# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 16:19:30 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: N-[(2R)-tetrahydrofuran-2-ylmethyl]cyclohexanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NC[C@H]1CCCO1)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
 47L  47L  N-[(2R)-tetrahydrofuran-2-ylmethyl]cyclohexanecarboxamide  ligand  36  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_47L
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
 47L  C4   C  CH2   0  -0.475   5.0718  -0.3105  -0.3614
 47L  C5   C  CH2   0  -0.176   4.0243  -1.4093  -0.3130
 47L  C6   C  CH1   0  -0.392  -1.9440   0.0732  -0.1757
 47L  C7   C  CH2   0  -0.416  -2.2419  -1.1114   0.7571
 47L  C8   C  CH2   0  -0.433  -3.4875  -1.8686   0.3090
 47L  C9   C  CH2   0  -0.430  -4.6916  -0.9407   0.1969
 47L  C10  C  CH2   0  -0.435  -4.3967   0.2325  -0.7316
 47L  C11  C  CH2   0  -0.414  -3.1541   0.9974  -0.2857
 47L  O    O  O     0  -0.504  -0.7833   1.7323   1.1298
 47L  C    C  C     0   0.576  -0.7155   0.8056   0.3319
 47L  N    N  NH1   0  -0.644   0.4552   0.3355  -0.1329
 47L  C1   C  CH2   0  -0.267   1.7427   0.7886   0.3392
 47L  C2   C  CR15  0   0.007   2.8294   0.5252  -0.6901
 47L  O1   O  O     0  -0.502   2.9084  -0.8627  -0.9942
 47L  C3   C  CH2   0  -0.502   4.2162   0.9421  -0.1655
 47L  H1   H  HCH2  0   0.245   5.8387  -0.4262   0.4037
 47L  H2   H  HCH2  0   0.238   5.5657  -0.2984  -1.3348
 47L  H3   H  HCH2  0   0.235   4.3223  -2.3296  -0.8169
 47L  H4   H  HCH2  0   0.204   3.7734  -1.6590   0.7263
 47L  H5   H  HCH1  0   0.245  -1.7240  -0.3340  -1.1707
 47L  H6   H  HCH2  0   0.235  -1.3840  -1.7879   0.7898
 47L  H7   H  HCH2  0   0.222  -2.3866  -0.7376   1.7765
 47L  H8   H  HCH2  0   0.213  -3.2959  -2.3365  -0.6626
 47L  H9   H  HCH2  0   0.231  -3.6955  -2.6805   1.0099
 47L  H10  H  HCH2  0   0.228  -5.5652  -1.4932  -0.1568
 47L  H11  H  HCH2  0   0.210  -4.9457  -0.5579   1.1915
 47L  H12  H  HCH2  0   0.210  -4.2540  -0.1380  -1.7527
 47L  H13  H  HCH2  0   0.229  -5.2525   0.9108  -0.7679
 47L  H14  H  HCH2  0   0.217  -3.3450   1.4610   0.6861
 47L  H15  H  HCH2  0   0.233  -2.9430   1.8091  -0.9865
 47L  H16  H  HNH1  0   0.394   0.4408  -0.4910  -0.7101
 47L  H17  H  HCH2  0   0.249   1.6964   1.8608   0.5338
 47L  H18  H  HCH2  0   0.232   2.0082   0.3037   1.2870
 47L  H19  H  HCR5  0   0.239   2.5734   1.0454  -1.6189
 47L  H20  H  HCH2  0   0.243   4.1622   1.2073   0.8933
 47L  H21  H  HCH2  0   0.256   4.6065   1.8081  -0.6976

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
 47L  C8   C7   single  1.525  0.020  1.525
 47L  C8   C9   single  1.524  0.020  1.524
 47L  N    C1   single  1.444  0.020  1.444
 47L  N    C    single  1.344  0.020  1.344
 47L  C7   C6   single  1.537  0.020  1.537
 47L  C1   C2   single  1.520  0.020  1.520
 47L  C6   C    single  1.518  0.020  1.518
 47L  C6   C11  single  1.527  0.020  1.527
 47L  C    O    double  1.225  0.020  1.225
 47L  C9   C10  single  1.525  0.020  1.525
 47L  C10  C11  single  1.526  0.020  1.526
 47L  O1   C2   single  1.423  0.020  1.423
 47L  O1   C5   single  1.417  0.020  1.417
 47L  C2   C3   single  1.540  0.020  1.540
 47L  C3   C4   single  1.530  0.020  1.530
 47L  C5   C4   single  1.519  0.020  1.519
 47L  C4   H1   single  0.970  0.020  1.090
 47L  C4   H2   single  0.970  0.020  1.090
 47L  C5   H3   single  0.970  0.020  1.090
 47L  C5   H4   single  0.970  0.020  1.090
 47L  C6   H5   single  0.970  0.020  1.090
 47L  C7   H6   single  0.970  0.020  1.090
 47L  C7   H7   single  0.970  0.020  1.090
 47L  C8   H8   single  0.970  0.020  1.090
 47L  C8   H9   single  0.970  0.020  1.090
 47L  C9   H10  single  0.970  0.020  1.090
 47L  C9   H11  single  0.970  0.020  1.090
 47L  C10  H12  single  0.970  0.020  1.090
 47L  C10  H13  single  0.970  0.020  1.090
 47L  C11  H14  single  0.970  0.020  1.090
 47L  C11  H15  single  0.970  0.020  1.090
 47L  N    H16  single  0.860  0.020  1.020
 47L  C1   H17  single  0.970  0.020  1.090
 47L  C1   H18  single  0.970  0.020  1.090
 47L  C2   H19  single  0.970  0.020  1.090
 47L  C3   H20  single  0.970  0.020  1.090
 47L  C3   H21  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
 47L  H2   C4   H1   107.99  3.000
 47L  H2   C4   C3   110.99  3.000
 47L  H1   C4   C3   113.01  3.000
 47L  H2   C4   C5   110.40  3.000
 47L  H1   C4   C5   112.72  3.000
 47L  C3   C4   C5   101.69  3.000
 47L  H4   C5   H3   107.93  3.000
 47L  H4   C5   O1   111.27  3.000
 47L  H3   C5   O1   108.57  3.000
 47L  H4   C5   C4   110.63  3.000
 47L  H3   C5   C4   114.03  3.000
 47L  O1   C5   C4   104.40  3.000
 47L  H5   C6   C    108.67  3.000
 47L  H5   C6   C11  108.55  3.000
 47L  C    C6   C11  111.93  3.000
 47L  H5   C6   C7   107.65  3.000
 47L  C11  C6   C7   110.90  3.000
 47L  C    C6   C7   109.02  3.000
 47L  H7   C7   H6   106.68  3.000
 47L  H7   C7   C8   109.57  3.000
 47L  H6   C7   C8   110.03  3.000
 47L  H7   C7   C6   109.11  3.000
 47L  H6   C7   C6   110.06  3.000
 47L  C8   C7   C6   111.27  3.000
 47L  H9   C8   H8   106.56  3.000
 47L  H9   C8   C9   110.44  3.000
 47L  H8   C8   C9   109.45  3.000
 47L  H9   C8   C7   109.63  3.000
 47L  H8   C8   C7   109.26  3.000
 47L  C9   C8   C7   111.38  3.000
 47L  H11  C9   H10  106.56  3.000
 47L  H11  C9   C10  109.20  3.000
 47L  H10  C9   C10  110.28  3.000
 47L  H11  C9   C8   109.22  3.000
 47L  H10  C9   C8   110.34  3.000
 47L  C10  C9   C8   111.12  3.000
 47L  H13  C10  H12  106.32  3.000
 47L  H13  C10  C11  109.66  3.000
 47L  H12  C10  C11  109.63  3.000
 47L  H13  C10  C9   110.27  3.000
 47L  H12  C10  C9   109.42  3.000
 47L  C11  C10  C9   111.42  3.000
 47L  H15  C11  H14  106.78  3.000
 47L  H15  C11  C10  110.01  3.000
 47L  H14  C11  C10  109.27  3.000
 47L  H15  C11  C6   110.05  3.000
 47L  H14  C11  C6   109.33  3.000
 47L  C10  C11  C6   111.29  3.000
 47L  N    C    O    122.55  3.000
 47L  O    C    C6   122.56  3.000
 47L  N    C    C6   114.86  3.000
 47L  H16  N    C1   117.19  3.000
 47L  H16  N    C    118.18  3.000
 47L  C1   N    C    123.61  3.000
 47L  H18  C1   H17  106.89  3.000
 47L  H18  C1   C2   109.60  3.000
 47L  H17  C1   C2   108.76  3.000
 47L  H18  C1   N    111.07  3.000
 47L  H17  C1   N    109.20  3.000
 47L  C2   C1   N    111.21  3.000
 47L  H19  C2   C3   111.77  3.000
 47L  H19  C2   O1   107.16  3.000
 47L  C3   C2   O1   106.67  3.000
 47L  H19  C2   C1   108.96  3.000
 47L  C3   C2   C1   111.48  3.000
 47L  O1   C2   C1   110.70  3.000
 47L  C2   O1   C5   108.49  3.000
 47L  H21  C3   H20  107.35  3.000
 47L  H21  C3   C2   111.81  3.000
 47L  H20  C3   C2   110.56  3.000
 47L  H21  C3   C4   112.85  3.000
 47L  H20  C3   C4   110.52  3.000
 47L  C2   C3   C4   103.79  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
 47L  CONST_01  C1   N    C    C6   180.00   0.0  0
 47L  CONST_02  H16  N    C    C6     0.00   0.0  0
 47L  CONST_03  C1   N    C    O      0.00   0.0  0
 47L  Var_01    C2   C3   C4   C5   -26.08  30.0  1
 47L  Var_02    C9   C8   C7   C6   -55.38  30.0  1
 47L  Var_03    C9   C10  C11  C6    55.69  30.0  1
 47L  Var_04    C10  C9   C8   C7    55.47  30.0  1
 47L  Var_05    C11  C10  C9   C8   -55.55  30.0  1
 47L  Var_06    C3   C4   C5   O1    38.22  30.0  1
 47L  Var_07    H3   C5   O1   C2  -158.39  30.0  1
 47L  Var_08    C2   C1   N    C   -157.47  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
 47L  chir_01  C6  C7  C   C11  positiv
 47L  chir_02  C2  O1  C3  C1   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
 47L  plan-1  C6   0.020
 47L  plan-1  O    0.020
 47L  plan-1  C    0.020
 47L  plan-1  N    0.020
 47L  plan-1  C1   0.020
 47L  plan-1  H16  0.020

