:25 2022
#   Inital geometry file: a 135 line input string
#   Ligand name: [(1R)-4-phenyl-1-{[N-(pyrazine-2-carbonyl)-D-norvalyl]amino}butyl]boronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@@H](NC(=O)c1cnccn1)C(=O)N[C@@H](CCCc2ccccc2)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
 UKS  UKS  '[(1R)-4-phenyl-1-{[N-(pyrazine-2-carbonyl)-D-norvalyl]amino}butyl]boronic acid'  ligand  56  29  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_UKS
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
 UKS  C2   C  CH1   0  -0.147  22.4372  331.7960  73.1468
 UKS  C3   C  C     0   0.557  23.3320  332.6598  72.2642
 UKS  C11  C  CH2   0  -0.424  23.6978  331.1716  68.4699
 UKS  C14  C  CR6   0   0.070  21.1841  334.2941  75.6589
 UKS  C17  C  CR16  0  -0.106  21.2508  334.1438  77.9155
 UKS  C18  C  CR16  0  -0.086  20.6353  335.3875  78.0108
 UKS  C20  C  CR16  0  -0.057  20.5703  335.5369  75.7565
 UKS  C21  C  CH2   0  -0.440  23.5774  329.6518  72.3327
 UKS  C22  C  CH3   0  -0.658  24.1505  328.3110  72.7697
 UKS  C23  C  CH2   0  -0.509  23.4165  330.6125  67.0728
 UKS  C24  C  CR6   0   0.127  24.3663  331.1292  66.0276
 UKS  C25  C  CR16  0  -0.301  25.6829  330.6706  65.9868
 UKS  C26  C  CR16  0  -0.239  26.5794  331.1546  65.0451
 UKS  C27  C  CR16  0  -0.272  26.1726  332.1116  64.1227
 UKS  C28  C  CR16  0  -0.239  24.8654  332.5764  64.1522
 UKS  C29  C  CR16  0  -0.310  23.9719  332.0878  65.0979
 UKS  B9   B  B     0   0.528  23.8212  334.8633  70.0182
 UKS  C10  C  CH2   0  -0.482  23.4865  332.6790  68.5686
 UKS  C4   C  CH2   0  -0.460  23.1740  330.5086  73.5252
 UKS  C7   C  C     0   0.550  21.4810  333.7002  74.3153
 UKS  C8   C  CH1   0  -0.267  23.8712  333.2622  69.9243
 UKS  N1   N  NH1   0  -0.660  22.0825  332.5083  74.3483
 UKS  N16  N  N     0  -0.378  21.5216  333.6040  76.7407
 UKS  N19  N  N     0  -0.348  20.2972  336.0810  76.9347
 UKS  N6   N  NH1   0  -0.628  23.0393  332.6526  70.9690
 UKS  O13  O  OH1   0  -0.643  24.1167  335.5024  71.1773
 UKS  O15  O  O     0  -0.469  21.1850  334.2851  73.2834
 UKS  O5   O  O     0  -0.525  24.2939  333.2637  72.7432
 UKS  H1   H  HCH1  0   0.276  21.5287  331.5270  72.5957
 UKS  H2   H  HCH2  0   0.232  23.0519  330.6470  69.1789
 UKS  H3   H  HCH2  0   0.222  24.7258  330.9304  68.7600
 UKS  H4   H  HCR6  0   0.285  21.5238  333.5865  78.8029
 UKS  H5   H  HCR6  0   0.287  20.4165  335.8214  78.9790
 UKS  H6   H  HCR6  0   0.283  20.2961  336.0973  74.8720
 UKS  H7   H  HCH2  0   0.230  24.3184  330.1749  71.7224
 UKS  H8   H  HCH2  0   0.225  22.7102  329.4884  71.6863
 UKS  H9   H  HCH3  0   0.231  24.4465  327.7094  71.9103
 UKS  H10  H  HCH3  0   0.220  25.0324  328.4452  73.3983
 UKS  H11  H  HCH3  0   0.221  23.4207  327.7367  73.3426
 UKS  H12  H  HCH2  0   0.238  22.3883  330.8510  66.7882
 UKS  H13  H  HCH2  0   0.247  23.4816  329.5222  67.1144
 UKS  H14  H  HCR6  0   0.244  26.0088  329.9213  66.6999
 UKS  H15  H  HCR6  0   0.249  27.5959  330.7820  65.0281
 UKS  H16  H  HCR6  0   0.250  26.8696  332.4896  63.3857
 UKS  H17  H  HCR6  0   0.249  24.5378  333.3211  63.4377
 UKS  H18  H  HCR6  0   0.245  22.9524  332.4560  65.1129
 UKS  H19  H  HCH2  0   0.246  24.0916  333.1793  67.8100
 UKS  H20  H  HCH2  0   0.227  22.4447  332.9226  68.3323
 UKS  H21  H  HCH2  0   0.251  22.5147  329.9295  74.1788
 UKS  H22  H  HCH2  0   0.241  24.0583  330.7646  74.1162
 UKS  H23  H  HCH1  0   0.254  24.9066  332.9522  70.1246
 UKS  H24  H  HNH1  0   0.414  22.2997  332.1060  75.2488
 UKS  H25  H  HNH1  0   0.407  22.1804  332.2097  70.6792
 UKS  H26  H  HOH1  0   0.483  23.5075  336.5308  69.0456
 UKS  H27  H  HOH1  0   0.479  24.3371  334.8595  71.8779
 UKS  O12  O  OH1   0  -0.620  23.4995  335.5772  68.9083

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
 UKS  C28  C27  aromatic  1.388  0.020  1.388
 UKS  C28  C29  aromatic  1.390  0.020  1.390
 UKS  C27  C26  aromatic  1.390  0.020  1.390
 UKS  C29  C24  aromatic  1.392  0.020  1.392
 UKS  C26  C25  aromatic  1.387  0.020  1.387
 UKS  C24  C25  aromatic  1.395  0.020  1.395
 UKS  C24  C23  single    1.504  0.020  1.504
 UKS  C23  C11  single    1.531  0.020  1.531
 UKS  C10  C11  single    1.525  0.020  1.525
 UKS  C10  C8   single    1.525  0.020  1.525
 UKS  B9   O12  single    1.358  0.020  1.358
 UKS  B9   C8   single    1.605  0.020  1.605
 UKS  B9   O13  single    1.356  0.020  1.356
 UKS  C8   N6   single    1.468  0.020  1.468
 UKS  N6   C3   single    1.328  0.020  1.328
 UKS  C21  C22  single    1.522  0.020  1.522
 UKS  C21  C4   single    1.523  0.020  1.523
 UKS  C3   O5   double    1.233  0.020  1.233
 UKS  C3   C2   single    1.525  0.020  1.525
 UKS  C2   C4   single    1.531  0.020  1.531
 UKS  C2   N1   single    1.441  0.020  1.441
 UKS  O15  C7   double    1.223  0.020  1.223
 UKS  N1   C7   single    1.335  0.020  1.335
 UKS  C7   C14  single    1.499  0.020  1.499
 UKS  C14  C20  aromatic  1.390  0.020  1.390
 UKS  C14  N16  aromatic  1.327  0.020  1.327
 UKS  C20  N19  aromatic  1.326  0.020  1.326
 UKS  N16  C17  aromatic  1.321  0.020  1.321
 UKS  N19  C18  aromatic  1.324  0.020  1.324
 UKS  C17  C18  aromatic  1.391  0.020  1.391
 UKS  C2   H1   single    0.970  0.020  1.090
 UKS  C11  H2   single    0.970  0.020  1.090
 UKS  C11  H3   single    0.970  0.020  1.090
 UKS  C17  H4   single    0.930  0.020  1.080
 UKS  C18  H5   single    0.930  0.020  1.080
 UKS  C20  H6   single    0.930  0.020  1.080
 UKS  C21  H7   single    0.970  0.020  1.090
 UKS  C21  H8   single    0.970  0.020  1.090
 UKS  C22  H9   single    0.970  0.020  1.090
 UKS  C22  H10  single    0.970  0.020  1.090
 UKS  C22  H11  single    0.970  0.020  1.090
 UKS  C23  H12  single    0.970  0.020  1.090
 UKS  C23  H13  single    0.970  0.020  1.090
 UKS  C25  H14  single    0.930  0.020  1.080
 UKS  C26  H15  single    0.930  0.020  1.080
 UKS  C27  H16  single    0.930  0.020  1.080
 UKS  C28  H17  single    0.930  0.020  1.080
 UKS  C29  H18  single    0.930  0.020  1.080
 UKS  C10  H19  single    0.970  0.020  1.090
 UKS  C10  H20  single    0.970  0.020  1.090
 UKS  C4   H21  single    0.970  0.020  1.090
 UKS  C4   H22  single    0.970  0.020  1.090
 UKS  C8   H23  single    0.970  0.020  1.090
 UKS  N1   H24  single    0.860  0.020  1.020
 UKS  N6   H25  single    0.860  0.020  1.020
 UKS  O12  H26  single    0.850  0.020  0.980
 UKS  O13  H27  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
 UKS  H1   C2   N1   109.66  3.000
 UKS  H1   C2   C4   108.48  3.000
 UKS  N1   C2   C4   109.15  3.000
 UKS  H1   C2   C3   109.53  3.000
 UKS  N1   C2   C3   110.30  3.000
 UKS  C4   C2   C3   109.69  3.000
 UKS  O5   C3   N6   123.62  3.000
 UKS  O5   C3   C2   120.70  3.000
 UKS  N6   C3   C2   115.60  3.000
 UKS  H3   C11  H2   106.08  3.000
 UKS  H3   C11  C10  109.31  3.000
 UKS  H2   C11  C10  110.51  3.000
 UKS  H3   C11  C23  109.50  3.000
 UKS  H2   C11  C23  107.94  3.000
 UKS  C10  C11  C23  113.24  3.000
 UKS  N16  C14  C7   118.33  3.000
 UKS  N16  C14  C20  121.35  3.000
 UKS  C7   C14  C20  120.33  3.000
 UKS  H4   C17  N16  117.83  3.000
 UKS  H4   C17  C18  121.04  3.000
 UKS  N16  C17  C18  121.14  3.000
 UKS  H5   C18  N19  117.71  3.000
 UKS  H5   C18  C17  120.59  3.000
 UKS  N19  C18  C17  121.71  3.000
 UKS  H6   C20  N19  117.48  3.000
 UKS  H6   C20  C14  121.17  3.000
 UKS  N19  C20  C14  121.35  3.000
 UKS  H8   C21  H7   106.20  3.000
 UKS  H8   C21  C4   109.68  3.000
 UKS  H7   C21  C4   110.33  3.000
 UKS  H8   C21  C22  109.67  3.000
 UKS  H7   C21  C22  109.06  3.000
 UKS  C4   C21  C22  111.75  3.000
 UKS  H11  C22  H10  107.63  3.000
 UKS  H11  C22  H9   107.77  3.000
 UKS  H10  C22  H9   107.61  3.000
 UKS  H11  C22  C21  111.25  3.000
 UKS  H10  C22  C21  111.18  3.000
 UKS  H9   C22  C21  111.22  3.000
 UKS  H13  C23  H12  106.48  3.000
 UKS  H13  C23  C24  109.36  3.000
 UKS  H12  C23  C24  109.77  3.000
 UKS  H13  C23  C11  108.58  3.000
 UKS  H12  C23  C11  109.31  3.000
 UKS  C24  C23  C11  113.12  3.000
 UKS  C29  C24  C25  118.31  3.000
 UKS  C25  C24  C23  120.24  3.000
 UKS  C29  C24  C23  121.44  3.000
 UKS  H14  C25  C26  119.55  3.000
 UKS  H14  C25  C24  119.44  3.000
 UKS  C26  C25  C24  121.01  3.000
 UKS  H15  C26  C27  120.08  3.000
 UKS  H15  C26  C25  119.82  3.000
 UKS  C27  C26  C25  120.10  3.000
 UKS  H16  C27  C28  120.26  3.000
 UKS  H16  C27  C26  120.25  3.000
 UKS  C28  C27  C26  119.48  3.000
 UKS  H17  C28  C29  119.75  3.000
 UKS  H17  C28  C27  120.09  3.000
 UKS  C29  C28  C27  120.15  3.000
 UKS  H18  C29  C28  119.64  3.000
 UKS  H18  C29  C24  119.41  3.000
 UKS  C28  C29  C24  120.95  3.000
 UKS  O13  B9   O12  120.15  3.000
 UKS  O13  B9   C8   120.89  3.000
 UKS  O12  B9   C8   118.94  3.000
 UKS  H20  C10  H19  105.98  3.000
 UKS  H20  C10  C8   110.28  3.000
 UKS  H19  C10  C8   107.62  3.000
 UKS  H20  C10  C11  109.73  3.000
 UKS  H19  C10  C11  109.33  3.000
 UKS  C8   C10  C11  113.61  3.000
 UKS  H22  C4   H21  106.75  3.000
 UKS  H22  C4   C21  109.91  3.000
 UKS  H21  C4   C21  109.25  3.000
 UKS  H22  C4   C2   109.01  3.000
 UKS  H21  C4   C2   107.62  3.000
 UKS  C21  C4   C2   114.02  3.000
 UKS  O15  C7   N1   123.84  3.000
 UKS  N1   C7   C14  114.88  3.000
 UKS  O15  C7   C14  121.28  3.000
 UKS  H23  C8   N6   106.68  3.000
 UKS  H23  C8   C10  106.96  3.000
 UKS  N6   C8   C10  109.32  3.000
 UKS  H23  C8   B9   107.46  3.000
 UKS  N6   C8   B9   110.79  3.000
 UKS  C10  C8   B9   115.20  3.000
 UKS  H24  N1   C7   118.32  3.000
 UKS  H24  N1   C2   119.58  3.000
 UKS  C7   N1   C2   122.10  3.000
 UKS  C17  N16  C14  117.42  3.000
 UKS  C20  N19  C18  117.04  3.000
 UKS  H25  N6   C8   117.41  3.000
 UKS  H25  N6   C3   118.05  3.000
 UKS  C8   N6   C3   124.54  3.000
 UKS  H27  O13  B9   110.63  3.000
 UKS  H26  O12  B9   113.69  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
 UKS  CONST_01  C18  N19  C20  C14     0.00   0.0  0
 UKS  CONST_02  C18  C17  N16  C14     0.00   0.0  0
 UKS  CONST_03  C20  C14  N16  C17     0.00   0.0  0
 UKS  CONST_04  C20  N19  C18  C17     0.00   0.0  0
 UKS  CONST_05  C27  C28  C29  C24     0.00   0.0  0
 UKS  CONST_06  C27  C26  C25  C24     0.00   0.0  0
 UKS  CONST_07  C28  C27  C26  C25     0.00   0.0  0
 UKS  CONST_08  C28  C29  C24  C25     0.00   0.0  0
 UKS  CONST_09  C29  C28  C27  C26     0.00   0.0  0
 UKS  CONST_10  C29  C24  C25  C26     0.00   0.0  0
 UKS  CONST_11  N19  C20  C14  N16     0.00   0.0  0
 UKS  CONST_12  N19  C18  C17  N16     0.00   0.0  0
 UKS  CONST_13  C7   C14  N16  C17   180.00   0.0  0
 UKS  CONST_14  C28  C29  C24  C23   180.00   0.0  0
 UKS  CONST_15  C26  C25  C24  C23   180.00   0.0  0
 UKS  CONST_16  N19  C20  C14  C7    180.00   0.0  0
 UKS  CONST_17  H4   C17  N16  C14   180.00   0.0  0
 UKS  CONST_18  H6   C20  N19  C18   180.00   0.0  0
 UKS  CONST_19  H5   C18  N19  C20   180.00   0.0  0
 UKS  CONST_20  H17  C28  C29  C24   180.00   0.0  0
 UKS  CONST_21  H15  C26  C25  C24   180.00   0.0  0
 UKS  CONST_22  H16  C27  C26  C25   180.00   0.0  0
 UKS  CONST_23  H18  C29  C24  C25   180.00   0.0  0
 UKS  CONST_24  H14  C25  C26  C27   180.00   0.0  0
 UKS  CONST_25  C14  C7   N1   C2    180.00   0.0  0
 UKS  CONST_26  H24  N1   C7   C14     0.00   0.0  0
 UKS  CONST_27  C8   N6   C3   C2    180.00   0.0  0
 UKS  CONST_28  O15  C7   N1   C2      0.00   0.0  0
 UKS  CONST_29  O5   C3   N6   C8      0.00   0.0  0
 UKS  CONST_30  H25  N6   C3   C2      0.00   0.0  0
 UKS  Var_01    C29  C24  C23  C11  -105.15  30.0  3
 UKS  Var_02    O15  C7   C14  C20    -0.50  30.0  2
 UKS  Var_03    C10  C11  C23  C24    64.64  30.0  3
 UKS  Var_04    C22  C21  C4   C2   -173.02  30.0  1
 UKS  Var_05    C8   C10  C11  C23  -175.36  30.0  1
 UKS  Var_06    H9   C22  C21  C4   -179.37  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
 UKS  chir_01  C2  C3  C4   N1  negativ
 UKS  chir_02  C8  N6  C10  B9  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
 UKS  plan-1  C14  0.020
 UKS  plan-1  C17  0.020
 UKS  plan-1  C18  0.020
 UKS  plan-1  C20  0.020
 UKS  plan-1  C7   0.020
 UKS  plan-1  N16  0.020
 UKS  plan-1  N19  0.020
 UKS  plan-1  H4   0.020
 UKS  plan-1  H5   0.020
 UKS  plan-1  H6   0.020
 UKS  plan-2  C23  0.020
 UKS  plan-2  C24  0.020
 UKS  plan-2  C25  0.020
 UKS  plan-2  C26  0.020
 UKS  plan-2  C27  0.020
 UKS  plan-2  C28  0.020
 UKS  plan-2  C29  0.020
 UKS  plan-2  H14  0.020
 UKS  plan-2  H15  0.020
 UKS  plan-2  H16  0.020
 UKS  plan-2  H17  0.020
 UKS  plan-2  H18  0.020
 UKS  plan-3  C2   0.020
 UKS  plan-3  C3   0.020
 UKS  plan-3  C8   0.020
 UKS  plan-3  N6   0.020
 UKS  plan-3  O5   0.020
 UKS  plan-3  H25  0.020
 UKS  plan-4  C2   0.020
 UKS  plan-4  C14  0.020
 UKS  plan-4  C7   0.020
 UKS  plan-4  N1   0.020
 UKS  plan-4  O15  0.020
 UKS  plan-4  H24  0.020

