# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 22:00:51 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: 1-[(1R)-1-cyclohexyl-2-(methylamino)-2-oxoethyl]-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)[C@@H](C1CCCCC1)N2CCC[C@H]2C(O)=O
#
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
 D8D  D8D  1-[(1R)-1-cyclohexyl-2-(methylamino)-2-oxoethyl]-L-proline  ligand  42  19  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D8D
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
 D8D  C4   C  CH2    0  -0.450   6.5668  -11.9468  33.4448
 D8D  C5   C  CH2    0  -0.429   5.7384  -10.8220  34.0762
 D8D  C6   C  CH2    0  -0.443   4.2838  -11.2494  34.3298
 D8D  N1   N  NT     0  -0.421   8.4347  -14.2296  34.0574
 D8D  C7   C  CH2    0  -0.442   3.8572  -12.3148  33.3286
 D8D  C8   C  CH2    0  -0.427   4.6907  -13.5945  33.4966
 D8D  C9   C  CH2    0  -0.256   9.4478  -15.0639  33.4298
 D8D  C10  C  CH2    0  -0.467  10.5918  -15.0787  34.4314
 D8D  C11  C  CH2    0  -0.469   9.8389  -15.0770  35.7560
 D8D  C12  C  CH1    0  -0.191   8.6830  -14.0965  35.4924
 D8D  C13  C  C      0   0.413   9.0994  -12.6810  35.9643
 D8D  O2   O  OC    -1  -0.621   8.8957  -12.4611  37.1784
 D8D  O1   O  O      0  -0.601   9.6428  -11.9057  35.1528
 D8D  C2   C  CH1    0  -0.176   7.0900  -14.4207  33.5665
 D8D  C1   C  C      0   0.548   6.5196  -15.7947  33.9481
 D8D  O    O  O      0  -0.497   6.2794  -16.1131  35.1083
 D8D  N    N  NH1    0  -0.624   6.3149  -16.6408  32.9267
 D8D  C    C  CH3    0  -0.515   5.7795  -17.9683  33.1121
 D8D  C3   C  CH1    0  -0.234   6.1248  -13.3047  33.9814
 D8D  H1   H  HCH2   0   0.252   7.6258  -11.7895  33.6377
 D8D  H2   H  HCH2   0   0.204   6.4406  -11.9441  32.3559
 D8D  H3   H  HCH2   0   0.216   6.1995  -10.5161  35.0189
 D8D  H4   H  HCH2   0   0.216   5.7629   -9.9446  33.4252
 D8D  H5   H  HCH2   0   0.225   3.6191  -10.3842  34.2805
 D8D  H6   H  HCH2   0   0.214   4.1794  -11.6519  35.3423
 D8D  H8   H  HCH2   0   0.215   3.9758  -11.9210  32.3149
 D8D  H9   H  HCH2   0   0.226   2.7959  -12.5473  33.4387
 D8D  H10  H  HCH2   0   0.225   4.1944  -14.2663  34.2007
 D8D  H11  H  HCH2   0   0.216   4.7262  -14.1242  32.5390
 D8D  H12  H  HCH2   0   0.186   9.1048  -16.0961  33.2582
 D8D  H13  H  HCH2   0   0.216   9.7414  -14.6660  32.4527
 D8D  H14  H  HCH2   0   0.229  11.2462  -15.9412  34.3029
 D8D  H15  H  HCH2   0   0.223  11.2000  -14.1774  34.3385
 D8D  H16  H  HCH2   0   0.220   9.4413  -16.0768  35.9541
 D8D  H17  H  HCH2   0   0.230  10.4527  -14.7968  36.6130
 D8D  H18  H  HCH1   0   0.219   7.8110  -14.3978  36.0741
 D8D  H20  H  HCH1   0   0.228   7.1527  -14.3765  32.4700
 D8D  H21  H  HNH1   0   0.400   6.5334  -16.3406  31.9918
 D8D  H22  H  HCH3   0   0.247   5.6595  -18.4340  32.1381
 D8D  H23  H  HCH3   0   0.235   6.4441  -18.5924  33.7107
 D8D  H24  H  HCH3   0   0.235   4.8060  -17.9415  33.6025
 D8D  H25  H  HCH1   0   0.227   6.1121  -13.2513  35.0763

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
 D8D  N    C    single  1.443  0.020  1.443
 D8D  N    C1   single  1.342  0.020  1.342
 D8D  C7   C8   single  1.536  0.020  1.536
 D8D  C7   C6   single  1.523  0.020  1.523
 D8D  C9   N1   single  1.455  0.020  1.455
 D8D  C9   C10  single  1.521  0.020  1.521
 D8D  C4   C3   single  1.525  0.020  1.525
 D8D  C4   C5   single  1.533  0.020  1.533
 D8D  C2   C1   single  1.536  0.020  1.536
 D8D  C2   N1   single  1.444  0.020  1.444
 D8D  C2   C3   single  1.533  0.020  1.533
 D8D  C8   C3   single  1.541  0.020  1.541
 D8D  C1   O    double  1.227  0.020  1.227
 D8D  N1   C12  single  1.462  0.020  1.462
 D8D  C5   C6   single  1.537  0.020  1.537
 D8D  C10  C11  single  1.524  0.020  1.524
 D8D  O1   C13  deloc   1.247  0.020  1.247
 D8D  C12  C11  single  1.538  0.020  1.538
 D8D  C12  C13  single  1.549  0.020  1.549
 D8D  C13  O2   deloc   1.251  0.020  1.251
 D8D  C4   H1   single  0.970  0.020  1.090
 D8D  C4   H2   single  0.970  0.020  1.090
 D8D  C5   H3   single  0.970  0.020  1.090
 D8D  C5   H4   single  0.970  0.020  1.090
 D8D  C6   H5   single  0.970  0.020  1.090
 D8D  C6   H6   single  0.970  0.020  1.090
 D8D  C7   H8   single  0.970  0.020  1.090
 D8D  C7   H9   single  0.970  0.020  1.090
 D8D  C8   H10  single  0.970  0.020  1.090
 D8D  C8   H11  single  0.970  0.020  1.090
 D8D  C9   H12  single  0.970  0.020  1.090
 D8D  C9   H13  single  0.970  0.020  1.090
 D8D  C10  H14  single  0.970  0.020  1.090
 D8D  C10  H15  single  0.970  0.020  1.090
 D8D  C11  H16  single  0.970  0.020  1.090
 D8D  C11  H17  single  0.970  0.020  1.090
 D8D  C12  H18  single  0.970  0.020  1.090
 D8D  C2   H20  single  0.970  0.020  1.090
 D8D  N    H21  single  0.860  0.020  1.020
 D8D  C    H22  single  0.970  0.020  1.090
 D8D  C    H23  single  0.970  0.020  1.090
 D8D  C    H24  single  0.970  0.020  1.090
 D8D  C3   H25  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
 D8D  H2   C4   H1   106.73  3.000
 D8D  H2   C4   C3   108.56  3.000
 D8D  H1   C4   C3   110.39  3.000
 D8D  H2   C4   C5   110.19  3.000
 D8D  H1   C4   C5   110.29  3.000
 D8D  C3   C4   C5   110.59  3.000
 D8D  H4   C5   H3   106.24  3.000
 D8D  H4   C5   C6   110.04  3.000
 D8D  H3   C5   C6   109.56  3.000
 D8D  H4   C5   C4   109.37  3.000
 D8D  H3   C5   C4   109.43  3.000
 D8D  C6   C5   C4   112.04  3.000
 D8D  H6   C6   H5   105.96  3.000
 D8D  H6   C6   C7   108.91  3.000
 D8D  H5   C6   C7   110.73  3.000
 D8D  H6   C6   C5   110.19  3.000
 D8D  H5   C6   C5   110.38  3.000
 D8D  C7   C6   C5   110.56  3.000
 D8D  C2   N1   C12  120.24  3.000
 D8D  C12  N1   C9   110.94  3.000
 D8D  C2   N1   C9   115.21  3.000
 D8D  H9   C7   H8   106.00  3.000
 D8D  H9   C7   C8   109.81  3.000
 D8D  H8   C7   C8   110.02  3.000
 D8D  H9   C7   C6   110.79  3.000
 D8D  H8   C7   C6   109.08  3.000
 D8D  C8   C7   C6   111.03  3.000
 D8D  H11  C8   H10  106.31  3.000
 D8D  H11  C8   C3   109.63  3.000
 D8D  H10  C8   C3   109.61  3.000
 D8D  H11  C8   C7   108.96  3.000
 D8D  H10  C8   C7   109.65  3.000
 D8D  C3   C8   C7   112.49  3.000
 D8D  H13  C9   H12  106.56  3.000
 D8D  H13  C9   C10  112.92  3.000
 D8D  H12  C9   C10  109.14  3.000
 D8D  H13  C9   N1   111.30  3.000
 D8D  H12  C9   N1   112.82  3.000
 D8D  C10  C9   N1   104.20  3.000
 D8D  H15  C10  H14  107.99  3.000
 D8D  H15  C10  C11  110.39  3.000
 D8D  H14  C10  C11  113.58  3.000
 D8D  H15  C10  C9   110.81  3.000
 D8D  H14  C10  C9   112.44  3.000
 D8D  C11  C10  C9   101.59  3.000
 D8D  H17  C11  H16  107.27  3.000
 D8D  H17  C11  C12  113.19  3.000
 D8D  H16  C11  C12  109.90  3.000
 D8D  H17  C11  C10  113.91  3.000
 D8D  H16  C11  C10  109.63  3.000
 D8D  C12  C11  C10  102.89  3.000
 D8D  H18  C12  C13  107.75  3.000
 D8D  H18  C12  C11  109.47  3.000
 D8D  C13  C12  C11  109.16  3.000
 D8D  H18  C12  N1   111.25  3.000
 D8D  C13  C12  N1   115.32  3.000
 D8D  C11  C12  N1   103.75  3.000
 D8D  O1   C13  O2   126.40  3.000
 D8D  O2   C13  C12  114.37  3.000
 D8D  O1   C13  C12  119.15  3.000
 D8D  H20  C2   C3   106.06  3.000
 D8D  H20  C2   C1   107.76  3.000
 D8D  C3   C2   C1   110.50  3.000
 D8D  H20  C2   N1   106.29  3.000
 D8D  C3   C2   N1   113.45  3.000
 D8D  C1   C2   N1   112.32  3.000
 D8D  N    C1   O    121.75  3.000
 D8D  O    C1   C2   122.68  3.000
 D8D  N    C1   C2   115.56  3.000
 D8D  H21  N    C    118.32  3.000
 D8D  H21  N    C1   119.09  3.000
 D8D  C    N    C1   122.59  3.000
 D8D  H24  C    H23  108.13  3.000
 D8D  H24  C    H22  108.37  3.000
 D8D  H23  C    H22  108.31  3.000
 D8D  H24  C    N    111.49  3.000
 D8D  H23  C    N    111.76  3.000
 D8D  H22  C    N    108.67  3.000
 D8D  H25  C3   C2   108.25  3.000
 D8D  H25  C3   C8   108.21  3.000
 D8D  C2   C3   C8   111.34  3.000
 D8D  H25  C3   C4   108.13  3.000
 D8D  C8   C3   C4   109.04  3.000
 D8D  C2   C3   C4   111.75  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
 D8D  CONST_01  C    N    C1   C2   180.00   0.0  0
 D8D  CONST_02  C    N    C1   O      0.00   0.0  0
 D8D  CONST_03  H21  N    C1   C2     0.00   0.0  0
 D8D  Var_01    C7   C6   C5   C4   -28.26  30.0  1
 D8D  Var_02    C8   C7   C6   C5    63.52  30.0  1
 D8D  Var_03    C3   C8   C7   C6   -31.39  30.0  1
 D8D  Var_04    C3   C4   C5   C6   -34.90  30.0  1
 D8D  Var_05    C11  C10  C9   N1    35.91  30.0  1
 D8D  Var_06    C12  C11  C10  C9   -40.22  30.0  1
 D8D  Var_07    C12  N1   C9   C10  -18.05  30.0  1
 D8D  Var_08    H22  C    N    C1   177.07  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
 D8D  chir_01  C12  N1  C11  C13  negativ
 D8D  chir_02  C2   N1  C1   C3   negativ
 D8D  chir_03  C3   C4  C2   C8   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
 D8D  plan-1  C2   0.020
 D8D  plan-1  C1   0.020
 D8D  plan-1  O    0.020
 D8D  plan-1  N    0.020
 D8D  plan-1  C    0.020
 D8D  plan-1  H21  0.020
 D8D  plan-2  C12  0.020
 D8D  plan-2  C13  0.020
 D8D  plan-2  O2   0.020
 D8D  plan-2  O1   0.020

