# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 02:17:37 2021
#   Inital geometry file: a 129 line input string
#   Ligand name: [(1~{S})-3-methyl-1-[[(2~{S})-3-phenyl-2-(pyrazin-2-ylcarbonylamino)propanoyl]amino]butyl]boronic acid
#   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
 FN3  FN3  '[(1~{S})-3-methyl-1-[[(2~{S})-3-phenyl-2-(pyrazin-2-ylcarbonylamino)propanoyl]amino]butyl]boronic acid'  ligand  53  28  .  2022-03-18  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FN3
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
 FN3  C10  C  CR16  0  -0.238  -34.6810  58.3538  -25.7749
 FN3  N12  N  NH1   0  -0.641  -38.8355  57.7053  -26.4302
 FN3  C13  C  CH1   0  -0.296  -41.0479  53.8490  -28.2801
 FN3  C15  C  CH2   0  -0.418  -42.3502  54.4629  -28.8256
 FN3  C17  C  CH3   0  -0.651  -43.5226  52.2207  -29.1834
 FN3  C21  C  C     0   0.555  -38.5998  58.9730  -26.7900
 FN3  C22  C  CR6   0   0.070  -38.7512  59.9640  -25.6739
 FN3  C26  C  CR16  0  -0.087  -38.9906  61.7596  -23.7376
 FN3  C28  C  CR16  0  -0.059  -38.5478  61.3183  -25.9098
 FN3  B14  B  B     0   0.530  -41.1323  53.1369  -26.8468
 FN3  C01  C  CH1   0  -0.202  -38.6003  56.5798  -27.2886
 FN3  C02  C  C     0   0.573  -39.7614  55.6009  -27.1805
 FN3  C05  C  CH2   0  -0.523  -37.2930  55.8474  -26.9098
 FN3  C06  C  CR6   0   0.141  -36.1194  56.7826  -26.9177
 FN3  C07  C  CR16  0  -0.295  -35.4303  57.0444  -28.0989
 FN3  C08  C  CR16  0  -0.242  -34.3756  57.9457  -28.1209
 FN3  C09  C  CR16  0  -0.270  -33.9994  58.6057  -26.9577
 FN3  C11  C  CR16  0  -0.306  -35.7322  57.4467  -25.7570
 FN3  C16  C  CH1   0  -0.245  -43.1108  53.5556  -29.7942
 FN3  C18  C  CH3   0  -0.651  -44.3313  54.2796  -30.3542
 FN3  C25  C  CR16  0  -0.107  -39.1925  60.4046  -23.4986
 FN3  N03  N  NH1   0  -0.637  -39.9627  54.8232  -28.2446
 FN3  N24  N  N     0  -0.382  -39.0706  59.5147  -24.4675
 FN3  N27  N  N     0  -0.352  -38.6684  62.2137  -24.9391
 FN3  O04  O  O     0  -0.491  -40.4111  55.4874  -26.1469
 FN3  O19  O  OH1   0  -0.623  -42.3284  53.0209  -26.2142
 FN3  O20  O  OH1   0  -0.628  -40.0423  52.5026  -26.3132
 FN3  O23  O  O     0  -0.466  -38.2947  59.3403  -27.9133
 FN3  H1   H  HCR6  0   0.252  -34.3928  58.8613  -24.8632
 FN3  H2   H  HNH1  0   0.405  -39.0706  57.5303  -25.4630
 FN3  H3   H  HCH1  0   0.257  -40.7137  53.0800  -28.9886
 FN3  H4   H  HCH2  0   0.226  -42.0949  55.3798  -29.3656
 FN3  H5   H  HCH2  0   0.223  -43.0078  54.7697  -28.0071
 FN3  H6   H  HCH3  0   0.226  -42.6677  51.6475  -28.8215
 FN3  H7   H  HCH3  0   0.215  -44.2047  52.3655  -28.3442
 FN3  H8   H  HCH3  0   0.223  -44.0329  51.6036  -29.9254
 FN3  H9   H  HCR6  0   0.288  -39.0936  62.4813  -22.9370
 FN3  H10  H  HCR6  0   0.284  -38.2831  61.6810  -26.8944
 FN3  H11  H  HCH1  0   0.293  -38.5167  56.9463  -28.3129
 FN3  H12  H  HCH2  0   0.266  -37.4130  55.3996  -25.9197
 FN3  H13  H  HCH2  0   0.269  -37.1361  55.0307  -27.6171
 FN3  H14  H  HCR6  0   0.245  -35.7204  56.5354  -29.0114
 FN3  H15  H  HCR6  0   0.252  -33.8455  58.1316  -29.0464
 FN3  H16  H  HCR6  0   0.253  -33.1768  59.3090  -26.9726
 FN3  H17  H  HCR6  0   0.246  -36.2534  57.2498  -24.8276
 FN3  H18  H  HCH1  0   0.212  -42.4338  53.3434  -30.6312
 FN3  H19  H  HCH3  0   0.222  -44.0565  55.2226  -30.8304
 FN3  H20  H  HCH3  0   0.224  -44.8433  53.6677  -31.0990
 FN3  H21  H  HCH3  0   0.213  -45.0495  54.5038  -29.5615
 FN3  H22  H  HCR6  0   0.287  -39.4538  60.0449  -22.5117
 FN3  H23  H  HNH1  0   0.403  -39.4796  55.0350  -29.1041
 FN3  H24  H  HOH1  0   0.485  -42.2789  52.5230  -25.3916
 FN3  H25  H  HOH1  0   0.471  -39.2478  52.5923  -26.8473

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
 FN3  C17  C16  single    1.525  0.020  1.525
 FN3  O19  B14  single    1.358  0.020  1.358
 FN3  C16  C18  single    1.526  0.020  1.526
 FN3  C16  C15  single    1.530  0.020  1.530
 FN3  C13  B14  single    1.603  0.020  1.603
 FN3  C13  N03  single    1.459  0.020  1.459
 FN3  C13  C15  single    1.540  0.020  1.540
 FN3  B14  O20  single    1.369  0.020  1.369
 FN3  N03  C02  single    1.333  0.020  1.333
 FN3  O23  C21  double    1.221  0.020  1.221
 FN3  C08  C07  aromatic  1.387  0.020  1.387
 FN3  C08  C09  aromatic  1.389  0.020  1.389
 FN3  C28  N27  aromatic  1.326  0.020  1.326
 FN3  C28  C22  aromatic  1.390  0.020  1.390
 FN3  C07  C06  aromatic  1.392  0.020  1.392
 FN3  C21  C22  single    1.500  0.020  1.500
 FN3  C21  N12  single    1.339  0.020  1.339
 FN3  C02  C01  single    1.523  0.020  1.523
 FN3  C02  O04  double    1.226  0.020  1.226
 FN3  C01  N12  single    1.435  0.020  1.435
 FN3  C01  C05  single    1.546  0.020  1.546
 FN3  N27  C26  aromatic  1.324  0.020  1.324
 FN3  C09  C10  aromatic  1.388  0.020  1.388
 FN3  C22  N24  aromatic  1.326  0.020  1.326
 FN3  C06  C05  single    1.501  0.020  1.501
 FN3  C06  C11  aromatic  1.392  0.020  1.392
 FN3  C10  C11  aromatic  1.389  0.020  1.389
 FN3  C26  C25  aromatic  1.391  0.020  1.391
 FN3  N24  C25  aromatic  1.321  0.020  1.321
 FN3  C10  H1   single    0.930  0.020  1.080
 FN3  N12  H2   single    0.860  0.020  1.020
 FN3  C13  H3   single    0.970  0.020  1.090
 FN3  C15  H4   single    0.970  0.020  1.090
 FN3  C15  H5   single    0.970  0.020  1.090
 FN3  C17  H6   single    0.970  0.020  1.090
 FN3  C17  H7   single    0.970  0.020  1.090
 FN3  C17  H8   single    0.970  0.020  1.090
 FN3  C26  H9   single    0.930  0.020  1.080
 FN3  C28  H10  single    0.930  0.020  1.080
 FN3  C01  H11  single    0.970  0.020  1.090
 FN3  C05  H12  single    0.970  0.020  1.090
 FN3  C05  H13  single    0.970  0.020  1.090
 FN3  C07  H14  single    0.930  0.020  1.080
 FN3  C08  H15  single    0.930  0.020  1.080
 FN3  C09  H16  single    0.930  0.020  1.080
 FN3  C11  H17  single    0.930  0.020  1.080
 FN3  C16  H18  single    0.970  0.020  1.090
 FN3  C18  H19  single    0.970  0.020  1.090
 FN3  C18  H20  single    0.970  0.020  1.090
 FN3  C18  H21  single    0.970  0.020  1.090
 FN3  C25  H22  single    0.930  0.020  1.080
 FN3  N03  H23  single    0.860  0.020  1.020
 FN3  O19  H24  single    0.850  0.020  0.980
 FN3  O20  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
 FN3  H1   C10  C11  119.80  3.000
 FN3  H1   C10  C09  120.12  3.000
 FN3  C11  C10  C09  120.08  3.000
 FN3  H2   N12  C01  118.35  3.000
 FN3  H2   N12  C21  117.52  3.000
 FN3  C01  N12  C21  123.58  3.000
 FN3  H3   C13  N03  104.90  3.000
 FN3  H3   C13  B14  106.38  3.000
 FN3  N03  C13  B14  108.31  3.000
 FN3  H3   C13  C15  107.95  3.000
 FN3  N03  C13  C15  111.81  3.000
 FN3  B14  C13  C15  116.71  3.000
 FN3  H5   C15  H4   105.93  3.000
 FN3  H5   C15  C16  109.96  3.000
 FN3  H4   C15  C16  107.49  3.000
 FN3  H5   C15  C13  110.80  3.000
 FN3  H4   C15  C13  108.16  3.000
 FN3  C16  C15  C13  114.11  3.000
 FN3  H8   C17  H7   107.79  3.000
 FN3  H8   C17  H6   107.14  3.000
 FN3  H7   C17  H6   107.71  3.000
 FN3  H8   C17  C16  110.42  3.000
 FN3  H7   C17  C16  111.15  3.000
 FN3  H6   C17  C16  112.41  3.000
 FN3  O23  C21  C22  120.74  3.000
 FN3  C22  C21  N12  114.07  3.000
 FN3  O23  C21  N12  125.19  3.000
 FN3  N24  C22  C28  121.31  3.000
 FN3  N24  C22  C21  118.51  3.000
 FN3  C28  C22  C21  120.18  3.000
 FN3  H9   C26  N27  117.73  3.000
 FN3  H9   C26  C25  120.57  3.000
 FN3  N27  C26  C25  121.70  3.000
 FN3  H10  C28  N27  117.51  3.000
 FN3  H10  C28  C22  121.13  3.000
 FN3  N27  C28  C22  121.37  3.000
 FN3  O20  B14  O19  118.68  3.000
 FN3  O20  B14  C13  120.82  3.000
 FN3  O19  B14  C13  120.06  3.000
 FN3  H11  C01  C05  108.93  3.000
 FN3  H11  C01  C02  109.94  3.000
 FN3  C05  C01  C02  108.84  3.000
 FN3  H11  C01  N12  108.10  3.000
 FN3  C05  C01  N12  111.33  3.000
 FN3  C02  C01  N12  109.69  3.000
 FN3  O04  C02  N03  122.60  3.000
 FN3  O04  C02  C01  121.56  3.000
 FN3  N03  C02  C01  115.69  3.000
 FN3  H13  C05  H12  107.22  3.000
 FN3  H13  C05  C06  110.51  3.000
 FN3  H12  C05  C06  110.24  3.000
 FN3  H13  C05  C01  108.50  3.000
 FN3  H12  C05  C01  108.86  3.000
 FN3  C06  C05  C01  111.40  3.000
 FN3  C11  C06  C07  118.68  3.000
 FN3  C11  C06  C05  120.69  3.000
 FN3  C07  C06  C05  120.58  3.000
 FN3  H14  C07  C08  119.67  3.000
 FN3  H14  C07  C06  119.55  3.000
 FN3  C08  C07  C06  120.78  3.000
 FN3  H15  C08  C09  120.10  3.000
 FN3  H15  C08  C07  119.82  3.000
 FN3  C09  C08  C07  120.08  3.000
 FN3  H16  C09  C08  120.20  3.000
 FN3  H16  C09  C10  120.19  3.000
 FN3  C08  C09  C10  119.62  3.000
 FN3  H17  C11  C06  119.64  3.000
 FN3  H17  C11  C10  119.60  3.000
 FN3  C06  C11  C10  120.76  3.000
 FN3  H18  C16  C18  107.79  3.000
 FN3  H18  C16  C17  107.63  3.000
 FN3  C18  C16  C17  110.27  3.000
 FN3  H18  C16  C15  106.92  3.000
 FN3  C18  C16  C15  110.41  3.000
 FN3  C17  C16  C15  113.57  3.000
 FN3  H21  C18  H20  107.56  3.000
 FN3  H21  C18  H19  107.74  3.000
 FN3  H20  C18  H19  107.74  3.000
 FN3  H21  C18  C16  110.91  3.000
 FN3  H20  C18  C16  111.08  3.000
 FN3  H19  C18  C16  111.64  3.000
 FN3  H22  C25  N24  117.84  3.000
 FN3  H22  C25  C26  121.03  3.000
 FN3  N24  C25  C26  121.12  3.000
 FN3  H23  N03  C02  119.04  3.000
 FN3  H23  N03  C13  118.42  3.000
 FN3  C02  N03  C13  121.42  3.000
 FN3  C25  N24  C22  117.46  3.000
 FN3  C28  N27  C26  117.04  3.000
 FN3  H24  O19  B14  113.39  3.000
 FN3  H25  O20  B14  113.45  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
 FN3  CONST_01  C07  C08  C09  C10     0.00   0.0  0
 FN3  CONST_02  C07  C06  C11  C10     0.00   0.0  0
 FN3  CONST_03  C26  N27  C28  C22     0.00   0.0  0
 FN3  CONST_04  C26  C25  N24  C22     0.00   0.0  0
 FN3  CONST_05  C25  C26  N27  C28     0.00   0.0  0
 FN3  CONST_06  C25  N24  C22  C28     0.00   0.0  0
 FN3  CONST_07  C09  C08  C07  C06     0.00   0.0  0
 FN3  CONST_08  C09  C10  C11  C06     0.00   0.0  0
 FN3  CONST_09  C11  C06  C07  C08     0.00   0.0  0
 FN3  CONST_10  C11  C10  C09  C08     0.00   0.0  0
 FN3  CONST_11  N27  C28  C22  N24     0.00   0.0  0
 FN3  CONST_12  N27  C26  C25  N24     0.00   0.0  0
 FN3  CONST_13  C05  C06  C11  C10   180.00   0.0  0
 FN3  CONST_14  N27  C28  C22  C21   180.00   0.0  0
 FN3  CONST_15  C25  N24  C22  C21   180.00   0.0  0
 FN3  CONST_16  C08  C07  C06  C05   180.00   0.0  0
 FN3  CONST_17  H15  C08  C09  C10   180.00   0.0  0
 FN3  CONST_18  H22  C25  N24  C22   180.00   0.0  0
 FN3  CONST_19  H10  C28  N27  C26   180.00   0.0  0
 FN3  CONST_20  H9   C26  N27  C28   180.00   0.0  0
 FN3  CONST_21  H1   C10  C11  C06   180.00   0.0  0
 FN3  CONST_22  H16  C09  C08  C07   180.00   0.0  0
 FN3  CONST_23  H17  C11  C06  C07   180.00   0.0  0
 FN3  CONST_24  H14  C07  C08  C09   180.00   0.0  0
 FN3  CONST_25  C01  N12  C21  C22   180.00   0.0  0
 FN3  CONST_26  H2   N12  C21  C22     0.00   0.0  0
 FN3  CONST_27  C01  C02  N03  C13   180.00   0.0  0
 FN3  CONST_28  O04  C02  N03  C13     0.00   0.0  0
 FN3  CONST_29  O23  C21  N12  C01     0.00   0.0  0
 FN3  CONST_30  H23  N03  C02  C01     0.00   0.0  0
 FN3  Var_01    C28  C22  C21  N12  -179.41  30.0  2
 FN3  Var_02    C07  C06  C05  C01   -85.42  30.0  2
 FN3  Var_03    C17  C16  C15  C13    59.40  30.0  1
 FN3  Var_04    H6   C17  C16  C15   -58.67  30.0  3
 FN3  Var_05    H19  C18  C16  C15    55.78  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
 FN3  chir_01  C13  B14  N03  C15  positiv
 FN3  chir_02  C01  N12  C02  C05  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
 FN3  plan-1  C21  0.020
 FN3  plan-1  C22  0.020
 FN3  plan-1  C26  0.020
 FN3  plan-1  C28  0.020
 FN3  plan-1  C25  0.020
 FN3  plan-1  N24  0.020
 FN3  plan-1  N27  0.020
 FN3  plan-1  H9   0.020
 FN3  plan-1  H10  0.020
 FN3  plan-1  H22  0.020
 FN3  plan-2  C10  0.020
 FN3  plan-2  C05  0.020
 FN3  plan-2  C06  0.020
 FN3  plan-2  C07  0.020
 FN3  plan-2  C08  0.020
 FN3  plan-2  C09  0.020
 FN3  plan-2  C11  0.020
 FN3  plan-2  H1   0.020
 FN3  plan-2  H14  0.020
 FN3  plan-2  H15  0.020
 FN3  plan-2  H16  0.020
 FN3  plan-2  H17  0.020
 FN3  plan-3  N12  0.020
 FN3  plan-3  C21  0.020
 FN3  plan-3  C22  0.020
 FN3  plan-3  C01  0.020
 FN3  plan-3  O23  0.020
 FN3  plan-3  H2   0.020
 FN3  plan-4  C13  0.020
 FN3  plan-4  C01  0.020
 FN3  plan-4  C02  0.020
 FN3  plan-4  N03  0.020
 FN3  plan-4  O04  0.020
 FN3  plan-4  H23  0.020

