# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 06:03:36 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: (2E)-4-{[3-(4-bromophenyl)-5-fluoro-1-methyl-1H-indazol-6-yl]oxy}-N-methyl-N-prop-2-en-1-ylbut-2-en-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CC=C)C\C=C\COc1cc2n(C)nc(c3ccc(Br)cc3)c2cc1F
#
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
 R04  R04  (2E)-4-{[3-(4-bromophenyl)-5-fluoro-1-methyl-1H-indazol-6-yl]oxy}-N-methyl-N-prop-2-en-1-ylbut-2-en-1-amine  ligand  51  28  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_R04
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
 R04  C3A   C   C2     0  -0.526   2.6868  -1.2406  -10.9666
 R04  C2A   C   C1     0  -0.179   2.4380  -0.6731   -9.7929
 R04  C1A   C   CH2    0  -0.323   1.1811   0.0642   -9.4516
 R04  N1    N   NT    -1  -0.414   0.5936  -0.4089   -8.2079
 R04  C1B   C   CH2    0  -0.325  -0.4363   0.5144   -7.7494
 R04  C2B   C   C1     0  -0.214  -0.9229   0.2140   -6.3649
 R04  C3B   C   C1     0  -0.241  -0.7527   1.0299   -5.3307
 R04  C4B   C   CH2    0  -0.247  -1.3088   0.7550   -3.9755
 R04  O     O   O2     0  -0.464  -0.2271   0.7789   -3.0495
 R04  C6C   C   CR6    0   0.248  -0.4981   0.5798   -1.7543
 R04  C7C   C   CR16   0  -0.467  -1.7454   0.3235   -1.2280
 R04  C7P   C   CR56   0   0.497  -1.8251   0.1315    0.1583
 R04  N1C   N   NR5    0  -0.391  -2.8979  -0.1063    0.9494
 R04  N2C   N   N      0  -0.271  -2.5458  -0.2360    2.2269
 R04  C3C   C   CR5    0   0.225  -1.2426  -0.0695    2.3031
 R04  C3P   C   CR56   0  -0.132  -0.7093   0.1751    1.0048
 R04  C4C   C   CR16   0  -0.505   0.5537   0.4580    0.4570
 R04  C5C   C   CR6    0   0.472   0.6274   0.6485   -0.8889
 R04  C1D   C   CR6    0   0.074  -0.5579  -0.1255    3.5943
 R04  C6D   C   CR16   0  -0.327   0.7745  -0.5252    3.6895
 R04  C5D   C   CR16   0  -0.209   1.4215  -0.5809    4.9149
 R04  C4D   C   CR6    0  -0.124   0.7249  -0.2389    6.0634
 R04  C3D   C   CR16   0  -0.214  -0.6056   0.1522    5.9999
 R04  C2D   C   CR16   0  -0.287  -1.2360   0.2081    4.7685
 R04  F     F   F      0  -0.314   1.8103   0.9192   -1.4628
 R04  BR27  BR  BR     0  -0.044   1.5957  -0.3092    7.7368
 R04  C1E   C   CH3    0  -0.526  -4.2592  -0.3367    0.5378
 R04  C1F   C   CH3    0  -0.532   0.0884  -1.7596   -8.3503
 R04  H3A1  H   H      0   0.238   3.6285  -1.7329  -11.1712
 R04  H3A2  H   H      0   0.235   1.9581  -1.2327  -11.7693
 R04  H2A   H   H      0   0.244   3.1884  -0.7079   -9.0080
 R04  H1A1  H   HCH2   0   0.205   0.4715   0.0132  -10.2950
 R04  H1A2  H   HCH2   0   0.246   1.4323   1.1220   -9.3189
 R04  H1B1  H   HCH2   0   0.246  -0.0196   1.5241   -7.7641
 R04  H1B2  H   HCH2   0   0.207  -1.3010   0.5203   -8.4370
 R04  H2B   H   H      0   0.255  -1.4691  -0.7134   -6.2140
 R04  H3B   H   H      0   0.256  -0.2200   1.9692   -5.4553
 R04  H4B1  H   HCH2   0   0.244  -2.0444   1.5212   -3.7023
 R04  H4B2  H   HCH2   0   0.244  -1.8134  -0.2169   -3.9528
 R04  H7C   H   HCR6   0   0.309  -2.6278   0.2704   -1.8501
 R04  H4C   H   HCR6   0   0.277   1.4473   0.5368    1.0617
 R04  H6D   H   HCR6   0   0.263   1.3225  -0.8252    2.8064
 R04  H5D   H   HCR6   0   0.283   2.4549  -0.8971    4.9597
 R04  H3D   H   HCR6   0   0.281  -1.1522   0.4192    6.8942
 R04  H2D   H   HCR6   0   0.263  -2.2690   0.5261    4.7213
 R04  H1E1  H   HCH3   0   0.258  -4.4243  -1.3822    0.2764
 R04  H1E2  H   HCH3   0   0.271  -4.9242  -0.0620    1.3516
 R04  H1E3  H   HCH3   0   0.259  -4.4935   0.2834   -0.3245
 R04  H1F1  H   HCH3   0   0.239  -0.2557  -2.1500   -7.3932
 R04  H1F2  H   HCH3   0   0.194  -0.7452  -1.8324   -9.0672
 R04  H1F3  H   HCH3   0   0.242   0.8811  -2.4207   -8.7001

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
 R04  C3A  C2A   double    1.327  0.020  1.327
 R04  C3A  H3A1  single    0.930  0.020  1.080
 R04  C3A  H3A2  single    0.930  0.020  1.080
 R04  C2A  C1A   single    1.497  0.020  1.497
 R04  C2A  H2A   single    0.930  0.020  1.080
 R04  C1A  N1    single    1.455  0.020  1.455
 R04  C1A  H1A1  single    0.970  0.020  1.090
 R04  C1A  H1A2  single    0.970  0.020  1.090
 R04  N1   C1B   single    1.457  0.020  1.457
 R04  N1   C1F   single    1.449  0.020  1.449
 R04  C1B  C2B   single    1.498  0.020  1.498
 R04  C1B  H1B1  single    0.970  0.020  1.090
 R04  C1B  H1B2  single    0.970  0.020  1.090
 R04  C2B  C3B   double    1.328  0.020  1.328
 R04  C2B  H2B   single    0.930  0.020  1.080
 R04  C3B  C4B   single    1.490  0.020  1.490
 R04  C3B  H3B   single    0.930  0.020  1.080
 R04  C4B  O     single    1.424  0.020  1.424
 R04  C4B  H4B1  single    0.970  0.020  1.090
 R04  C4B  H4B2  single    0.970  0.020  1.090
 R04  O    C6C   single    1.338  0.020  1.338
 R04  C6C  C7C   aromatic  1.378  0.020  1.378
 R04  C6C  C5C   aromatic  1.421  0.020  1.421
 R04  C7C  C7P   aromatic  1.402  0.020  1.402
 R04  C7C  H7C   single    0.930  0.020  1.080
 R04  C7P  N1C   aromatic  1.354  0.020  1.354
 R04  C7P  C3P   aromatic  1.401  0.020  1.401
 R04  N1C  N2C   aromatic  1.332  0.020  1.332
 R04  N1C  C1E   single    1.441  0.020  1.441
 R04  N2C  C3C   aromatic  1.316  0.020  1.316
 R04  C3C  C3P   aromatic  1.425  0.020  1.425
 R04  C3C  C1D   single    1.463  0.020  1.463
 R04  C3P  C4C   aromatic  1.405  0.020  1.405
 R04  C4C  C5C   aromatic  1.361  0.020  1.361
 R04  C4C  H4C   single    0.930  0.020  1.080
 R04  C5C  F     single    1.342  0.020  1.342
 R04  C1D  C6D   aromatic  1.394  0.020  1.394
 R04  C1D  C2D   aromatic  1.396  0.020  1.396
 R04  C6D  C5D   aromatic  1.387  0.020  1.387
 R04  C6D  H6D   single    0.930  0.020  1.080
 R04  C5D  C4D   aromatic  1.386  0.020  1.386
 R04  C5D  H5D   single    0.930  0.020  1.080
 R04  C4D  C3D   aromatic  1.388  0.020  1.388
 R04  C4D  BR27  single    1.888  0.020  1.888
 R04  C3D  C2D   aromatic  1.385  0.020  1.385
 R04  C3D  H3D   single    0.930  0.020  1.080
 R04  C2D  H2D   single    0.930  0.020  1.080
 R04  C1E  H1E1  single    0.970  0.020  1.090
 R04  C1E  H1E2  single    0.970  0.020  1.090
 R04  C1E  H1E3  single    0.970  0.020  1.090
 R04  C1F  H1F1  single    0.970  0.020  1.090
 R04  C1F  H1F2  single    0.970  0.020  1.090
 R04  C1F  H1F3  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
 R04  H3A2  C3A  H3A1  116.63  3.000
 R04  H3A2  C3A  C2A   121.71  3.000
 R04  H3A1  C3A  C2A   121.66  3.000
 R04  H2A   C2A  C1A   115.54  3.000
 R04  H2A   C2A  C3A   119.72  3.000
 R04  C1A   C2A  C3A   124.73  3.000
 R04  H1A2  C1A  H1A1  106.54  3.000
 R04  H1A2  C1A  N1    107.65  3.000
 R04  H1A1  C1A  N1    112.26  3.000
 R04  H1A2  C1A  C2A   108.11  3.000
 R04  H1A1  C1A  C2A   110.06  3.000
 R04  N1    C1A  C2A   111.96  3.000
 R04  C1F   N1   C1B   112.03  3.000
 R04  C1F   N1   C1A   111.10  3.000
 R04  C1B   N1   C1A   110.39  3.000
 R04  H1B2  C1B  H1B1  106.57  3.000
 R04  H1B2  C1B  C2B   108.79  3.000
 R04  H1B1  C1B  C2B   108.77  3.000
 R04  H1B2  C1B  N1    111.15  3.000
 R04  H1B1  C1B  N1    108.17  3.000
 R04  C2B   C1B  N1    113.16  3.000
 R04  H2B   C2B  C3B   118.72  3.000
 R04  H2B   C2B  C1B   117.56  3.000
 R04  C3B   C2B  C1B   123.70  3.000
 R04  H3B   C3B  C4B   116.52  3.000
 R04  H3B   C3B  C2B   120.29  3.000
 R04  C4B   C3B  C2B   123.15  3.000
 R04  H4B2  C4B  H4B1  107.80  3.000
 R04  H4B2  C4B  O     110.57  3.000
 R04  H4B1  C4B  O     109.62  3.000
 R04  H4B2  C4B  C3B   110.75  3.000
 R04  H4B1  C4B  C3B   110.36  3.000
 R04  O     C4B  C3B   107.74  3.000
 R04  C6C   O    C4B   118.23  3.000
 R04  C5C   C6C  C7C   119.55  3.000
 R04  C5C   C6C  O     114.94  3.000
 R04  C7C   C6C  O     125.50  3.000
 R04  H7C   C7C  C7P   121.07  3.000
 R04  H7C   C7C  C6C   121.89  3.000
 R04  C7P   C7C  C6C   117.04  3.000
 R04  C3P   C7P  N1C   106.47  3.000
 R04  C3P   C7P  C7C   123.22  3.000
 R04  N1C   C7P  C7C   130.31  3.000
 R04  C1E   N1C  N2C   120.55  3.000
 R04  C1E   N1C  C7P   127.58  3.000
 R04  N2C   N1C  C7P   111.60  3.000
 R04  C3C   N2C  N1C   107.76  3.000
 R04  C1D   C3C  C3P   129.48  3.000
 R04  C1D   C3C  N2C   120.66  3.000
 R04  C3P   C3C  N2C   109.85  3.000
 R04  C4C   C3P  C3C   136.56  3.000
 R04  C4C   C3P  C7P   119.11  3.000
 R04  C3C   C3P  C7P   104.30  3.000
 R04  H4C   C4C  C5C   119.85  3.000
 R04  H4C   C4C  C3P   122.62  3.000
 R04  C5C   C4C  C3P   117.53  3.000
 R04  F     C5C  C4C   119.91  3.000
 R04  F     C5C  C6C   116.56  3.000
 R04  C4C   C5C  C6C   123.53  3.000
 R04  C2D   C1D  C6D   118.37  3.000
 R04  C2D   C1D  C3C   120.38  3.000
 R04  C6D   C1D  C3C   121.24  3.000
 R04  H6D   C6D  C5D   118.29  3.000
 R04  H6D   C6D  C1D   120.52  3.000
 R04  C5D   C6D  C1D   121.17  3.000
 R04  H5D   C5D  C4D   121.20  3.000
 R04  H5D   C5D  C6D   119.60  3.000
 R04  C4D   C5D  C6D   119.20  3.000
 R04  BR27  C4D  C3D   119.55  3.000
 R04  BR27  C4D  C5D   119.57  3.000
 R04  C3D   C4D  C5D   120.88  3.000
 R04  H3D   C3D  C2D   119.69  3.000
 R04  H3D   C3D  C4D   121.07  3.000
 R04  C2D   C3D  C4D   119.23  3.000
 R04  H2D   C2D  C3D   119.04  3.000
 R04  H2D   C2D  C1D   119.82  3.000
 R04  C3D   C2D  C1D   121.14  3.000
 R04  H1E3  C1E  H1E2  108.54  3.000
 R04  H1E3  C1E  H1E1  108.91  3.000
 R04  H1E2  C1E  H1E1  109.23  3.000
 R04  H1E3  C1E  N1C   109.81  3.000
 R04  H1E2  C1E  N1C   108.91  3.000
 R04  H1E1  C1E  N1C   111.40  3.000
 R04  H1F3  C1F  H1F2  107.54  3.000
 R04  H1F3  C1F  H1F1  107.13  3.000
 R04  H1F2  C1F  H1F1  108.00  3.000
 R04  H1F3  C1F  N1    110.08  3.000
 R04  H1F2  C1F  N1    112.91  3.000
 R04  H1F1  C1F  N1    110.96  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
 R04  CONST_01  N1C   C7P  C7C  C6C  180.00   0.0  0
 R04  CONST_02  C3P   C7P  C7C  C6C    0.00   0.0  0
 R04  CONST_03  C3P   C4C  C5C  C6C    0.00   0.0  0
 R04  CONST_04  C4C   C5C  C6C  C7C    0.00   0.0  0
 R04  CONST_05  N2C   N1C  C7P  C7C  180.00   0.0  0
 R04  CONST_06  C3C   C3P  C7P  C7C  180.00   0.0  0
 R04  CONST_07  C4C   C3P  C7P  C7C    0.00   0.0  0
 R04  CONST_08  C5C   C6C  C7C  C7P    0.00   0.0  0
 R04  CONST_09  C3C   N2C  N1C  C7P    0.00   0.0  0
 R04  CONST_10  N2C   C3C  C3P  C7P    0.00   0.0  0
 R04  CONST_11  C1D   C3C  C3P  C7P  180.00   0.0  0
 R04  CONST_12  C5C   C4C  C3P  C7P    0.00   0.0  0
 R04  CONST_13  C3C   C3P  C7P  N1C    0.00   0.0  0
 R04  CONST_14  C4C   C3P  C7P  N1C  180.00   0.0  0
 R04  CONST_15  C3P   C3C  N2C  N1C    0.00   0.0  0
 R04  CONST_16  C1D   C3C  N2C  N1C  180.00   0.0  0
 R04  CONST_17  C3P   C7P  N1C  N2C    0.00   0.0  0
 R04  CONST_18  C4C   C3P  C3C  N2C  180.00   0.0  0
 R04  CONST_21  C5C   C4C  C3P  C3C  180.00   0.0  0
 R04  CONST_22  C5D   C6D  C1D  C3C  180.00   0.0  0
 R04  CONST_23  C3D   C2D  C1D  C3C  180.00   0.0  0
 R04  CONST_26  C1D   C3C  C3P  C4C    0.00   0.0  0
 R04  CONST_27  C4D   C5D  C6D  C1D    0.00   0.0  0
 R04  CONST_28  C4D   C3D  C2D  C1D    0.00   0.0  0
 R04  CONST_29  C3D   C2D  C1D  C6D    0.00   0.0  0
 R04  CONST_30  C3D   C4D  C5D  C6D    0.00   0.0  0
 R04  CONST_31  C2D   C1D  C6D  C5D    0.00   0.0  0
 R04  CONST_32  C2D   C3D  C4D  C5D    0.00   0.0  0
 R04  CONST_33  C7P   C7C  C6C  O    180.00   0.0  0
 R04  CONST_34  C4C   C5C  C6C  O    180.00   0.0  0
 R04  CONST_35  F     C5C  C6C  C7C  180.00   0.0  0
 R04  CONST_36  C1E   N1C  C7P  C7C    0.00   0.0  0
 R04  CONST_37  C1E   N1C  N2C  C3C  180.00   0.0  0
 R04  CONST_38  C1E   N1C  C7P  C3P  180.00   0.0  0
 R04  CONST_39  F     C5C  C4C  C3P  180.00   0.0  0
 R04  CONST_40  BR27  C4D  C5D  C6D  180.00   0.0  0
 R04  CONST_41  BR27  C4D  C3D  C2D  180.00   0.0  0
 R04  CONST_42  H4C   C4C  C5C  C6C  180.00   0.0  0
 R04  CONST_43  H7C   C7C  C7P  N1C    0.00   0.0  0
 R04  CONST_44  H6D   C6D  C1D  C3C    0.00   0.0  0
 R04  CONST_45  H2D   C2D  C1D  C3C    0.00   0.0  0
 R04  CONST_46  H5D   C5D  C6D  C1D  180.00   0.0  0
 R04  CONST_47  H3D   C3D  C2D  C1D  180.00   0.0  0
 R04  Var_01    C7C   C6C  O    C4B    1.37  30.0  2
 R04  Var_02    H1E1  C1E  N1C  C7P   84.23  30.0  2
 R04  Var_03    H4B1  C4B  O    C6C   58.64  30.0  1
 R04  Var_04    C4B   C3B  C2B  C1B  176.41   0.0  2
 R04  Var_05    N1    C1A  C2A  C3A  129.00  30.0  3
 R04  Var_06    C3B   C2B  C1B  N1   115.18  30.0  3
 R04  Var_07    O     C4B  C3B  C2B  124.12  30.0  3
 R04  Var_08    H3A1  C3A  C2A  C1A  177.84   0.0  2

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
 R04  chir_01  N1  C1A  C1B  C1F  negativ

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
 R04  plan-1  C3C   0.020
 R04  plan-1  C1D   0.020
 R04  plan-1  C6D   0.020
 R04  plan-1  C5D   0.020
 R04  plan-1  C4D   0.020
 R04  plan-1  C3D   0.020
 R04  plan-1  C2D   0.020
 R04  plan-1  BR27  0.020
 R04  plan-1  H6D   0.020
 R04  plan-1  H5D   0.020
 R04  plan-1  H3D   0.020
 R04  plan-1  H2D   0.020
 R04  plan-2  O     0.020
 R04  plan-2  C6C   0.020
 R04  plan-2  C7C   0.020
 R04  plan-2  C7P   0.020
 R04  plan-2  N1C   0.020
 R04  plan-2  N2C   0.020
 R04  plan-2  C3C   0.020
 R04  plan-2  C3P   0.020
 R04  plan-2  C4C   0.020
 R04  plan-2  C5C   0.020
 R04  plan-2  C1D   0.020
 R04  plan-2  F     0.020
 R04  plan-2  C1E   0.020
 R04  plan-2  H7C   0.020
 R04  plan-2  H4C   0.020
 R04  plan-3  C3A   0.020
 R04  plan-3  C2A   0.020
 R04  plan-3  C1A   0.020
 R04  plan-3  H3A1  0.020
 R04  plan-3  H3A2  0.020
 R04  plan-3  H2A   0.020
 R04  plan-4  C1B   0.020
 R04  plan-4  C2B   0.020
 R04  plan-4  C3B   0.020
 R04  plan-4  C4B   0.020
 R04  plan-4  H2B   0.020
 R04  plan-4  H3B   0.020

