# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 16:37:07 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (3S)-3-({3-[(1R)-3-amino-1-hydroxypropyl]phenoxy}methyl)hexan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@@H](CCO)COc1cccc(c1)[C@H](O)CCN
#
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
 8E4  8E4  (3S)-3-({3-[(1R)-3-amino-1-hydroxypropyl]phenoxy}methyl)hexan-1-ol  ligand  47  20  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8E4
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
 8E4  C9   C  CH2   0  -0.427   5.9852   0.0904  -0.4391
 8E4  C7   C  CH1   0  -0.284   3.4225  -0.0590  -0.2376
 8E4  C5   C  CR6   0   0.414  -0.1026   0.9498  -0.0137
 8E4  C1   C  CH2   0  -0.469  -4.4824  -0.4784   0.3806
 8E4  C15  C  CR16  0  -0.346  -2.5924   2.1133   0.4577
 8E4  O2   O  OH1   0  -0.679   2.6027  -3.7397  -0.0976
 8E4  C11  C  CH2   0  -0.454   3.3401  -1.5101   0.2481
 8E4  C8   C  CH2   0  -0.412   4.7220   0.6030   0.2435
 8E4  C10  C  CH3   0  -0.661   7.2378   0.7968   0.0613
 8E4  C6   C  CH2   0  -0.156   2.2631   0.8090   0.2255
 8E4  O1   O  O2    0  -0.479   1.0480   0.3162  -0.3093
 8E4  C4   C  CR16  0  -0.427  -1.2705   0.3536  -0.4962
 8E4  C13  C  CR16  0  -0.394  -0.1863   2.1327   0.7149
 8E4  C14  C  CR16  0  -0.228  -1.4365   2.7016   0.9393
 8E4  C3   C  CR6   0   0.170  -2.5117   0.9214  -0.2640
 8E4  C2   C  CH1   0  -0.056  -3.7591   0.2257  -0.7656
 8E4  O    O  OH1   0  -0.662  -4.6048   1.1004  -1.4835
 8E4  N    N  NH2   0  -0.802  -6.2498  -2.0259   1.0613
 8E4  H1   H  HCH2  0   0.219   6.0944  -0.9855  -0.2810
 8E4  H2   H  HCH2  0   0.215   5.8904   0.2312  -1.5200
 8E4  H3   H  HCH1  0   0.227   3.4309  -0.0475  -1.3355
 8E4  H4   H  HCH2  0   0.239  -3.7586  -1.0808   0.9359
 8E4  H5   H  HCH2  0   0.225  -4.8608   0.2727   1.0860
 8E4  H6   H  HCR6  0   0.241  -3.5486   2.5832   0.6532
 8E4  H7   H  HOH1  0   0.451   1.9107  -4.2933  -0.4695
 8E4  H10  H  HCH2  0   0.232   4.3199  -1.9721   0.1004
 8E4  H11  H  HCH2  0   0.221   3.1546  -1.5198   1.3280
 8E4  H12  H  HCH2  0   0.216   4.8134   0.4735   1.3282
 8E4  H13  H  HCH2  0   0.223   4.6590   1.6833   0.0738
 8E4  H14  H  HCH3  0   0.217   7.1857   1.8717  -0.1212
 8E4  H15  H  HCH3  0   0.217   7.3682   0.6521   1.1354
 8E4  H16  H  HCH3  0   0.228   8.1329   0.4199  -0.4347
 8E4  H17  H  HCH2  0   0.216   2.2172   0.8220   1.3225
 8E4  H18  H  HCH2  0   0.226   2.4268   1.8403  -0.1083
 8E4  H19  H  HCR6  0   0.255  -1.1923  -0.5679  -1.0631
 8E4  H20  H  HCR6  0   0.276   0.6945   2.6228   1.1061
 8E4  H21  H  HCR6  0   0.257  -1.4974   3.6236   1.5034
 8E4  H22  H  HCH1  0   0.238  -3.4502  -0.5365  -1.4890
 8E4  H23  H  HOH1  0   0.447  -5.1127   1.6294  -0.8597
 8E4  H24  H  HCH2  0   0.196  -6.3278  -0.7880  -0.6874
 8E4  H25  H  HCH2  0   0.216  -5.2207  -2.1478  -0.7385
 8E4  H26  H  HNH2  0   0.338  -6.7167  -1.3278   1.6276
 8E4  H27  H  HNH2  0   0.346  -6.9857  -2.6377   0.7316
 8E4  C12  C  CH2   0  -0.142   2.3286  -2.3982  -0.4585
 8E4  C    C  CH2   0  -0.273  -5.6243  -1.3724  -0.0809
 8E4  H8   H  HCH2  0   0.182   2.4177  -2.2540  -1.5443
 8E4  H9   H  HCH2  0   0.203   1.3073  -2.1242  -0.1845

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
 8E4  C12  O2   single    1.416  0.020  1.416
 8E4  C12  C11  single    1.520  0.020  1.520
 8E4  C7   C11  single    1.532  0.020  1.532
 8E4  C7   C6   single    1.521  0.020  1.521
 8E4  C7   C8   single    1.536  0.020  1.536
 8E4  N    C    single    1.457  0.020  1.457
 8E4  C9   C8   single    1.525  0.020  1.525
 8E4  C9   C10  single    1.523  0.020  1.523
 8E4  C6   O1   single    1.416  0.020  1.416
 8E4  C    C1   single    1.522  0.020  1.522
 8E4  C1   C2   single    1.527  0.020  1.527
 8E4  O    C2   single    1.413  0.020  1.413
 8E4  O1   C5   single    1.346  0.020  1.346
 8E4  C4   C5   aromatic  1.397  0.020  1.397
 8E4  C4   C3   aromatic  1.385  0.020  1.385
 8E4  C2   C3   single    1.514  0.020  1.514
 8E4  C5   C13  aromatic  1.392  0.020  1.392
 8E4  C3   C15  aromatic  1.396  0.020  1.396
 8E4  C13  C14  aromatic  1.392  0.020  1.392
 8E4  C15  C14  aromatic  1.383  0.020  1.383
 8E4  C9   H1   single    0.970  0.020  1.090
 8E4  C9   H2   single    0.970  0.020  1.090
 8E4  C7   H3   single    0.970  0.020  1.090
 8E4  C1   H4   single    0.970  0.020  1.090
 8E4  C1   H5   single    0.970  0.020  1.090
 8E4  C15  H6   single    0.930  0.020  1.080
 8E4  O2   H7   single    0.850  0.020  0.980
 8E4  C12  H8   single    0.970  0.020  1.090
 8E4  C12  H9   single    0.970  0.020  1.090
 8E4  C11  H10  single    0.970  0.020  1.090
 8E4  C11  H11  single    0.970  0.020  1.090
 8E4  C8   H12  single    0.970  0.020  1.090
 8E4  C8   H13  single    0.970  0.020  1.090
 8E4  C10  H14  single    0.970  0.020  1.090
 8E4  C10  H15  single    0.970  0.020  1.090
 8E4  C10  H16  single    0.970  0.020  1.090
 8E4  C6   H17  single    0.970  0.020  1.090
 8E4  C6   H18  single    0.970  0.020  1.090
 8E4  C4   H19  single    0.930  0.020  1.080
 8E4  C13  H20  single    0.930  0.020  1.080
 8E4  C14  H21  single    0.930  0.020  1.080
 8E4  C2   H22  single    0.970  0.020  1.090
 8E4  O    H23  single    0.850  0.020  0.980
 8E4  C    H24  single    0.970  0.020  1.090
 8E4  C    H25  single    0.970  0.020  1.090
 8E4  N    H26  single    0.890  0.020  1.040
 8E4  N    H27  single    0.890  0.020  1.040

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
 8E4  H2   C9   H1   106.16  3.000
 8E4  H2   C9   C10  109.65  3.000
 8E4  H1   C9   C10  109.09  3.000
 8E4  H2   C9   C8   109.10  3.000
 8E4  H1   C9   C8   110.42  3.000
 8E4  C10  C9   C8   112.24  3.000
 8E4  H3   C7   C6   107.72  3.000
 8E4  H3   C7   C8   107.59  3.000
 8E4  C6   C7   C8   107.68  3.000
 8E4  H3   C7   C11  109.10  3.000
 8E4  C8   C7   C11  110.76  3.000
 8E4  C6   C7   C11  113.77  3.000
 8E4  C13  C5   C4   119.54  3.000
 8E4  C13  C5   O1   124.49  3.000
 8E4  C4   C5   O1   115.96  3.000
 8E4  H5   C1   H4   106.19  3.000
 8E4  H5   C1   C    109.77  3.000
 8E4  H4   C1   C    109.09  3.000
 8E4  H5   C1   C2   109.27  3.000
 8E4  H4   C1   C2   108.77  3.000
 8E4  C    C1   C2   113.49  3.000
 8E4  H6   C15  C3   120.98  3.000
 8E4  H6   C15  C14  119.36  3.000
 8E4  C3   C15  C14  119.66  3.000
 8E4  H7   O2   C12  107.92  3.000
 8E4  H11  C11  H10  106.33  3.000
 8E4  H11  C11  C12  109.89  3.000
 8E4  H10  C11  C12  106.66  3.000
 8E4  H11  C11  C7   109.25  3.000
 8E4  H10  C11  C7   108.00  3.000
 8E4  C12  C11  C7   116.21  3.000
 8E4  H13  C8   H12  105.94  3.000
 8E4  H13  C8   C7   109.15  3.000
 8E4  H12  C8   C7   109.25  3.000
 8E4  H13  C8   C9   108.05  3.000
 8E4  H12  C8   C9   109.52  3.000
 8E4  C7   C8   C9   114.57  3.000
 8E4  H16  C10  H15  107.68  3.000
 8E4  H16  C10  H14  107.66  3.000
 8E4  H15  C10  H14  107.50  3.000
 8E4  H16  C10  C9   111.43  3.000
 8E4  H15  C10  C9   111.11  3.000
 8E4  H14  C10  C9   111.27  3.000
 8E4  H18  C6   H17  107.42  3.000
 8E4  H18  C6   O1   109.90  3.000
 8E4  H17  C6   O1   110.21  3.000
 8E4  H18  C6   C7   109.30  3.000
 8E4  H17  C6   C7   110.06  3.000
 8E4  O1   C6   C7   109.91  3.000
 8E4  C6   O1   C5   119.12  3.000
 8E4  H19  C4   C3   120.04  3.000
 8E4  H19  C4   C5   118.86  3.000
 8E4  C3   C4   C5   121.10  3.000
 8E4  H20  C13  C14  119.22  3.000
 8E4  H20  C13  C5   121.71  3.000
 8E4  C14  C13  C5   119.07  3.000
 8E4  H21  C14  C13  118.86  3.000
 8E4  H21  C14  C15  119.77  3.000
 8E4  C13  C14  C15  121.37  3.000
 8E4  C2   C3   C4   119.65  3.000
 8E4  C2   C3   C15  121.08  3.000
 8E4  C4   C3   C15  119.26  3.000
 8E4  H22  C2   O    105.31  3.000
 8E4  H22  C2   C3   107.83  3.000
 8E4  O    C2   C3   112.16  3.000
 8E4  H22  C2   C1   107.96  3.000
 8E4  C3   C2   C1   110.69  3.000
 8E4  O    C2   C1   112.54  3.000
 8E4  H23  O    C2   109.07  3.000
 8E4  H27  N    H26  105.28  3.000
 8E4  H27  N    C    109.14  3.000
 8E4  H26  N    C    109.09  3.000
 8E4  H9   C12  H8   106.90  3.000
 8E4  H9   C12  C11  111.04  3.000
 8E4  H8   C12  C11  109.19  3.000
 8E4  H9   C12  O2   110.78  3.000
 8E4  H8   C12  O2   111.12  3.000
 8E4  C11  C12  O2   107.83  3.000
 8E4  H25  C    H24  106.36  3.000
 8E4  H25  C    N    108.17  3.000
 8E4  H24  C    N    113.38  3.000
 8E4  H25  C    C1   108.78  3.000
 8E4  H24  C    C1   109.62  3.000
 8E4  N    C    C1   110.36  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
 8E4  CONST_01  C15  C3   C4   C5      0.00   0.0  0
 8E4  CONST_02  C15  C14  C13  C5      0.00   0.0  0
 8E4  CONST_03  C14  C13  C5   C4      0.00   0.0  0
 8E4  CONST_04  C14  C15  C3   C4      0.00   0.0  0
 8E4  CONST_05  C3   C4   C5   C13     0.00   0.0  0
 8E4  CONST_06  C3   C15  C14  C13     0.00   0.0  0
 8E4  CONST_07  C2   C3   C4   C5    180.00   0.0  0
 8E4  CONST_08  C3   C4   C5   O1    180.00   0.0  0
 8E4  CONST_09  C14  C13  C5   O1    180.00   0.0  0
 8E4  CONST_10  C2   C3   C15  C14   180.00   0.0  0
 8E4  CONST_11  H21  C14  C13  C5    180.00   0.0  0
 8E4  CONST_12  H19  C4   C3   C15   180.00   0.0  0
 8E4  CONST_13  H20  C13  C14  C15   180.00   0.0  0
 8E4  CONST_14  H6   C15  C3   C4    180.00   0.0  0
 8E4  Var_01    C4   C5   O1   C6   -175.57  30.0  2
 8E4  Var_02    H17  C6   O1   C5     58.46  30.0  1
 8E4  Var_03    O2   C12  C11  C7    167.02  30.0  1
 8E4  Var_04    C10  C9   C8   C7    179.11  30.0  1
 8E4  Var_05    N    C    C1   C2    179.03  30.0  1
 8E4  Var_06    H26  N    C    C1     67.27  30.0  3
 8E4  Var_07    H14  C10  C9   C8    -59.87  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
 8E4  chir_01  C7  C11  C6  C8  negativ
 8E4  chir_02  C2  O    C1  C3  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
 8E4  plan-1  C5   0.020
 8E4  plan-1  C15  0.020
 8E4  plan-1  O1   0.020
 8E4  plan-1  C4   0.020
 8E4  plan-1  C13  0.020
 8E4  plan-1  C14  0.020
 8E4  plan-1  C3   0.020
 8E4  plan-1  C2   0.020
 8E4  plan-1  H6   0.020
 8E4  plan-1  H19  0.020
 8E4  plan-1  H20  0.020
 8E4  plan-1  H21  0.020

