# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 11:46:57 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 4-(2-aminoethyl)-2-cyclohexylphenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCc1ccc(O)c(c1)C2CCCCC2
#
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
 AED  AED  4-(2-aminoethyl)-2-cyclohexylphenol  ligand  37  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AED
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
 AED  C4    C  CR6   0   0.273   0.0421   2.0304  -0.0628
 AED  C5    C  CH2   0  -0.407   2.3056  -0.3182   1.2702
 AED  C6    C  CH2   0  -0.409   1.8657  -0.9790  -1.1194
 AED  C7    C  CR6   0   0.123  -2.0296   0.2224   0.4817
 AED  C8    C  CR16  0  -0.366  -1.2686   2.4773   0.0820
 AED  C10   C  CH2   0  -0.434   3.7421  -0.8158   1.1451
 AED  C13   C  CH2   0  -0.515  -3.1353  -0.7654   0.7261
 AED  C15   C  CH2   0  -0.267  -3.7397  -1.2768  -0.5797
 AED  O9    O  OH1   0  -0.633   1.0561   2.8918  -0.3115
 AED  C12   C  CR16  0  -0.317  -2.2915   1.5819   0.3500
 AED  N16   N  NH2   0  -0.800  -4.7891  -2.2490  -0.3162
 AED  C3    C  CR16  0  -0.369  -0.7130  -0.2006   0.3268
 AED  C1    C  CR6   0   0.105   0.3403   0.6675   0.0510
 AED  C2    C  CH1   0  -0.322   1.7514   0.1460  -0.0840
 AED  C14   C  CH2   0  -0.430   3.8546  -1.9244   0.1037
 AED  C11   C  CH2   0  -0.434   3.3047  -1.4702  -1.2445
 AED  H5A   H  HCH2  0   0.230   2.2476   0.5012   1.9914
 AED  H6    H  HCH2  0   0.210   1.2278  -1.8207  -0.8300
 AED  H6A   H  HCH2  0   0.230   1.4987  -0.6288  -2.0876
 AED  H8    H  HCR6  0   0.261  -1.4901   3.5354  -0.0120
 AED  H10   H  HCH2  0   0.209   4.3904   0.0194   0.8575
 AED  H10A  H  HCH2  0   0.227   4.1014  -1.1668   2.1156
 AED  H13   H  HCH2  0   0.234  -2.7633  -1.6185   1.2993
 AED  H13A  H  HCH2  0   0.234  -3.9236  -0.3007   1.3262
 AED  H15   H  HCH2  0   0.195  -4.0735  -0.4138  -1.1738
 AED  H15A  H  HCH2  0   0.218  -2.9556  -1.7660  -1.1638
 AED  HO9   H  HOH1  0   0.472   0.7194   3.7933  -0.3548
 AED  H12   H  HCR6  0   0.245  -3.3042   1.9526   0.4613
 AED  HN16  H  HNH2  0   0.339  -5.5718  -1.7850   0.1285
 AED  HN1A  H  HNH2  0   0.347  -5.1464  -2.6054  -1.1933
 AED  H3    H  HCR6  0   0.234  -0.5023  -1.2607   0.4294
 AED  H2    H  HCH1  0   0.233   2.3945   0.9598  -0.4311
 AED  H14   H  HCH2  0   0.226   4.8944  -2.2448   0.0015
 AED  H14A  H  HCH2  0   0.208   3.2916  -2.7998   0.4457
 AED  H11   H  HCH2  0   0.227   3.3580  -2.2859  -1.9696
 AED  H11A  H  HCH2  0   0.209   3.9303  -0.6620  -1.6388
 AED  H5    H  HCH2  0   0.211   1.6746  -1.1238   1.6620

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
 AED  C4   C8    aromatic  1.392  0.020  1.392
 AED  C4   O9    single    1.354  0.020  1.354
 AED  C4   C1    aromatic  1.400  0.020  1.400
 AED  C5   C10   single    1.525  0.020  1.525
 AED  C5   C2    single    1.535  0.020  1.535
 AED  C6   C2    single    1.533  0.020  1.533
 AED  C6   C11   single    1.526  0.020  1.526
 AED  C7   C13   single    1.503  0.020  1.503
 AED  C7   C12   aromatic  1.391  0.020  1.391
 AED  C7   C3    aromatic  1.391  0.020  1.391
 AED  C8   C12   aromatic  1.386  0.020  1.386
 AED  C10  C14   single    1.525  0.020  1.525
 AED  C13  C15   single    1.527  0.020  1.527
 AED  C15  N16   single    1.455  0.020  1.455
 AED  C3   C1    aromatic  1.393  0.020  1.393
 AED  C1   C2    single    1.510  0.020  1.510
 AED  C14  C11   single    1.525  0.020  1.525
 AED  C5   H5    single    0.970  0.020  1.090
 AED  C5   H5A   single    0.970  0.020  1.090
 AED  C6   H6    single    0.970  0.020  1.090
 AED  C6   H6A   single    0.970  0.020  1.090
 AED  C8   H8    single    0.930  0.020  1.080
 AED  C10  H10   single    0.970  0.020  1.090
 AED  C10  H10A  single    0.970  0.020  1.090
 AED  C13  H13   single    0.970  0.020  1.090
 AED  C13  H13A  single    0.970  0.020  1.090
 AED  C15  H15   single    0.970  0.020  1.090
 AED  C15  H15A  single    0.970  0.020  1.090
 AED  O9   HO9   single    0.850  0.020  0.980
 AED  C12  H12   single    0.930  0.020  1.080
 AED  N16  HN16  single    0.890  0.020  1.040
 AED  N16  HN1A  single    0.890  0.020  1.040
 AED  C3   H3    single    0.930  0.020  1.080
 AED  C2   H2    single    0.970  0.020  1.090
 AED  C14  H14   single    0.970  0.020  1.090
 AED  C14  H14A  single    0.970  0.020  1.090
 AED  C11  H11   single    0.970  0.020  1.090
 AED  C11  H11A  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
 AED  C1    C4   O9    118.35  3.000
 AED  C1    C4   C8    120.31  3.000
 AED  O9    C4   C8    121.34  3.000
 AED  H5A   C5   H5    106.54  3.000
 AED  H5A   C5   C2    109.65  3.000
 AED  H5    C5   C2    109.26  3.000
 AED  H5A   C5   C10   110.40  3.000
 AED  H5    C5   C10   109.38  3.000
 AED  C2    C5   C10   111.49  3.000
 AED  H6A   C6   H6    106.54  3.000
 AED  H6A   C6   C11   110.31  3.000
 AED  H6    C6   C11   108.88  3.000
 AED  H6A   C6   C2    109.76  3.000
 AED  H6    C6   C2    110.01  3.000
 AED  C11   C6   C2    111.22  3.000
 AED  C3    C7   C12   117.70  3.000
 AED  C3    C7   C13   120.96  3.000
 AED  C12   C7   C13   121.29  3.000
 AED  H8    C8   C12   119.75  3.000
 AED  H8    C8   C4    119.74  3.000
 AED  C12   C8   C4    120.51  3.000
 AED  H10A  C10  H10   106.46  3.000
 AED  H10A  C10  C14   110.41  3.000
 AED  H10   C10  C14   109.34  3.000
 AED  H10A  C10  C5    109.97  3.000
 AED  H10   C10  C5    109.27  3.000
 AED  C14   C10  C5    111.26  3.000
 AED  H13A  C13  H13   106.79  3.000
 AED  H13A  C13  C15   109.03  3.000
 AED  H13   C13  C15   108.77  3.000
 AED  H13A  C13  C7    109.89  3.000
 AED  H13   C13  C7    110.36  3.000
 AED  C15   C13  C7    111.86  3.000
 AED  H15A  C15  H15   106.28  3.000
 AED  H15A  C15  N16   108.37  3.000
 AED  H15   C15  N16   113.79  3.000
 AED  H15A  C15  C13   108.83  3.000
 AED  H15   C15  C13   108.62  3.000
 AED  N16   C15  C13   110.76  3.000
 AED  HO9   O9   C4    109.99  3.000
 AED  H12   C12  C8    119.24  3.000
 AED  H12   C12  C7    120.03  3.000
 AED  C8    C12  C7    120.73  3.000
 AED  HN1A  N16  HN16  105.61  3.000
 AED  HN1A  N16  C15   109.46  3.000
 AED  HN16  N16  C15   109.32  3.000
 AED  H3    C3   C1    118.72  3.000
 AED  H3    C3   C7    118.03  3.000
 AED  C1    C3   C7    123.25  3.000
 AED  C2    C1   C3    120.61  3.000
 AED  C2    C1   C4    121.86  3.000
 AED  C3    C1   C4    117.51  3.000
 AED  H2    C2   C1    108.71  3.000
 AED  H2    C2   C6    106.73  3.000
 AED  C1    C2   C6    112.54  3.000
 AED  H2    C2   C5    107.02  3.000
 AED  C1    C2   C5    111.28  3.000
 AED  C6    C2   C5    110.30  3.000
 AED  H14A  C14  H14   106.49  3.000
 AED  H14A  C14  C11   109.18  3.000
 AED  H14   C14  C11   110.35  3.000
 AED  H14A  C14  C10   109.25  3.000
 AED  H14   C14  C10   110.31  3.000
 AED  C11   C14  C10   111.13  3.000
 AED  H11A  C11  H11   106.50  3.000
 AED  H11A  C11  C14   109.39  3.000
 AED  H11   C11  C14   110.28  3.000
 AED  H11A  C11  C6    109.31  3.000
 AED  H11   C11  C6    109.93  3.000
 AED  C14   C11  C6    111.31  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
 AED  CONST_01  C7    C12  C8   C4     0.00   0.0  0
 AED  CONST_02  C7    C3   C1   C4     0.00   0.0  0
 AED  CONST_03  C3    C1   C4   C8     0.00   0.0  0
 AED  CONST_04  C3    C7   C12  C8     0.00   0.0  0
 AED  CONST_05  C1    C3   C7   C12    0.00   0.0  0
 AED  CONST_06  C1    C4   C8   C12    0.00   0.0  0
 AED  CONST_07  C2    C1   C3   C7   180.00   0.0  0
 AED  CONST_08  C2    C1   C4   C8   180.00   0.0  0
 AED  CONST_09  C13   C7   C12  C8   180.00   0.0  0
 AED  CONST_10  C1    C3   C7   C13  180.00   0.0  0
 AED  CONST_11  C12   C8   C4   O9   180.00   0.0  0
 AED  CONST_12  C3    C1   C4   O9   180.00   0.0  0
 AED  CONST_13  C2    C1   C4   O9     0.00   0.0  0
 AED  CONST_14  H12   C12  C8   C4   180.00   0.0  0
 AED  CONST_15  H3    C3   C1   C4   180.00   0.0  0
 AED  CONST_16  H8    C8   C12  C7   180.00   0.0  0
 AED  Var_01    C11   C14  C10  C5    55.29  30.0  1
 AED  Var_02    C10   C14  C11  C6   -55.62  30.0  1
 AED  Var_03    C14   C10  C5   C2   -55.69  30.0  1
 AED  Var_04    C14   C11  C6   C2    56.20  30.0  1
 AED  Var_05    C12   C7   C13  C15   88.44  30.0  2
 AED  Var_06    N16   C15  C13  C7   178.93  30.0  3
 AED  Var_07    HN16  N16  C15  C13   67.31  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
 AED  chir_01  C2  C5  C6  C1  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
 AED  plan-1  C4   0.020
 AED  plan-1  C7   0.020
 AED  plan-1  C8   0.020
 AED  plan-1  C13  0.020
 AED  plan-1  O9   0.020
 AED  plan-1  C12  0.020
 AED  plan-1  C3   0.020
 AED  plan-1  C1   0.020
 AED  plan-1  C2   0.020
 AED  plan-1  H8   0.020
 AED  plan-1  H12  0.020
 AED  plan-1  H3   0.020

