# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 00:15:24 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 1-[6-(2-chloro-4-methoxyphenoxy)hexyl]-1H-imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(OCCCCCCn2ccnc2)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
 S57  S57  1-[6-(2-chloro-4-methoxyphenoxy)hexyl]-1H-imidazole  ligand  42  21  .  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_S57
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
 S57  C1    C   CH3   0  -0.416   1.1482  -0.0883   7.9201
 S57  O4    O   O2    0  -0.482   1.9300  -0.0241   6.7452
 S57  C4A   C   CR6   0   0.347   1.2971   0.0019   5.5546
 S57  C3A   C   CR16  0  -0.319  -0.0865   0.0229   5.4053
 S57  C2A   C   CR6   0  -0.136  -0.6369   0.0512   4.1330
 S57  CL    CL  CL    0  -0.086  -2.3587   0.0767   3.9651
 S57  C1A   C   CR6   0   0.453   0.1483   0.0593   2.9825
 S57  C6A   C   CR16  0  -0.346   1.5318   0.0386   3.1518
 S57  C5A   C   CR16  0  -0.304   2.0970   0.0100   4.4153
 S57  O1    O   O2    0  -0.448  -0.4876   0.0862   1.7997
 S57  C6B   C   CH2   0  -0.152   0.2850   0.0597   0.6090
 S57  C5B   C   CH2   0  -0.445  -0.6636   0.0665  -0.5708
 S57  C4B   C   CH2   0  -0.421   0.0938   0.0335  -1.8930
 S57  C3B   C   CH2   0  -0.417  -0.8377   0.0389  -3.0985
 S57  C2B   C   CH2   0  -0.418  -0.0841   0.0012  -4.4212
 S57  C1B   C   CH2   0  -0.284  -1.0358   0.0129  -5.6095
 S57  N1    N   NR5   0  -0.399  -0.3401  -0.0190  -6.8809
 S57  C2C   C   CR15  0   0.112  -0.0283   1.0446  -7.6502
 S57  N3    N   N     0  -0.397   0.6697   0.7032  -8.7038
 S57  C4C   C   CR15  0  -0.167   0.8246  -0.6503  -8.6076
 S57  C5C   C   CR15  0  -0.093   0.2085  -1.1169  -7.4812
 S57  H11   H   HCH3  0   0.258   1.8437  -0.1181   8.7549
 S57  H12   H   HCH3  0   0.218   0.5050   0.7885   8.0328
 S57  H13   H   HCH3  0   0.218   0.5271  -0.9878   7.9491
 S57  H3A   H   HCR6  0   0.274  -0.7533   0.0179   6.2561
 S57  H6A   H   HCR6  0   0.254   2.1932   0.0436   2.2965
 S57  H5A   H   HCR6  0   0.241   3.1747  -0.0057   4.5168
 S57  H6B1  H   HCH2  0   0.203   0.9491   0.9307   0.5659
 S57  H6B2  H   HCH2  0   0.203   0.9139  -0.8378   0.5837
 S57  H5B1  H   HCH2  0   0.231  -1.3306  -0.7983  -0.5069
 S57  H5B2  H   HCH2  0   0.232  -1.2932   0.9602  -0.5285
 S57  H4B1  H   HCH2  0   0.214   0.7685   0.8938  -1.9533
 S57  H4B2  H   HCH2  0   0.212   0.7297  -0.8573  -1.9308
 S57  H3B1  H   HCH2  0   0.214  -1.5144  -0.8200  -3.0378
 S57  H3B2  H   HCH2  0   0.214  -1.4719   0.9312  -3.0630
 S57  H2B1  H   HCH2  0   0.229   0.5903   0.8599  -4.4919
 S57  H2B2  H   HCH2  0   0.225   0.5414  -0.8957  -4.4654
 S57  H1B1  H   HCH2  0   0.240  -1.7103  -0.8432  -5.5661
 S57  H1B2  H   HCH2  0   0.240  -1.6562   0.9098  -5.5924
 S57  H2C   H   HCR5  0   0.237  -0.3456   2.0454  -7.3960
 S57  H4C   H   HCR5  0   0.221   1.3629  -1.2187  -9.3505
 S57  H5C   H   HCR5  0   0.243   0.1081  -2.1076  -7.0701

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
 S57  C1   O4    single    1.413  0.020  1.413
 S57  C1   H11   single    0.970  0.020  1.090
 S57  C1   H12   single    0.970  0.020  1.090
 S57  C1   H13   single    0.970  0.020  1.090
 S57  O4   C4A   single    1.349  0.020  1.349
 S57  C4A  C3A   aromatic  1.392  0.020  1.392
 S57  C4A  C5A   aromatic  1.392  0.020  1.392
 S57  C3A  C2A   aromatic  1.386  0.020  1.386
 S57  C3A  H3A   single    0.930  0.020  1.080
 S57  C2A  CL    single    1.730  0.020  1.730
 S57  C2A  C1A   aromatic  1.393  0.020  1.393
 S57  C1A  C6A   aromatic  1.394  0.020  1.394
 S57  C1A  O1    single    1.343  0.020  1.343
 S57  C6A  C5A   aromatic  1.384  0.020  1.384
 S57  C6A  H6A   single    0.930  0.020  1.080
 S57  C5A  H5A   single    0.930  0.020  1.080
 S57  O1   C6B   single    1.420  0.020  1.420
 S57  C6B  C5B   single    1.514  0.020  1.514
 S57  C6B  H6B1  single    0.970  0.020  1.090
 S57  C6B  H6B2  single    0.970  0.020  1.090
 S57  C5B  C4B   single    1.524  0.020  1.524
 S57  C5B  H5B1  single    0.970  0.020  1.090
 S57  C5B  H5B2  single    0.970  0.020  1.090
 S57  C4B  C3B   single    1.523  0.020  1.523
 S57  C4B  H4B1  single    0.970  0.020  1.090
 S57  C4B  H4B2  single    0.970  0.020  1.090
 S57  C3B  C2B   single    1.523  0.020  1.523
 S57  C3B  H3B1  single    0.970  0.020  1.090
 S57  C3B  H3B2  single    0.970  0.020  1.090
 S57  C2B  C1B   single    1.522  0.020  1.522
 S57  C2B  H2B1  single    0.970  0.020  1.090
 S57  C2B  H2B2  single    0.970  0.020  1.090
 S57  C1B  N1    single    1.450  0.020  1.450
 S57  C1B  H1B1  single    0.970  0.020  1.090
 S57  C1B  H1B2  single    0.970  0.020  1.090
 S57  N1   C2C   aromatic  1.349  0.020  1.349
 S57  N1   C5C   aromatic  1.366  0.020  1.366
 S57  C2C  N3    aromatic  1.309  0.020  1.309
 S57  C2C  H2C   single    0.930  0.020  1.080
 S57  N3   C4C   aromatic  1.366  0.020  1.366
 S57  C4C  C5C   aromatic  1.366  0.020  1.366
 S57  C4C  H4C   single    0.930  0.020  1.080
 S57  C5C  H5C   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
 S57  H13   C1   H12   108.83  3.000
 S57  H13   C1   H11   108.70  3.000
 S57  H12   C1   H11   108.62  3.000
 S57  H13   C1   O4    111.95  3.000
 S57  H12   C1   O4    112.01  3.000
 S57  H11   C1   O4    106.61  3.000
 S57  C4A   O4   C1    118.39  3.000
 S57  C5A   C4A  C3A   118.90  3.000
 S57  C5A   C4A  O4    116.93  3.000
 S57  C3A   C4A  O4    124.16  3.000
 S57  H3A   C3A  C2A   118.52  3.000
 S57  H3A   C3A  C4A   121.92  3.000
 S57  C2A   C3A  C4A   119.56  3.000
 S57  C1A   C2A  CL    118.73  3.000
 S57  C1A   C2A  C3A   122.30  3.000
 S57  CL    C2A  C3A   118.97  3.000
 S57  O1    C1A  C6A   125.25  3.000
 S57  O1    C1A  C2A   117.43  3.000
 S57  C6A   C1A  C2A   117.32  3.000
 S57  H6A   C6A  C5A   118.18  3.000
 S57  H6A   C6A  C1A   120.73  3.000
 S57  C5A   C6A  C1A   121.09  3.000
 S57  H5A   C5A  C6A   119.49  3.000
 S57  H5A   C5A  C4A   119.69  3.000
 S57  C6A   C5A  C4A   120.83  3.000
 S57  C6B   O1   C1A   118.72  3.000
 S57  H6B2  C6B  H6B1  107.58  3.000
 S57  H6B2  C6B  C5B   110.20  3.000
 S57  H6B1  C6B  C5B   110.21  3.000
 S57  H6B2  C6B  O1    110.29  3.000
 S57  H6B1  C6B  O1    110.36  3.000
 S57  C5B   C6B  O1    108.21  3.000
 S57  H5B2  C5B  H5B1  107.01  3.000
 S57  H5B2  C5B  C4B   109.71  3.000
 S57  H5B1  C5B  C4B   109.67  3.000
 S57  H5B2  C5B  C6B   109.52  3.000
 S57  H5B1  C5B  C6B   109.45  3.000
 S57  C4B   C5B  C6B   111.38  3.000
 S57  H4B2  C4B  H4B1  106.23  3.000
 S57  H4B2  C4B  C3B   109.30  3.000
 S57  H4B1  C4B  C3B   109.29  3.000
 S57  H4B2  C4B  C5B   109.64  3.000
 S57  H4B1  C4B  C5B   109.69  3.000
 S57  C3B   C4B  C5B   112.49  3.000
 S57  H3B2  C3B  H3B1  106.22  3.000
 S57  H3B2  C3B  C2B   109.56  3.000
 S57  H3B1  C3B  C2B   109.54  3.000
 S57  H3B2  C3B  C4B   109.35  3.000
 S57  H3B1  C3B  C4B   109.34  3.000
 S57  C2B   C3B  C4B   112.62  3.000
 S57  H2B2  C2B  H2B1  106.76  3.000
 S57  H2B2  C2B  C1B   109.39  3.000
 S57  H2B1  C2B  C1B   109.20  3.000
 S57  H2B2  C2B  C3B   109.77  3.000
 S57  H2B1  C2B  C3B   109.98  3.000
 S57  C1B   C2B  C3B   111.62  3.000
 S57  H1B2  C1B  H1B1  107.04  3.000
 S57  H1B2  C1B  N1    107.75  3.000
 S57  H1B1  C1B  N1    108.32  3.000
 S57  H1B2  C1B  C2B   110.46  3.000
 S57  H1B1  C1B  C2B   110.46  3.000
 S57  N1    C1B  C2B   112.61  3.000
 S57  C5C   N1   C2C   106.86  3.000
 S57  C5C   N1   C1B   126.57  3.000
 S57  C2C   N1   C1B   126.42  3.000
 S57  H2C   C2C  N3    125.99  3.000
 S57  H2C   C2C  N1    121.89  3.000
 S57  N3    C2C  N1    112.12  3.000
 S57  C4C   N3   C2C   105.21  3.000
 S57  H4C   C4C  C5C   127.78  3.000
 S57  H4C   C4C  N3    122.01  3.000
 S57  C5C   C4C  N3    110.21  3.000
 S57  H5C   C5C  C4C   132.13  3.000
 S57  H5C   C5C  N1    122.26  3.000
 S57  C4C   C5C  N1    105.60  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
 S57  CONST_01  C1A  C2A  C3A  C4A     0.00   0.0  0
 S57  CONST_02  C1A  C6A  C5A  C4A     0.00   0.0  0
 S57  CONST_03  C6A  C5A  C4A  C3A     0.00   0.0  0
 S57  CONST_04  C6A  C1A  C2A  C3A     0.00   0.0  0
 S57  CONST_05  C5A  C4A  C3A  C2A     0.00   0.0  0
 S57  CONST_06  C5A  C6A  C1A  C2A     0.00   0.0  0
 S57  CONST_07  C4C  N3   C2C  N1      0.00   0.0  0
 S57  CONST_08  N3   C4C  C5C  N1      0.00   0.0  0
 S57  CONST_09  C4C  C5C  N1   C2C     0.00   0.0  0
 S57  CONST_10  C5C  C4C  N3   C2C     0.00   0.0  0
 S57  CONST_11  C5C  N1   C2C  N3      0.00   0.0  0
 S57  CONST_12  C2A  C3A  C4A  O4    180.00   0.0  0
 S57  CONST_13  C6A  C5A  C4A  O4    180.00   0.0  0
 S57  CONST_14  CL   C2A  C3A  C4A   180.00   0.0  0
 S57  CONST_15  O1   C1A  C2A  C3A   180.00   0.0  0
 S57  CONST_16  C6A  C1A  C2A  CL    180.00   0.0  0
 S57  CONST_17  O1   C1A  C6A  C5A   180.00   0.0  0
 S57  CONST_18  N3   C2C  N1   C1B   180.00   0.0  0
 S57  CONST_19  C4C  C5C  N1   C1B   180.00   0.0  0
 S57  CONST_20  H6A  C6A  C5A  C4A   180.00   0.0  0
 S57  CONST_21  H5A  C5A  C4A  C3A   180.00   0.0  0
 S57  CONST_22  H3A  C3A  C2A  C1A   180.00   0.0  0
 S57  CONST_23  H4C  C4C  C5C  N1    180.00   0.0  0
 S57  CONST_24  H5C  C5C  N1   C2C   180.00   0.0  0
 S57  CONST_25  H2C  C2C  N3   C4C   180.00   0.0  0
 S57  Var_01    C3A  C4A  O4   C1      2.66  30.0  2
 S57  Var_02    C2C  N1   C1B  C2B   -96.06  30.0  2
 S57  Var_03    C5B  C6B  O1   C1A   178.73  30.0  3
 S57  Var_04    N1   C1B  C2B  C3B   179.85  30.0  3
 S57  Var_05    H11  C1   O4   C4A   178.98  30.0  3
 S57  Var_06    C4B  C5B  C6B  O1   -179.77  30.0  3
 S57  Var_07    C3B  C4B  C5B  C6B   179.97  30.0  3
 S57  Var_08    C2B  C3B  C4B  C5B  -179.80  30.0  3
 S57  Var_09    C1B  C2B  C3B  C4B  -179.78  30.0  3

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
 S57  plan-1  C1B  0.020
 S57  plan-1  N1   0.020
 S57  plan-1  C2C  0.020
 S57  plan-1  N3   0.020
 S57  plan-1  C4C  0.020
 S57  plan-1  C5C  0.020
 S57  plan-1  H2C  0.020
 S57  plan-1  H4C  0.020
 S57  plan-1  H5C  0.020
 S57  plan-2  O4   0.020
 S57  plan-2  C4A  0.020
 S57  plan-2  C3A  0.020
 S57  plan-2  C2A  0.020
 S57  plan-2  CL   0.020
 S57  plan-2  C1A  0.020
 S57  plan-2  C6A  0.020
 S57  plan-2  C5A  0.020
 S57  plan-2  O1   0.020
 S57  plan-2  H3A  0.020
 S57  plan-2  H6A  0.020
 S57  plan-2  H5A  0.020

