# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 15:01:53 2021
#   Inital geometry file: a 144 line input string
#   Ligand name: [(1~{R})-1-[[(2~{S})-2-[[2,5-bis(chloranyl)phenyl]carbonylamino]-3-(1~{H}-indol-3-yl)propanoyl]amino]-3-methyl-butyl]boronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)c3cc(Cl)ccc3Cl)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
 E4U  E4U  '[(1~{R})-1-[[(2~{S})-2-[[2,5-bis(chloranyl)phenyl]carbonylamino]-3-(1~{H}-indol-3-yl)propanoyl]amino]-3-methyl-butyl]boronic acid'  ligand  59  33  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E4U
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
 E4U  N3   N   NH1   0  -0.656  -53.7095  -60.1881  -1.6728
 E4U  C6   C   CH1   0  -0.267  -52.6929  -61.0667  -2.2617
 E4U  C8   C   CH2   0  -0.446  -53.3591  -61.9659  -3.2977
 E4U  C10  C   CH3   0  -0.667  -51.6911  -63.8548  -2.9673
 E4U  C15  C   CR6   0   0.055  -52.6293  -55.5730   0.5156
 E4U  C17  C   CH2   0  -0.602  -55.8476  -58.4555  -0.9618
 E4U  C21  C   CR56  0   0.354  -58.1961  -55.8608   0.3743
 E4U  C22  C   CR56  0   0.031  -57.0323  -56.1954  -0.3531
 E4U  C24  C   CR16  0  -0.286  -57.8100  -53.5469   0.0112
 E4U  C26  C   CR16  0  -0.373  -56.2607  -55.1688  -0.9079
 E4U  C28  C   CR16  0  -0.200  -51.8490  -53.2874   0.5921
 E4U  B7   B   B     0   0.536  -51.5018  -60.1289  -2.7811
 E4U  C1   C   CH1   0  -0.171  -54.6783  -58.6888   0.0058
 E4U  C11  C   CH3   0  -0.651  -53.2219  -63.8355  -4.9484
 E4U  C18  C   CR5   0   0.032  -56.9277  -57.6243  -0.3506
 E4U  C19  C   CR15  0  -0.078  -58.0060  -58.0797   0.3562
 E4U  C2   C   C     0   0.560  -53.5484  -59.5989  -0.4885
 E4U  C23  C   CR16  0  -0.306  -58.5978  -54.5386   0.5637
 E4U  C25  C   CR16  0  -0.266  -56.6510  -53.8584  -0.7202
 E4U  C27  C   CR6   0  -0.084  -52.4150  -54.3437  -0.1052
 E4U  C29  C   CR16  0  -0.217  -51.4645  -53.4464   1.9126
 E4U  C30  C   CR6   0  -0.019  -51.6601  -54.6708   2.5290
 E4U  C31  C   CR16  0  -0.254  -52.2393  -55.7244   1.8440
 E4U  C9   C   CH1   0  -0.251  -52.4257  -62.9732  -3.9732
 E4U  N20  N   NR15  0  -0.686  -58.7625  -57.0292   0.7917
 E4U  N5   N   NH1   0  -0.629  -54.1039  -57.4586   0.4992
 E4U  O12  O   OH1   0  -0.630  -50.5881  -59.6165  -1.9122
 E4U  O13  O   OH1   0  -0.620  -51.4327  -59.8090  -4.0994
 E4U  O16  O   O     0  -0.455  -52.8443  -57.0665  -1.3273
 E4U  O4   O   O     0  -0.517  -52.5778  -59.8040   0.2354
 E4U  CL2  CL  CL    0  -0.098  -52.8730  -54.0604  -1.7464
 E4U  CL3  CL  CL    0  -0.110  -51.1742  -54.8911   4.1722
 E4U  H1   H   HNH1  0   0.419  -54.4466  -59.8711  -2.2825
 E4U  H2   H   HCH1  0   0.249  -52.3255  -61.6942  -1.4445
 E4U  H3   H   HCH2  0   0.228  -53.8301  -61.3508  -4.0724
 E4U  H4   H   HCH2  0   0.222  -54.1713  -62.5172  -2.8079
 E4U  H5   H   HCH3  0   0.229  -51.0254  -63.2846  -2.3176
 E4U  H6   H   HCH3  0   0.216  -52.3972  -64.3915  -2.3287
 E4U  H7   H   HCH3  0   0.230  -51.0772  -64.5985  -3.4787
 E4U  H8   H   HCH2  0   0.266  -56.2612  -59.4283  -1.2396
 E4U  H9   H   HCH2  0   0.261  -55.4909  -57.9848  -1.8821
 E4U  H10  H   HCR6  0   0.248  -58.0937  -52.5105   0.1416
 E4U  H11  H   HCR6  0   0.230  -55.3753  -55.3960  -1.4865
 E4U  H12  H   HCR6  0   0.298  -51.7035  -52.3327   0.1059
 E4U  H13  H   HCH1  0   0.303  -55.0837  -59.2010   0.8832
 E4U  H14  H   HCH3  0   0.226  -52.5672  -64.5055  -5.5076
 E4U  H15  H   HCH3  0   0.213  -53.9522  -64.4525  -4.4185
 E4U  H16  H   HCH3  0   0.224  -53.7656  -63.2247  -5.6712
 E4U  H17  H   HCR5  0   0.282  -58.2972  -59.0943   0.5801
 E4U  H18  H   HCR6  0   0.258  -59.4941  -54.2963   1.1207
 E4U  H19  H   HCR6  0   0.239  -56.0549  -53.0576  -1.1390
 E4U  H20  H   HCR6  0   0.297  -51.0177  -52.6198   2.4471
 E4U  H21  H   HCR6  0   0.298  -52.3705  -56.6782   2.3379
 E4U  H22  H   HCH1  0   0.230  -51.6787  -62.4205  -4.5514
 E4U  H23  H   HNR5  0   0.409  -59.6122  -57.1136   1.3238
 E4U  H24  H   HNH1  0   0.415  -54.4354  -57.1055   1.3814
 E4U  H25  H   HOH1  0   0.472  -50.8464  -59.7927  -0.9975
 E4U  H26  H   HOH1  0   0.485  -50.7311  -59.1821  -4.3071
 E4U  C14  C   C     0   0.531  -53.2029  -56.7564  -0.2042

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
 E4U  C11  C9   single    1.526  0.020  1.526
 E4U  O13  B7   single    1.358  0.020  1.358
 E4U  C9   C8   single    1.531  0.020  1.531
 E4U  C9   C10  single    1.526  0.020  1.526
 E4U  C8   C6   single    1.525  0.020  1.525
 E4U  B7   C6   single    1.602  0.020  1.602
 E4U  B7   O12  single    1.361  0.020  1.361
 E4U  CL2  C27  single    1.727  0.020  1.727
 E4U  C6   N3   single    1.467  0.020  1.467
 E4U  N3   C2   single    1.333  0.020  1.333
 E4U  C17  C18  single    1.494  0.020  1.494
 E4U  C17  C1   single    1.536  0.020  1.536
 E4U  C2   C1   single    1.533  0.020  1.533
 E4U  C2   O4   double    1.228  0.020  1.228
 E4U  C19  C18  aromatic  1.367  0.020  1.367
 E4U  C19  N20  aromatic  1.366  0.020  1.366
 E4U  O16  C14  double    1.219  0.020  1.219
 E4U  C18  C22  aromatic  1.433  0.020  1.433
 E4U  C1   N5   single    1.445  0.020  1.445
 E4U  C27  C28  aromatic  1.386  0.020  1.386
 E4U  C27  C15  aromatic  1.394  0.020  1.394
 E4U  C14  N5   single    1.341  0.020  1.341
 E4U  C14  C15  single    1.499  0.020  1.499
 E4U  C28  C29  aromatic  1.385  0.020  1.385
 E4U  N20  C21  aromatic  1.364  0.020  1.364
 E4U  C15  C31  aromatic  1.393  0.020  1.393
 E4U  C22  C21  aromatic  1.413  0.020  1.413
 E4U  C22  C26  aromatic  1.399  0.020  1.399
 E4U  C21  C23  aromatic  1.395  0.020  1.395
 E4U  C26  C25  aromatic  1.380  0.020  1.380
 E4U  C29  C30  aromatic  1.385  0.020  1.385
 E4U  C31  C30  aromatic  1.384  0.020  1.384
 E4U  C23  C24  aromatic  1.382  0.020  1.382
 E4U  C30  CL3  single    1.728  0.020  1.728
 E4U  C25  C24  aromatic  1.405  0.020  1.405
 E4U  N3   H1   single    0.860  0.020  1.020
 E4U  C6   H2   single    0.970  0.020  1.090
 E4U  C8   H3   single    0.970  0.020  1.090
 E4U  C8   H4   single    0.970  0.020  1.090
 E4U  C10  H5   single    0.970  0.020  1.090
 E4U  C10  H6   single    0.970  0.020  1.090
 E4U  C10  H7   single    0.970  0.020  1.090
 E4U  C17  H8   single    0.970  0.020  1.090
 E4U  C17  H9   single    0.970  0.020  1.090
 E4U  C24  H10  single    0.930  0.020  1.080
 E4U  C26  H11  single    0.930  0.020  1.080
 E4U  C28  H12  single    0.930  0.020  1.080
 E4U  C1   H13  single    0.970  0.020  1.090
 E4U  C11  H14  single    0.970  0.020  1.090
 E4U  C11  H15  single    0.970  0.020  1.090
 E4U  C11  H16  single    0.970  0.020  1.090
 E4U  C19  H17  single    0.930  0.020  1.080
 E4U  C23  H18  single    0.930  0.020  1.080
 E4U  C25  H19  single    0.930  0.020  1.080
 E4U  C29  H20  single    0.930  0.020  1.080
 E4U  C31  H21  single    0.930  0.020  1.080
 E4U  C9   H22  single    0.970  0.020  1.090
 E4U  N20  H23  single    0.860  0.020  1.020
 E4U  N5   H24  single    0.860  0.020  1.020
 E4U  O12  H25  single    0.850  0.020  0.980
 E4U  O13  H26  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
 E4U  H1   N3   C2   119.15  3.000
 E4U  H1   N3   C6   116.89  3.000
 E4U  C2   N3   C6   122.54  3.000
 E4U  H2   C6   B7   109.16  3.000
 E4U  H2   C6   C8   108.42  3.000
 E4U  B7   C6   C8   116.72  3.000
 E4U  H2   C6   N3   106.04  3.000
 E4U  B7   C6   N3   107.14  3.000
 E4U  C8   C6   N3   108.85  3.000
 E4U  H4   C8   H3   106.24  3.000
 E4U  H4   C8   C9   108.53  3.000
 E4U  H3   C8   C9   108.64  3.000
 E4U  H4   C8   C6   108.45  3.000
 E4U  H3   C8   C6   109.70  3.000
 E4U  C9   C8   C6   114.93  3.000
 E4U  H7   C10  H6   107.61  3.000
 E4U  H7   C10  H5   106.97  3.000
 E4U  H6   C10  H5   107.63  3.000
 E4U  H7   C10  C9   110.82  3.000
 E4U  H6   C10  C9   110.97  3.000
 E4U  H5   C10  C9   112.60  3.000
 E4U  C31  C15  C27  118.53  3.000
 E4U  C31  C15  C14  118.64  3.000
 E4U  C27  C15  C14  122.76  3.000
 E4U  H9   C17  H8   107.01  3.000
 E4U  H9   C17  C18  109.92  3.000
 E4U  H8   C17  C18  109.00  3.000
 E4U  H9   C17  C1   110.33  3.000
 E4U  H8   C17  C1   108.25  3.000
 E4U  C18  C17  C1   112.17  3.000
 E4U  N20  C21  C23  130.61  3.000
 E4U  C23  C21  C22  122.12  3.000
 E4U  N20  C21  C22  107.27  3.000
 E4U  C18  C22  C26  133.81  3.000
 E4U  C26  C22  C21  119.00  3.000
 E4U  C18  C22  C21  107.19  3.000
 E4U  H10  C24  C25  119.41  3.000
 E4U  H10  C24  C23  119.32  3.000
 E4U  C25  C24  C23  121.28  3.000
 E4U  H11  C26  C25  120.24  3.000
 E4U  H11  C26  C22  120.63  3.000
 E4U  C25  C26  C22  119.13  3.000
 E4U  H12  C28  C29  119.53  3.000
 E4U  H12  C28  C27  120.10  3.000
 E4U  C29  C28  C27  120.37  3.000
 E4U  O13  B7   O12  119.78  3.000
 E4U  O12  B7   C6   120.83  3.000
 E4U  O13  B7   C6   119.35  3.000
 E4U  H13  C1   N5   105.79  3.000
 E4U  H13  C1   C2   104.70  3.000
 E4U  N5   C1   C2   108.82  3.000
 E4U  H13  C1   C17  107.12  3.000
 E4U  N5   C1   C17  112.87  3.000
 E4U  C2   C1   C17  116.64  3.000
 E4U  H16  C11  H15  107.70  3.000
 E4U  H16  C11  H14  107.65  3.000
 E4U  H15  C11  H14  107.63  3.000
 E4U  H16  C11  C9   111.53  3.000
 E4U  H15  C11  C9   110.96  3.000
 E4U  H14  C11  C9   111.19  3.000
 E4U  C19  C18  C22  105.99  3.000
 E4U  C22  C18  C17  127.37  3.000
 E4U  C19  C18  C17  126.62  3.000
 E4U  H17  C19  N20  120.50  3.000
 E4U  H17  C19  C18  129.29  3.000
 E4U  N20  C19  C18  110.21  3.000
 E4U  O4   C2   C1   119.45  3.000
 E4U  O4   C2   N3   123.06  3.000
 E4U  C1   C2   N3   117.39  3.000
 E4U  H18  C23  C24  121.13  3.000
 E4U  H18  C23  C21  121.36  3.000
 E4U  C24  C23  C21  117.51  3.000
 E4U  H19  C25  C26  119.60  3.000
 E4U  H19  C25  C24  119.44  3.000
 E4U  C26  C25  C24  120.96  3.000
 E4U  CL2  C27  C28  117.46  3.000
 E4U  C28  C27  C15  120.71  3.000
 E4U  CL2  C27  C15  121.81  3.000
 E4U  H20  C29  C30  120.96  3.000
 E4U  H20  C29  C28  119.90  3.000
 E4U  C30  C29  C28  119.14  3.000
 E4U  CL3  C30  C31  119.43  3.000
 E4U  CL3  C30  C29  119.76  3.000
 E4U  C31  C30  C29  120.80  3.000
 E4U  H21  C31  C30  119.73  3.000
 E4U  H21  C31  C15  119.82  3.000
 E4U  C30  C31  C15  120.44  3.000
 E4U  H22  C9   C11  107.69  3.000
 E4U  H22  C9   C10  108.15  3.000
 E4U  C11  C9   C10  110.24  3.000
 E4U  H22  C9   C8   108.48  3.000
 E4U  C10  C9   C8   112.51  3.000
 E4U  C11  C9   C8   109.62  3.000
 E4U  H23  N20  C19  124.88  3.000
 E4U  H23  N20  C21  125.77  3.000
 E4U  C19  N20  C21  109.34  3.000
 E4U  H24  N5   C14  119.82  3.000
 E4U  H24  N5   C1   117.85  3.000
 E4U  C14  N5   C1   122.26  3.000
 E4U  H25  O12  B7   110.85  3.000
 E4U  H26  O13  B7   113.55  3.000
 E4U  O16  C14  N5   123.19  3.000
 E4U  N5   C14  C15  114.74  3.000
 E4U  O16  C14  C15  122.04  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
 E4U  CONST_01  C29  C28  C27  C15    0.00   0.0  0
 E4U  CONST_02  C29  C30  C31  C15    0.00   0.0  0
 E4U  CONST_03  C18  C19  N20  C21    0.00   0.0  0
 E4U  CONST_04  C19  C18  C22  C21    0.00   0.0  0
 E4U  CONST_05  C25  C26  C22  C21    0.00   0.0  0
 E4U  CONST_06  C25  C24  C23  C21    0.00   0.0  0
 E4U  CONST_07  N20  C19  C18  C22    0.00   0.0  0
 E4U  CONST_08  C19  N20  C21  C22    0.00   0.0  0
 E4U  CONST_09  C24  C23  C21  C22    0.00   0.0  0
 E4U  CONST_10  C24  C25  C26  C22    0.00   0.0  0
 E4U  CONST_11  N20  C21  C23  C24  180.00   0.0  0
 E4U  CONST_12  C19  C18  C22  C26  180.00   0.0  0
 E4U  CONST_13  N20  C21  C22  C26  180.00   0.0  0
 E4U  CONST_14  C23  C21  C22  C26    0.00   0.0  0
 E4U  CONST_15  C23  C24  C25  C26    0.00   0.0  0
 E4U  CONST_16  C31  C15  C27  C28    0.00   0.0  0
 E4U  CONST_17  C31  C30  C29  C28    0.00   0.0  0
 E4U  CONST_18  N20  C21  C22  C18    0.00   0.0  0
 E4U  CONST_19  C23  C21  C22  C18  180.00   0.0  0
 E4U  CONST_20  C25  C26  C22  C18  180.00   0.0  0
 E4U  CONST_21  C23  C21  N20  C19  180.00   0.0  0
 E4U  CONST_22  C30  C29  C28  C27    0.00   0.0  0
 E4U  CONST_23  C30  C31  C15  C27    0.00   0.0  0
 E4U  CONST_24  CL3  C30  C31  C15  180.00   0.0  0
 E4U  CONST_25  N20  C19  C18  C17  180.00   0.0  0
 E4U  CONST_26  C21  C22  C18  C17  180.00   0.0  0
 E4U  CONST_27  C26  C22  C18  C17    0.00   0.0  0
 E4U  CONST_28  C14  C15  C27  C28  180.00   0.0  0
 E4U  CONST_29  CL3  C30  C29  C28  180.00   0.0  0
 E4U  CONST_30  C30  C31  C15  C14  180.00   0.0  0
 E4U  CONST_31  CL2  C27  C28  C29  180.00   0.0  0
 E4U  CONST_32  CL2  C27  C15  C31  180.00   0.0  0
 E4U  CONST_33  H12  C28  C27  C15  180.00   0.0  0
 E4U  CONST_34  H17  C19  N20  C21  180.00   0.0  0
 E4U  CONST_35  H11  C26  C22  C21  180.00   0.0  0
 E4U  CONST_36  H10  C24  C23  C21  180.00   0.0  0
 E4U  CONST_37  H23  N20  C21  C22  180.00   0.0  0
 E4U  CONST_38  H18  C23  C21  C22  180.00   0.0  0
 E4U  CONST_39  H19  C25  C26  C22  180.00   0.0  0
 E4U  CONST_40  H20  C29  C28  C27  180.00   0.0  0
 E4U  CONST_41  H21  C31  C15  C27  180.00   0.0  0
 E4U  CONST_42  C1   N5   C14  C15  180.00   0.0  0
 E4U  CONST_43  H24  N5   C14  C15    0.00   0.0  0
 E4U  CONST_44  C1   C2   N3   C6   180.00   0.0  0
 E4U  CONST_45  O4   C2   N3   C6     0.00   0.0  0
 E4U  CONST_46  O16  C14  N5   C1     0.00   0.0  0
 E4U  CONST_47  H1   N3   C2   C1     0.00   0.0  0
 E4U  Var_01    C1   C17  C18  C22   88.38  30.0  2
 E4U  Var_02    O16  C14  C15  C27   43.35  30.0  2
 E4U  Var_03    C11  C9   C8   C6   178.19  30.0  2
 E4U  Var_04    H14  C11  C9   C8   175.13  30.0  3
 E4U  Var_05    H5   C10  C9   C8   -63.40  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
 E4U  chir_01  C6  C8  B7   N3  negativ
 E4U  chir_02  C1  N5  C17  C2  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
 E4U  plan-1  C15  0.020
 E4U  plan-1  C28  0.020
 E4U  plan-1  C27  0.020
 E4U  plan-1  C29  0.020
 E4U  plan-1  C30  0.020
 E4U  plan-1  C31  0.020
 E4U  plan-1  CL2  0.020
 E4U  plan-1  CL3  0.020
 E4U  plan-1  H12  0.020
 E4U  plan-1  H20  0.020
 E4U  plan-1  H21  0.020
 E4U  plan-1  C14  0.020
 E4U  plan-2  C17  0.020
 E4U  plan-2  C21  0.020
 E4U  plan-2  C22  0.020
 E4U  plan-2  C24  0.020
 E4U  plan-2  C26  0.020
 E4U  plan-2  C18  0.020
 E4U  plan-2  C19  0.020
 E4U  plan-2  C23  0.020
 E4U  plan-2  C25  0.020
 E4U  plan-2  N20  0.020
 E4U  plan-2  H10  0.020
 E4U  plan-2  H11  0.020
 E4U  plan-2  H17  0.020
 E4U  plan-2  H18  0.020
 E4U  plan-2  H19  0.020
 E4U  plan-2  H23  0.020
 E4U  plan-3  N3   0.020
 E4U  plan-3  C6   0.020
 E4U  plan-3  C1   0.020
 E4U  plan-3  C2   0.020
 E4U  plan-3  O4   0.020
 E4U  plan-3  H1   0.020
 E4U  plan-4  C15  0.020
 E4U  plan-4  C1   0.020
 E4U  plan-4  N5   0.020
 E4U  plan-4  O16  0.020
 E4U  plan-4  H24  0.020
 E4U  plan-4  C14  0.020

