# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 14:38:16 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (1R)-3-amino-1-{3-[(2-propylpentyl)oxy]phenyl}propan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC(CCC)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
 8D7  8D7  (1R)-3-amino-1-{3-[(2-propylpentyl)oxy]phenyl}propan-1-ol  ligand  49  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_8D7
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
 8D7  C16  C  CR16  0  -0.412   1.3936  -0.1709   0.3346
 8D7  C10  C  CR16  0  -0.225   1.5415   2.1233   1.8538
 8D7  C8   C  CR6   0   0.410   0.2362   0.5729   0.5701
 8D7  C7   C  CH2   0  -0.164  -2.1242   0.7543   0.2873
 8D7  C6   C  CH3   0  -0.661  -4.4116  -3.7306   0.3737
 8D7  C5   C  CH2   0  -0.426  -4.2418  -2.4239  -0.3892
 8D7  O1   O  OH1   0  -0.664   4.7987  -0.5765   1.5756
 8D7  C13  C  CH1   0  -0.026   3.8502  -0.5970   0.5328
 8D7  C14  C  CH2   0  -0.475   4.4447  -0.1613  -0.8063
 8D7  C15  C  CH2   0  -0.274   5.6011  -1.0342  -1.2729
 8D7  N    N  NH2   0  -0.801   6.0762  -0.5887  -2.5764
 8D7  C12  C  CR6   0   0.137   2.6173   0.2243   0.8524
 8D7  C11  C  CR16  0  -0.350   2.6895   1.3831   1.6233
 8D7  C9   C  CR16  0  -0.397   0.3113   1.7340   1.3364
 8D7  O    O  O2    0  -0.479  -0.8975   0.0912   0.0271
 8D7  C3   C  CH1   0  -0.266  -3.2593  -0.0543  -0.3232
 8D7  C4   C  CH2   0  -0.409  -3.4172  -1.4030   0.3861
 8D7  C2   C  CH2   0  -0.427  -4.5522   0.7681  -0.2667
 8D7  C1   C  CH2   0  -0.425  -4.6515   1.8789  -1.3071
 8D7  C    C  CH3   0  -0.661  -5.9399   2.6790  -1.1745
 8D7  H1   H  HCR6  0   0.250   1.3230  -1.0767  -0.2591
 8D7  H2   H  HCR6  0   0.256   1.5950   3.0234   2.4531
 8D7  H3   H  HCH2  0   0.215  -2.2821   0.8525   1.3692
 8D7  H4   H  HCH2  0   0.229  -2.0948   1.7660  -0.1326
 8D7  H5   H  HCH3  0   0.227  -4.9958  -4.4548  -0.1951
 8D7  H6   H  HCH3  0   0.216  -3.4451  -4.1869   0.5964
 8D7  H7   H  HCH3  0   0.216  -4.9227  -3.5669   1.3244
 8D7  H8   H  HCH2  0   0.214  -3.7554  -2.6205  -1.3496
 8D7  H9   H  HCH2  0   0.215  -5.2274  -2.0164  -0.6289
 8D7  H10  H  HOH1  0   0.449   5.3268   0.2258   1.5079
 8D7  H11  H  HCH1  0   0.238   3.5389  -1.6435   0.4411
 8D7  H12  H  HCH2  0   0.240   3.6559  -0.1816  -1.5626
 8D7  H13  H  HCH2  0   0.228   4.7699   0.8845  -0.7303
 8D7  H14  H  HCH2  0   0.196   6.3863  -1.0494  -0.5063
 8D7  H15  H  HCH2  0   0.216   5.2470  -2.0644  -1.3718
 8D7  H16  H  HNH2  0   0.338   6.4963   0.3282  -2.4794
 8D7  H17  H  HNH2  0   0.347   6.8271  -1.1949  -2.8818
 8D7  H19  H  HCR6  0   0.237   3.6280   1.7118   2.0503
 8D7  H20  H  HCR6  0   0.276  -0.5625   2.3370   1.5421
 8D7  H21  H  HCH1  0   0.222  -3.0132  -0.2384  -1.3778
 8D7  H22  H  HCH2  0   0.208  -3.8714  -1.2334   1.3701
 8D7  H23  H  HCH2  0   0.225  -2.4333  -1.8390   0.5821
 8D7  H24  H  HCH2  0   0.230  -5.4098   0.1023  -0.3981
 8D7  H25  H  HCH2  0   0.213  -4.6633   1.1928   0.7384
 8D7  H26  H  HCH2  0   0.216  -3.7980   2.5567  -1.2258
 8D7  H27  H  HCH2  0   0.216  -4.5933   1.4367  -2.3062
 8D7  H28  H  HCH3  0   0.217  -6.8166   2.0363  -1.2776
 8D7  H29  H  HCH3  0   0.217  -6.0033   3.1641  -0.1984
 8D7  H30  H  HCH3  0   0.227  -6.0098   3.4573  -1.9351

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
 8D7  C1   C    single    1.522  0.020  1.522
 8D7  C1   C2   single    1.525  0.020  1.525
 8D7  C3   C2   single    1.533  0.020  1.533
 8D7  C3   C7   single    1.522  0.020  1.522
 8D7  C3   C4   single    1.532  0.020  1.532
 8D7  N    C15  single    1.457  0.020  1.457
 8D7  C5   C4   single    1.524  0.020  1.524
 8D7  C5   C6   single    1.523  0.020  1.523
 8D7  C7   O    single    1.419  0.020  1.419
 8D7  C15  C14  single    1.522  0.020  1.522
 8D7  C14  C13  single    1.529  0.020  1.529
 8D7  O1   C13  single    1.410  0.020  1.410
 8D7  O    C8   single    1.346  0.020  1.346
 8D7  C16  C8   aromatic  1.396  0.020  1.396
 8D7  C16  C12  aromatic  1.386  0.020  1.386
 8D7  C13  C12  single    1.515  0.020  1.515
 8D7  C8   C9   aromatic  1.393  0.020  1.393
 8D7  C12  C11  aromatic  1.394  0.020  1.394
 8D7  C9   C10  aromatic  1.390  0.020  1.390
 8D7  C11  C10  aromatic  1.385  0.020  1.385
 8D7  C16  H1   single    0.930  0.020  1.080
 8D7  C10  H2   single    0.930  0.020  1.080
 8D7  C7   H3   single    0.970  0.020  1.090
 8D7  C7   H4   single    0.970  0.020  1.090
 8D7  C6   H5   single    0.970  0.020  1.090
 8D7  C6   H6   single    0.970  0.020  1.090
 8D7  C6   H7   single    0.970  0.020  1.090
 8D7  C5   H8   single    0.970  0.020  1.090
 8D7  C5   H9   single    0.970  0.020  1.090
 8D7  O1   H10  single    0.850  0.020  0.980
 8D7  C13  H11  single    0.970  0.020  1.090
 8D7  C14  H12  single    0.970  0.020  1.090
 8D7  C14  H13  single    0.970  0.020  1.090
 8D7  C15  H14  single    0.970  0.020  1.090
 8D7  C15  H15  single    0.970  0.020  1.090
 8D7  N    H16  single    0.890  0.020  1.040
 8D7  N    H17  single    0.890  0.020  1.040
 8D7  C11  H19  single    0.930  0.020  1.080
 8D7  C9   H20  single    0.930  0.020  1.080
 8D7  C3   H21  single    0.970  0.020  1.090
 8D7  C4   H22  single    0.970  0.020  1.090
 8D7  C4   H23  single    0.970  0.020  1.090
 8D7  C2   H24  single    0.970  0.020  1.090
 8D7  C2   H25  single    0.970  0.020  1.090
 8D7  C1   H26  single    0.970  0.020  1.090
 8D7  C1   H27  single    0.970  0.020  1.090
 8D7  C    H28  single    0.970  0.020  1.090
 8D7  C    H29  single    0.970  0.020  1.090
 8D7  C    H30  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
 8D7  H1   C16  C12  119.98  3.000
 8D7  H1   C16  C8   118.89  3.000
 8D7  C12  C16  C8   121.13  3.000
 8D7  H2   C10  C9   118.85  3.000
 8D7  H2   C10  C11  119.70  3.000
 8D7  C9   C10  C11  121.45  3.000
 8D7  O    C8   C9   124.44  3.000
 8D7  C9   C8   C16  119.49  3.000
 8D7  O    C8   C16  116.08  3.000
 8D7  H4   C7   H3   107.40  3.000
 8D7  H4   C7   C3   110.91  3.000
 8D7  H3   C7   C3   109.61  3.000
 8D7  H4   C7   O    109.77  3.000
 8D7  H3   C7   O    110.31  3.000
 8D7  C3   C7   O    108.85  3.000
 8D7  H7   C6   H6   107.42  3.000
 8D7  H7   C6   H5   107.64  3.000
 8D7  H6   C6   H5   107.65  3.000
 8D7  H7   C6   C5   111.09  3.000
 8D7  H6   C6   C5   111.23  3.000
 8D7  H5   C6   C5   111.61  3.000
 8D7  H9   C5   H8   105.99  3.000
 8D7  H9   C5   C4   110.46  3.000
 8D7  H8   C5   C4   109.04  3.000
 8D7  H9   C5   C6   109.22  3.000
 8D7  H8   C5   C6   109.58  3.000
 8D7  C4   C5   C6   112.35  3.000
 8D7  H10  O1   C13  109.22  3.000
 8D7  H11  C13  C12  107.71  3.000
 8D7  H11  C13  C14  108.03  3.000
 8D7  C12  C13  C14  110.28  3.000
 8D7  H11  C13  O1   105.48  3.000
 8D7  C12  C13  O1   112.55  3.000
 8D7  C14  C13  O1   112.47  3.000
 8D7  H13  C14  H12  106.23  3.000
 8D7  H13  C14  C15  110.02  3.000
 8D7  H12  C14  C15  108.99  3.000
 8D7  H13  C14  C13  109.04  3.000
 8D7  H12  C14  C13  108.68  3.000
 8D7  C15  C14  C13  113.61  3.000
 8D7  H15  C15  H14  106.36  3.000
 8D7  H15  C15  N    108.22  3.000
 8D7  H14  C15  N    113.32  3.000
 8D7  H15  C15  C14  108.77  3.000
 8D7  H14  C15  C14  109.72  3.000
 8D7  N    C15  C14  110.28  3.000
 8D7  H17  N    H16  105.26  3.000
 8D7  H17  N    C15  109.19  3.000
 8D7  H16  N    C15  109.04  3.000
 8D7  C11  C12  C13  121.68  3.000
 8D7  C11  C12  C16  119.29  3.000
 8D7  C13  C12  C16  119.00  3.000
 8D7  H19  C11  C12  121.04  3.000
 8D7  H19  C11  C10  119.39  3.000
 8D7  C12  C11  C10  119.57  3.000
 8D7  H20  C9   C8   121.72  3.000
 8D7  H20  C9   C10  119.22  3.000
 8D7  C8   C9   C10  119.06  3.000
 8D7  C7   O    C8   119.14  3.000
 8D7  H21  C3   C2   108.31  3.000
 8D7  H21  C3   C4   108.66  3.000
 8D7  C2   C3   C4   111.60  3.000
 8D7  H21  C3   C7   107.89  3.000
 8D7  C4   C3   C7   111.04  3.000
 8D7  C2   C3   C7   109.22  3.000
 8D7  H23  C4   H22  105.86  3.000
 8D7  H23  C4   C3   109.94  3.000
 8D7  H22  C4   C3   108.78  3.000
 8D7  H23  C4   C5   108.10  3.000
 8D7  H22  C4   C5   109.62  3.000
 8D7  C3   C4   C5   114.20  3.000
 8D7  H25  C2   H24  105.45  3.000
 8D7  H25  C2   C1   109.66  3.000
 8D7  H24  C2   C1   108.09  3.000
 8D7  H25  C2   C3   109.08  3.000
 8D7  H24  C2   C3   109.29  3.000
 8D7  C1   C2   C3   114.86  3.000
 8D7  H27  C1   H26  106.08  3.000
 8D7  H27  C1   C    109.69  3.000
 8D7  H26  C1   C    109.18  3.000
 8D7  H27  C1   C2   108.97  3.000
 8D7  H26  C1   C2   110.50  3.000
 8D7  C    C1   C2   112.24  3.000
 8D7  H30  C    H29  107.62  3.000
 8D7  H30  C    H28  107.62  3.000
 8D7  H29  C    H28  107.42  3.000
 8D7  H30  C    C1   111.63  3.000
 8D7  H29  C    C1   111.13  3.000
 8D7  H28  C    C1   111.22  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
 8D7  CONST_01  C10  C9   C8   C16     0.00   0.0  0
 8D7  CONST_02  C10  C11  C12  C16     0.00   0.0  0
 8D7  CONST_03  C11  C12  C16  C8      0.00   0.0  0
 8D7  CONST_04  C11  C10  C9   C8      0.00   0.0  0
 8D7  CONST_05  C9   C8   C16  C12     0.00   0.0  0
 8D7  CONST_06  C9   C10  C11  C12     0.00   0.0  0
 8D7  CONST_07  O    C8   C9   C10   180.00   0.0  0
 8D7  CONST_08  C13  C12  C11  C10   180.00   0.0  0
 8D7  CONST_09  C13  C12  C16  C8    180.00   0.0  0
 8D7  CONST_10  O    C8   C16  C12   180.00   0.0  0
 8D7  CONST_11  H20  C9   C8   C16   180.00   0.0  0
 8D7  CONST_12  H19  C11  C12  C16   180.00   0.0  0
 8D7  CONST_13  H2   C10  C9   C8    180.00   0.0  0
 8D7  CONST_14  H1   C16  C12  C11   180.00   0.0  0
 8D7  Var_01    C9   C8   O    C7     -3.13  30.0  2
 8D7  Var_02    C3   C7   O    C8   -174.66  30.0  1
 8D7  Var_03    C1   C2   C3   C7     76.28  30.0  3
 8D7  Var_04    C5   C4   C3   C7   -163.55  30.0  3
 8D7  Var_05    C3   C4   C5   C6   -178.06  30.0  3
 8D7  Var_06    N    C15  C14  C13   177.74  30.0  1
 8D7  Var_07    C    C1   C2   C3   -178.52  30.0  1
 8D7  Var_08    H16  N    C15  C14    67.01  30.0  3
 8D7  Var_09    H5   C6   C5   C4   -179.52  30.0  3
 8D7  Var_10    H28  C    C1   C2    -58.65  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
 8D7  chir_01  C13  C14  O1  C12  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
 8D7  plan-1  C16  0.020
 8D7  plan-1  C10  0.020
 8D7  plan-1  C8   0.020
 8D7  plan-1  C13  0.020
 8D7  plan-1  C12  0.020
 8D7  plan-1  C11  0.020
 8D7  plan-1  C9   0.020
 8D7  plan-1  O    0.020
 8D7  plan-1  H1   0.020
 8D7  plan-1  H2   0.020
 8D7  plan-1  H19  0.020
 8D7  plan-1  H20  0.020

