# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 13:49:03 2020
#   Inital geometry file: a 154 line input string
#   Ligand name: N-[(2-chlorobiphenyl-4-yl)methyl]-beta-alanyl-N-(3-carboxyphenyl)-beta-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(NC(=O)CCNC(=O)CCNCc2ccc(c(Cl)c2)c3ccccc3)c1
#
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
 54S  54S  N-[(2-chlorobiphenyl-4-yl)methyl]-beta-alanyl-N-(3-carboxyphenyl)-beta-alaninamide  ligand  60  34  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_54S
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
 54S  C11  C   CH2   0  -0.243   -1.3601   1.6298   0.2347
 54S  C12  C   CH2   0  -0.302   -3.7467   1.9437   0.4298
 54S  C13  C   CR6   0   0.055   -5.0889   1.2600   0.4300
 54S  C14  C   CR16  0  -0.283   -6.1698   1.8093   1.1106
 54S  C16  C   CR6   0   0.140   -7.6325   0.0256   0.3512
 54S  C17  C   CR6   0  -0.105   -6.5310  -0.5210  -0.3066
 54S  C18  C   CR16  0  -0.233   -5.2818   0.0772  -0.2748
 54S  C19  C   CR6   0   0.063   -8.9808  -0.5819   0.3304
 54S  C20  C   CR16  0  -0.285   -9.6607  -0.7879  -0.8698
 54S  C21  C   CR16  0  -0.243  -10.9397  -1.3242  -0.8718
 54S  C22  C   CR16  0  -0.263  -11.5576  -1.6656   0.3250
 54S  C23  C   CR16  0  -0.242  -10.8904  -1.4597   1.5245
 54S  CL   CL  CL    0  -0.132   -6.6815  -2.0239  -1.1650
 54S  C24  C   CR16  0  -0.294   -9.6111  -0.9197   1.5266
 54S  C15  C   CR16  0  -0.298   -7.4144   1.2031   1.0662
 54S  N2   N   NH1   0  -0.601   -2.6543   0.9960   0.3961
 54S  C10  C   CH2   0  -0.605   -0.2702   0.5736   0.1756
 54S  C9   C   C     0   0.565    1.0990   1.1485  -0.1168
 54S  O3   O   O     0  -0.504    1.2568   2.1881  -0.7431
 54S  N1   N   NH1   0  -0.652    2.1302   0.4104   0.3235
 54S  C8   C   CH2   0  -0.230    3.5109   0.7584   0.0644
 54S  C7   C   CH2   0  -0.643    4.3957  -0.4451   0.3366
 54S  C6   C   C     0   0.566    5.8574  -0.1589   0.0694
 54S  O2   O   O     0  -0.463    6.2593   0.9282  -0.2995
 54S  N    N   NH1   0  -0.753    6.6604  -1.2348   0.2832
 54S  C5   C   CR6   0   0.401    8.0469  -1.3450   0.1650
 54S  C4   C   CR16  0  -0.336    8.6160  -2.5628   0.5494
 54S  C3   C   CR16  0  -0.229    9.9810  -2.7634   0.4645
 54S  C2   C   CR16  0  -0.285   10.8148  -1.7582  -0.0024
 54S  C25  C   CR16  0  -0.335    8.8785  -0.3341  -0.3092
 54S  C1   C   CR6   0  -0.065   10.2539  -0.5453  -0.3882
 54S  C    C   C     0   0.538   11.0848   0.5760  -0.9003
 54S  O1   O   O     0  -0.437   10.6360   1.6380  -1.2596
 54S  O    O   OH1   0  -0.594   12.3793   0.2926  -0.9235
 54S  H1   H   HCH2  0   0.229   -1.3717   2.1961  -0.6991
 54S  H2   H   HCH2  0   0.202   -1.1380   2.3522   1.0347
 54S  H3   H   HCH2  0   0.248   -3.6757   2.5693  -0.4666
 54S  H4   H   HCH2  0   0.220   -3.6962   2.6375   1.2822
 54S  H5   H   HCR6  0   0.255   -6.0420   2.7214   1.6807
 54S  H6   H   HCR6  0   0.269   -4.4476  -0.3809  -0.7888
 54S  H7   H   HCR6  0   0.254   -9.1950  -0.5156  -1.8081
 54S  H8   H   HCR6  0   0.258  -11.4562  -1.4734  -1.8112
 54S  H9   H   HCR6  0   0.258  -12.5542  -2.0878   0.3214
 54S  H10  H   HCR6  0   0.258  -11.3633  -1.7204   2.4624
 54S  H11  H   HCR6  0   0.255   -9.0947  -0.7679   2.4665
 54S  H12  H   HCR6  0   0.261   -8.2455   1.6554   1.5926
 54S  H13  H   HNH1  0   0.346   -2.6612   0.4556   1.2540
 54S  H15  H   HCH2  0   0.255   -0.2500  -0.0009   1.1058
 54S  H16  H   HCH2  0   0.275   -0.5057  -0.1416  -0.6192
 54S  H17  H   HNH1  0   0.402    1.9366  -0.4076   0.8783
 54S  H18  H   HCH2  0   0.246    3.6137   1.0715  -0.9750
 54S  H19  H   HCH2  0   0.242    3.8183   1.6033   0.6860
 54S  H20  H   HCH2  0   0.289    4.2883  -0.7685   1.3773
 54S  H21  H   HCH2  0   0.290    4.0799  -1.2925  -0.2800
 54S  H22  H   HNH1  0   0.421    6.1962  -2.0758   0.5927
 54S  H23  H   HCR6  0   0.281    7.9816  -3.3598   0.9196
 54S  H24  H   HCR6  0   0.271   10.3974  -3.7137   0.7697
 54S  H25  H   HCR6  0   0.268   11.8799  -1.9299  -0.0600
 54S  H26  H   HCR6  0   0.288    8.4718   0.6134  -0.6201
 54S  H27  H   HOH1  0   0.488   12.8761   1.0522  -1.2619

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
 54S  CL   C17  single    1.737  0.020  1.737
 54S  C17  C18  aromatic  1.385  0.020  1.385
 54S  C17  C16  aromatic  1.395  0.020  1.395
 54S  C18  C13  aromatic  1.390  0.020  1.390
 54S  C23  C24  aromatic  1.389  0.020  1.389
 54S  C23  C22  aromatic  1.388  0.020  1.388
 54S  C24  C19  aromatic  1.394  0.020  1.394
 54S  C22  C21  aromatic  1.390  0.020  1.390
 54S  C21  C20  aromatic  1.387  0.020  1.387
 54S  C19  C20  aromatic  1.395  0.020  1.395
 54S  C19  C16  single    1.479  0.020  1.479
 54S  C16  C15  aromatic  1.395  0.020  1.395
 54S  C13  C12  single    1.506  0.020  1.506
 54S  C13  C14  aromatic  1.390  0.020  1.390
 54S  C12  N2   single    1.447  0.020  1.447
 54S  C15  C14  aromatic  1.385  0.020  1.385
 54S  N2   C11  single    1.450  0.020  1.450
 54S  C11  C10  single    1.519  0.020  1.519
 54S  O3   C9   double    1.224  0.020  1.224
 54S  C10  C9   single    1.514  0.020  1.514
 54S  C9   N1   single    1.342  0.020  1.342
 54S  N1   C8   single    1.447  0.020  1.447
 54S  C8   C7   single    1.518  0.020  1.518
 54S  C7   C6   single    1.513  0.020  1.513
 54S  C6   N    single    1.359  0.020  1.359
 54S  C6   O2   double    1.216  0.020  1.216
 54S  N    C5   single    1.396  0.020  1.396
 54S  C5   C25  aromatic  1.392  0.020  1.392
 54S  C5   C4   aromatic  1.398  0.020  1.398
 54S  C25  C1   aromatic  1.394  0.020  1.394
 54S  O1   C    double    1.208  0.020  1.208
 54S  C4   C3   aromatic  1.382  0.020  1.382
 54S  C1   C    single    1.487  0.020  1.487
 54S  C1   C2   aromatic  1.391  0.020  1.391
 54S  C    O    single    1.325  0.020  1.325
 54S  C3   C2   aromatic  1.387  0.020  1.387
 54S  C11  H1   single    0.970  0.020  1.090
 54S  C11  H2   single    0.970  0.020  1.090
 54S  C12  H3   single    0.970  0.020  1.090
 54S  C12  H4   single    0.970  0.020  1.090
 54S  C14  H5   single    0.930  0.020  1.080
 54S  C18  H6   single    0.930  0.020  1.080
 54S  C20  H7   single    0.930  0.020  1.080
 54S  C21  H8   single    0.930  0.020  1.080
 54S  C22  H9   single    0.930  0.020  1.080
 54S  C23  H10  single    0.930  0.020  1.080
 54S  C24  H11  single    0.930  0.020  1.080
 54S  C15  H12  single    0.930  0.020  1.080
 54S  N2   H13  single    0.890  0.020  1.040
 54S  C10  H15  single    0.970  0.020  1.090
 54S  C10  H16  single    0.970  0.020  1.090
 54S  N1   H17  single    0.860  0.020  1.020
 54S  C8   H18  single    0.970  0.020  1.090
 54S  C8   H19  single    0.970  0.020  1.090
 54S  C7   H20  single    0.970  0.020  1.090
 54S  C7   H21  single    0.970  0.020  1.090
 54S  N    H22  single    0.860  0.020  1.020
 54S  C4   H23  single    0.930  0.020  1.080
 54S  C3   H24  single    0.930  0.020  1.080
 54S  C2   H25  single    0.930  0.020  1.080
 54S  C25  H26  single    0.930  0.020  1.080
 54S  O    H27  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
 54S  H2   C11  H1   106.46  3.000
 54S  H2   C11  C10  109.87  3.000
 54S  H1   C11  C10  109.57  3.000
 54S  H2   C11  N2   112.71  3.000
 54S  H1   C11  N2   108.20  3.000
 54S  C10  C11  N2   109.93  3.000
 54S  H4   C12  H3   105.72  3.000
 54S  H4   C12  N2   113.36  3.000
 54S  H3   C12  N2   107.82  3.000
 54S  H4   C12  C13  109.09  3.000
 54S  H3   C12  C13  108.48  3.000
 54S  N2   C12  C13  112.06  3.000
 54S  C18  C13  C14  118.45  3.000
 54S  C14  C13  C12  120.90  3.000
 54S  C18  C13  C12  120.65  3.000
 54S  H5   C14  C15  119.43  3.000
 54S  H5   C14  C13  119.90  3.000
 54S  C15  C14  C13  120.66  3.000
 54S  C15  C16  C19  119.77  3.000
 54S  C15  C16  C17  116.69  3.000
 54S  C19  C16  C17  123.53  3.000
 54S  CL   C17  C18  117.58  3.000
 54S  C18  C17  C16  122.15  3.000
 54S  CL   C17  C16  120.24  3.000
 54S  H6   C18  C17  120.11  3.000
 54S  H6   C18  C13  119.61  3.000
 54S  C17  C18  C13  120.27  3.000
 54S  C24  C19  C20  118.84  3.000
 54S  C20  C19  C16  121.15  3.000
 54S  C24  C19  C16  119.98  3.000
 54S  H7   C20  C21  119.53  3.000
 54S  H7   C20  C19  119.94  3.000
 54S  C21  C20  C19  120.53  3.000
 54S  H8   C21  C22  120.10  3.000
 54S  H8   C21  C20  119.65  3.000
 54S  C22  C21  C20  120.25  3.000
 54S  H9   C22  C23  120.23  3.000
 54S  H9   C22  C21  120.16  3.000
 54S  C23  C22  C21  119.62  3.000
 54S  H10  C23  C24  119.67  3.000
 54S  H10  C23  C22  120.21  3.000
 54S  C24  C23  C22  120.12  3.000
 54S  H11  C24  C23  119.68  3.000
 54S  H11  C24  C19  119.68  3.000
 54S  C23  C24  C19  120.64  3.000
 54S  H12  C15  C16  118.80  3.000
 54S  H12  C15  C14  119.43  3.000
 54S  C16  C15  C14  121.77  3.000
 54S  H13  N2   C12  108.92  3.000
 54S  H13  N2   C11  109.46  3.000
 54S  C12  N2   C11  112.97  3.000
 54S  H16  C10  H15  106.16  3.000
 54S  H16  C10  C9   107.60  3.000
 54S  H15  C10  C9   110.31  3.000
 54S  H16  C10  C11  109.16  3.000
 54S  H15  C10  C11  110.22  3.000
 54S  C9   C10  C11  113.11  3.000
 54S  N1   C9   O3   122.40  3.000
 54S  N1   C9   C10  115.01  3.000
 54S  O3   C9   C10  122.56  3.000
 54S  H17  N1   C8   118.51  3.000
 54S  H17  N1   C9   118.66  3.000
 54S  C8   N1   C9   122.82  3.000
 54S  H19  C8   H18  107.08  3.000
 54S  H19  C8   C7   110.30  3.000
 54S  H18  C8   C7   110.10  3.000
 54S  H19  C8   N1   110.63  3.000
 54S  H18  C8   N1   109.24  3.000
 54S  C7   C8   N1   109.46  3.000
 54S  H21  C7   H20  106.17  3.000
 54S  H21  C7   C6   109.00  3.000
 54S  H20  C7   C6   108.57  3.000
 54S  H21  C7   C8   110.16  3.000
 54S  H20  C7   C8   110.32  3.000
 54S  C6   C7   C8   112.41  3.000
 54S  N    C6   O2   124.05  3.000
 54S  O2   C6   C7   122.80  3.000
 54S  N    C6   C7   113.15  3.000
 54S  H22  N    C5   114.65  3.000
 54S  H22  N    C6   115.85  3.000
 54S  C5   N    C6   129.49  3.000
 54S  C25  C5   C4   118.88  3.000
 54S  C4   C5   N    116.73  3.000
 54S  C25  C5   N    124.39  3.000
 54S  H23  C4   C3   119.49  3.000
 54S  H23  C4   C5   119.75  3.000
 54S  C3   C4   C5   120.76  3.000
 54S  H24  C3   C2   120.03  3.000
 54S  H24  C3   C4   119.36  3.000
 54S  C2   C3   C4   120.61  3.000
 54S  H25  C2   C1   121.43  3.000
 54S  H25  C2   C3   119.70  3.000
 54S  C1   C2   C3   118.88  3.000
 54S  H26  C25  C1   119.31  3.000
 54S  H26  C25  C5   120.77  3.000
 54S  C1   C25  C5   119.91  3.000
 54S  C    C1   C25  117.18  3.000
 54S  C    C1   C2   121.86  3.000
 54S  C25  C1   C2   120.96  3.000
 54S  O    C    O1   123.08  3.000
 54S  O    C    C1   113.00  3.000
 54S  O1   C    C1   123.92  3.000
 54S  H27  O    C    109.84  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
 54S  CONST_01  C16  C17  C18  C13     0.00   0.0  0
 54S  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 54S  CONST_03  C17  C18  C13  C14     0.00   0.0  0
 54S  CONST_04  C17  C16  C15  C14     0.00   0.0  0
 54S  CONST_05  C19  C16  C15  C14   180.00   0.0  0
 54S  CONST_06  C23  C24  C19  C16   180.00   0.0  0
 54S  CONST_07  C21  C20  C19  C16   180.00   0.0  0
 54S  CONST_10  C19  C16  C17  C18   180.00   0.0  0
 54S  CONST_11  C15  C16  C17  C18     0.00   0.0  0
 54S  CONST_12  C15  C14  C13  C18     0.00   0.0  0
 54S  CONST_13  C22  C23  C24  C19     0.00   0.0  0
 54S  CONST_14  C22  C21  C20  C19     0.00   0.0  0
 54S  CONST_15  C23  C22  C21  C20     0.00   0.0  0
 54S  CONST_16  C23  C24  C19  C20     0.00   0.0  0
 54S  CONST_18  C24  C23  C22  C21     0.00   0.0  0
 54S  CONST_19  C24  C19  C20  C21     0.00   0.0  0
 54S  CONST_21  C2   C1   C25  C5      0.00   0.0  0
 54S  CONST_22  C2   C3   C4   C5      0.00   0.0  0
 54S  CONST_23  C1   C25  C5   C4      0.00   0.0  0
 54S  CONST_24  C1   C2   C3   C4      0.00   0.0  0
 54S  CONST_25  C25  C5   C4   C3      0.00   0.0  0
 54S  CONST_26  C25  C1   C2   C3      0.00   0.0  0
 54S  CONST_27  C17  C18  C13  C12   180.00   0.0  0
 54S  CONST_28  C15  C14  C13  C12   180.00   0.0  0
 54S  CONST_29  CL   C17  C18  C13   180.00   0.0  0
 54S  CONST_30  CL   C17  C16  C19     0.00   0.0  0
 54S  CONST_31  C15  C16  C17  CL    180.00   0.0  0
 54S  CONST_32  C1   C25  C5   N     180.00   0.0  0
 54S  CONST_33  C3   C4   C5   N     180.00   0.0  0
 54S  CONST_34  C    C1   C25  C5    180.00   0.0  0
 54S  CONST_35  C    C1   C2   C3    180.00   0.0  0
 54S  CONST_36  H12  C15  C14  C13   180.00   0.0  0
 54S  CONST_37  H6   C18  C13  C14   180.00   0.0  0
 54S  CONST_38  H11  C24  C19  C16     0.00   0.0  0
 54S  CONST_39  H7   C20  C19  C16     0.00   0.0  0
 54S  CONST_40  H5   C14  C15  C16   180.00   0.0  0
 54S  CONST_41  H10  C23  C24  C19   180.00   0.0  0
 54S  CONST_42  H8   C21  C20  C19   180.00   0.0  0
 54S  CONST_43  H9   C22  C21  C20   180.00   0.0  0
 54S  CONST_44  H24  C3   C4   C5    180.00   0.0  0
 54S  CONST_45  H26  C25  C5   C4    180.00   0.0  0
 54S  CONST_46  H25  C2   C3   C4    180.00   0.0  0
 54S  CONST_47  H23  C4   C3   C2    180.00   0.0  0
 54S  CONST_48  C25  C5   N    C6      0.00   0.0  0
 54S  CONST_49  C4   C5   N    C6    180.00   0.0  0
 54S  CONST_50  H22  N    C5   C4      0.00   0.0  0
 54S  CONST_51  C5   N    C6   C7    180.00   0.0  0
 54S  CONST_52  C5   N    C6   O2      0.00   0.0  0
 54S  CONST_53  H27  O    C    C1    180.00   0.0  0
 54S  CONST_54  C8   N1   C9   C10   180.00   0.0  0
 54S  CONST_55  C8   N1   C9   O3      0.00   0.0  0
 54S  CONST_56  H17  N1   C9   C10     0.00   0.0  0
 54S  Var_01    N2   C12  C13  C14   146.67  30.0  2
 54S  Var_02    O1   C    C1   C2    179.11  30.0  2
 54S  Var_03    C13  C12  N2   C11   173.09  30.0  1
 54S  Var_04    O3   C9   C10  C11   -27.19  30.0  3
 54S  Var_05    C10  C11  N2   C12  -178.68  30.0  3
 54S  Var_06    C9   C10  C11  N2    174.83  30.0  3
 54S  Var_07    C7   C8   N1   C9   -163.99  30.0  3
 54S  Var_08    C6   C7   C8   N1    179.29  30.0  3
 54S  Var_09    N    C6   C7   C8   -178.78  30.0  3

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
 54S  plan-1  C12  0.020
 54S  plan-1  C13  0.020
 54S  plan-1  C14  0.020
 54S  plan-1  C16  0.020
 54S  plan-1  C17  0.020
 54S  plan-1  C18  0.020
 54S  plan-1  C19  0.020
 54S  plan-1  CL   0.020
 54S  plan-1  C15  0.020
 54S  plan-1  H5   0.020
 54S  plan-1  H6   0.020
 54S  plan-1  H12  0.020
 54S  plan-2  C16  0.020
 54S  plan-2  C19  0.020
 54S  plan-2  C20  0.020
 54S  plan-2  C21  0.020
 54S  plan-2  C22  0.020
 54S  plan-2  C23  0.020
 54S  plan-2  C24  0.020
 54S  plan-2  H7   0.020
 54S  plan-2  H8   0.020
 54S  plan-2  H9   0.020
 54S  plan-2  H10  0.020
 54S  plan-2  H11  0.020
 54S  plan-3  N    0.020
 54S  plan-3  C5   0.020
 54S  plan-3  C4   0.020
 54S  plan-3  C3   0.020
 54S  plan-3  C2   0.020
 54S  plan-3  C25  0.020
 54S  plan-3  C1   0.020
 54S  plan-3  C    0.020
 54S  plan-3  H23  0.020
 54S  plan-3  H24  0.020
 54S  plan-3  H25  0.020
 54S  plan-3  H26  0.020
 54S  plan-4  C10  0.020
 54S  plan-4  C9   0.020
 54S  plan-4  O3   0.020
 54S  plan-4  N1   0.020
 54S  plan-4  C8   0.020
 54S  plan-4  H17  0.020
 54S  plan-5  C7   0.020
 54S  plan-5  C6   0.020
 54S  plan-5  O2   0.020
 54S  plan-5  N    0.020
 54S  plan-5  C5   0.020
 54S  plan-5  H22  0.020
 54S  plan-6  C1   0.020
 54S  plan-6  C    0.020
 54S  plan-6  O1   0.020
 54S  plan-6  O    0.020
 54S  plan-6  H27  0.020

