# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 05:22:06 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 4-bromo-3-(carboxymethoxy)-5-{3-[cyclohexyl(methylcarbamoyl)amino]phenyl}thiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)N(C1CCCCC1)c2cccc(c2)c3sc(C(O)=O)c(OCC(O)=O)c3Br
#
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
 35B  35B  '4-bromo-3-(carboxymethoxy)-5-{3-[cyclohexyl(methylcarbamoyl)amino]phenyl}thiophene-2-carboxylic acid'  ligand  52  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_35B
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
 35B  C1    C   CH3    0  -0.506   5.8129   3.9400  -0.0244
 35B  C2    C   C      0   0.712   4.4192   2.1084   0.7628
 35B  C3    C   C      0   0.329   2.9223   0.3765   1.3779
 35B  C4    C   C1     0  -0.282   2.9454  -0.2013   2.6402
 35B  C5    C   C1     0  -0.244   1.7642  -0.6451   3.2191
 35B  C6    C   C1     0  -0.295   0.5603  -0.5152   2.5448
 35B  N1    N   NH1    0  -0.674   5.4841   2.5364   0.0482
 35B  C7    C   C      0   0.082   0.5281   0.0580   1.2730
 35B  O1    O   O      0  -0.541   3.7366   2.8877   1.4205
 35B  C8    C   C1     0  -0.320   1.7173   0.5056   0.7003
 35B  C9    C   CR5    0  -0.207  -0.7338   0.2050   0.5425
 35B  C10   C   CR5    0  -0.138  -1.6810  -0.7278   0.2327
 35B  C11   C   CR5    0   0.437  -2.7780  -0.2210  -0.5303
 35B  C12   C   CR5    0  -0.441  -2.6528   1.1200  -0.7745
 35B  C13   C   C      0   0.424  -3.5201   2.1014  -1.5164
 35B  C14   C   CH2    0  -0.290  -4.9331  -1.0170  -0.1458
 35B  C15   C   C      0   0.368  -5.9913  -1.9796  -0.6973
 35B  C16   C   CH1    0  -0.114   4.8823  -0.3093   0.0809
 35B  C17   C   CH2    0  -0.434   6.3299  -0.4653   0.5518
 35B  C18   C   CH2    0  -0.438   6.9433  -1.7215  -0.0632
 35B  C19   C   CH2    0  -0.433   6.8482  -1.7039  -1.5858
 35B  C20   C   CH2    0  -0.436   5.4023  -1.5392  -2.0418
 35B  C21   C   CH2    0  -0.433   4.7695  -0.2847  -1.4456
 35B  N2    N   NT     0  -0.605   4.1351   0.7651   0.7484
 35B  S1    S   S2     0   0.243  -1.1988   1.7360  -0.0951
 35B  O2    O   OC    -1  -0.598  -3.0541   3.2574  -1.5631
 35B  O3    O   O      0  -0.568  -4.5852   1.6823  -1.9951
 35B  O4    O   O2     0  -0.460  -3.7641  -1.0232  -0.9600
 35B  O5    O   OC    -1  -0.627  -7.0209  -2.0456   0.0044
 35B  O6    O   O      0  -0.596  -5.7492  -2.5841  -1.7522
 35B  BR1   BR  BR     0  -0.029  -1.5580  -2.5486   0.6486
 35B  H1    H   HCH3   0   0.229   5.0161   4.5350  -0.4748
 35B  H1A   H   HCH3   0   0.235   6.0310   4.3523   0.9601
 35B  H4    H   H      0   0.260   3.8862  -0.3019   3.1669
 35B  H5    H   H      0   0.263   1.7809  -1.0862   4.2071
 35B  H6    H   H      0   0.259  -0.3580  -0.8411   3.0146
 35B  H8    H   H      0   0.254   1.7117   0.9407  -0.2919
 35B  H14   H   HCH2   0   0.227  -5.3486  -0.0060  -0.1020
 35B  H14A  H   HCH2   0   0.214  -4.6800  -1.3118   0.8798
 35B  H16   H   HCH1   0   0.258   4.3729  -1.2220   0.4036
 35B  H17   H   HCH2   0   0.217   6.9414   0.3975   0.2760
 35B  H17A  H   HCH2   0   0.242   6.3497  -0.5259   1.6427
 35B  H18   H   HCH2   0   0.235   7.9845  -1.8150   0.2531
 35B  H18A  H   HCH2   0   0.217   6.4208  -2.6043   0.3201
 35B  H19   H   HCH2   0   0.213   7.4515  -0.8781  -1.9787
 35B  H19A  H   HCH2   0   0.233   7.2708  -2.6224  -1.9995
 35B  H20   H   HCH2   0   0.236   5.3436  -1.5007  -3.1315
 35B  H20A  H   HCH2   0   0.218   4.8239  -2.4151  -1.7279
 35B  H21   H   HCH2   0   0.245   3.7165  -0.2161  -1.7301
 35B  H21A  H   HCH2   0   0.216   5.2622   0.5956  -1.8705
 35B  H1B   H   HCH3   0   0.244   6.7038   4.0446  -0.6379
 35B  HN    H   HNH1   0   0.400   5.9334   1.9308  -0.6126

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
 35B  C1   N1    single    1.443  0.020  1.443
 35B  C1   H1    single    0.970  0.020  1.090
 35B  C1   H1A   single    0.970  0.020  1.090
 35B  N1   C2    single    1.352  0.020  1.352
 35B  O1   C2    double    1.227  0.020  1.227
 35B  C2   N2    single    1.373  0.020  1.373
 35B  C4   C3    aromatic  1.388  0.020  1.388
 35B  C3   N2    single    1.421  0.020  1.421
 35B  C3   C8    aromatic  1.388  0.020  1.388
 35B  C5   C4    aromatic  1.388  0.020  1.388
 35B  C4   H4    single    0.930  0.020  1.080
 35B  C5   C6    aromatic  1.386  0.020  1.386
 35B  C5   H5    single    0.930  0.020  1.080
 35B  C6   C7    aromatic  1.395  0.020  1.395
 35B  C6   H6    single    0.930  0.020  1.080
 35B  C7   C8    aromatic  1.394  0.020  1.394
 35B  C7   C9    single    1.465  0.020  1.465
 35B  C8   H8    single    0.930  0.020  1.080
 35B  S1   C9    aromatic  1.722  0.020  1.722
 35B  C9   C10   aromatic  1.365  0.020  1.365
 35B  C10  C11   aromatic  1.429  0.020  1.429
 35B  C10  BR1   single    1.872  0.020  1.872
 35B  C12  C11   aromatic  1.369  0.020  1.369
 35B  C11  O4    single    1.342  0.020  1.342
 35B  S1   C12   aromatic  1.719  0.020  1.719
 35B  C13  C12   single    1.505  0.020  1.505
 35B  O3   C13   deloc     1.241  0.020  1.241
 35B  C13  O2    deloc     1.247  0.020  1.247
 35B  C14  O4    single    1.425  0.020  1.425
 35B  C14  C15   single    1.533  0.020  1.533
 35B  C14  H14   single    0.970  0.020  1.090
 35B  C14  H14A  single    0.970  0.020  1.090
 35B  O6   C15   deloc     1.240  0.020  1.240
 35B  C15  O5    deloc     1.248  0.020  1.248
 35B  N2   C16   single    1.469  0.020  1.469
 35B  C17  C16   single    1.530  0.020  1.530
 35B  C16  C21   single    1.531  0.020  1.531
 35B  C16  H16   single    0.970  0.020  1.090
 35B  C17  C18   single    1.527  0.020  1.527
 35B  C17  H17   single    0.970  0.020  1.090
 35B  C17  H17A  single    0.970  0.020  1.090
 35B  C18  C19   single    1.526  0.020  1.526
 35B  C18  H18   single    0.970  0.020  1.090
 35B  C18  H18A  single    0.970  0.020  1.090
 35B  C19  C20   single    1.525  0.020  1.525
 35B  C19  H19   single    0.970  0.020  1.090
 35B  C19  H19A  single    0.970  0.020  1.090
 35B  C21  C20   single    1.526  0.020  1.526
 35B  C20  H20   single    0.970  0.020  1.090
 35B  C20  H20A  single    0.970  0.020  1.090
 35B  C21  H21   single    0.970  0.020  1.090
 35B  C21  H21A  single    0.970  0.020  1.090
 35B  C1   H1B   single    0.970  0.020  1.090
 35B  N1   HN    single    0.860  0.020  1.020

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
 35B  H1B   C1   H1A  108.03  3.000
 35B  H1B   C1   H1   108.24  3.000
 35B  H1A   C1   H1   108.23  3.000
 35B  H1B   C1   N1   107.98  3.000
 35B  H1A   C1   N1   111.60  3.000
 35B  H1    C1   N1   112.61  3.000
 35B  N2    C2   O1   120.78  3.000
 35B  N2    C2   N1   117.85  3.000
 35B  O1    C2   N1   121.36  3.000
 35B  N2    C3   C8   119.95  3.000
 35B  C8    C3   C4   119.79  3.000
 35B  N2    C3   C4   120.17  3.000
 35B  H4    C4   C5   120.45  3.000
 35B  H4    C4   C3   119.69  3.000
 35B  C5    C4   C3   119.87  3.000
 35B  H5    C5   C6   119.73  3.000
 35B  H5    C5   C4   119.86  3.000
 35B  C6    C5   C4   120.41  3.000
 35B  H6    C6   C7   120.00  3.000
 35B  H6    C6   C5   119.85  3.000
 35B  C7    C6   C5   120.13  3.000
 35B  HN    N1   C2   120.67  3.000
 35B  HN    N1   C1   116.88  3.000
 35B  C2    N1   C1   120.92  3.000
 35B  C9    C7   C8   119.85  3.000
 35B  C9    C7   C6   121.03  3.000
 35B  C8    C7   C6   119.12  3.000
 35B  H8    C8   C7   120.05  3.000
 35B  H8    C8   C3   119.26  3.000
 35B  C7    C8   C3   120.68  3.000
 35B  S1    C9   C10  109.64  3.000
 35B  C10   C9   C7   129.95  3.000
 35B  S1    C9   C7   120.40  3.000
 35B  BR1   C10  C11  120.93  3.000
 35B  BR1   C10  C9   124.66  3.000
 35B  C11   C10  C9   114.30  3.000
 35B  O4    C11  C12  126.57  3.000
 35B  O4    C11  C10  121.54  3.000
 35B  C12   C11  C10  111.87  3.000
 35B  S1    C12  C13  116.64  3.000
 35B  C13   C12  C11  132.38  3.000
 35B  S1    C12  C11  110.97  3.000
 35B  O3    C13  O2   128.27  3.000
 35B  O2    C13  C12  114.05  3.000
 35B  O3    C13  C12  117.68  3.000
 35B  H14A  C14  H14  107.37  3.000
 35B  H14A  C14  O4   110.11  3.000
 35B  H14   C14  O4   109.79  3.000
 35B  H14A  C14  C15  109.08  3.000
 35B  H14   C14  C15  109.42  3.000
 35B  O4    C14  C15  110.98  3.000
 35B  O6    C15  O5   127.87  3.000
 35B  O5    C15  C14  113.60  3.000
 35B  O6    C15  C14  118.52  3.000
 35B  H16   C16  N2   103.85  3.000
 35B  H16   C16  C21  105.85  3.000
 35B  N2    C16  C21  113.82  3.000
 35B  H16   C16  C17  105.35  3.000
 35B  C21   C16  C17  112.22  3.000
 35B  N2    C16  C17  114.58  3.000
 35B  H17A  C17  H17  106.59  3.000
 35B  H17A  C17  C18  110.43  3.000
 35B  H17   C17  C18  108.84  3.000
 35B  H17A  C17  C16  109.27  3.000
 35B  H17   C17  C16  111.79  3.000
 35B  C18   C17  C16  109.87  3.000
 35B  H18A  C18  H18  106.53  3.000
 35B  H18A  C18  C19  109.20  3.000
 35B  H18   C18  C19  110.45  3.000
 35B  H18A  C18  C17  109.29  3.000
 35B  H18   C18  C17  109.68  3.000
 35B  C19   C18  C17  111.55  3.000
 35B  H19A  C19  H19  106.55  3.000
 35B  H19A  C19  C20  110.14  3.000
 35B  H19   C19  C20  109.47  3.000
 35B  H19A  C19  C18  110.13  3.000
 35B  H19   C19  C18  109.41  3.000
 35B  C20   C19  C18  111.02  3.000
 35B  H20A  C20  H20  106.60  3.000
 35B  H20A  C20  C21  109.05  3.000
 35B  H20   C20  C21  109.79  3.000
 35B  H20A  C20  C19  109.18  3.000
 35B  H20   C20  C19  110.68  3.000
 35B  C21   C20  C19  111.41  3.000
 35B  H21A  C21  H21  106.38  3.000
 35B  H21A  C21  C20  108.83  3.000
 35B  H21   C21  C20  110.45  3.000
 35B  H21A  C21  C16  111.52  3.000
 35B  H21   C21  C16  109.37  3.000
 35B  C20   C21  C16  110.23  3.000
 35B  C16   N2   C3   115.81  3.000
 35B  C16   N2   C2   127.95  3.000
 35B  C3    N2   C2   116.08  3.000
 35B  C12   S1   C9    93.21  3.000
 35B  C14   O4   C11  114.67  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
 35B  CONST_01  C6   C5   C4   C3      0.00   0.0  0
 35B  CONST_02  C6   C7   C8   C3      0.00   0.0  0
 35B  CONST_03  C9   C7   C8   C3    180.00   0.0  0
 35B  CONST_04  C7   C8   C3   C4      0.00   0.0  0
 35B  CONST_05  C7   C6   C5   C4      0.00   0.0  0
 35B  CONST_06  C8   C3   C4   C5      0.00   0.0  0
 35B  CONST_07  C8   C7   C6   C5      0.00   0.0  0
 35B  CONST_08  C9   C7   C6   C5    180.00   0.0  0
 35B  CONST_11  C12  S1   C9   C7    180.00   0.0  0
 35B  CONST_12  C11  C10  C9   C7    180.00   0.0  0
 35B  CONST_15  C11  C12  S1   C9      0.00   0.0  0
 35B  CONST_16  C12  C11  C10  C9      0.00   0.0  0
 35B  CONST_17  C12  S1   C9   C10     0.00   0.0  0
 35B  CONST_18  S1   C12  C11  C10     0.00   0.0  0
 35B  CONST_19  S1   C9   C10  C11     0.00   0.0  0
 35B  CONST_20  N2   C3   C4   C5    180.00   0.0  0
 35B  CONST_21  N2   C3   C8   C7    180.00   0.0  0
 35B  CONST_22  BR1  C10  C9   C7      0.00   0.0  0
 35B  CONST_23  C13  C12  S1   C9    180.00   0.0  0
 35B  CONST_24  O4   C11  C10  C9    180.00   0.0  0
 35B  CONST_25  C13  C12  C11  C10   180.00   0.0  0
 35B  CONST_26  BR1  C10  C11  C12   180.00   0.0  0
 35B  CONST_27  BR1  C10  C9   S1    180.00   0.0  0
 35B  CONST_28  O4   C11  C12  S1    180.00   0.0  0
 35B  CONST_31  H5   C5   C4   C3    180.00   0.0  0
 35B  CONST_32  H8   C8   C3   C4    180.00   0.0  0
 35B  CONST_33  H6   C6   C5   C4    180.00   0.0  0
 35B  CONST_34  H4   C4   C5   C6    180.00   0.0  0
 35B  CONST_37  O1   C2   N2   C3      0.00   0.0  0
 35B  CONST_38  C16  N2   C2   O1    180.00   0.0  0
 35B  CONST_39  N1   C2   N2   C3    180.00   0.0  0
 35B  CONST_40  C16  N2   C2   N1      0.00   0.0  0
 35B  CONST_41  O1   C2   N1   C1      0.00   0.0  0
 35B  CONST_42  N2   C2   N1   C1    180.00   0.0  0
 35B  CONST_43  HN   N1   C2   O1    180.00   0.0  0
 35B  Var_01    C19  C18  C17  C16    55.76  30.0  1
 35B  Var_02    C19  C20  C21  C16   -55.40  30.0  1
 35B  Var_03    C20  C19  C18  C17   -56.35  30.0  1
 35B  Var_04    C21  C20  C19  C18    56.03  30.0  1
 35B  Var_05    O3   C13  C12  C11     2.09  30.0  3
 35B  Var_06    C15  C14  O4   C11  -178.91  30.0  1
 35B  Var_07    O6   C15  C14  O4     -2.43  30.0  3
 35B  Var_08    H1   C1   N1   C2    -61.17  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
 35B  chir_01  C16  N2  C17  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
 35B  plan-1  C7   0.020
 35B  plan-1  C9   0.020
 35B  plan-1  C10  0.020
 35B  plan-1  C11  0.020
 35B  plan-1  C12  0.020
 35B  plan-1  C13  0.020
 35B  plan-1  S1   0.020
 35B  plan-1  O4   0.020
 35B  plan-1  BR1  0.020
 35B  plan-2  C3   0.020
 35B  plan-2  C4   0.020
 35B  plan-2  C5   0.020
 35B  plan-2  C6   0.020
 35B  plan-2  C7   0.020
 35B  plan-2  C8   0.020
 35B  plan-2  C9   0.020
 35B  plan-2  N2   0.020
 35B  plan-2  H4   0.020
 35B  plan-2  H5   0.020
 35B  plan-2  H6   0.020
 35B  plan-2  H8   0.020
 35B  plan-3  C1   0.020
 35B  plan-3  C2   0.020
 35B  plan-3  C3   0.020
 35B  plan-3  N1   0.020
 35B  plan-3  O1   0.020
 35B  plan-3  C16  0.020
 35B  plan-3  N2   0.020
 35B  plan-3  HN   0.020
 35B  plan-4  C12  0.020
 35B  plan-4  C13  0.020
 35B  plan-4  O2   0.020
 35B  plan-4  O3   0.020
 35B  plan-5  C14  0.020
 35B  plan-5  C15  0.020
 35B  plan-5  O5   0.020
 35B  plan-5  O6   0.020

