# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 23:40:25 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 3-[6-chloranyl-2-cyclopropyl-1-(1-ethylpyrazol-4-yl)-7-fluoranyl-indol-3-yl]sulfanyl-2-fluoranyl-benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCn1cc(cn1)n2c(C3CC3)c(Sc4cccc(C(O)=O)c4F)c5ccc(Cl)c(F)c25
#
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
 6Y7  6Y7  '3-[6-chloranyl-2-cyclopropyl-1-(1-ethylpyrazol-4-yl)-7-fluoranyl-indol-3-yl]sulfanyl-2-fluoranyl-benzoic acid'  ligand  49  32  .  2022-07-23  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_6Y7
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
 6Y7  C1   C   CR56   0   0.168  -1.6293  -0.7907  -0.1465
 6Y7  C2   C   CR5    0  -0.049  -2.8277   1.3370   0.1796
 6Y7  C4   C   CH2    0  -0.292  -6.0336   2.9155  -0.1697
 6Y7  C6   C   CR15   0  -0.015  -3.0987   1.9031   1.4334
 6Y7  C7   C   CR5    0   0.524  -0.5087   1.0872  -0.6604
 6Y7  C8   C   CH1    0  -0.412  -0.3464   2.5393  -0.7942
 6Y7  C9   C   CH2    0  -0.462   0.4089   3.1611  -1.9420
 6Y7  C10  C   CH2    0  -0.466   0.9784   3.2238  -0.5700
 6Y7  C11  C   CR5    0  -0.404   0.3392   0.0301  -0.9132
 6Y7  C12  C   CR6    0  -0.313   2.9557  -0.0659  -0.1008
 6Y7  C13  C   CR16   0  -0.229   2.4696   0.0284   1.1939
 6Y7  CL   CL  CL     0  -0.101  -3.3609  -4.2595   0.6867
 6Y7  C22  C   CR6    0  -0.282  -2.2038  -3.0750   0.1967
 6Y7  C    C   CR6    0   0.622  -2.5579  -1.7432   0.2489
 6Y7  F    F   F      0  -0.285  -3.7709  -1.3874   0.6721
 6Y7  C21  C   CR16   0  -0.234  -0.9345  -3.4688  -0.2443
 6Y7  C20  C   CR16   0  -0.379  -0.0075  -2.5272  -0.6381
 6Y7  C19  C   CR56   0   0.187  -0.3564  -1.1767  -0.5915
 6Y7  S    S   S2     0   0.056   1.9553   0.0746  -1.5603
 6Y7  C18  C   CR6    0   0.562   4.3176  -0.2718  -0.2967
 6Y7  F1   F   F      0  -0.300   4.7046  -0.3411  -1.5797
 6Y7  C16  C   CR6    0  -0.296   5.2223  -0.4019   0.7473
 6Y7  C17  C   C      0   0.417   6.7259  -0.6336   0.5628
 6Y7  O1   O   O      0  -0.581   7.1725  -0.6100  -0.5958
 6Y7  O    O   OC    -1  -0.587   7.3694  -0.8224   1.6111
 6Y7  C15  C   CR16   0  -0.284   4.6953  -0.3112   2.0374
 6Y7  C14  C   CR16   0  -0.252   3.3467  -0.0958   2.2623
 6Y7  N    N   NR5    0  -0.702  -1.7058   0.5811  -0.2004
 6Y7  N2   N   N      0  -0.281  -4.2575   2.5305   1.4146
 6Y7  N1   N   NR5    0  -0.265  -4.7307   2.3795   0.1802
 6Y7  C3   C   CR15   0   0.088  -3.9110   1.6679  -0.6037
 6Y7  C5   C   CH3    0  -0.663  -7.1593   2.2079   0.5609
 6Y7  H1   H   HCH2   0   0.265  -6.0344   3.9827   0.0518
 6Y7  H2   H   HCH2   0   0.261  -6.1420   2.8059  -1.2474
 6Y7  H3   H   HCR5   0   0.277  -2.4906   1.8737   2.3252
 6Y7  H4   H   HCH1   0   0.293  -1.2105   3.1009  -0.4628
 6Y7  H5   H   HCH2   0   0.259   0.8774   2.4977  -2.6566
 6Y7  H6   H   HCH2   0   0.267  -0.0180   4.0583  -2.3705
 6Y7  H7   H   HCH2   0   0.268   0.9513   4.1648  -0.0362
 6Y7  H8   H   HCH2   0   0.263   1.8368   2.6045  -0.3468
 6Y7  H9   H   HCR6   0   0.274   1.4141   0.1955   1.3645
 6Y7  H10  H   HCR6   0   0.282  -0.6919  -4.5222  -0.2733
 6Y7  H11  H   HCR6   0   0.258   0.9714  -2.8337  -0.9819
 6Y7  H13  H   HCR6   0   0.256   5.3733  -0.4111   2.8732
 6Y7  H14  H   HCR6   0   0.257   2.9696  -0.0220   3.2739
 6Y7  H15  H   HCR5   0   0.310  -4.1354   1.4457  -1.6344
 6Y7  H16  H   HCH3   0   0.235  -7.1653   1.1415   0.3361
 6Y7  H17  H   HCH3   0   0.239  -7.0713   2.3345   1.6389
 6Y7  H18  H   HCH3   0   0.243  -8.1157   2.6261   0.2494

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
 6Y7  O1   C17  deloc     1.242  0.020  1.242
 6Y7  C17  O    deloc     1.244  0.020  1.244
 6Y7  C17  C16  single    1.532  0.020  1.532
 6Y7  C15  C16  aromatic  1.397  0.020  1.397
 6Y7  C15  C14  aromatic  1.384  0.020  1.384
 6Y7  C16  C18  aromatic  1.388  0.020  1.388
 6Y7  C14  C13  aromatic  1.388  0.020  1.388
 6Y7  C18  F1   single    1.342  0.020  1.342
 6Y7  C18  C12  aromatic  1.391  0.020  1.391
 6Y7  C13  C12  aromatic  1.386  0.020  1.386
 6Y7  C12  S    single    1.775  0.020  1.775
 6Y7  S    C11  single    1.741  0.020  1.741
 6Y7  C8   C10  single    1.508  0.020  1.508
 6Y7  C8   C7   single    1.467  0.020  1.467
 6Y7  C8   C9   single    1.508  0.020  1.508
 6Y7  C11  C7   aromatic  1.379  0.020  1.379
 6Y7  C11  C19  aromatic  1.430  0.020  1.430
 6Y7  C10  C9   single    1.487  0.020  1.487
 6Y7  C7   N    aromatic  1.379  0.020  1.379
 6Y7  C20  C19  aromatic  1.396  0.020  1.396
 6Y7  C20  C21  aromatic  1.379  0.020  1.379
 6Y7  C19  C1   aromatic  1.403  0.020  1.403
 6Y7  N    C1   aromatic  1.375  0.020  1.375
 6Y7  N    C2   single    1.405  0.020  1.405
 6Y7  C6   C2   aromatic  1.402  0.020  1.402
 6Y7  C6   N2   aromatic  1.318  0.020  1.318
 6Y7  C21  C22  aromatic  1.400  0.020  1.400
 6Y7  C1   C    aromatic  1.388  0.020  1.388
 6Y7  C2   C3   aromatic  1.377  0.020  1.377
 6Y7  C22  C    aromatic  1.379  0.020  1.379
 6Y7  C22  CL   single    1.727  0.020  1.727
 6Y7  C    F    single    1.333  0.020  1.333
 6Y7  N2   N1   aromatic  1.331  0.020  1.331
 6Y7  C3   N1   aromatic  1.339  0.020  1.339
 6Y7  N1   C4   single    1.452  0.020  1.452
 6Y7  C4   C5   single    1.517  0.020  1.517
 6Y7  C4   H1   single    0.970  0.020  1.090
 6Y7  C4   H2   single    0.970  0.020  1.090
 6Y7  C6   H3   single    0.930  0.020  1.080
 6Y7  C8   H4   single    0.970  0.020  1.090
 6Y7  C9   H5   single    0.970  0.020  1.090
 6Y7  C9   H6   single    0.970  0.020  1.090
 6Y7  C10  H7   single    0.970  0.020  1.090
 6Y7  C10  H8   single    0.970  0.020  1.090
 6Y7  C13  H9   single    0.930  0.020  1.080
 6Y7  C21  H10  single    0.930  0.020  1.080
 6Y7  C20  H11  single    0.930  0.020  1.080
 6Y7  C15  H13  single    0.930  0.020  1.080
 6Y7  C14  H14  single    0.930  0.020  1.080
 6Y7  C3   H15  single    0.930  0.020  1.080
 6Y7  C5   H16  single    0.970  0.020  1.090
 6Y7  C5   H17  single    0.970  0.020  1.090
 6Y7  C5   H18  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
 6Y7  N    C1   C19  108.22  3.000
 6Y7  N    C1   C    131.20  3.000
 6Y7  C19  C1   C    120.58  3.000
 6Y7  C3   C2   N    127.12  3.000
 6Y7  C3   C2   C6   105.05  3.000
 6Y7  N    C2   C6   127.83  3.000
 6Y7  H2   C4   H1   107.44  3.000
 6Y7  H2   C4   C5   110.84  3.000
 6Y7  H1   C4   C5   110.99  3.000
 6Y7  H2   C4   N1   106.91  3.000
 6Y7  H1   C4   N1   108.25  3.000
 6Y7  C5   C4   N1   112.19  3.000
 6Y7  H3   C6   N2   121.32  3.000
 6Y7  H3   C6   C2   128.23  3.000
 6Y7  N2   C6   C2   110.45  3.000
 6Y7  N    C7   C11  108.28  3.000
 6Y7  N    C7   C8   119.33  3.000
 6Y7  C11  C7   C8   132.39  3.000
 6Y7  H4   C8   C10  114.85  3.000
 6Y7  H4   C8   C9   114.76  3.000
 6Y7  C10  C8   C9    59.07  3.000
 6Y7  H4   C8   C7   113.40  3.000
 6Y7  C9   C8   C7   122.20  3.000
 6Y7  C10  C8   C7   122.20  3.000
 6Y7  H6   C9   H5   114.70  3.000
 6Y7  H6   C9   C10  118.78  3.000
 6Y7  H5   C9   C10  118.01  3.000
 6Y7  H6   C9   C8   116.46  3.000
 6Y7  H5   C9   C8   117.83  3.000
 6Y7  C10  C9   C8    60.46  3.000
 6Y7  H8   C10  H7   114.57  3.000
 6Y7  H8   C10  C9   118.04  3.000
 6Y7  H7   C10  C9   118.84  3.000
 6Y7  H8   C10  C8   117.90  3.000
 6Y7  H7   C10  C8   116.50  3.000
 6Y7  C9   C10  C8    60.47  3.000
 6Y7  S    C11  C19  123.83  3.000
 6Y7  C19  C11  C7   107.87  3.000
 6Y7  S    C11  C7   128.27  3.000
 6Y7  C18  C12  S    116.59  3.000
 6Y7  S    C12  C13  124.40  3.000
 6Y7  C18  C12  C13  119.01  3.000
 6Y7  H9   C13  C14  120.59  3.000
 6Y7  H9   C13  C12  119.98  3.000
 6Y7  C14  C13  C12  119.42  3.000
 6Y7  C21  C22  C    121.08  3.000
 6Y7  C    C22  CL   118.66  3.000
 6Y7  C21  C22  CL   120.26  3.000
 6Y7  F    C    C22  120.23  3.000
 6Y7  F    C    C1   121.07  3.000
 6Y7  C22  C    C1   118.70  3.000
 6Y7  H10  C21  C20  120.45  3.000
 6Y7  H10  C21  C22  119.06  3.000
 6Y7  C20  C21  C22  120.49  3.000
 6Y7  H11  C20  C19  120.73  3.000
 6Y7  H11  C20  C21  120.37  3.000
 6Y7  C19  C20  C21  118.90  3.000
 6Y7  C20  C19  C11  133.45  3.000
 6Y7  C20  C19  C1   120.25  3.000
 6Y7  C11  C19  C1   106.30  3.000
 6Y7  C12  S    C11  102.44  3.000
 6Y7  C16  C18  F1   121.77  3.000
 6Y7  F1   C18  C12  115.13  3.000
 6Y7  C16  C18  C12  123.11  3.000
 6Y7  C15  C16  C17  119.42  3.000
 6Y7  C15  C16  C18  116.29  3.000
 6Y7  C17  C16  C18  124.29  3.000
 6Y7  O    C17  O1   127.07  3.000
 6Y7  O    C17  C16  115.40  3.000
 6Y7  O1   C17  C16  117.53  3.000
 6Y7  H13  C15  C14  119.99  3.000
 6Y7  H13  C15  C16  118.14  3.000
 6Y7  C14  C15  C16  121.86  3.000
 6Y7  H14  C14  C15  120.14  3.000
 6Y7  H14  C14  C13  119.55  3.000
 6Y7  C15  C14  C13  120.31  3.000
 6Y7  C7   N    C2   125.87  3.000
 6Y7  C2   N    C1   124.79  3.000
 6Y7  C7   N    C1   109.33  3.000
 6Y7  N1   N2   C6   105.78  3.000
 6Y7  C3   N1   N2   112.69  3.000
 6Y7  C3   N1   C4   127.20  3.000
 6Y7  N2   N1   C4   120.06  3.000
 6Y7  H15  C3   N1   122.81  3.000
 6Y7  H15  C3   C2   131.15  3.000
 6Y7  N1   C3   C2   106.04  3.000
 6Y7  H18  C5   H17  108.02  3.000
 6Y7  H18  C5   H16  108.18  3.000
 6Y7  H17  C5   H16  108.56  3.000
 6Y7  H18  C5   C4   109.55  3.000
 6Y7  H17  C5   C4   111.25  3.000
 6Y7  H16  C5   C4   111.17  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
 6Y7  CONST_01  C7   C11  C19  C1     0.00   0.0  0
 6Y7  CONST_02  C21  C20  C19  C1     0.00   0.0  0
 6Y7  CONST_03  C11  C7   N    C1     0.00   0.0  0
 6Y7  CONST_06  C21  C22  C    C1     0.00   0.0  0
 6Y7  CONST_07  C11  C7   N    C2   180.00   0.0  0
 6Y7  CONST_08  C19  C1   N    C2   180.00   0.0  0
 6Y7  CONST_09  C    C1   N    C2     0.00   0.0  0
 6Y7  CONST_10  N1   N2   C6   C2     0.00   0.0  0
 6Y7  CONST_11  N2   N1   C3   C2     0.00   0.0  0
 6Y7  CONST_13  N1   C3   C2   C6     0.00   0.0  0
 6Y7  CONST_14  C3   N1   N2   C6     0.00   0.0  0
 6Y7  CONST_15  C20  C19  C11  C7   180.00   0.0  0
 6Y7  CONST_16  C19  C1   N    C7     0.00   0.0  0
 6Y7  CONST_17  C    C1   N    C7   180.00   0.0  0
 6Y7  CONST_19  C21  C20  C19  C11  180.00   0.0  0
 6Y7  CONST_20  N    C1   C19  C11    0.00   0.0  0
 6Y7  CONST_21  C    C1   C19  C11  180.00   0.0  0
 6Y7  CONST_22  C15  C16  C18  C12    0.00   0.0  0
 6Y7  CONST_23  C15  C14  C13  C12    0.00   0.0  0
 6Y7  CONST_24  C16  C15  C14  C13    0.00   0.0  0
 6Y7  CONST_25  C16  C18  C12  C13    0.00   0.0  0
 6Y7  CONST_26  C19  C20  C21  C22    0.00   0.0  0
 6Y7  CONST_27  C19  C1   C    C22    0.00   0.0  0
 6Y7  CONST_28  N    C1   C    C22  180.00   0.0  0
 6Y7  CONST_29  C20  C19  C1   C      0.00   0.0  0
 6Y7  CONST_30  C20  C21  C22  C      0.00   0.0  0
 6Y7  CONST_31  N    C1   C19  C20  180.00   0.0  0
 6Y7  CONST_32  N    C7   C11  C19    0.00   0.0  0
 6Y7  CONST_33  C14  C15  C16  C18    0.00   0.0  0
 6Y7  CONST_34  C14  C13  C12  C18    0.00   0.0  0
 6Y7  CONST_35  N2   C6   C2   N    180.00   0.0  0
 6Y7  CONST_36  N1   C3   C2   N    180.00   0.0  0
 6Y7  CONST_37  C3   C2   C6   N2     0.00   0.0  0
 6Y7  CONST_38  C8   C7   N    C1   180.00   0.0  0
 6Y7  CONST_39  C8   C7   N    C2     0.00   0.0  0
 6Y7  CONST_40  C19  C11  C7   C8   180.00   0.0  0
 6Y7  CONST_41  S    C11  C19  C1   180.00   0.0  0
 6Y7  CONST_42  CL   C22  C    C1   180.00   0.0  0
 6Y7  CONST_43  C4   N1   C3   C2   180.00   0.0  0
 6Y7  CONST_44  C6   N2   N1   C4   180.00   0.0  0
 6Y7  CONST_45  S    C11  C7   C8     0.00   0.0  0
 6Y7  CONST_46  C17  C16  C18  C12  180.00   0.0  0
 6Y7  CONST_47  F1   C18  C12  C13  180.00   0.0  0
 6Y7  CONST_48  C20  C21  C22  CL   180.00   0.0  0
 6Y7  CONST_49  C19  C1   C    F    180.00   0.0  0
 6Y7  CONST_50  N    C1   C    F      0.00   0.0  0
 6Y7  CONST_51  C21  C22  C    F    180.00   0.0  0
 6Y7  CONST_52  S    C11  C19  C20    0.00   0.0  0
 6Y7  CONST_53  C16  C18  C12  S    180.00   0.0  0
 6Y7  CONST_54  C14  C13  C12  S    180.00   0.0  0
 6Y7  CONST_55  N    C7   C11  S    180.00   0.0  0
 6Y7  CONST_56  C15  C16  C18  F1   180.00   0.0  0
 6Y7  CONST_57  C14  C15  C16  C17  180.00   0.0  0
 6Y7  CONST_58  H11  C20  C19  C1   180.00   0.0  0
 6Y7  CONST_59  H15  C3   C2   C6   180.00   0.0  0
 6Y7  CONST_60  H14  C14  C13  C12  180.00   0.0  0
 6Y7  CONST_61  H13  C15  C14  C13  180.00   0.0  0
 6Y7  CONST_62  H10  C21  C22  C    180.00   0.0  0
 6Y7  CONST_63  H9   C13  C12  C18  180.00   0.0  0
 6Y7  CONST_64  H3   C6   C2   N      0.00   0.0  0
 6Y7  Var_01    C9   C10  C8   C7   110.90  30.0  1
 6Y7  Var_02    C11  C7   C8   C9    38.28  30.0  2
 6Y7  Var_03    C18  C12  S    C11  170.24  30.0  3
 6Y7  Var_04    C19  C11  S    C12  -83.09  30.0  2
 6Y7  Var_05    O1   C17  C16  C18    5.22  30.0  3
 6Y7  Var_06    C5   C4   N1   N2   -66.54  30.0  2
 6Y7  Var_07    H16  C5   C4   N1   -59.13  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
 6Y7  chir_01  C8  C10  C7  C9  both

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
 6Y7  plan-1  C2   0.020
 6Y7  plan-1  C4   0.020
 6Y7  plan-1  C6   0.020
 6Y7  plan-1  N    0.020
 6Y7  plan-1  N2   0.020
 6Y7  plan-1  N1   0.020
 6Y7  plan-1  C3   0.020
 6Y7  plan-1  H3   0.020
 6Y7  plan-1  H15  0.020
 6Y7  plan-2  C12  0.020
 6Y7  plan-2  C13  0.020
 6Y7  plan-2  S    0.020
 6Y7  plan-2  C18  0.020
 6Y7  plan-2  F1   0.020
 6Y7  plan-2  C16  0.020
 6Y7  plan-2  C17  0.020
 6Y7  plan-2  C15  0.020
 6Y7  plan-2  C14  0.020
 6Y7  plan-2  H9   0.020
 6Y7  plan-2  H13  0.020
 6Y7  plan-2  H14  0.020
 6Y7  plan-3  C1   0.020
 6Y7  plan-3  C2   0.020
 6Y7  plan-3  C7   0.020
 6Y7  plan-3  C8   0.020
 6Y7  plan-3  C11  0.020
 6Y7  plan-3  CL   0.020
 6Y7  plan-3  C22  0.020
 6Y7  plan-3  C    0.020
 6Y7  plan-3  F    0.020
 6Y7  plan-3  C21  0.020
 6Y7  plan-3  C20  0.020
 6Y7  plan-3  C19  0.020
 6Y7  plan-3  S    0.020
 6Y7  plan-3  N    0.020
 6Y7  plan-3  H10  0.020
 6Y7  plan-3  H11  0.020
 6Y7  plan-4  C16  0.020
 6Y7  plan-4  C17  0.020
 6Y7  plan-4  O1   0.020
 6Y7  plan-4  O    0.020

