# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 02:27:39 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: N-[(1R)-1-borono-3-methylbutyl]-Nalpha-(pyrazine-2-carbonyl)-D-phenylalaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)[C@@H](Cc1ccccc1)NC(=O)c2cnccn2)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
 UFY  UFY  N-[(1R)-1-borono-3-methylbutyl]-Nalpha-(pyrazine-2-carbonyl)-D-phenylalaninamide  ligand  53  28  .  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_UFY
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
 UFY  C1   C  CR16  0  -0.105  22.7899  334.3601  77.6577
 UFY  C2   C  CR16  0  -0.086  22.4113  335.5904  78.1847
 UFY  C11  C  CH2   0  -0.477  23.0697  334.6922  67.8591
 UFY  C12  C  CH1   0  -0.280  23.5788  335.0520  69.2512
 UFY  C17  C  CH3   0  -0.665  24.5148  332.5949  67.7256
 UFY  C19  C  CH1   0  -0.167  22.3949  333.1890  72.3589
 UFY  C20  C  C     0   0.553  23.2771  334.1001  71.5091
 UFY  C22  C  CH2   0  -0.566  22.8808  331.7413  72.2097
 UFY  C23  C  CR6   0   0.138  21.9419  330.7578  72.8527
 UFY  C24  C  CR16  0  -0.297  20.7205  330.4670  72.2468
 UFY  C25  C  CR16  0  -0.237  19.8307  329.5797  72.8326
 UFY  C26  C  CR16  0  -0.266  20.1509  328.9672  74.0390
 UFY  C27  C  CR16  0  -0.237  21.3651  329.2468  74.6491
 UFY  C28  C  CR16  0  -0.322  22.2542  330.1373  74.0584
 UFY  B14  B  B     0   0.536  23.6013  336.6215  69.5795
 UFY  C4   C  CR16  0  -0.057  21.8019  336.2943  76.1252
 UFY  C5   C  CR6   0   0.069  22.1793  335.0660  75.5968
 UFY  C7   C  C     0   0.550  22.0411  334.7980  74.1293
 UFY  C9   C  CH3   0  -0.674  22.0273  332.3321  67.9423
 UFY  N13  N  NH1   0  -0.633  22.8128  334.3529  70.2882
 UFY  N18  N  NH1   0  -0.651  22.4366  333.5821  73.7403
 UFY  N3   N  N     0  -0.348  21.9194  336.5533  77.4206
 UFY  N6   N  N     0  -0.379  22.6721  334.1048  76.3672
 UFY  O15  O  OH1   0  -0.638  24.0993  337.0704  70.7614
 UFY  O16  O  OH1   0  -0.618  23.1202  337.5066  68.6691
 UFY  O8   O  O     0  -0.466  21.5949  335.6415  73.3659
 UFY  H1   H  HCR6  0   0.285  23.1912  333.5802  78.2928
 UFY  H2   H  HCR6  0   0.287  22.5125  335.7904  79.2445
 UFY  H3   H  HCH2  0   0.242  23.6645  335.2798  67.1553
 UFY  H4   H  HCH2  0   0.231  22.0384  335.0398  67.7351
 UFY  H5   H  HCH1  0   0.256  24.6124  334.6949  69.3376
 UFY  H6   H  HCH3  0   0.230  24.5997  331.6117  67.2601
 UFY  H7   H  HCH3  0   0.225  25.3373  333.2085  67.3528
 UFY  H8   H  HCH3  0   0.217  24.6617  332.4567  68.7993
 UFY  H9   H  HCH1  0   0.288  21.3631  333.2496  71.9955
 UFY  H10  H  HCH2  0   0.289  22.9676  331.5211  71.1436
 UFY  H11  H  HCH2  0   0.276  23.8842  331.6512  72.6329
 UFY  H12  H  HCR6  0   0.251  20.4672  330.9376  71.3030
 UFY  H13  H  HCR6  0   0.254  18.8878  329.3627  72.3471
 UFY  H14  H  HCR6  0   0.254  19.4583  328.2732  74.4973
 UFY  H15  H  HCR6  0   0.254  21.6242  328.7713  75.5864
 UFY  H16  H  HCR6  0   0.252  23.2038  330.3465  74.5378
 UFY  H17  H  HCH1  0   0.223  23.0475  333.2428  66.3319
 UFY  H18  H  HCR6  0   0.283  21.4013  337.0769  75.4936
 UFY  H19  H  HCH3  0   0.224  21.0497  332.7921  67.7851
 UFY  H20  H  HCH3  0   0.229  22.0266  331.3750  67.4181
 UFY  H21  H  HCH3  0   0.221  22.1272  332.1096  69.0053
 UFY  H22  H  HNH1  0   0.410  21.8672  334.0815  70.0676
 UFY  H23  H  HNH1  0   0.416  22.8305  332.9636  74.4346
 UFY  H24  H  HOH1  0   0.475  24.4140  336.3356  71.3134
 UFY  H25  H  HOH1  0   0.483  23.1769  338.4251  68.9548
 UFY  O21  O  O     0  -0.516  24.3633  334.5025  71.9217
 UFY  C10  C  CH1   0  -0.217  23.1573  333.2198  67.4217

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
 UFY  C10  C17  single    1.525  0.020  1.525
 UFY  C10  C11  single    1.538  0.020  1.538
 UFY  C10  C9   single    1.528  0.020  1.528
 UFY  C11  C12  single    1.525  0.020  1.525
 UFY  O16  B14  single    1.358  0.020  1.358
 UFY  C12  B14  single    1.604  0.020  1.604
 UFY  C12  N13  single    1.467  0.020  1.467
 UFY  B14  O15  single    1.359  0.020  1.359
 UFY  N13  C20  single    1.331  0.020  1.331
 UFY  C20  O21  double    1.230  0.020  1.230
 UFY  C20  C19  single    1.527  0.020  1.527
 UFY  C19  C22  single    1.534  0.020  1.534
 UFY  C19  N18  single    1.437  0.020  1.437
 UFY  C22  C23  single    1.504  0.020  1.504
 UFY  C24  C23  aromatic  1.394  0.020  1.394
 UFY  C24  C25  aromatic  1.387  0.020  1.387
 UFY  C23  C28  aromatic  1.391  0.020  1.391
 UFY  C25  C26  aromatic  1.390  0.020  1.390
 UFY  C28  C27  aromatic  1.390  0.020  1.390
 UFY  N18  C7   single    1.336  0.020  1.336
 UFY  O8   C7   double    1.222  0.020  1.222
 UFY  C26  C27  aromatic  1.387  0.020  1.387
 UFY  C7   C5   single    1.498  0.020  1.498
 UFY  C5   N6   aromatic  1.327  0.020  1.327
 UFY  C5   C4   aromatic  1.389  0.020  1.389
 UFY  N6   C1   aromatic  1.321  0.020  1.321
 UFY  C4   N3   aromatic  1.326  0.020  1.326
 UFY  C1   C2   aromatic  1.391  0.020  1.391
 UFY  N3   C2   aromatic  1.324  0.020  1.324
 UFY  C1   H1   single    0.930  0.020  1.080
 UFY  C2   H2   single    0.930  0.020  1.080
 UFY  C11  H3   single    0.970  0.020  1.090
 UFY  C11  H4   single    0.970  0.020  1.090
 UFY  C12  H5   single    0.970  0.020  1.090
 UFY  C17  H6   single    0.970  0.020  1.090
 UFY  C17  H7   single    0.970  0.020  1.090
 UFY  C17  H8   single    0.970  0.020  1.090
 UFY  C19  H9   single    0.970  0.020  1.090
 UFY  C22  H10  single    0.970  0.020  1.090
 UFY  C22  H11  single    0.970  0.020  1.090
 UFY  C24  H12  single    0.930  0.020  1.080
 UFY  C25  H13  single    0.930  0.020  1.080
 UFY  C26  H14  single    0.930  0.020  1.080
 UFY  C27  H15  single    0.930  0.020  1.080
 UFY  C28  H16  single    0.930  0.020  1.080
 UFY  C10  H17  single    0.970  0.020  1.090
 UFY  C4   H18  single    0.930  0.020  1.080
 UFY  C9   H19  single    0.970  0.020  1.090
 UFY  C9   H20  single    0.970  0.020  1.090
 UFY  C9   H21  single    0.970  0.020  1.090
 UFY  N13  H22  single    0.860  0.020  1.020
 UFY  N18  H23  single    0.860  0.020  1.020
 UFY  O15  H24  single    0.850  0.020  0.980
 UFY  O16  H25  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
 UFY  H1   C1   N6   117.83  3.000
 UFY  H1   C1   C2   121.04  3.000
 UFY  N6   C1   C2   121.12  3.000
 UFY  H2   C2   N3   117.71  3.000
 UFY  H2   C2   C1   120.57  3.000
 UFY  N3   C2   C1   121.72  3.000
 UFY  H4   C11  H3   105.59  3.000
 UFY  H4   C11  C10  108.97  3.000
 UFY  H3   C11  C10  107.49  3.000
 UFY  H4   C11  C12  110.04  3.000
 UFY  H3   C11  C12  106.22  3.000
 UFY  C10  C11  C12  117.79  3.000
 UFY  H5   C12  N13  106.33  3.000
 UFY  H5   C12  B14  106.81  3.000
 UFY  N13  C12  B14  109.22  3.000
 UFY  H5   C12  C11  108.03  3.000
 UFY  N13  C12  C11  111.01  3.000
 UFY  B14  C12  C11  114.99  3.000
 UFY  H8   C17  H7   107.78  3.000
 UFY  H8   C17  H6   107.15  3.000
 UFY  H7   C17  H6   107.58  3.000
 UFY  H8   C17  C10  111.55  3.000
 UFY  H7   C17  C10  111.85  3.000
 UFY  H6   C17  C10  110.70  3.000
 UFY  H9   C19  N18  109.33  3.000
 UFY  H9   C19  C22  108.56  3.000
 UFY  N18  C19  C22  110.02  3.000
 UFY  H9   C19  C20  109.06  3.000
 UFY  N18  C19  C20  110.80  3.000
 UFY  C22  C19  C20  109.03  3.000
 UFY  O21  C20  N13  123.64  3.000
 UFY  O21  C20  C19  121.27  3.000
 UFY  N13  C20  C19  114.99  3.000
 UFY  H11  C22  H10  106.77  3.000
 UFY  H11  C22  C23  110.72  3.000
 UFY  H10  C22  C23  109.58  3.000
 UFY  H11  C22  C19  109.33  3.000
 UFY  H10  C22  C19  108.08  3.000
 UFY  C23  C22  C19  112.19  3.000
 UFY  C28  C23  C24  118.70  3.000
 UFY  C28  C23  C22  121.46  3.000
 UFY  C24  C23  C22  119.84  3.000
 UFY  H12  C24  C25  119.71  3.000
 UFY  H12  C24  C23  119.49  3.000
 UFY  C25  C24  C23  120.80  3.000
 UFY  H13  C25  C26  120.10  3.000
 UFY  H13  C25  C24  119.85  3.000
 UFY  C26  C25  C24  120.05  3.000
 UFY  H14  C26  C27  120.20  3.000
 UFY  H14  C26  C25  120.17  3.000
 UFY  C27  C26  C25  119.63  3.000
 UFY  H15  C27  C28  119.76  3.000
 UFY  H15  C27  C26  120.12  3.000
 UFY  C28  C27  C26  120.13  3.000
 UFY  H16  C28  C27  119.73  3.000
 UFY  H16  C28  C23  119.58  3.000
 UFY  C27  C28  C23  120.69  3.000
 UFY  O16  B14  O15  119.85  3.000
 UFY  O15  B14  C12  120.43  3.000
 UFY  O16  B14  C12  119.72  3.000
 UFY  H18  C4   N3   117.49  3.000
 UFY  H18  C4   C5   121.18  3.000
 UFY  N3   C4   C5   121.33  3.000
 UFY  N6   C5   C7   118.26  3.000
 UFY  N6   C5   C4   121.37  3.000
 UFY  C7   C5   C4   120.37  3.000
 UFY  O8   C7   N18  123.66  3.000
 UFY  O8   C7   C5   121.48  3.000
 UFY  N18  C7   C5   114.87  3.000
 UFY  H21  C9   H20  106.81  3.000
 UFY  H21  C9   H19  107.96  3.000
 UFY  H20  C9   H19  107.44  3.000
 UFY  H21  C9   C10  112.51  3.000
 UFY  H20  C9   C10  110.26  3.000
 UFY  H19  C9   C10  111.61  3.000
 UFY  H22  N13  C20  118.49  3.000
 UFY  H22  N13  C12  117.61  3.000
 UFY  C20  N13  C12  123.86  3.000
 UFY  H23  N18  C7   118.20  3.000
 UFY  H23  N18  C19  120.31  3.000
 UFY  C7   N18  C19  121.34  3.000
 UFY  C4   N3   C2   117.04  3.000
 UFY  C5   N6   C1   117.42  3.000
 UFY  H24  O15  B14  111.29  3.000
 UFY  H25  O16  B14  113.69  3.000
 UFY  H17  C10  C9   106.08  3.000
 UFY  H17  C10  C17  107.22  3.000
 UFY  C9   C10  C17  110.63  3.000
 UFY  H17  C10  C11  104.89  3.000
 UFY  C9   C10  C11  114.64  3.000
 UFY  C17  C10  C11  112.72  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
 UFY  CONST_01  C4   C5   N6   C1      0.00   0.0  0
 UFY  CONST_02  C4   N3   C2   C1      0.00   0.0  0
 UFY  CONST_03  C5   N6   C1   C2      0.00   0.0  0
 UFY  CONST_04  C5   C4   N3   C2      0.00   0.0  0
 UFY  CONST_05  C26  C25  C24  C23     0.00   0.0  0
 UFY  CONST_06  C26  C27  C28  C23     0.00   0.0  0
 UFY  CONST_07  C27  C28  C23  C24     0.00   0.0  0
 UFY  CONST_08  C27  C26  C25  C24     0.00   0.0  0
 UFY  CONST_09  C28  C23  C24  C25     0.00   0.0  0
 UFY  CONST_10  C28  C27  C26  C25     0.00   0.0  0
 UFY  CONST_11  N6   C5   C4   N3      0.00   0.0  0
 UFY  CONST_12  N6   C1   C2   N3      0.00   0.0  0
 UFY  CONST_13  C7   C5   N6   C1    180.00   0.0  0
 UFY  CONST_14  C25  C24  C23  C22   180.00   0.0  0
 UFY  CONST_15  C27  C28  C23  C22   180.00   0.0  0
 UFY  CONST_16  N3   C4   C5   C7    180.00   0.0  0
 UFY  CONST_17  H18  C4   N3   C2    180.00   0.0  0
 UFY  CONST_18  H13  C25  C24  C23   180.00   0.0  0
 UFY  CONST_19  H15  C27  C28  C23   180.00   0.0  0
 UFY  CONST_20  H16  C28  C23  C24   180.00   0.0  0
 UFY  CONST_21  H14  C26  C25  C24   180.00   0.0  0
 UFY  CONST_22  H12  C24  C25  C26   180.00   0.0  0
 UFY  CONST_23  H2   C2   N3   C4    180.00   0.0  0
 UFY  CONST_24  H1   C1   N6   C5    180.00   0.0  0
 UFY  CONST_25  C5   C7   N18  C19   180.00   0.0  0
 UFY  CONST_26  H23  N18  C7   C5      0.00   0.0  0
 UFY  CONST_27  O21  C20  N13  C12     0.00   0.0  0
 UFY  CONST_28  C19  C20  N13  C12   180.00   0.0  0
 UFY  CONST_29  O8   C7   N18  C19     0.00   0.0  0
 UFY  CONST_30  H22  N13  C20  C19     0.00   0.0  0
 UFY  Var_01    C24  C23  C22  C19    73.63  30.0  2
 UFY  Var_02    N18  C7   C5   C4    180.00  30.0  2
 UFY  Var_03    C17  C10  C11  C12   -46.44  30.0  1
 UFY  Var_04    H6   C17  C10  C11  -170.72  30.0  3
 UFY  Var_05    H19  C9   C10  C11    47.88  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
 UFY  chir_01  C12  C11  B14  N13  negativ
 UFY  chir_02  C19  N18  C20  C22  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
 UFY  plan-1  C22  0.020
 UFY  plan-1  C23  0.020
 UFY  plan-1  C24  0.020
 UFY  plan-1  C25  0.020
 UFY  plan-1  C26  0.020
 UFY  plan-1  C27  0.020
 UFY  plan-1  C28  0.020
 UFY  plan-1  H12  0.020
 UFY  plan-1  H13  0.020
 UFY  plan-1  H14  0.020
 UFY  plan-1  H15  0.020
 UFY  plan-1  H16  0.020
 UFY  plan-2  C1   0.020
 UFY  plan-2  C2   0.020
 UFY  plan-2  C4   0.020
 UFY  plan-2  C5   0.020
 UFY  plan-2  C7   0.020
 UFY  plan-2  N3   0.020
 UFY  plan-2  N6   0.020
 UFY  plan-2  H1   0.020
 UFY  plan-2  H2   0.020
 UFY  plan-2  H18  0.020
 UFY  plan-3  C12  0.020
 UFY  plan-3  C19  0.020
 UFY  plan-3  C20  0.020
 UFY  plan-3  N13  0.020
 UFY  plan-3  H22  0.020
 UFY  plan-3  O21  0.020
 UFY  plan-4  C19  0.020
 UFY  plan-4  C5   0.020
 UFY  plan-4  C7   0.020
 UFY  plan-4  N18  0.020
 UFY  plan-4  O8   0.020
 UFY  plan-4  H23  0.020

