# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 19:28:17 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 4-[6,6-dimethyl-4-oxidanylidene-3-(trifluoromethyl)-5,7-dihydroindazol-1-yl]-2-[(4-oxidanylcyclohexyl)amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)CC(=O)c2c(C1)n(nc2C(F)(F)F)c3ccc(C(N)=O)c(N[C@@H]4CC[C@@H](O)CC4)c3
#
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
 E0G  E0G  4-[6,6-dimethyl-4-oxidanylidene-3-(trifluoromethyl)-5,7-dihydroindazol-1-yl]-2-[(4-oxidanylcyclohexyl)amino]benzamide  ligand  60  33  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E0G
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
 E0G  C8   C  CH1   0  -0.045   3.6733  -0.5564  -0.5635
 E0G  C5   C  CR6   0   0.415   2.4026   1.4107   0.2669
 E0G  C6   C  CR6   0  -0.145   2.3689   2.7734   0.6830
 E0G  N1   N  NH2   0  -0.807   3.5997   4.6428   1.5794
 E0G  C2   C  CR16  0  -0.319  -0.0487   2.6589   0.9582
 E0G  O2   O  O     0  -0.503   4.6268   3.2862   0.1190
 E0G  N2   N  NH1   0  -0.722   3.5536   0.8041  -0.0889
 E0G  N3   N  NR5   0  -0.490  -1.1891   0.5555   0.5576
 E0G  C3   C  CR6   0   0.358   0.0013   1.3217   0.5863
 E0G  C4   C  CR16  0  -0.409   1.1852   0.7033   0.2458
 E0G  N4   N  N     0  -0.264  -1.1758  -0.6920   1.0446
 E0G  C10  C  CH2   0  -0.464   3.8180  -3.0011   0.0358
 E0G  C11  C  CH1   0   0.086   5.1025  -3.1347  -0.7660
 E0G  C12  C  CH2   0  -0.479   5.1345  -2.1109  -1.8947
 E0G  C13  C  CH2   0  -0.469   4.9603  -0.6904  -1.3710
 E0G  C14  C  CR5   0   0.009  -2.3864  -1.1510   0.8673
 E0G  C15  C  CR5   0  -0.320  -3.2162  -0.1897   0.2531
 E0G  C16  C  CR5   0   0.512  -2.3936   0.9020   0.0640
 E0G  C19  C  CH2   0  -0.549  -5.0767   1.1231  -0.7503
 E0G  C1   C  CR16  0  -0.286   1.1430   3.3567   0.9927
 E0G  F1   F  F     0  -0.305  -1.6976  -3.1305   1.8928
 E0G  F2   F  F     0  -0.309  -3.7406  -2.5221   2.1899
 E0G  F3   F  F     0  -0.310  -3.1133  -3.2947   0.2810
 E0G  O3   O  OH1   0  -0.678   5.1843  -4.4603  -1.2497
 E0G  C7   C  C     0   0.523   3.6195   3.5757   0.7657
 E0G  C9   C  CH2   0  -0.453   3.6559  -1.5824   0.5711
 E0G  C17  C  CH2   0  -0.494  -2.7921   2.1675  -0.5988
 E0G  C18  C  CT    0  -0.145  -4.0056   1.9197  -1.5145
 E0G  C20  C  C     0   0.347  -4.6037  -0.1974  -0.1879
 E0G  C22  C  CH3   0  -0.644  -4.5898   3.2670  -1.9295
 E0G  C23  C  CT    0   1.077  -2.7352  -2.5302   1.3099
 E0G  H1   H  HCH1  0   0.230   2.8382  -0.7712  -1.2438
 E0G  H2   H  HNH2  0   0.406   4.4374   5.1919   1.6838
 E0G  H3   H  HNH2  0   0.413   2.8668   4.8055   2.2472
 E0G  H4   H  HCR6  0   0.275  -0.9737   3.1381   1.2433
 E0G  H5   H  HNH1  0   0.403   4.3621   1.4058  -0.1518
 E0G  H6   H  HCR6  0   0.284   1.1634  -0.3348  -0.0506
 E0G  H7   H  HCH2  0   0.220   2.9651  -3.2568  -0.6032
 E0G  H8   H  HCH2  0   0.241   3.8170  -3.7120   0.8658
 E0G  H9   H  HCH1  0   0.188   5.9458  -2.9231  -0.0894
 E0G  H10  H  HCH2  0   0.239   6.0778  -2.1847  -2.4439
 E0G  H11  H  HCH2  0   0.223   4.3339  -2.3390  -2.6067
 E0G  H12  H  HCH2  0   0.250   4.9502   0.0143  -2.2058
 E0G  H13  H  HCH2  0   0.229   5.8122  -0.4185  -0.7372
 E0G  H14  H  HCH2  0   0.282  -5.4248   1.7160   0.1057
 E0G  H15  H  HCH2  0   0.271  -5.9485   0.9507  -1.3849
 E0G  H16  H  HCH3  0   0.234  -3.1057   0.1962  -2.5397
 E0G  H17  H  HCH3  0   0.237  -4.4283   0.9607  -3.4150
 E0G  H18  H  HCH3  0   0.237  -2.8503   1.7420  -3.3422
 E0G  H19  H  HCR6  0   0.266   1.1011   4.4023   1.2679
 E0G  H20  H  HOH1  0   0.446   6.0022  -4.5458  -1.7498
 E0G  H21  H  HCH2  0   0.226   4.4711  -1.3509   1.2645
 E0G  H22  H  HCH2  0   0.243   2.7310  -1.5080   1.1484
 E0G  H23  H  HCH2  0   0.287  -3.0500   2.9079   0.1660
 E0G  H24  H  HCH2  0   0.284  -1.9633   2.5908  -1.1718
 E0G  H25  H  HCH3  0   0.238  -5.4324   3.1299  -2.6091
 E0G  H26  H  HCH3  0   0.232  -4.9442   3.8332  -1.0661
 E0G  H27  H  HCH3  0   0.236  -3.8424   3.8725  -2.4460
 E0G  C21  C  CH3   0  -0.636  -3.5711   1.1566  -2.7682
 E0G  O1   O  O     0  -0.401  -5.3242  -1.1690  -0.0817

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
 E0G  O2   C7   double    1.232  0.020  1.232
 E0G  N1   C7   single    1.342  0.020  1.342
 E0G  C7   C6   single    1.488  0.020  1.488
 E0G  C9   C10  single    1.525  0.020  1.525
 E0G  C9   C8   single    1.530  0.020  1.530
 E0G  C11  C10  single    1.520  0.020  1.520
 E0G  C11  O3   single    1.413  0.020  1.413
 E0G  C11  C12  single    1.524  0.020  1.524
 E0G  N2   C8   single    1.446  0.020  1.446
 E0G  N2   C5   single    1.349  0.020  1.349
 E0G  C13  C12  single    1.524  0.020  1.524
 E0G  C13  C8   single    1.525  0.020  1.525
 E0G  C6   C5   aromatic  1.425  0.020  1.425
 E0G  C6   C1   aromatic  1.392  0.020  1.392
 E0G  C5   C4   aromatic  1.408  0.020  1.408
 E0G  C1   C2   aromatic  1.381  0.020  1.381
 E0G  C4   C3   aromatic  1.378  0.020  1.378
 E0G  C2   C3   aromatic  1.389  0.020  1.389
 E0G  C3   N3   single    1.416  0.020  1.416
 E0G  N3   C16  aromatic  1.347  0.020  1.347
 E0G  N3   N4   aromatic  1.339  0.020  1.339
 E0G  C17  C16  single    1.483  0.020  1.483
 E0G  C17  C18  single    1.540  0.020  1.540
 E0G  C21  C18  single    1.531  0.020  1.531
 E0G  C22  C18  single    1.526  0.020  1.526
 E0G  C16  C15  aromatic  1.380  0.020  1.380
 E0G  N4   C14  aromatic  1.307  0.020  1.307
 E0G  C18  C19  single    1.538  0.020  1.538
 E0G  C15  C14  aromatic  1.411  0.020  1.411
 E0G  C15  C20  single    1.456  0.020  1.456
 E0G  C14  C23  single    1.490  0.020  1.490
 E0G  C19  C20  single    1.511  0.020  1.511
 E0G  F1   C23  single    1.333  0.020  1.333
 E0G  C20  O1   double    1.214  0.020  1.214
 E0G  C23  F3   single    1.336  0.020  1.336
 E0G  C23  F2   single    1.336  0.020  1.336
 E0G  C8   H1   single    0.970  0.020  1.090
 E0G  N1   H2   single    0.860  0.020  1.020
 E0G  N1   H3   single    0.860  0.020  1.020
 E0G  C2   H4   single    0.930  0.020  1.080
 E0G  N2   H5   single    0.860  0.020  1.020
 E0G  C4   H6   single    0.930  0.020  1.080
 E0G  C10  H7   single    0.970  0.020  1.090
 E0G  C10  H8   single    0.970  0.020  1.090
 E0G  C11  H9   single    0.970  0.020  1.090
 E0G  C12  H10  single    0.970  0.020  1.090
 E0G  C12  H11  single    0.970  0.020  1.090
 E0G  C13  H12  single    0.970  0.020  1.090
 E0G  C13  H13  single    0.970  0.020  1.090
 E0G  C19  H14  single    0.970  0.020  1.090
 E0G  C19  H15  single    0.970  0.020  1.090
 E0G  C21  H16  single    0.970  0.020  1.090
 E0G  C21  H17  single    0.970  0.020  1.090
 E0G  C21  H18  single    0.970  0.020  1.090
 E0G  C1   H19  single    0.930  0.020  1.080
 E0G  O3   H20  single    0.850  0.020  0.980
 E0G  C9   H21  single    0.970  0.020  1.090
 E0G  C9   H22  single    0.970  0.020  1.090
 E0G  C17  H23  single    0.970  0.020  1.090
 E0G  C17  H24  single    0.970  0.020  1.090
 E0G  C22  H25  single    0.970  0.020  1.090
 E0G  C22  H26  single    0.970  0.020  1.090
 E0G  C22  H27  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
 E0G  H1   C8   C9   108.64  3.000
 E0G  H1   C8   C13  107.24  3.000
 E0G  C9   C8   C13  110.08  3.000
 E0G  H1   C8   N2   108.93  3.000
 E0G  C13  C8   N2   109.04  3.000
 E0G  C9   C8   N2   112.75  3.000
 E0G  C4   C5   N2   120.53  3.000
 E0G  C4   C5   C6   117.66  3.000
 E0G  N2   C5   C6   121.81  3.000
 E0G  C7   C6   C1   120.11  3.000
 E0G  C1   C6   C5   119.09  3.000
 E0G  C7   C6   C5   120.79  3.000
 E0G  H3   N1   H2   116.72  3.000
 E0G  H3   N1   C7   122.85  3.000
 E0G  H2   N1   C7   118.95  3.000
 E0G  H4   C2   C1   120.54  3.000
 E0G  H4   C2   C3   121.92  3.000
 E0G  C1   C2   C3   117.51  3.000
 E0G  H5   N2   C5   115.57  3.000
 E0G  H5   N2   C8   118.29  3.000
 E0G  C5   N2   C8   125.48  3.000
 E0G  C16  N3   N4   112.44  3.000
 E0G  N4   N3   C3   119.23  3.000
 E0G  C16  N3   C3   128.31  3.000
 E0G  C4   C3   N3   118.32  3.000
 E0G  N3   C3   C2   119.74  3.000
 E0G  C4   C3   C2   121.94  3.000
 E0G  H6   C4   C3   118.80  3.000
 E0G  H6   C4   C5   120.30  3.000
 E0G  C3   C4   C5   120.90  3.000
 E0G  C14  N4   N3   105.58  3.000
 E0G  H8   C10  H7   106.88  3.000
 E0G  H8   C10  C9   109.78  3.000
 E0G  H7   C10  C9   109.82  3.000
 E0G  H8   C10  C11  110.13  3.000
 E0G  H7   C10  C11  109.24  3.000
 E0G  C9   C10  C11  110.90  3.000
 E0G  H9   C11  O3   110.24  3.000
 E0G  H9   C11  C12  108.04  3.000
 E0G  O3   C11  C12  112.05  3.000
 E0G  H9   C11  C10  107.82  3.000
 E0G  C12  C11  C10  110.44  3.000
 E0G  O3   C11  C10  108.17  3.000
 E0G  H11  C12  H10  106.85  3.000
 E0G  H11  C12  C13  109.51  3.000
 E0G  H10  C12  C13  109.51  3.000
 E0G  H11  C12  C11  109.03  3.000
 E0G  H10  C12  C11  110.15  3.000
 E0G  C13  C12  C11  111.67  3.000
 E0G  H13  C13  H12  106.80  3.000
 E0G  H13  C13  C12  109.94  3.000
 E0G  H12  C13  C12  109.86  3.000
 E0G  H13  C13  C8   109.14  3.000
 E0G  H12  C13  C8   109.88  3.000
 E0G  C12  C13  C8   111.12  3.000
 E0G  C23  C14  C15  128.50  3.000
 E0G  C23  C14  N4   120.11  3.000
 E0G  C15  C14  N4   111.38  3.000
 E0G  C20  C15  C16  122.06  3.000
 E0G  C20  C15  C14  133.54  3.000
 E0G  C16  C15  C14  104.37  3.000
 E0G  C17  C16  C15  125.17  3.000
 E0G  C15  C16  N3   106.22  3.000
 E0G  C17  C16  N3   128.58  3.000
 E0G  H15  C19  H14  106.57  3.000
 E0G  H15  C19  C20  109.15  3.000
 E0G  H14  C19  C20  106.32  3.000
 E0G  H15  C19  C18  110.42  3.000
 E0G  H14  C19  C18  109.18  3.000
 E0G  C20  C19  C18  114.80  3.000
 E0G  H19  C1   C2   117.45  3.000
 E0G  H19  C1   C6   119.70  3.000
 E0G  C2   C1   C6   122.84  3.000
 E0G  H20  O3   C11  108.08  3.000
 E0G  O2   C7   N1   121.16  3.000
 E0G  N1   C7   C6   116.74  3.000
 E0G  O2   C7   C6   122.10  3.000
 E0G  H22  C9   H21  106.33  3.000
 E0G  H22  C9   C10  109.80  3.000
 E0G  H21  C9   C10  109.87  3.000
 E0G  H22  C9   C8   110.84  3.000
 E0G  H21  C9   C8   108.63  3.000
 E0G  C10  C9   C8   111.24  3.000
 E0G  H24  C17  H23  106.43  3.000
 E0G  H24  C17  C18  110.37  3.000
 E0G  H23  C17  C18  109.78  3.000
 E0G  H24  C17  C16  111.16  3.000
 E0G  H23  C17  C16  109.15  3.000
 E0G  C18  C17  C16  109.88  3.000
 E0G  C22  C18  C17  108.74  3.000
 E0G  C22  C18  C21  109.03  3.000
 E0G  C17  C18  C21  110.09  3.000
 E0G  C22  C18  C19  109.01  3.000
 E0G  C21  C18  C19  110.27  3.000
 E0G  C17  C18  C19  109.67  3.000
 E0G  O1   C20  C19  123.10  3.000
 E0G  O1   C20  C15  122.90  3.000
 E0G  C19  C20  C15  113.97  3.000
 E0G  H27  C22  H26  107.98  3.000
 E0G  H27  C22  H25  107.68  3.000
 E0G  H26  C22  H25  107.89  3.000
 E0G  H27  C22  C18  110.87  3.000
 E0G  H26  C22  C18  111.54  3.000
 E0G  H25  C22  C18  110.74  3.000
 E0G  F3   C23  F2   107.31  3.000
 E0G  F2   C23  F1   107.48  3.000
 E0G  F3   C23  F1   107.42  3.000
 E0G  F2   C23  C14  111.48  3.000
 E0G  F3   C23  C14  111.54  3.000
 E0G  F1   C23  C14  111.38  3.000
 E0G  H18  C21  H17  107.65  3.000
 E0G  H18  C21  H16  107.49  3.000
 E0G  H17  C21  H16  107.52  3.000
 E0G  H18  C21  C18  110.53  3.000
 E0G  H17  C21  C18  110.60  3.000
 E0G  H16  C21  C18  112.84  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
 E0G  CONST_01  C2   C1   C6   C5     0.00   0.0  0
 E0G  CONST_02  C2   C3   C4   C5     0.00   0.0  0
 E0G  CONST_03  N3   C3   C4   C5   180.00   0.0  0
 E0G  CONST_04  C3   C4   C5   C6     0.00   0.0  0
 E0G  CONST_05  C3   C2   C1   C6     0.00   0.0  0
 E0G  CONST_08  C1   C2   C3   N3   180.00   0.0  0
 E0G  CONST_09  C14  C15  C16  N3     0.00   0.0  0
 E0G  CONST_10  C15  C14  N4   N3     0.00   0.0  0
 E0G  CONST_11  C15  C16  N3   C3   180.00   0.0  0
 E0G  CONST_12  C14  N4   N3   C3   180.00   0.0  0
 E0G  CONST_13  C1   C6   C5   C4     0.00   0.0  0
 E0G  CONST_14  C1   C2   C3   C4     0.00   0.0  0
 E0G  CONST_17  C15  C16  N3   N4     0.00   0.0  0
 E0G  CONST_18  C16  C15  C14  N4     0.00   0.0  0
 E0G  CONST_19  C16  N3   N4   C14    0.00   0.0  0
 E0G  CONST_20  C17  C16  N3   C3     0.00   0.0  0
 E0G  CONST_21  C7   C6   C1   C2   180.00   0.0  0
 E0G  CONST_22  C1   C6   C5   N2   180.00   0.0  0
 E0G  CONST_23  C3   C4   C5   N2   180.00   0.0  0
 E0G  CONST_24  C23  C14  N4   N3   180.00   0.0  0
 E0G  CONST_25  C7   C6   C5   C4   180.00   0.0  0
 E0G  CONST_26  C23  C14  C15  C16  180.00   0.0  0
 E0G  CONST_27  C23  C14  C15  C20    0.00   0.0  0
 E0G  CONST_28  C6   C5   N2   C8   180.00   0.0  0
 E0G  CONST_29  C4   C5   N2   C8     0.00   0.0  0
 E0G  CONST_30  H19  C1   C6   C5   180.00   0.0  0
 E0G  CONST_31  H6   C4   C5   C6   180.00   0.0  0
 E0G  CONST_32  H4   C2   C1   C6   180.00   0.0  0
 E0G  CONST_33  H5   N2   C5   C6     0.00   0.0  0
 E0G  CONST_34  H2   N1   C7   C6   180.00   0.0  0
 E0G  CONST_35  H3   N1   C7   C6     0.00   0.0  0
 E0G  Var_01    C11  C10  C9   C8    57.24  30.0  1
 E0G  Var_02    C11  C12  C13  C8   -56.08  30.0  1
 E0G  Var_03    C18  C17  C16  N3   155.48  30.0  1
 E0G  Var_04    C19  C20  C15  C14  177.46  30.0  1
 E0G  Var_05    C18  C19  C20  C15   34.16  30.0  1
 E0G  Var_06    C19  C18  C17  C16   48.10  30.0  1
 E0G  Var_07    C20  C19  C18  C17  -56.77  30.0  1
 E0G  Var_08    O2   C7   C6   C5    23.09  30.0  2
 E0G  Var_09    F1   C23  C14  N4     1.56  30.0  2
 E0G  Var_10    H16  C21  C18  C19  -62.64  30.0  3
 E0G  Var_11    H25  C22  C18  C19  -62.47  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
 E0G  chir_01  C8   C9  N2   C13  negativ
 E0G  chir_02  C11  O3  C10  C12  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
 E0G  plan-1  C5   0.020
 E0G  plan-1  C6   0.020
 E0G  plan-1  C2   0.020
 E0G  plan-1  N2   0.020
 E0G  plan-1  N3   0.020
 E0G  plan-1  C3   0.020
 E0G  plan-1  C4   0.020
 E0G  plan-1  C1   0.020
 E0G  plan-1  C7   0.020
 E0G  plan-1  H4   0.020
 E0G  plan-1  H6   0.020
 E0G  plan-1  H19  0.020
 E0G  plan-2  N3   0.020
 E0G  plan-2  C3   0.020
 E0G  plan-2  N4   0.020
 E0G  plan-2  C14  0.020
 E0G  plan-2  C15  0.020
 E0G  plan-2  C16  0.020
 E0G  plan-2  C17  0.020
 E0G  plan-2  C20  0.020
 E0G  plan-2  C23  0.020
 E0G  plan-3  C6   0.020
 E0G  plan-3  N1   0.020
 E0G  plan-3  O2   0.020
 E0G  plan-3  C7   0.020
 E0G  plan-3  H2   0.020
 E0G  plan-3  H3   0.020
 E0G  plan-4  C8   0.020
 E0G  plan-4  C5   0.020
 E0G  plan-4  N2   0.020
 E0G  plan-4  H5   0.020
 E0G  plan-5  C15  0.020
 E0G  plan-5  C19  0.020
 E0G  plan-5  C20  0.020
 E0G  plan-5  O1   0.020

