# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 22:37:23 2021
#   Inital geometry file: a 150 line input string
#   Ligand name: N-({(1S)-5-[acetyl(4-bromobenzyl)amino]-1-carboxypentyl}carbamoyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N(CCCC[C@H](NC(=O)N[C@@H](CCC(O)=O)C(O)=O)C(O)=O)Cc1ccc(Br)cc1
#
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
 JB7  JB7  'N-({(1S)-5-[acetyl(4-bromobenzyl)amino]-1-carboxypentyl}carbamoyl)-L-glutamic acid'  ligand  61  33  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JB7
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
 JB7  C1   C   C     0   0.541  16.2331  20.7738  39.3936
 JB7  C2   C   CH1   0  -0.162  15.7372  20.4488  37.9926
 JB7  C3   C   CH2   0  -0.497  14.4229  19.6622  38.0718
 JB7  C4   C   CH2   0  -0.569  14.5278  18.3335  38.8236
 JB7  C5   C   C     0   0.545  13.2803  17.4953  38.7456
 JB7  C15  C   CR16  0  -0.281  24.9219  15.6413  39.0645
 JB7  C17  C   CR6   0  -0.123  24.2022  13.9260  37.5628
 JB7  C18  C   CR16  0  -0.212  25.0120  14.4396  36.5636
 JB7  O8   O   O     0  -0.503  25.1789  20.0778  40.3033
 JB7  C21  C   CH3   0  -0.809  26.7624  18.4576  41.0415
 JB7  N3   N   NT    0  -0.438  25.7911  18.5438  38.7811
 JB7  C13  C   CH2   0  -0.416  26.5797  17.4050  38.3547
 JB7  C14  C   CR6   0   0.137  25.7452  16.1790  38.0787
 JB7  C19  C   CR16  0  -0.305  25.7782  15.5673  36.8331
 JB7  C16  C   CR16  0  -0.212  24.1496  14.5184  38.8181
 JB7  C12  C   CH2   0  -0.288  24.9133  19.1410  37.7837
 JB7  C11  C   CH2   0  -0.423  23.4444  18.7583  37.9295
 JB7  C9   C   CH2   0  -0.426  21.1139  19.0594  37.0156
 JB7  C7   C   CH1   0  -0.192  20.1718  19.8391  36.0897
 JB7  C8   C   C     0   0.546  20.5558  19.6483  34.6336
 JB7  O7   O   OH1   0  -0.590  20.2079  18.4513  34.1825
 JB7  O6   O   O     0  -0.436  21.1352  20.4706  33.9709
 JB7  N2   N   NH1   0  -0.687  18.7905  19.4723  36.2950
 JB7  O5   O   O     0  -0.536  18.2237  21.3913  37.3895
 JB7  N1   N   NH1   0  -0.691  16.7294  19.7066  37.2709
 JB7  O2   O   O     0  -0.433  17.0180  20.1079  40.0159
 JB7  O1   O   OH1   0  -0.591  15.6419  21.8613  39.8693
 JB7  O3   O   OH1   0  -0.589  12.1771  18.2063  38.9468
 JB7  O4   O   O     0  -0.445  13.2688  16.3057  38.5481
 JB7  H1   H   HCH1  0   0.293  15.5116  21.3913  37.4841
 JB7  H2   H   HCH2  0   0.277  13.6732  20.3031  38.5348
 JB7  H3   H   HCH2  0   0.277  14.0905  19.4887  37.0454
 JB7  H4   H   HCH2  0   0.269  15.3506  17.7233  38.4527
 JB7  H5   H   HCH2  0   0.289  14.7279  18.5096  39.8851
 JB7  H6   H   HCR6  0   0.261  24.8677  16.1027  40.0432
 JB7  H7   H   HCR6  0   0.280  25.0517  13.9835  35.5836
 JB7  H8   H   HCH3  0   0.272  26.6457  18.9824  41.9861
 JB7  H9   H   HCH3  0   0.261  26.5364  17.4036  41.2082
 JB7  H10  H   HCH3  0   0.271  27.8095  18.5240  40.7425
 JB7  H11  H   HCH2  0   0.292  27.3313  17.1777  39.1075
 JB7  H12  H   HCH2  0   0.276  27.1332  17.6757  37.4521
 JB7  H13  H   HCR6  0   0.266  26.4071  15.9742  36.0502
 JB7  H14  H   HCR6  0   0.280  23.5170  14.1180  39.5987
 JB7  H15  H   HCH2  0   0.243  25.2774  18.8270  36.8029
 JB7  H16  H   HCH2  0   0.247  25.0166  20.2272  37.8201
 JB7  H17  H   HCH2  0   0.231  23.0899  19.0412  38.9234
 JB7  H18  H   HCH2  0   0.228  23.3352  17.6738  37.8506
 JB7  H19  H   HCH2  0   0.228  22.9533  19.1584  35.8783
 JB7  H20  H   HCH2  0   0.227  22.6923  20.5221  36.9493
 JB7  H21  H   HCH2  0   0.247  20.7879  19.2645  38.0389
 JB7  H22  H   HCH2  0   0.236  20.9827  17.9850  36.8557
 JB7  H23  H   HCH1  0   0.288  20.2667  20.9026  36.3051
 JB7  H24  H   HOH1  0   0.487  20.4719  18.3475  33.2555
 JB7  H25  H   HNH1  0   0.397  18.5502  18.5008  36.1680
 JB7  H26  H   HNH1  0   0.404  16.4782  18.8208  36.8633
 JB7  H27  H   HOH1  0   0.483  15.9180  22.0193  40.7848
 JB7  H28  H   HOH1  0   0.483  11.3986  17.6306  38.9037
 JB7  C6   C   C     0   0.765  17.9410  20.2602  37.0108
 JB7  C10  C   CH2   0  -0.443  22.5833  19.4355  36.8706
 JB7  BR   BR  BR    0  -0.048  23.1488  12.3971  37.2147
 JB7  C20  C   C     0   0.521  25.8462  19.0915  40.0182

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
 JB7  O6   C8   double    1.205  0.020  1.205
 JB7  O7   C8   single    1.326  0.020  1.326
 JB7  C8   C7   single    1.518  0.020  1.518
 JB7  C7   N2   single    1.444  0.020  1.444
 JB7  C7   C9   single    1.534  0.020  1.534
 JB7  N2   C6   single    1.362  0.020  1.362
 JB7  C6   N1   single    1.357  0.020  1.357
 JB7  C6   O5   double    1.226  0.020  1.226
 JB7  C9   C10  single    1.524  0.020  1.524
 JB7  C10  C11  single    1.524  0.020  1.524
 JB7  N1   C2   single    1.434  0.020  1.434
 JB7  C18  C19  aromatic  1.390  0.020  1.390
 JB7  C18  C17  aromatic  1.385  0.020  1.385
 JB7  C19  C14  aromatic  1.388  0.020  1.388
 JB7  C11  C12  single    1.525  0.020  1.525
 JB7  BR   C17  single    1.889  0.020  1.889
 JB7  C12  N3   single    1.457  0.020  1.457
 JB7  C17  C16  aromatic  1.389  0.020  1.389
 JB7  C2   C3   single    1.534  0.020  1.534
 JB7  C2   C1   single    1.521  0.020  1.521
 JB7  C3   C4   single    1.530  0.020  1.530
 JB7  C14  C13  single    1.509  0.020  1.509
 JB7  C14  C15  aromatic  1.392  0.020  1.392
 JB7  C4   C5   single    1.505  0.020  1.505
 JB7  C13  N3   single    1.449  0.020  1.449
 JB7  O4   C5   double    1.206  0.020  1.206
 JB7  N3   C20  single    1.354  0.020  1.354
 JB7  C1   O2   double    1.203  0.020  1.203
 JB7  C1   O1   single    1.326  0.020  1.326
 JB7  C5   O3   single    1.328  0.020  1.328
 JB7  C16  C15  aromatic  1.385  0.020  1.385
 JB7  C20  O8   double    1.224  0.020  1.224
 JB7  C20  C21  single    1.513  0.020  1.513
 JB7  C2   H1   single    0.970  0.020  1.090
 JB7  C3   H2   single    0.970  0.020  1.090
 JB7  C3   H3   single    0.970  0.020  1.090
 JB7  C4   H4   single    0.970  0.020  1.090
 JB7  C4   H5   single    0.970  0.020  1.090
 JB7  C15  H6   single    0.930  0.020  1.080
 JB7  C18  H7   single    0.930  0.020  1.080
 JB7  C21  H8   single    0.970  0.020  1.090
 JB7  C21  H9   single    0.970  0.020  1.090
 JB7  C21  H10  single    0.970  0.020  1.090
 JB7  C13  H11  single    0.970  0.020  1.090
 JB7  C13  H12  single    0.970  0.020  1.090
 JB7  C19  H13  single    0.930  0.020  1.080
 JB7  C16  H14  single    0.930  0.020  1.080
 JB7  C12  H15  single    0.970  0.020  1.090
 JB7  C12  H16  single    0.970  0.020  1.090
 JB7  C11  H17  single    0.970  0.020  1.090
 JB7  C11  H18  single    0.970  0.020  1.090
 JB7  C10  H19  single    0.970  0.020  1.090
 JB7  C10  H20  single    0.970  0.020  1.090
 JB7  C9   H21  single    0.970  0.020  1.090
 JB7  C9   H22  single    0.970  0.020  1.090
 JB7  C7   H23  single    0.970  0.020  1.090
 JB7  O7   H24  single    0.850  0.020  0.980
 JB7  N2   H25  single    0.890  0.020  1.040
 JB7  N1   H26  single    0.860  0.020  1.020
 JB7  O1   H27  single    0.850  0.020  0.980
 JB7  O3   H28  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
 JB7  O1   C1   O2   124.02  3.000
 JB7  O1   C1   C2   111.12  3.000
 JB7  O2   C1   C2   124.81  3.000
 JB7  H1   C2   N1   110.77  3.000
 JB7  H1   C2   C3   106.79  3.000
 JB7  N1   C2   C3   110.70  3.000
 JB7  H1   C2   C1   108.13  3.000
 JB7  C3   C2   C1   109.96  3.000
 JB7  N1   C2   C1   110.40  3.000
 JB7  H3   C3   H2   106.45  3.000
 JB7  H3   C3   C4   110.15  3.000
 JB7  H2   C3   C4   110.44  3.000
 JB7  H3   C3   C2   107.08  3.000
 JB7  H2   C3   C2   108.05  3.000
 JB7  C4   C3   C2   114.33  3.000
 JB7  H5   C4   H4   106.39  3.000
 JB7  H5   C4   C5   106.94  3.000
 JB7  H4   C4   C5   107.24  3.000
 JB7  H5   C4   C3   110.45  3.000
 JB7  H4   C4   C3   111.77  3.000
 JB7  C5   C4   C3   113.66  3.000
 JB7  O4   C5   O3   123.03  3.000
 JB7  O3   C5   C4   112.50  3.000
 JB7  O4   C5   C4   124.46  3.000
 JB7  H6   C15  C16  118.56  3.000
 JB7  H6   C15  C14  120.32  3.000
 JB7  C16  C15  C14  121.12  3.000
 JB7  C16  C17  BR   119.38  3.000
 JB7  C16  C17  C18  121.06  3.000
 JB7  BR   C17  C18  119.56  3.000
 JB7  H7   C18  C19  119.84  3.000
 JB7  H7   C18  C17  121.25  3.000
 JB7  C19  C18  C17  118.91  3.000
 JB7  H10  C21  H9   107.43  3.000
 JB7  H10  C21  H8   108.17  3.000
 JB7  H9   C21  H8   108.15  3.000
 JB7  H10  C21  C20  111.74  3.000
 JB7  H9   C21  C20  112.51  3.000
 JB7  H8   C21  C20  108.69  3.000
 JB7  C12  N3   C13  116.65  3.000
 JB7  C13  N3   C20  124.37  3.000
 JB7  C12  N3   C20  118.96  3.000
 JB7  H12  C13  H11  105.86  3.000
 JB7  H12  C13  C14  109.29  3.000
 JB7  H11  C13  C14  109.82  3.000
 JB7  H12  C13  N3   108.90  3.000
 JB7  H11  C13  N3   109.67  3.000
 JB7  C14  C13  N3   113.05  3.000
 JB7  C19  C14  C13  120.61  3.000
 JB7  C13  C14  C15  120.75  3.000
 JB7  C19  C14  C15  118.63  3.000
 JB7  H13  C19  C14  119.78  3.000
 JB7  H13  C19  C18  118.98  3.000
 JB7  C14  C19  C18  121.23  3.000
 JB7  H14  C16  C17  121.09  3.000
 JB7  H14  C16  C15  119.86  3.000
 JB7  C17  C16  C15  119.04  3.000
 JB7  H16  C12  H15  106.52  3.000
 JB7  H16  C12  C11  109.73  3.000
 JB7  H15  C12  C11  109.56  3.000
 JB7  H16  C12  N3   109.15  3.000
 JB7  H15  C12  N3   107.22  3.000
 JB7  C11  C12  N3   114.34  3.000
 JB7  H18  C11  H17  106.88  3.000
 JB7  H18  C11  C10  109.54  3.000
 JB7  H17  C11  C10  109.50  3.000
 JB7  H18  C11  C12  109.78  3.000
 JB7  H17  C11  C12  109.55  3.000
 JB7  C10  C11  C12  111.49  3.000
 JB7  H22  C9   H21  106.57  3.000
 JB7  H22  C9   C7   109.71  3.000
 JB7  H21  C9   C7   106.64  3.000
 JB7  H22  C9   C10  110.13  3.000
 JB7  H21  C9   C10  109.29  3.000
 JB7  C7   C9   C10  114.17  3.000
 JB7  H23  C7   N2   107.66  3.000
 JB7  H23  C7   C8   106.88  3.000
 JB7  N2   C7   C8   110.28  3.000
 JB7  H23  C7   C9   108.87  3.000
 JB7  N2   C7   C9   111.88  3.000
 JB7  C8   C7   C9   111.09  3.000
 JB7  O6   C8   O7   123.74  3.000
 JB7  O7   C8   C7   111.93  3.000
 JB7  O6   C8   C7   124.31  3.000
 JB7  H24  O7   C8   110.52  3.000
 JB7  H25  N2   C7   117.04  3.000
 JB7  H25  N2   C6   118.34  3.000
 JB7  C7   N2   C6   121.64  3.000
 JB7  H26  N1   C6   120.26  3.000
 JB7  H26  N1   C2   119.11  3.000
 JB7  C6   N1   C2   120.20  3.000
 JB7  H27  O1   C1   110.22  3.000
 JB7  H28  O3   C5   110.04  3.000
 JB7  N1   C6   O5   121.53  3.000
 JB7  O5   C6   N2   123.53  3.000
 JB7  N1   C6   N2   114.94  3.000
 JB7  H20  C10  H19  106.42  3.000
 JB7  H20  C10  C9   109.52  3.000
 JB7  H19  C10  C9   110.47  3.000
 JB7  H20  C10  C11  109.57  3.000
 JB7  H19  C10  C11  109.05  3.000
 JB7  C9   C10  C11  111.66  3.000
 JB7  N3   C20  C21  118.24  3.000
 JB7  C21  C20  O8   120.67  3.000
 JB7  N3   C20  O8   121.09  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
 JB7  CONST_01  C18  C19  C14  C15     0.00   0.0  0
 JB7  CONST_02  C18  C17  C16  C15     0.00   0.0  0
 JB7  CONST_03  C14  C19  C18  C17     0.00   0.0  0
 JB7  CONST_04  C14  C15  C16  C17     0.00   0.0  0
 JB7  CONST_05  C16  C17  C18  C19     0.00   0.0  0
 JB7  CONST_06  C16  C15  C14  C19     0.00   0.0  0
 JB7  CONST_07  BR   C17  C16  C15   180.00   0.0  0
 JB7  CONST_08  C13  C14  C19  C18   180.00   0.0  0
 JB7  CONST_09  C16  C15  C14  C13   180.00   0.0  0
 JB7  CONST_10  BR   C17  C18  C19   180.00   0.0  0
 JB7  CONST_11  H13  C19  C14  C15   180.00   0.0  0
 JB7  CONST_12  H6   C15  C16  C17   180.00   0.0  0
 JB7  CONST_13  H14  C16  C17  C18   180.00   0.0  0
 JB7  CONST_14  H7   C18  C19  C14   180.00   0.0  0
 JB7  CONST_15  O5   C6   N1   C2      0.00   0.0  0
 JB7  CONST_16  C12  N3   C20  O8      0.00   0.0  0
 JB7  CONST_17  C13  N3   C20  O8    180.00   0.0  0
 JB7  CONST_18  C12  N3   C20  C21   180.00   0.0  0
 JB7  CONST_19  C13  N3   C20  C21     0.00   0.0  0
 JB7  CONST_20  O5   C6   N2   C7      0.00   0.0  0
 JB7  CONST_21  N2   C6   N1   C2    180.00   0.0  0
 JB7  CONST_22  N1   C6   N2   C7    180.00   0.0  0
 JB7  CONST_23  H25  N2   C6   O5    180.00   0.0  0
 JB7  CONST_24  H26  N1   C6   O5    180.00   0.0  0
 JB7  CONST_25  H27  O1   C1   C2    180.00   0.0  0
 JB7  CONST_26  H28  O3   C5   C4    180.00   0.0  0
 JB7  CONST_27  H24  O7   C8   C7    180.00   0.0  0
 JB7  Var_01    N3   C13  C14  C15   -57.34  30.0  2
 JB7  Var_02    C14  C13  N3   C20   113.05  30.0  2
 JB7  Var_03    C5   C4   C3   C2   -172.77  30.0  3
 JB7  Var_04    O4   C5   C4   C3    136.56  30.0  3
 JB7  Var_05    C11  C12  N3   C20   -79.43  30.0  1
 JB7  Var_06    C10  C11  C12  N3    179.04  30.0  1
 JB7  Var_07    C9   C10  C11  C12  -179.81  30.0  1
 JB7  Var_08    C7   C9   C10  C11   172.92  30.0  1
 JB7  Var_09    H8   C21  C20  O8      3.40  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
 JB7  chir_01  C2  N1  C3  C1  negativ
 JB7  chir_02  C7  N2  C8  C9  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
 JB7  plan-1  C15  0.020
 JB7  plan-1  C17  0.020
 JB7  plan-1  C18  0.020
 JB7  plan-1  C13  0.020
 JB7  plan-1  C14  0.020
 JB7  plan-1  C19  0.020
 JB7  plan-1  C16  0.020
 JB7  plan-1  H6   0.020
 JB7  plan-1  H7   0.020
 JB7  plan-1  H13  0.020
 JB7  plan-1  H14  0.020
 JB7  plan-1  BR   0.020
 JB7  plan-2  C7   0.020
 JB7  plan-2  C8   0.020
 JB7  plan-2  O7   0.020
 JB7  plan-2  O6   0.020
 JB7  plan-2  H24  0.020
 JB7  plan-3  C2   0.020
 JB7  plan-3  C7   0.020
 JB7  plan-3  N2   0.020
 JB7  plan-3  O5   0.020
 JB7  plan-3  N1   0.020
 JB7  plan-3  H25  0.020
 JB7  plan-3  H26  0.020
 JB7  plan-3  C6   0.020
 JB7  plan-4  O8   0.020
 JB7  plan-4  C21  0.020
 JB7  plan-4  N3   0.020
 JB7  plan-4  C13  0.020
 JB7  plan-4  C12  0.020
 JB7  plan-4  C20  0.020
 JB7  plan-5  C1   0.020
 JB7  plan-5  C2   0.020
 JB7  plan-5  O2   0.020
 JB7  plan-5  O1   0.020
 JB7  plan-5  H27  0.020
 JB7  plan-6  C4   0.020
 JB7  plan-6  C5   0.020
 JB7  plan-6  O3   0.020
 JB7  plan-6  O4   0.020
 JB7  plan-6  H28  0.020

