# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 08:15:54 2022
#   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  58  33  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.401  17.1243  19.8483  39.5894
 JB7  C2   C   CH1    0  -0.186  16.3141  20.2581  38.3310
 JB7  C3   C   CH2    0  -0.430  14.8682  19.7590  38.4308
 JB7  C4   C   CH2    0  -0.598  14.7069  18.2487  38.5432
 JB7  C5   C   C      0   0.413  13.2575  17.7406  38.7046
 JB7  C15  C   CR16   0  -0.280  24.5909  15.7162  39.2323
 JB7  C17  C   CR6    0  -0.121  23.7294  14.2384  37.5622
 JB7  C18  C   CR16   0  -0.212  24.5363  14.8267  36.6029
 JB7  O8   O   O      0  -0.498  24.8246  20.3121  40.3679
 JB7  C21  C   CH3    0  -0.811  26.3195  18.7126  41.3023
 JB7  N3   N   NT     0  -0.435  25.5137  18.6879  38.9752
 JB7  C13  C   CH2    0  -0.414  26.2847  17.4962  38.6737
 JB7  C14  C   CR6    0   0.124  25.4105  16.3283  38.2878
 JB7  C19  C   CR16   0  -0.292  25.3752  15.8690  36.9783
 JB7  C16  C   CR16   0  -0.214  23.7503  14.6726  38.8814
 JB7  C12  C   CH2    0  -0.292  24.7462  19.2547  37.8743
 JB7  C11  C   CH2    0  -0.420  23.2720  18.8666  37.8665
 JB7  C9   C   CH2    0  -0.426  21.0739  19.0407  36.6484
 JB7  C7   C   CH1    0  -0.171  20.2170  19.6680  35.5327
 JB7  C8   C   C      0   0.406  20.5345  19.0165  34.1658
 JB7  O7   O   OC    -1  -0.598  19.7364  18.1478  33.7586
 JB7  O6   O   O      0  -0.598  21.5816  19.3937  33.6069
 JB7  N2   N   NH1    0  -0.683  18.8103  19.5125  35.8244
 JB7  O5   O   O      0  -0.559  18.6769  21.2282  37.2981
 JB7  N1   N   NH1    0  -0.672  16.9083  19.8128  37.0864
 JB7  O2   O   O      0  -0.604  17.9745  18.9458  39.4682
 JB7  O1   O   OC    -1  -0.615  16.8190  20.4568  40.6360
 JB7  O3   O   OC    -1  -0.603  12.3427  18.5866  38.7343
 JB7  O4   O   O      0  -0.625  13.1288  16.5014  38.7949
 JB7  H1   H   HCH1   0   0.219  16.2699  21.3501  38.3075
 JB7  H2   H   HCH2   0   0.212  14.4160  20.2354  39.3018
 JB7  H3   H   HCH2   0   0.208  14.3110  20.1244  37.5637
 JB7  H4   H   HCH2   0   0.210  15.1287  17.7425  37.6666
 JB7  H5   H   HCH2   0   0.222  15.2861  17.8688  39.3911
 JB7  H6   H   HCR6   0   0.268  24.5972  16.0577  40.2608
 JB7  H7   H   HCR6   0   0.278  24.5194  14.4912  35.5745
 JB7  H8   H   HCH3   0   0.269  26.1661  19.3082  42.1983
 JB7  H9   H   HCH3   0   0.266  26.0426  17.6823  41.5261
 JB7  H10  H   HCH3   0   0.265  27.3840  18.7206  41.0646
 JB7  H11  H   HCH2   0   0.288  26.8963  17.2268  39.5313
 JB7  H12  H   HCH2   0   0.271  26.9776  17.7162  37.8566
 JB7  H13  H   HCR6   0   0.265  26.0032  16.3337  36.2275
 JB7  H14  H   HCR6   0   0.279  23.1220  14.2096  39.6306
 JB7  H15  H   HCH2   0   0.241  25.2174  18.9213  36.9463
 JB7  H16  H   HCH2   0   0.244  24.8411  20.3415  37.8936
 JB7  H17  H   HCH2   0   0.220  22.7978  19.2125  38.7886
 JB7  H18  H   HCH2   0   0.224  23.1778  17.7780  37.8572
 JB7  H19  H   HCH2   0   0.218  23.0347  19.1208  35.7436
 JB7  H20  H   HCH2   0   0.206  22.6148  20.5390  36.6787
 JB7  H21  H   HCH2   0   0.218  20.6329  19.3240  37.6085
 JB7  H22  H   HCH2   0   0.206  20.9907  17.9495  36.5897
 JB7  H23  H   HCH1   0   0.214  20.4510  20.7343  35.4739
 JB7  H25  H   HNH1   0   0.366  18.3865  18.6879  35.4269
 JB7  H26  H   HNH1   0   0.367  16.7025  18.8568  36.8396
 JB7  C6   C   C      0   0.719  18.1764  20.2303  36.7831
 JB7  C20  C   C      0   0.520  25.4890  19.3006  40.1827
 JB7  C10  C   CH2    0  -0.422  22.5413  19.4458  36.6617
 JB7  BR   BR  BR     0  -0.048  22.5792  12.8231  37.0690

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   deloc     1.245  0.020  1.245
 JB7  O7   C8   deloc     1.248  0.020  1.248
 JB7  C8   C7   single    1.547  0.020  1.547
 JB7  C7   N2   single    1.445  0.020  1.445
 JB7  C7   C9   single    1.540  0.020  1.540
 JB7  N2   C6   single    1.355  0.020  1.355
 JB7  C6   N1   single    1.369  0.020  1.369
 JB7  C6   O5   double    1.229  0.020  1.229
 JB7  C9   C10  single    1.522  0.020  1.522
 JB7  C10  C11  single    1.523  0.020  1.523
 JB7  N1   C2   single    1.449  0.020  1.449
 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    1.524  0.020  1.524
 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    1.533  0.020  1.533
 JB7  C2   C1   single    1.552  0.020  1.552
 JB7  C3   C4   single    1.523  0.020  1.523
 JB7  C14  C13  single    1.509  0.020  1.509
 JB7  C14  C15  aromatic  1.392  0.020  1.392
 JB7  C4   C5   single    1.544  0.020  1.544
 JB7  C13  N3   single    1.451  0.020  1.451
 JB7  O4   C5   deloc     1.249  0.020  1.249
 JB7  N3   C20  single    1.354  0.020  1.354
 JB7  C1   O2   deloc     1.246  0.020  1.246
 JB7  C1   O1   deloc     1.249  0.020  1.249
 JB7  C5   O3   deloc     1.246  0.020  1.246
 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  N2   H25  single    0.860  0.020  1.020
 JB7  N1   H26  single    0.890  0.020  1.040

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   126.98  3.000
 JB7  O1   C1   C2   115.05  3.000
 JB7  O2   C1   C2   117.95  3.000
 JB7  H1   C2   N1   107.76  3.000
 JB7  H1   C2   C3   106.77  3.000
 JB7  N1   C2   C3   110.04  3.000
 JB7  H1   C2   C1   107.60  3.000
 JB7  C3   C2   C1   110.72  3.000
 JB7  N1   C2   C1   113.66  3.000
 JB7  H3   C3   H2   106.01  3.000
 JB7  H3   C3   C4   109.63  3.000
 JB7  H2   C3   C4   109.28  3.000
 JB7  H3   C3   C2   108.68  3.000
 JB7  H2   C3   C2   107.51  3.000
 JB7  C4   C3   C2   115.31  3.000
 JB7  H5   C4   H4   104.80  3.000
 JB7  H5   C4   C5   107.54  3.000
 JB7  H4   C4   C5   107.02  3.000
 JB7  H5   C4   C3   110.19  3.000
 JB7  H4   C4   C3   110.98  3.000
 JB7  C5   C4   C3   115.68  3.000
 JB7  O4   C5   O3   126.58  3.000
 JB7  O3   C5   C4   117.91  3.000
 JB7  O4   C5   C4   115.51  3.000
 JB7  H6   C15  C16  118.78  3.000
 JB7  H6   C15  C14  120.12  3.000
 JB7  C16  C15  C14  121.10  3.000
 JB7  C16  C17  BR   119.43  3.000
 JB7  C16  C17  C18  121.09  3.000
 JB7  BR   C17  C18  119.48  3.000
 JB7  H7   C18  C19  119.93  3.000
 JB7  H7   C18  C17  121.18  3.000
 JB7  C19  C18  C17  118.90  3.000
 JB7  H10  C21  H9   107.43  3.000
 JB7  H10  C21  H8   108.27  3.000
 JB7  H9   C21  H8   108.23  3.000
 JB7  H10  C21  C20  111.81  3.000
 JB7  H9   C21  C20  112.32  3.000
 JB7  H8   C21  C20  108.64  3.000
 JB7  C12  N3   C13  116.26  3.000
 JB7  C13  N3   C20  124.51  3.000
 JB7  C12  N3   C20  119.22  3.000
 JB7  H12  C13  H11  106.43  3.000
 JB7  H12  C13  C14  109.37  3.000
 JB7  H11  C13  C14  109.62  3.000
 JB7  H12  C13  N3   109.07  3.000
 JB7  H11  C13  N3   109.79  3.000
 JB7  C14  C13  N3   112.39  3.000
 JB7  C19  C14  C13  120.80  3.000
 JB7  C13  C14  C15  120.52  3.000
 JB7  C19  C14  C15  118.65  3.000
 JB7  H13  C19  C14  119.80  3.000
 JB7  H13  C19  C18  118.97  3.000
 JB7  C14  C19  C18  121.23  3.000
 JB7  H14  C16  C17  121.01  3.000
 JB7  H14  C16  C15  119.96  3.000
 JB7  C17  C16  C15  119.03  3.000
 JB7  H16  C12  H15  106.34  3.000
 JB7  H16  C12  C11  109.74  3.000
 JB7  H15  C12  C11  109.57  3.000
 JB7  H16  C12  N3   109.17  3.000
 JB7  H15  C12  N3   107.21  3.000
 JB7  C11  C12  N3   114.47  3.000
 JB7  H18  C11  H17  106.56  3.000
 JB7  H18  C11  C10  109.30  3.000
 JB7  H17  C11  C10  109.80  3.000
 JB7  H18  C11  C12  109.69  3.000
 JB7  H17  C11  C12  109.56  3.000
 JB7  C10  C11  C12  111.78  3.000
 JB7  H22  C9   H21  105.92  3.000
 JB7  H22  C9   C7   108.93  3.000
 JB7  H21  C9   C7   107.81  3.000
 JB7  H22  C9   C10  109.79  3.000
 JB7  H21  C9   C10  108.18  3.000
 JB7  C7   C9   C10  115.73  3.000
 JB7  H23  C7   N2   108.92  3.000
 JB7  H23  C7   C8   108.62  3.000
 JB7  N2   C7   C8   109.44  3.000
 JB7  H23  C7   C9   108.49  3.000
 JB7  N2   C7   C9   110.58  3.000
 JB7  C8   C7   C9   110.75  3.000
 JB7  O6   C8   O7   127.02  3.000
 JB7  O7   C8   C7   116.76  3.000
 JB7  O6   C8   C7   116.20  3.000
 JB7  H25  N2   C7   114.67  3.000
 JB7  H25  N2   C6   121.02  3.000
 JB7  C7   N2   C6   122.76  3.000
 JB7  H26  N1   C6   115.08  3.000
 JB7  H26  N1   C2   114.69  3.000
 JB7  C6   N1   C2   118.44  3.000
 JB7  N1   C6   O5   122.13  3.000
 JB7  O5   C6   N2   122.41  3.000
 JB7  N1   C6   N2   115.37  3.000
 JB7  N3   C20  C21  118.29  3.000
 JB7  C21  C20  O8   120.47  3.000
 JB7  N3   C20  O8   121.24  3.000
 JB7  H20  C10  H19  106.24  3.000
 JB7  H20  C10  C9   109.28  3.000
 JB7  H19  C10  C9   110.43  3.000
 JB7  H20  C10  C11  109.56  3.000
 JB7  H19  C10  C11  109.58  3.000
 JB7  C9   C10  C11  111.60  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_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_22  N1   C6   N2   C7    180.00   0.0  0
 JB7  CONST_23  H25  N2   C6   O5    180.00   0.0  0
 JB7  Var_01    N3   C13  C14  C15   -68.95  30.0  2
 JB7  Var_02    C14  C13  N3   C20   117.50  30.0  2
 JB7  Var_03    C5   C4   C3   C2    177.50  30.0  3
 JB7  Var_04    O4   C5   C4   C3    179.92  30.0  3
 JB7  Var_05    C11  C12  N3   C20   -82.76  30.0  1
 JB7  Var_06    C10  C11  C12  N3   -177.72  30.0  1
 JB7  Var_07    C9   C10  C11  C12   179.25  30.0  1
 JB7  Var_08    C7   C9   C10  C11   175.22  30.0  2
 JB7  Var_09    H8   C21  C20  O8      2.04  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-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-6  C4   0.020
 JB7  plan-6  C5   0.020
 JB7  plan-6  O3   0.020
 JB7  plan-6  O4   0.020

