# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 05:33:53 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 1-[(2R)-2-[(2,4-dichlorobenzyl)oxy]-2-(2,4-dichlorophenyl)ethyl]-1H-imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(CO[C@@H](Cn2ccnc2)c3ccc(Cl)cc3Cl)c(Cl)c1
#
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
 X89  X89  1-[(2R)-2-[(2,4-dichlorobenzyl)oxy]-2-(2,4-dichlorophenyl)ethyl]-1H-imidazole  ligand  39  25  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X89
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
 X89  O     O   O2    0  -0.485   0.0990   0.2396  -0.3922
 X89  C1    C   CH2   0  -0.330  -1.3752   1.7246  -1.4776
 X89  N1    N   NR5   0  -0.394  -0.3351   2.6858  -1.7479
 X89  C2    C   CR15  0   0.107   0.7514   2.4945  -2.5262
 X89  N3    N   N     0  -0.457   1.5588   3.5226  -2.5012
 X89  C4    C   CR15  0  -0.215   0.9729   4.4212  -1.6535
 X89  C5    C   CR15  0  -0.109  -0.2013   3.9193  -1.1721
 X89  CL2A  CL  CL    0  -0.109  -3.4766   2.0391   1.4203
 X89  CL2B  CL  CL    0  -0.111   2.2626  -1.2516   3.1431
 X89  CL4A  CL  CL    0  -0.111  -5.7441  -2.7724   0.8220
 X89  CL4B  CL  CL    0  -0.117   6.2791  -2.2094  -0.2749
 X89  C1A   C   CR6   0   0.158  -2.2629   0.0107   0.0855
 X89  C1B   C   CR6   0   0.117   2.0834  -0.7114   0.4988
 X89  C2A   C   CR6   0  -0.120  -3.3832   0.4219   0.8003
 X89  C2B   C   CR6   0  -0.101   2.8831  -1.2080   1.5250
 X89  C3A   C   CR16  0  -0.145  -4.4593  -0.4197   1.0361
 X89  C3B   C   CR16  0  -0.149   4.1699  -1.6711   1.3086
 X89  C4A   C   CR6   0  -0.062  -4.4118  -1.7091   0.5348
 X89  C4B   C   CR6   0  -0.065   4.6727  -1.6383   0.0184
 X89  C5A   C   CR16  0  -0.183  -3.3199  -2.1558  -0.1913
 X89  C5B   C   CR16  0  -0.182   3.9111  -1.1561  -1.0315
 X89  C6A   C   CR16  0  -0.315  -2.2611  -1.2905  -0.4085
 X89  C6B   C   CR16  0  -0.330   2.6265  -0.6975  -0.7813
 X89  CBA   C   CH1   0   0.005  -1.1001   0.9354  -0.1989
 X89  CBB   C   CH2   0  -0.153   0.6979  -0.2123   0.7933
 X89  H1    H   HCH2  0   0.287  -2.3276   2.2475  -1.3940
 X89  H1A   H   HCH2  0   0.290  -1.4538   1.0428  -2.3257
 X89  H2    H   HCR5  0   0.277   0.8917   1.5894  -3.0980
 X89  H4    H   HCR5  0   0.251   1.4178   5.3811  -1.4402
 X89  H5    H   HCR5  0   0.287  -0.9390   4.3250  -0.4993
 X89  HC3   H   HCR6  0   0.304  -5.3148  -0.0731   1.5988
 X89  HC3A  H   HCR6  0   0.302   4.7646  -2.0471   2.1295
 X89  HC5   H   HCR6  0   0.288  -3.2910  -3.1624  -0.5844
 X89  HC5A  H   HCR6  0   0.285   4.3082  -1.1338  -2.0368
 X89  HC6   H   HCR6  0   0.279  -1.4079  -1.6438  -0.9725
 X89  HC6A  H   HCR6  0   0.271   2.0423  -0.3213  -1.6086
 X89  HCB   H   HCH1  0   0.250  -0.9854   1.6434   0.6336
 X89  HCBA  H   HCH2  0   0.245   0.7500   0.6001   1.5312
 X89  HCBB  H   HCH2  0   0.240   0.1087  -1.0158   1.2548

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
 X89  O    CBA   single    1.400  0.020  1.400
 X89  O    CBB   single    1.403  0.020  1.403
 X89  N1   C1    single    1.442  0.020  1.442
 X89  C1   CBA   single    1.528  0.020  1.528
 X89  C1   H1    single    0.970  0.020  1.090
 X89  C1   H1A   single    0.970  0.020  1.090
 X89  C2   N1    aromatic  1.350  0.020  1.350
 X89  C5   N1    aromatic  1.368  0.020  1.368
 X89  N3   C2    aromatic  1.307  0.020  1.307
 X89  C2   H2    single    0.930  0.020  1.080
 X89  N3   C4    aromatic  1.367  0.020  1.367
 X89  C4   C5    aromatic  1.365  0.020  1.365
 X89  C4   H4    single    0.930  0.020  1.080
 X89  C5   H5    single    0.930  0.020  1.080
 X89  C2A  CL2A  single    1.735  0.020  1.735
 X89  C2B  CL2B  single    1.734  0.020  1.734
 X89  C4A  CL4A  single    1.729  0.020  1.729
 X89  C4B  CL4B  single    1.730  0.020  1.730
 X89  CBA  C1A   single    1.513  0.020  1.513
 X89  C6A  C1A   aromatic  1.392  0.020  1.392
 X89  C1A  C2A   aromatic  1.391  0.020  1.391
 X89  C6B  C1B   aromatic  1.391  0.020  1.391
 X89  C1B  CBB   single    1.502  0.020  1.502
 X89  C1B  C2B   aromatic  1.392  0.020  1.392
 X89  C2A  C3A   aromatic  1.386  0.020  1.386
 X89  C3B  C2B   aromatic  1.385  0.020  1.385
 X89  C4A  C3A   aromatic  1.384  0.020  1.384
 X89  C3A  HC3   single    0.930  0.020  1.080
 X89  C4B  C3B   aromatic  1.385  0.020  1.385
 X89  C3B  HC3A  single    0.930  0.020  1.080
 X89  C5A  C4A   aromatic  1.385  0.020  1.385
 X89  C5B  C4B   aromatic  1.384  0.020  1.384
 X89  C6A  C5A   aromatic  1.385  0.020  1.385
 X89  C5A  HC5   single    0.930  0.020  1.080
 X89  C5B  C6B   aromatic  1.387  0.020  1.387
 X89  C5B  HC5A  single    0.930  0.020  1.080
 X89  C6A  HC6   single    0.930  0.020  1.080
 X89  C6B  HC6A  single    0.930  0.020  1.080
 X89  CBA  HCB   single    0.970  0.020  1.090
 X89  CBB  HCBA  single    0.970  0.020  1.090
 X89  CBB  HCBB  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
 X89  CBB   O    CBA   114.15  3.000
 X89  H1A   C1   H1    107.25  3.000
 X89  H1A   C1   CBA   109.93  3.000
 X89  H1    C1   CBA   109.94  3.000
 X89  H1A   C1   N1    108.83  3.000
 X89  H1    C1   N1    108.96  3.000
 X89  CBA   C1   N1    111.81  3.000
 X89  C5    N1   C2    106.96  3.000
 X89  C5    N1   C1    126.36  3.000
 X89  C2    N1   C1    126.45  3.000
 X89  H2    C2   N3    126.09  3.000
 X89  H2    C2   N1    121.91  3.000
 X89  N3    C2   N1    111.99  3.000
 X89  C4    N3   C2    105.32  3.000
 X89  H4    C4   C5    127.74  3.000
 X89  H4    C4   N3    122.04  3.000
 X89  C5    C4   N3    110.22  3.000
 X89  H5    C5   C4    132.12  3.000
 X89  H5    C5   N1    122.36  3.000
 X89  C4    C5   N1    105.50  3.000
 X89  CBA   C1A  C6A   120.25  3.000
 X89  C6A   C1A  C2A   117.37  3.000
 X89  CBA   C1A  C2A   122.34  3.000
 X89  CBB   C1B  C6B   122.51  3.000
 X89  CBB   C1B  C2B   120.25  3.000
 X89  C6B   C1B  C2B   117.24  3.000
 X89  C3A   C2A  C1A   122.21  3.000
 X89  C3A   C2A  CL2A  117.61  3.000
 X89  C1A   C2A  CL2A  120.18  3.000
 X89  C3B   C2B  C1B   122.54  3.000
 X89  C3B   C2B  CL2B  118.04  3.000
 X89  C1B   C2B  CL2B  119.42  3.000
 X89  HC3   C3A  C4A   120.95  3.000
 X89  HC3   C3A  C2A   120.55  3.000
 X89  C4A   C3A  C2A   118.51  3.000
 X89  HC3A  C3B  C4B   121.05  3.000
 X89  HC3A  C3B  C2B   120.59  3.000
 X89  C4B   C3B  C2B   118.36  3.000
 X89  C5A   C4A  C3A   121.14  3.000
 X89  C5A   C4A  CL4A  119.75  3.000
 X89  C3A   C4A  CL4A  119.10  3.000
 X89  C5B   C4B  C3B   121.01  3.000
 X89  C5B   C4B  CL4B  119.83  3.000
 X89  C3B   C4B  CL4B  119.16  3.000
 X89  HC5   C5A  C6A   120.30  3.000
 X89  HC5   C5A  C4A   120.79  3.000
 X89  C6A   C5A  C4A   118.91  3.000
 X89  HC5A  C5B  C6B   120.08  3.000
 X89  HC5A  C5B  C4B   120.70  3.000
 X89  C6B   C5B  C4B   119.22  3.000
 X89  HC6   C6A  C5A   118.73  3.000
 X89  HC6   C6A  C1A   119.42  3.000
 X89  C5A   C6A  C1A   121.85  3.000
 X89  HC6A  C6B  C5B   118.55  3.000
 X89  HC6A  C6B  C1B   119.81  3.000
 X89  C5B   C6B  C1B   121.64  3.000
 X89  HCB   CBA  C1A   109.37  3.000
 X89  HCB   CBA  C1    108.67  3.000
 X89  C1A   CBA  C1    109.56  3.000
 X89  HCB   CBA  O     109.60  3.000
 X89  C1A   CBA  O     112.37  3.000
 X89  C1    CBA  O     107.18  3.000
 X89  HCBB  CBB  HCBA  106.52  3.000
 X89  HCBB  CBB  C1B   109.53  3.000
 X89  HCBA  CBB  C1B   109.49  3.000
 X89  HCBB  CBB  O     111.21  3.000
 X89  HCBA  CBB  O     110.46  3.000
 X89  C1B   CBB  O     109.59  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
 X89  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 X89  CONST_02  N3    C4   C5   N1      0.00   0.0  0
 X89  CONST_03  C4    C5   N1   C2      0.00   0.0  0
 X89  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 X89  CONST_05  C5    N1   C2   N3      0.00   0.0  0
 X89  CONST_06  C4A   C5A  C6A  C1A     0.00   0.0  0
 X89  CONST_07  C4A   C3A  C2A  C1A     0.00   0.0  0
 X89  CONST_08  C4B   C5B  C6B  C1B     0.00   0.0  0
 X89  CONST_09  C4B   C3B  C2B  C1B     0.00   0.0  0
 X89  CONST_10  C5A   C6A  C1A  C2A     0.00   0.0  0
 X89  CONST_11  C5A   C4A  C3A  C2A     0.00   0.0  0
 X89  CONST_12  C5B   C6B  C1B  C2B     0.00   0.0  0
 X89  CONST_13  C5B   C4B  C3B  C2B     0.00   0.0  0
 X89  CONST_14  C6A   C1A  C2A  C3A     0.00   0.0  0
 X89  CONST_15  C6A   C5A  C4A  C3A     0.00   0.0  0
 X89  CONST_16  C6B   C1B  C2B  C3B     0.00   0.0  0
 X89  CONST_17  C6B   C5B  C4B  C3B     0.00   0.0  0
 X89  CONST_18  N3    C2   N1   C1    180.00   0.0  0
 X89  CONST_19  C4    C5   N1   C1    180.00   0.0  0
 X89  CONST_20  C6A   C1A  C2A  CL2A  180.00   0.0  0
 X89  CONST_21  C4A   C3A  C2A  CL2A  180.00   0.0  0
 X89  CONST_22  C6B   C1B  C2B  CL2B  180.00   0.0  0
 X89  CONST_23  C4B   C3B  C2B  CL2B  180.00   0.0  0
 X89  CONST_24  C2A   C3A  C4A  CL4A  180.00   0.0  0
 X89  CONST_25  C6A   C5A  C4A  CL4A  180.00   0.0  0
 X89  CONST_26  C2B   C3B  C4B  CL4B  180.00   0.0  0
 X89  CONST_27  C6B   C5B  C4B  CL4B  180.00   0.0  0
 X89  CONST_28  CBA   C1A  C2A  C3A   180.00   0.0  0
 X89  CONST_29  CBB   C1B  C2B  C3B   180.00   0.0  0
 X89  CONST_30  CBA   C1A  C6A  C5A   180.00   0.0  0
 X89  CONST_31  CBB   C1B  C6B  C5B   180.00   0.0  0
 X89  CONST_32  H4    C4   C5   N1    180.00   0.0  0
 X89  CONST_33  H5    C5   N1   C2    180.00   0.0  0
 X89  CONST_34  H2    C2   N3   C4    180.00   0.0  0
 X89  CONST_35  HC5   C5A  C6A  C1A   180.00   0.0  0
 X89  CONST_36  HC3   C3A  C2A  C1A   180.00   0.0  0
 X89  CONST_37  HC5A  C5B  C6B  C1B   180.00   0.0  0
 X89  CONST_38  HC3A  C3B  C2B  C1B   180.00   0.0  0
 X89  CONST_39  HC6   C6A  C1A  C2A   180.00   0.0  0
 X89  CONST_40  HC6A  C6B  C1B  C2B   180.00   0.0  0
 X89  Var_01    C6B   C1B  CBB  O      -0.00  30.0  3
 X89  Var_02    CBA   C1   N1   C2     93.36  30.0  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
 X89  chir_01  CBA  O  C1  C1A  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
 X89  plan-1  C1    0.020
 X89  plan-1  N1    0.020
 X89  plan-1  C2    0.020
 X89  plan-1  N3    0.020
 X89  plan-1  C4    0.020
 X89  plan-1  C5    0.020
 X89  plan-1  H2    0.020
 X89  plan-1  H4    0.020
 X89  plan-1  H5    0.020
 X89  plan-2  CL2A  0.020
 X89  plan-2  CL4A  0.020
 X89  plan-2  C1A   0.020
 X89  plan-2  C2A   0.020
 X89  plan-2  C3A   0.020
 X89  plan-2  C4A   0.020
 X89  plan-2  C5A   0.020
 X89  plan-2  C6A   0.020
 X89  plan-2  CBA   0.020
 X89  plan-2  HC3   0.020
 X89  plan-2  HC5   0.020
 X89  plan-2  HC6   0.020
 X89  plan-3  CL2B  0.020
 X89  plan-3  CL4B  0.020
 X89  plan-3  C1B   0.020
 X89  plan-3  C2B   0.020
 X89  plan-3  C3B   0.020
 X89  plan-3  C4B   0.020
 X89  plan-3  C5B   0.020
 X89  plan-3  C6B   0.020
 X89  plan-3  CBB   0.020
 X89  plan-3  HC3A  0.020
 X89  plan-3  HC5A  0.020
 X89  plan-3  HC6A  0.020

