# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 07:20:16 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: 3-({(3R)-1-[(5-bromothiophen-2-yl)carbonyl]pyrrolidin-3-yl}oxy)-N-methyl-2'-[(methylsulfonyl)amino]biphenyl-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1ccc(cc1O[C@@H]2CCN(C2)C(=O)c3sc(Br)cc3)c4ccccc4N[S](C)(=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
 EL1  EL1  3-({(3R)-1-[(5-bromothiophen-2-yl)carbonyl]pyrrolidin-3-yl}oxy)-N-methyl-2'-[(methylsulfonyl)amino]biphenyl-4-carboxamide  ligand  59  35  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EL1
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
 EL1  C01  C   CH3   0  -0.516  -2.4419   5.9651  -2.4125
 EL1  N05  N   NH1   0  -0.612  -2.5025   4.5809  -2.0055
 EL1  C07  C   C     0   0.506  -1.4024   3.8561  -1.7629
 EL1  O08  O   O     0  -0.480  -0.2703   4.3050  -1.8582
 EL1  C09  C   CR6   0  -0.171  -1.6673   2.4263  -1.4027
 EL1  C10  C   CR16  0  -0.234  -2.4046   1.6196  -2.2567
 EL1  C12  C   CR16  0  -0.353  -2.5983   0.2722  -1.9887
 EL1  C14  C   CR6   0   0.085  -2.0762  -0.2788  -0.8247
 EL1  C15  C   CR16  0  -0.423  -1.3476   0.5264   0.0491
 EL1  C17  C   CR6   0   0.413  -1.1213   1.8670  -0.2400
 EL1  O18  O   O2    0  -0.467  -0.4312   2.7008   0.5567
 EL1  C19  C   CH1   0  -0.007   0.3129   2.1904   1.6403
 EL1  C21  C   CH2   0  -0.508   0.9786   3.3345   2.3818
 EL1  C24  C   CH2   0  -0.270   2.0892   2.6393   3.1517
 EL1  N27  N   NT    0  -0.501   2.4601   1.5220   2.2811
 EL1  C28  C   CH2   0  -0.301   1.5004   1.3184   1.2097
 EL1  C31  C   C     0   0.576   3.4995   0.7396   2.6198
 EL1  O32  O   O     0  -0.487   4.1248   0.9299   3.6568
 EL1  C33  C   CR5   0  -0.335   3.9240  -0.3769   1.7377
 EL1  C34  C   CR15  0  -0.165   4.7779  -1.3573   2.1668
 EL1  C36  C   CR15  0  -0.144   5.1254  -2.2926   1.1666
 EL1  C38  C   CR5   0  -0.328   4.5359  -1.9894  -0.0234
 EL1  BR   BR  BR    0   0.040   4.6972  -2.9147  -1.6238
 EL1  S40  S   S2    0   0.293   3.5514  -0.5942   0.0622
 EL1  C41  C   CR6   0   0.064  -2.2586  -1.7088  -0.4911
 EL1  C42  C   CR16  0  -0.298  -1.1353  -2.5107  -0.2933
 EL1  C44  C   CR16  0  -0.234  -1.2581  -3.8493   0.0422
 EL1  C46  C   CR16  0  -0.270  -2.5199  -4.4118   0.1747
 EL1  C48  C   CR16  0  -0.238  -3.6484  -3.6342  -0.0268
 EL1  C50  C   CR6   0   0.211  -3.5278  -2.2864  -0.3502
 EL1  N51  N   NC1   0  -0.832  -4.7161  -1.5282  -0.5191
 EL1  S53  S   S     0   1.317  -5.5768  -1.0308   0.8169
 EL1  C54  C   CH3   0  -0.795  -4.5490   0.1467   1.6621
 EL1  O58  O   OS    0  -0.662  -6.7416  -0.3414   0.2891
 EL1  O59  O   OS    0  -0.652  -5.7484  -2.1858   1.6799
 EL1  H1   H   HCH3  0   0.253  -3.4466   6.2955  -2.6588
 EL1  H2   H   HCH3  0   0.239  -2.0528   6.6055  -1.6193
 EL1  H3   H   HCH3  0   0.242  -1.8119   6.0899  -3.2925
 EL1  H4   H   HNH1  0   0.411  -3.4058   4.1732  -1.8310
 EL1  H5   H   HCR6  0   0.274  -2.8107   2.0400  -3.1680
 EL1  H6   H   HCR6  0   0.275  -3.1237  -0.3445  -2.7075
 EL1  H7   H   HCR6  0   0.293  -0.9858   0.0857   0.9684
 EL1  H8   H   HCH1  0   0.261  -0.3341   1.6288   2.3246
 EL1  H9   H   HCH2  0   0.259   1.3987   4.0390   1.6605
 EL1  H10  H   HCH2  0   0.275   0.2962   3.8748   3.0358
 EL1  H11  H   HCH2  0   0.264   2.9403   3.2944   3.3332
 EL1  H12  H   HCH2  0   0.252   1.7383   2.2690   4.1181
 EL1  H13  H   HCH2  0   0.266   1.2270   0.2679   1.1168
 EL1  H14  H   HCH2  0   0.265   1.8786   1.6716   0.2440
 EL1  H15  H   HCR5  0   0.281   5.1525  -1.4049   3.1786
 EL1  H16  H   HCR5  0   0.294   5.7784  -3.1385   1.3222
 EL1  H17  H   HCR6  0   0.251  -0.1506  -2.0755  -0.4129
 EL1  H18  H   HCR6  0   0.266  -0.3718  -4.4518   0.1893
 EL1  H19  H   HCR6  0   0.266  -2.6282  -5.4590   0.4235
 EL1  H20  H   HCR6  0   0.271  -4.6327  -4.0723   0.0589
 EL1  H21  H   HNC1  0   0.422  -4.6834  -0.8011  -1.2255
 EL1  H22  H   HCH3  0   0.315  -5.0781   0.4641   2.5593
 EL1  H23  H   HCH3  0   0.291  -3.6092  -0.3248   1.9392
 EL1  H24  H   HCH3  0   0.292  -4.3699   0.9995   1.0123

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
 EL1  C54  S53  single    1.777  0.020  1.777
 EL1  BR   C38  single    1.856  0.020  1.856
 EL1  O59  S53  double    1.452  0.020  1.452
 EL1  S53  O58  double    1.453  0.020  1.453
 EL1  S53  N51  single    1.665  0.020  1.665
 EL1  C38  S40  aromatic  1.710  0.020  1.710
 EL1  C38  C36  aromatic  1.362  0.020  1.362
 EL1  S40  C33  aromatic  1.730  0.020  1.730
 EL1  N51  C50  single    1.420  0.020  1.420
 EL1  C36  C34  aromatic  1.413  0.020  1.413
 EL1  C48  C50  aromatic  1.391  0.020  1.391
 EL1  C48  C46  aromatic  1.385  0.020  1.385
 EL1  C50  C41  aromatic  1.402  0.020  1.402
 EL1  C33  C34  aromatic  1.369  0.020  1.369
 EL1  C33  C31  single    1.485  0.020  1.485
 EL1  O32  C31  double    1.226  0.020  1.226
 EL1  C46  C44  aromatic  1.388  0.020  1.388
 EL1  C31  N27  single    1.344  0.020  1.344
 EL1  C41  C14  single    1.480  0.020  1.480
 EL1  C41  C42  aromatic  1.394  0.020  1.394
 EL1  C14  C12  aromatic  1.390  0.020  1.390
 EL1  C14  C15  aromatic  1.394  0.020  1.394
 EL1  C12  C10  aromatic  1.387  0.020  1.387
 EL1  N27  C28  single    1.453  0.020  1.453
 EL1  N27  C24  single    1.464  0.020  1.464
 EL1  C44  C42  aromatic  1.385  0.020  1.385
 EL1  C15  C17  aromatic  1.390  0.020  1.390
 EL1  C10  C09  aromatic  1.387  0.020  1.387
 EL1  C28  C19  single    1.535  0.020  1.535
 EL1  O08  C07  double    1.222  0.020  1.222
 EL1  C17  C09  aromatic  1.401  0.020  1.401
 EL1  C17  O18  single    1.344  0.020  1.344
 EL1  C24  C21  single    1.520  0.020  1.520
 EL1  C09  C07  single    1.498  0.020  1.498
 EL1  O18  C19  single    1.410  0.020  1.410
 EL1  C07  N05  single    1.340  0.020  1.340
 EL1  C19  C21  single    1.517  0.020  1.517
 EL1  N05  C01  single    1.444  0.020  1.444
 EL1  C01  H1   single    0.970  0.020  1.090
 EL1  C01  H2   single    0.970  0.020  1.090
 EL1  C01  H3   single    0.970  0.020  1.090
 EL1  N05  H4   single    0.860  0.020  1.020
 EL1  C10  H5   single    0.930  0.020  1.080
 EL1  C12  H6   single    0.930  0.020  1.080
 EL1  C15  H7   single    0.930  0.020  1.080
 EL1  C19  H8   single    0.970  0.020  1.090
 EL1  C21  H9   single    0.970  0.020  1.090
 EL1  C21  H10  single    0.970  0.020  1.090
 EL1  C24  H11  single    0.970  0.020  1.090
 EL1  C24  H12  single    0.970  0.020  1.090
 EL1  C28  H13  single    0.970  0.020  1.090
 EL1  C28  H14  single    0.970  0.020  1.090
 EL1  C34  H15  single    0.930  0.020  1.080
 EL1  C36  H16  single    0.930  0.020  1.080
 EL1  C42  H17  single    0.930  0.020  1.080
 EL1  C44  H18  single    0.930  0.020  1.080
 EL1  C46  H19  single    0.930  0.020  1.080
 EL1  C48  H20  single    0.930  0.020  1.080
 EL1  N51  H21  single    0.890  0.020  1.040
 EL1  C54  H22  single    0.970  0.020  1.090
 EL1  C54  H23  single    0.970  0.020  1.090
 EL1  C54  H24  single    0.970  0.020  1.090

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
 EL1  H3   C01  H2   108.28  3.000
 EL1  H3   C01  H1   108.48  3.000
 EL1  H2   C01  H1   108.43  3.000
 EL1  H3   C01  N05  111.21  3.000
 EL1  H2   C01  N05  111.88  3.000
 EL1  H1   C01  N05  108.46  3.000
 EL1  H4   N05  C07  119.11  3.000
 EL1  H4   N05  C01  118.36  3.000
 EL1  C07  N05  C01  122.36  3.000
 EL1  C09  C07  O08  122.24  3.000
 EL1  C09  C07  N05  114.50  3.000
 EL1  O08  C07  N05  123.24  3.000
 EL1  C17  C09  C10  119.08  3.000
 EL1  C17  C09  C07  120.77  3.000
 EL1  C10  C09  C07  120.07  3.000
 EL1  H5   C10  C12  119.17  3.000
 EL1  H5   C10  C09  119.46  3.000
 EL1  C12  C10  C09  121.34  3.000
 EL1  H6   C12  C14  120.82  3.000
 EL1  H6   C12  C10  119.51  3.000
 EL1  C14  C12  C10  119.64  3.000
 EL1  C41  C14  C15  118.78  3.000
 EL1  C15  C14  C12  119.50  3.000
 EL1  C41  C14  C12  121.72  3.000
 EL1  H7   C15  C17  121.01  3.000
 EL1  H7   C15  C14  118.18  3.000
 EL1  C17  C15  C14  120.79  3.000
 EL1  O18  C17  C15  123.96  3.000
 EL1  O18  C17  C09  116.39  3.000
 EL1  C15  C17  C09  119.62  3.000
 EL1  C19  O18  C17  120.13  3.000
 EL1  H8   C19  C28  109.91  3.000
 EL1  H8   C19  C21  109.88  3.000
 EL1  C28  C19  C21  103.06  3.000
 EL1  H8   C19  O18  110.71  3.000
 EL1  C21  C19  O18  109.52  3.000
 EL1  C28  C19  O18  113.48  3.000
 EL1  H10  C21  H9   108.52  3.000
 EL1  H10  C21  C24  112.38  3.000
 EL1  H9   C21  C24  110.40  3.000
 EL1  H10  C21  C19  113.13  3.000
 EL1  H9   C21  C19  109.42  3.000
 EL1  C24  C21  C19  102.90  3.000
 EL1  H12  C24  H11  107.90  3.000
 EL1  H12  C24  N27  110.40  3.000
 EL1  H11  C24  N27  111.11  3.000
 EL1  H12  C24  C21  111.62  3.000
 EL1  H11  C24  C21  112.35  3.000
 EL1  N27  C24  C21  103.47  3.000
 EL1  C31  N27  C28  127.95  3.000
 EL1  C28  N27  C24  112.22  3.000
 EL1  C31  N27  C24  119.35  3.000
 EL1  H14  C28  H13  108.80  3.000
 EL1  H14  C28  N27  112.14  3.000
 EL1  H13  C28  N27  111.34  3.000
 EL1  H14  C28  C19  109.34  3.000
 EL1  H13  C28  C19  112.18  3.000
 EL1  N27  C28  C19  102.98  3.000
 EL1  C33  C31  O32  118.26  3.000
 EL1  O32  C31  N27  121.14  3.000
 EL1  C33  C31  N27  120.60  3.000
 EL1  S40  C33  C34  110.36  3.000
 EL1  C34  C33  C31  122.04  3.000
 EL1  S40  C33  C31  127.46  3.000
 EL1  H15  C34  C36  123.28  3.000
 EL1  H15  C34  C33  122.79  3.000
 EL1  C36  C34  C33  113.93  3.000
 EL1  H16  C36  C38  124.19  3.000
 EL1  H16  C36  C34  124.42  3.000
 EL1  C38  C36  C34  111.39  3.000
 EL1  S40  C38  BR   120.01  3.000
 EL1  S40  C38  C36  112.77  3.000
 EL1  BR   C38  C36  127.22  3.000
 EL1  C38  S40  C33   91.54  3.000
 EL1  C50  C41  C42  118.57  3.000
 EL1  C42  C41  C14  119.25  3.000
 EL1  C50  C41  C14  122.18  3.000
 EL1  H17  C42  C44  119.70  3.000
 EL1  H17  C42  C41  119.05  3.000
 EL1  C44  C42  C41  121.25  3.000
 EL1  H18  C44  C46  120.41  3.000
 EL1  H18  C44  C42  119.90  3.000
 EL1  C46  C44  C42  119.69  3.000
 EL1  H19  C46  C48  119.69  3.000
 EL1  H19  C46  C44  120.36  3.000
 EL1  C48  C46  C44  119.95  3.000
 EL1  H20  C48  C50  119.35  3.000
 EL1  H20  C48  C46  120.19  3.000
 EL1  C50  C48  C46  120.46  3.000
 EL1  N51  C50  C48  118.19  3.000
 EL1  C48  C50  C41  120.08  3.000
 EL1  N51  C50  C41  121.73  3.000
 EL1  H21  N51  S53  111.18  3.000
 EL1  H21  N51  C50  116.02  3.000
 EL1  S53  N51  C50  119.78  3.000
 EL1  O59  S53  O58  119.91  3.000
 EL1  O58  S53  C54  108.79  3.000
 EL1  O59  S53  C54  108.23  3.000
 EL1  O58  S53  N51  105.35  3.000
 EL1  O59  S53  N51  107.48  3.000
 EL1  C54  S53  N51  106.30  3.000
 EL1  H24  C54  H23  110.49  3.000
 EL1  H24  C54  H22  110.11  3.000
 EL1  H23  C54  H22  109.66  3.000
 EL1  H24  C54  S53  109.32  3.000
 EL1  H23  C54  S53  109.50  3.000
 EL1  H22  C54  S53  107.70  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
 EL1  CONST_01  C14  C12  C10  C09     0.00   0.0  0
 EL1  CONST_02  C14  C15  C17  C09     0.00   0.0  0
 EL1  CONST_03  C41  C14  C12  C10   180.00   0.0  0
 EL1  CONST_04  C15  C14  C12  C10     0.00   0.0  0
 EL1  CONST_05  C15  C17  C09  C10     0.00   0.0  0
 EL1  CONST_08  C17  C15  C14  C12     0.00   0.0  0
 EL1  CONST_09  C17  C09  C10  C12     0.00   0.0  0
 EL1  CONST_10  C48  C50  C41  C14   180.00   0.0  0
 EL1  CONST_11  C44  C42  C41  C14   180.00   0.0  0
 EL1  CONST_14  C41  C14  C15  C17   180.00   0.0  0
 EL1  CONST_15  C36  C38  S40  C33     0.00   0.0  0
 EL1  CONST_16  C38  C36  C34  C33     0.00   0.0  0
 EL1  CONST_17  S40  C38  C36  C34     0.00   0.0  0
 EL1  CONST_18  C38  S40  C33  C34     0.00   0.0  0
 EL1  CONST_19  S40  C33  C34  C36     0.00   0.0  0
 EL1  CONST_20  C46  C48  C50  C41     0.00   0.0  0
 EL1  CONST_21  C46  C44  C42  C41     0.00   0.0  0
 EL1  CONST_22  C48  C50  C41  C42     0.00   0.0  0
 EL1  CONST_23  C48  C46  C44  C42     0.00   0.0  0
 EL1  CONST_24  C50  C48  C46  C44     0.00   0.0  0
 EL1  CONST_25  C50  C41  C42  C44     0.00   0.0  0
 EL1  CONST_26  C12  C10  C09  C07   180.00   0.0  0
 EL1  CONST_27  C15  C17  C09  C07   180.00   0.0  0
 EL1  CONST_28  O18  C17  C09  C10   180.00   0.0  0
 EL1  CONST_29  N51  C50  C41  C14     0.00   0.0  0
 EL1  CONST_30  O18  C17  C15  C14   180.00   0.0  0
 EL1  CONST_31  C38  S40  C33  C31   180.00   0.0  0
 EL1  CONST_32  C36  C34  C33  C31   180.00   0.0  0
 EL1  CONST_33  BR   C38  S40  C33   180.00   0.0  0
 EL1  CONST_34  BR   C38  C36  C34   180.00   0.0  0
 EL1  CONST_35  N51  C50  C41  C42   180.00   0.0  0
 EL1  CONST_36  N51  C50  C48  C46   180.00   0.0  0
 EL1  CONST_37  C33  C31  N27  C24   180.00   0.0  0
 EL1  CONST_38  C33  C31  N27  C28     0.00   0.0  0
 EL1  CONST_39  H6   C12  C10  C09   180.00   0.0  0
 EL1  CONST_40  H7   C15  C17  C09   180.00   0.0  0
 EL1  CONST_41  H17  C42  C41  C14     0.00   0.0  0
 EL1  CONST_42  H5   C10  C12  C14   180.00   0.0  0
 EL1  CONST_43  H16  C36  C34  C33   180.00   0.0  0
 EL1  CONST_44  H15  C34  C36  C38   180.00   0.0  0
 EL1  CONST_45  H20  C48  C50  C41   180.00   0.0  0
 EL1  CONST_46  H18  C44  C42  C41   180.00   0.0  0
 EL1  CONST_47  H19  C46  C44  C42   180.00   0.0  0
 EL1  CONST_48  O32  C31  N27  C24     0.00   0.0  0
 EL1  CONST_49  O32  C31  N27  C28   180.00   0.0  0
 EL1  CONST_53  C09  C07  N05  C01   180.00   0.0  0
 EL1  CONST_54  H4   N05  C07  C09     0.00   0.0  0
 EL1  CONST_55  O08  C07  N05  C01     0.00   0.0  0
 EL1  Var_01    C24  N27  C28  C19   -12.35  30.0  1
 EL1  Var_02    N27  C24  C21  C19    31.66  30.0  1
 EL1  Var_03    C28  N27  C24  C21   -12.06  30.0  1
 EL1  Var_04    S40  C33  C31  N27    18.77  30.0  2
 EL1  Var_05    C10  C09  C07  N05    55.92  30.0  2
 EL1  Var_06    C54  S53  N51  C50    66.95  30.0  2
 EL1  Var_07    H1   C01  N05  C07   173.45  30.0  3
 EL1  Var_08    H22  C54  S53  N51  -178.22  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
 EL1  chir_01  C19  C28  O18  C21  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
 EL1  plan-1  C31  0.020
 EL1  plan-1  C33  0.020
 EL1  plan-1  C34  0.020
 EL1  plan-1  C36  0.020
 EL1  plan-1  C38  0.020
 EL1  plan-1  BR   0.020
 EL1  plan-1  S40  0.020
 EL1  plan-1  H15  0.020
 EL1  plan-1  H16  0.020
 EL1  plan-2  C07  0.020
 EL1  plan-2  C09  0.020
 EL1  plan-2  C10  0.020
 EL1  plan-2  C12  0.020
 EL1  plan-2  C14  0.020
 EL1  plan-2  C15  0.020
 EL1  plan-2  C17  0.020
 EL1  plan-2  O18  0.020
 EL1  plan-2  C41  0.020
 EL1  plan-2  H5   0.020
 EL1  plan-2  H6   0.020
 EL1  plan-2  H7   0.020
 EL1  plan-3  C14  0.020
 EL1  plan-3  C41  0.020
 EL1  plan-3  C42  0.020
 EL1  plan-3  C44  0.020
 EL1  plan-3  C46  0.020
 EL1  plan-3  C48  0.020
 EL1  plan-3  C50  0.020
 EL1  plan-3  N51  0.020
 EL1  plan-3  H17  0.020
 EL1  plan-3  H18  0.020
 EL1  plan-3  H19  0.020
 EL1  plan-3  H20  0.020
 EL1  plan-4  C24  0.020
 EL1  plan-4  N27  0.020
 EL1  plan-4  C28  0.020
 EL1  plan-4  C31  0.020
 EL1  plan-4  O32  0.020
 EL1  plan-4  C33  0.020
 EL1  plan-5  C50  0.020
 EL1  plan-5  N51  0.020
 EL1  plan-5  S53  0.020
 EL1  plan-5  H21  0.020
 EL1  plan-6  C01  0.020
 EL1  plan-6  N05  0.020
 EL1  plan-6  C07  0.020
 EL1  plan-6  O08  0.020
 EL1  plan-6  C09  0.020
 EL1  plan-6  H4   0.020

