# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 14:45:42 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (4-bromophenyl)[4-({(2E)-4-[cyclopropyl(methyl)amino]but-2-en-1-yl}oxy)phenyl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C/C=C/COc1ccc(cc1)C(=O)c2ccc(Br)cc2)C3CC3
#
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
 R88  R88  (4-bromophenyl)[4-({(2E)-4-[cyclopropyl(methyl)amino]but-2-en-1-yl}oxy)phenyl]methanone  ligand  47  25  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_R88
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
 R88  C1A   C   CR6    0  -0.033   1.3432  -0.1150    3.6676
 R88  C1    C   C      0   0.360   2.3046   0.0798    2.5454
 R88  O2    O   O      0  -0.397   3.5001   0.0768    2.7736
 R88  C1B   C   CR6    0  -0.060   1.7919   0.2805    1.1752
 R88  C6B   C   CR16   0  -0.249   2.5889   0.9536    0.2409
 R88  C5B   C   CR16   0  -0.338   2.1648   1.1293   -1.0558
 R88  C4B   C   CR6    0   0.403   0.9327   0.6075   -1.4719
 R88  C2C   C   CH2    0  -0.247  -0.6648   0.3832   -3.2280
 R88  C3C   C   C1     0  -0.242  -0.7961   0.8418   -4.6391
 R88  C4C   C   C1     0  -0.219  -1.0442   0.0245   -5.6556
 R88  C5C   C   CH2    0  -0.317  -1.2678   0.4721   -7.0650
 R88  N1D   N   NT    -1  -0.421  -0.4799  -0.3030   -8.0074
 R88  C1F   C   CH3    0  -0.521   0.9440  -0.0973   -7.8365
 R88  C1E   C   CH1    0  -0.074  -0.8843  -0.0582   -9.3560
 R88  C2E   C   CH2    0  -0.499  -0.7022  -1.1546  -10.3543
 R88  C3B   C   CR16   0  -0.373   0.1402  -0.0884   -0.5597
 R88  C2B   C   CR16   0  -0.267   0.5713  -0.2374    0.7496
 R88  C6A   C   CR16   0  -0.266   1.7097  -0.9364    4.7325
 R88  C5A   C   CR16   0  -0.217   0.8724  -1.1014    5.8221
 R88  C4A   C   CR6    0  -0.112  -0.3322  -0.4106    5.8572
 R88  O1C   O   O2     0  -0.462   0.6072   0.8189   -2.7517
 R88  C3E   C   CH2    0  -0.500  -2.0781  -0.7890   -9.8781
 R88  BR23  BR  BR     0  -0.028  -1.4730  -0.6172    7.3430
 R88  C3A   C   CR16   0  -0.212  -0.7095   0.4301    4.8211
 R88  C2A   C   CR16   0  -0.278   0.1296   0.5662    3.7254
 R88  H6    H   HCR6   0   0.266   3.5448   1.3618    0.5420
 R88  H5    H   HCR6   0   0.271   2.7780   1.6713   -1.7644
 R88  H151  H   HCH2   0   0.242  -1.4569   0.8198   -2.6087
 R88  H152  H   HCH2   0   0.244  -0.7499  -0.7066   -3.1630
 R88  H16   H   H      0   0.253  -0.7098   1.9117   -4.8102
 R88  H17   H   H      0   0.251  -1.1236  -1.0463   -5.4814
 R88  H201  H   HCH2   0   0.209  -1.0786   1.5555   -7.1486
 R88  H202  H   HCH2   0   0.252  -2.3233   0.3186   -7.3115
 R88  H271  H   HCH3   0   0.237   1.4933  -0.7339   -8.5303
 R88  H272  H   HCH3   0   0.194   1.2555   0.9440   -8.0115
 R88  H273  H   HCH3   0   0.236   1.2493  -0.3663   -6.8249
 R88  H25   H   HCH1   0   0.229  -0.7385   0.9604   -9.7275
 R88  H261  H   HCH2   0   0.247  -0.4148  -0.8871  -11.3629
 R88  H262  H   HCH2   0   0.247  -0.2818  -2.0868   -9.9974
 R88  H3    H   HCR6   0   0.288  -0.8054  -0.5265   -0.8464
 R88  H2    H   HCR6   0   0.277  -0.0541  -0.7977    1.4321
 R88  H13   H   HCR6   0   0.275   2.6516  -1.4686    4.7089
 R88  H12   H   HCR6   0   0.286   1.1642  -1.7569    6.6314
 R88  H3E1  H   HCH2   0   0.247  -2.5717  -1.4780   -9.2040
 R88  H3E2  H   HCH2   0   0.247  -2.7418  -0.2692  -10.5570
 R88  H10   H   HCR6   0   0.287  -1.6403   0.9795    4.8552
 R88  H9    H   HCR6   0   0.284  -0.1652   1.2329    2.9257

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
 R88  C1A  C1    single    1.490  0.020  1.490
 R88  C1A  C6A   aromatic  1.394  0.020  1.394
 R88  C1A  C2A   aromatic  1.393  0.020  1.393
 R88  C1   O2    double    1.217  0.020  1.217
 R88  C1   C1B   single    1.477  0.020  1.477
 R88  C1B  C6B   aromatic  1.400  0.020  1.400
 R88  C1B  C2B   aromatic  1.393  0.020  1.393
 R88  C6B  C5B   aromatic  1.376  0.020  1.376
 R88  C6B  H6    single    0.930  0.020  1.080
 R88  C5B  C4B   aromatic  1.401  0.020  1.401
 R88  C5B  H5    single    0.930  0.020  1.080
 R88  C4B  C3B   aromatic  1.394  0.020  1.394
 R88  C4B  O1C   single    1.337  0.020  1.337
 R88  C2C  C3C   single    1.490  0.020  1.490
 R88  C2C  O1C   single    1.426  0.020  1.426
 R88  C2C  H151  single    0.970  0.020  1.090
 R88  C2C  H152  single    0.970  0.020  1.090
 R88  C3C  C4C   double    1.328  0.020  1.328
 R88  C3C  H16   single    0.930  0.020  1.080
 R88  C4C  C5C   single    1.496  0.020  1.496
 R88  C4C  H17   single    0.930  0.020  1.080
 R88  C5C  N1D   single    1.452  0.020  1.452
 R88  C5C  H201  single    0.970  0.020  1.090
 R88  C5C  H202  single    0.970  0.020  1.090
 R88  N1D  C1F   single    1.449  0.020  1.449
 R88  N1D  C1E   single    1.429  0.020  1.429
 R88  C1F  H271  single    0.970  0.020  1.090
 R88  C1F  H272  single    0.970  0.020  1.090
 R88  C1F  H273  single    0.970  0.020  1.090
 R88  C1E  C2E   single    1.494  0.020  1.494
 R88  C1E  C3E   single    1.494  0.020  1.494
 R88  C1E  H25   single    0.970  0.020  1.090
 R88  C2E  C3E   single    1.501  0.020  1.501
 R88  C2E  H261  single    0.970  0.020  1.090
 R88  C2E  H262  single    0.970  0.020  1.090
 R88  C3B  C2B   aromatic  1.386  0.020  1.386
 R88  C3B  H3    single    0.930  0.020  1.080
 R88  C2B  H2    single    0.930  0.020  1.080
 R88  C6A  C5A   aromatic  1.384  0.020  1.384
 R88  C6A  H13   single    0.930  0.020  1.080
 R88  C5A  C4A   aromatic  1.389  0.020  1.389
 R88  C5A  H12   single    0.930  0.020  1.080
 R88  C4A  BR23  single    1.885  0.020  1.885
 R88  C4A  C3A   aromatic  1.387  0.020  1.387
 R88  C3E  H3E1  single    0.970  0.020  1.090
 R88  C3E  H3E2  single    0.970  0.020  1.090
 R88  C3A  C2A   aromatic  1.387  0.020  1.387
 R88  C3A  H10   single    0.930  0.020  1.080
 R88  C2A  H9    single    0.930  0.020  1.080

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
 R88  C2A   C1A  C6A   119.05  3.000
 R88  C2A   C1A  C1    121.96  3.000
 R88  C6A   C1A  C1    118.86  3.000
 R88  C1B   C1   O2    121.02  3.000
 R88  C1B   C1   C1A   119.50  3.000
 R88  O2    C1   C1A   119.48  3.000
 R88  C2B   C1B  C6B   118.27  3.000
 R88  C2B   C1B  C1    122.50  3.000
 R88  C6B   C1B  C1    119.13  3.000
 R88  H6    C6B  C5B   119.11  3.000
 R88  H6    C6B  C1B   119.89  3.000
 R88  C5B   C6B  C1B   120.98  3.000
 R88  H5    C5B  C4B   119.35  3.000
 R88  H5    C5B  C6B   120.42  3.000
 R88  C4B   C5B  C6B   120.24  3.000
 R88  O1C   C4B  C3B   124.51  3.000
 R88  O1C   C4B  C5B   116.06  3.000
 R88  C3B   C4B  C5B   119.43  3.000
 R88  H152  C2C  H151  107.86  3.000
 R88  H152  C2C  O1C   110.70  3.000
 R88  H151  C2C  O1C   109.51  3.000
 R88  H152  C2C  C3C   110.84  3.000
 R88  H151  C2C  C3C   110.42  3.000
 R88  O1C   C2C  C3C   107.52  3.000
 R88  H16   C3C  C4C   120.02  3.000
 R88  H16   C3C  C2C   116.43  3.000
 R88  C4C   C3C  C2C   123.52  3.000
 R88  H17   C4C  C5C   115.76  3.000
 R88  H17   C4C  C3C   119.80  3.000
 R88  C5C   C4C  C3C   124.41  3.000
 R88  H202  C5C  H201  106.62  3.000
 R88  H202  C5C  N1D   107.59  3.000
 R88  H201  C5C  N1D   112.46  3.000
 R88  H202  C5C  C4C   108.32  3.000
 R88  H201  C5C  C4C   109.86  3.000
 R88  N1D   C5C  C4C   111.75  3.000
 R88  C1E   N1D  C1F   111.41  3.000
 R88  C1E   N1D  C5C   111.56  3.000
 R88  C1F   N1D  C5C   112.39  3.000
 R88  H273  C1F  H272  107.56  3.000
 R88  H273  C1F  H271  107.78  3.000
 R88  H272  C1F  H271  107.97  3.000
 R88  H273  C1F  N1D   110.46  3.000
 R88  H272  C1F  N1D   113.18  3.000
 R88  H271  C1F  N1D   109.71  3.000
 R88  H25   C1E  C3E   116.31  3.000
 R88  H25   C1E  C2E   116.12  3.000
 R88  C3E   C1E  C2E    60.32  3.000
 R88  H25   C1E  N1D   116.25  3.000
 R88  C3E   C1E  N1D   118.17  3.000
 R88  C2E   C1E  N1D   118.06  3.000
 R88  H262  C2E  H261  114.63  3.000
 R88  H262  C2E  C3E   117.44  3.000
 R88  H261  C2E  C3E   118.61  3.000
 R88  H262  C2E  C1E   117.31  3.000
 R88  H261  C2E  C1E   118.28  3.000
 R88  C3E   C2E  C1E    59.84  3.000
 R88  H3    C3B  C2B   118.62  3.000
 R88  H3    C3B  C4B   121.73  3.000
 R88  C2B   C3B  C4B   119.65  3.000
 R88  H2    C2B  C3B   118.13  3.000
 R88  H2    C2B  C1B   120.43  3.000
 R88  C3B   C2B  C1B   121.41  3.000
 R88  H13   C6A  C5A   119.02  3.000
 R88  H13   C6A  C1A   120.13  3.000
 R88  C5A   C6A  C1A   120.84  3.000
 R88  H12   C5A  C4A   121.10  3.000
 R88  H12   C5A  C6A   119.87  3.000
 R88  C4A   C5A  C6A   119.03  3.000
 R88  C3A   C4A  BR23  119.40  3.000
 R88  C3A   C4A  C5A   121.24  3.000
 R88  BR23  C4A  C5A   119.36  3.000
 R88  C2C   O1C  C4B   119.23  3.000
 R88  H3E2  C3E  H3E1  114.62  3.000
 R88  H3E2  C3E  C2E   118.68  3.000
 R88  H3E1  C3E  C2E   117.40  3.000
 R88  H3E2  C3E  C1E   118.31  3.000
 R88  H3E1  C3E  C1E   117.25  3.000
 R88  C2E   C3E  C1E    59.84  3.000
 R88  H10   C3A  C2A   119.73  3.000
 R88  H10   C3A  C4A   121.24  3.000
 R88  C2A   C3A  C4A   119.03  3.000
 R88  H9    C2A  C3A   118.66  3.000
 R88  H9    C2A  C1A   120.53  3.000
 R88  C3A   C2A  C1A   120.79  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
 R88  CONST_01  C4A   C5A  C6A  C1A      0.00   0.0  0
 R88  CONST_02  C4A   C3A  C2A  C1A      0.00   0.0  0
 R88  CONST_03  C4B   C5B  C6B  C1B      0.00   0.0  0
 R88  CONST_04  C4B   C3B  C2B  C1B      0.00   0.0  0
 R88  CONST_05  C3B   C2B  C1B  C6B      0.00   0.0  0
 R88  CONST_06  C3B   C4B  C5B  C6B      0.00   0.0  0
 R88  CONST_07  C2B   C1B  C6B  C5B      0.00   0.0  0
 R88  CONST_08  C2B   C3B  C4B  C5B      0.00   0.0  0
 R88  CONST_09  C3A   C2A  C1A  C6A      0.00   0.0  0
 R88  CONST_10  C3A   C4A  C5A  C6A      0.00   0.0  0
 R88  CONST_11  C2A   C1A  C6A  C5A      0.00   0.0  0
 R88  CONST_12  C2A   C3A  C4A  C5A      0.00   0.0  0
 R88  CONST_13  C5A   C6A  C1A  C1     180.00   0.0  0
 R88  CONST_14  C3A   C2A  C1A  C1     180.00   0.0  0
 R88  CONST_15  C5B   C6B  C1B  C1     180.00   0.0  0
 R88  CONST_16  C3B   C2B  C1B  C1     180.00   0.0  0
 R88  CONST_17  O1C   C4B  C5B  C6B    180.00   0.0  0
 R88  CONST_18  O1C   C4B  C3B  C2B    180.00   0.0  0
 R88  CONST_19  BR23  C4A  C5A  C6A    180.00   0.0  0
 R88  CONST_20  C2A   C3A  C4A  BR23   180.00   0.0  0
 R88  CONST_21  H12   C5A  C6A  C1A    180.00   0.0  0
 R88  CONST_22  H10   C3A  C2A  C1A    180.00   0.0  0
 R88  CONST_23  H5    C5B  C6B  C1B    180.00   0.0  0
 R88  CONST_24  H3    C3B  C2B  C1B    180.00   0.0  0
 R88  CONST_25  H2    C2B  C1B  C6B    180.00   0.0  0
 R88  CONST_26  H6    C6B  C5B  C4B    180.00   0.0  0
 R88  CONST_27  H9    C2A  C1A  C6A    180.00   0.0  0
 R88  CONST_28  H13   C6A  C5A  C4A    180.00   0.0  0
 R88  Var_01    C6B   C1B  C1   C1A    155.62  30.0  2
 R88  Var_02    C6A   C1A  C1   C1B    147.45  30.0  2
 R88  Var_03    C3E   C2E  C1E  N1D    108.17  30.0  1
 R88  Var_04    H3E1  C3E  C2E  C1E   -107.17  30.0  1
 R88  Var_05    C3B   C4B  O1C  C2C      3.86  30.0  1
 R88  Var_06    C3C   C2C  O1C  C4B    175.58  30.0  2
 R88  Var_07    C5C   C4C  C3C  C2C    175.84   0.0  2
 R88  Var_08    N1D   C5C  C4C  C3C    132.17  30.0  3
 R88  Var_09    O1C   C2C  C3C  C4C    123.96  30.0  1

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
 R88  chir_01  N1D  C5C  C1F  C1E  positiv
 R88  chir_02  C1E  N1D  C2E  C3E  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
 R88  plan-1  C1A   0.020
 R88  plan-1  C1    0.020
 R88  plan-1  C6A   0.020
 R88  plan-1  C5A   0.020
 R88  plan-1  C4A   0.020
 R88  plan-1  BR23  0.020
 R88  plan-1  C3A   0.020
 R88  plan-1  C2A   0.020
 R88  plan-1  H13   0.020
 R88  plan-1  H12   0.020
 R88  plan-1  H10   0.020
 R88  plan-1  H9    0.020
 R88  plan-2  C1    0.020
 R88  plan-2  C1B   0.020
 R88  plan-2  C6B   0.020
 R88  plan-2  C5B   0.020
 R88  plan-2  C4B   0.020
 R88  plan-2  C3B   0.020
 R88  plan-2  C2B   0.020
 R88  plan-2  O1C   0.020
 R88  plan-2  H6    0.020
 R88  plan-2  H5    0.020
 R88  plan-2  H3    0.020
 R88  plan-2  H2    0.020
 R88  plan-3  C1A   0.020
 R88  plan-3  C1    0.020
 R88  plan-3  O2    0.020
 R88  plan-3  C1B   0.020
 R88  plan-4  C2C   0.020
 R88  plan-4  C3C   0.020
 R88  plan-4  C4C   0.020
 R88  plan-4  C5C   0.020
 R88  plan-4  H16   0.020
 R88  plan-4  H17   0.020

