# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 02:59:28 2021
#   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  43  19  .  2022-03-18  2022-11-17
;
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  -0.447   6.6123  -11.9599  33.3508
 D8D  C5   C  CH2   0  -0.430   5.8140  -10.8299  34.0156
 D8D  C6   C  CH2   0  -0.449   4.4009  -11.2846  34.4101
 D8D  N1   N  NR5   0  -0.419   8.4960  -14.2211  34.0305
 D8D  C7   C  CH2   0  -0.443   3.8862  -12.3354  33.4335
 D8D  C8   C  CH2   0  -0.428   4.7508  -13.6080  33.4730
 D8D  C9   C  CH2   0  -0.259   9.5317  -15.0587  33.4375
 D8D  C10  C  CH2   0  -0.474  10.6464  -15.0694  34.4709
 D8D  C11  C  CH2   0  -0.473   9.8646  -15.0546  35.7785
 D8D  C12  C  CR15  0  -0.224   8.6950  -14.1020  35.4629
 D8D  C13  C  C     0   0.563   9.0975  -12.6937  35.8607
 D8D  O2   O  OH1   0  -0.598   8.7784  -12.4414  37.1287
 D8D  O1   O  O     0  -0.441   9.6808  -11.9044  35.1620
 D8D  C2   C  CH1   0  -0.185   7.1619  -14.4281  33.5121
 D8D  C1   C  C     0   0.553   6.5984  -15.8025  33.8962
 D8D  O    O  O     0  -0.499   6.4873  -16.1588  35.0650
 D8D  N    N  NH1   0  -0.620   6.2415  -16.5920  32.8760
 D8D  C    C  CH3   0  -0.518   5.6601  -17.8991  33.0715
 D8D  C3   C  CH1   0  -0.247   6.1923  -13.3129  33.9191
 D8D  H1   H  HCH2  0   0.249   7.6820  -11.8002  33.4794
 D8D  H2   H  HCH2  0   0.216   6.4321  -11.9703  32.2699
 D8D  H3   H  HCH2  0   0.219   6.3459  -10.4771  34.9031
 D8D  H4   H  HCH2  0   0.220   5.7556   -9.9775  33.3344
 D8D  H5   H  HCH2  0   0.229   3.7235  -10.4289  34.4458
 D8D  H6   H  HCH2  0   0.217   4.4107  -11.7050  35.4205
 D8D  H8   H  HCH2  0   0.218   3.8917  -11.9117  32.4252
 D8D  H9   H  HCH2  0   0.230   2.8459  -12.5870  33.6492
 D8D  H10  H  HCH2  0   0.230   4.2992  -14.3433  34.1435
 D8D  H11  H  HCH2  0   0.220   4.7620  -14.0623  32.4776
 D8D  H12  H  HCH2  0   0.201   9.1846  -16.0868  33.2590
 D8D  H13  H  HCH2  0   0.233   9.8510  -14.6587  32.4714
 D8D  H14  H  HCH2  0   0.247  11.2945  -15.9399  34.3747
 D8D  H15  H  HCH2  0   0.237  11.2700  -14.1782  34.3819
 D8D  H16  H  HCH2  0   0.251   9.4540  -16.0450  35.9845
 D8D  H17  H  HCH2  0   0.256  10.4537  -14.7556  36.6461
 D8D  H18  H  HCR5  0   0.282   7.8144  -14.3915  36.0366
 D8D  H19  H  HOH1  0   0.477   9.1085  -11.5673  37.3854
 D8D  H20  H  HCH1  0   0.244   7.2506  -14.3856  32.4191
 D8D  H21  H  HNH1  0   0.403   6.3595  -16.2598  31.9340
 D8D  H22  H  HCH3  0   0.251   5.4097  -18.3149  32.1001
 D8D  H23  H  HCH3  0   0.238   6.3546  -18.5787  33.5668
 D8D  H24  H  HCH3  0   0.238   4.7489  -17.8467  33.6684
 D8D  H25  H  HCH1  0   0.232   6.1998  -13.2438  35.0137

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  1.444  0.020  1.444
 D8D  N    C1   single  1.338  0.020  1.338
 D8D  C7   C8   single  1.539  0.020  1.539
 D8D  C7   C6   single  1.524  0.020  1.524
 D8D  C9   N1   single  1.458  0.020  1.458
 D8D  C9   C10  single  1.520  0.020  1.520
 D8D  C4   C3   single  1.526  0.020  1.526
 D8D  C4   C5   single  1.535  0.020  1.535
 D8D  C2   C1   single  1.534  0.020  1.534
 D8D  C2   N1   single  1.446  0.020  1.446
 D8D  C2   C3   single  1.533  0.020  1.533
 D8D  C8   C3   single  1.538  0.020  1.538
 D8D  C1   O    double  1.227  0.020  1.227
 D8D  N1   C12  single  1.451  0.020  1.451
 D8D  C5   C6   single  1.536  0.020  1.536
 D8D  C10  C11  single  1.524  0.020  1.524
 D8D  O1   C13  double  1.205  0.020  1.205
 D8D  C12  C11  single  1.541  0.020  1.541
 D8D  C12  C13  single  1.518  0.020  1.518
 D8D  C13  O2   single  1.332  0.020  1.332
 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  O2   H19  single  0.850  0.020  0.980
 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   106.22  3.000
 D8D  H2   C4   C3   108.28  3.000
 D8D  H1   C4   C3   110.87  3.000
 D8D  H2   C4   C5   110.41  3.000
 D8D  H1   C4   C5   110.59  3.000
 D8D  C3   C4   C5   110.37  3.000
 D8D  H4   C5   H3   106.28  3.000
 D8D  H4   C5   C6   109.99  3.000
 D8D  H3   C5   C6   109.55  3.000
 D8D  H4   C5   C4   109.39  3.000
 D8D  H3   C5   C4   109.65  3.000
 D8D  C6   C5   C4   111.82  3.000
 D8D  H6   C6   H5   106.05  3.000
 D8D  H6   C6   C7   109.25  3.000
 D8D  H5   C6   C7   110.59  3.000
 D8D  H6   C6   C5   110.04  3.000
 D8D  H5   C6   C5   110.32  3.000
 D8D  C7   C6   C5   110.50  3.000
 D8D  C2   N1   C12  119.48  3.000
 D8D  C12  N1   C9   110.56  3.000
 D8D  C2   N1   C9   115.29  3.000
 D8D  H9   C7   H8   106.03  3.000
 D8D  H9   C7   C8   109.86  3.000
 D8D  H8   C7   C8   109.95  3.000
 D8D  H9   C7   C6   110.74  3.000
 D8D  H8   C7   C6   108.78  3.000
 D8D  C8   C7   C6   111.34  3.000
 D8D  H11  C8   H10  106.44  3.000
 D8D  H11  C8   C3   109.51  3.000
 D8D  H10  C8   C3   109.79  3.000
 D8D  H11  C8   C7   109.01  3.000
 D8D  H10  C8   C7   109.88  3.000
 D8D  C3   C8   C7   112.05  3.000
 D8D  H13  C9   H12  106.90  3.000
 D8D  H13  C9   C10  112.90  3.000
 D8D  H12  C9   C10  109.59  3.000
 D8D  H13  C9   N1   110.90  3.000
 D8D  H12  C9   N1   112.27  3.000
 D8D  C10  C9   N1   104.39  3.000
 D8D  H15  C10  H14  107.78  3.000
 D8D  H15  C10  C11  110.81  3.000
 D8D  H14  C10  C11  112.88  3.000
 D8D  H15  C10  C9   110.97  3.000
 D8D  H14  C10  C9   112.45  3.000
 D8D  C11  C10  C9   101.95  3.000
 D8D  H17  C11  H16  107.56  3.000
 D8D  H17  C11  C12  113.79  3.000
 D8D  H16  C11  C12  108.30  3.000
 D8D  H17  C11  C10  114.10  3.000
 D8D  H16  C11  C10  110.25  3.000
 D8D  C12  C11  C10  102.69  3.000
 D8D  H18  C12  C13  108.83  3.000
 D8D  H18  C12  C11  109.94  3.000
 D8D  C13  C12  C11  108.58  3.000
 D8D  H18  C12  N1   112.76  3.000
 D8D  C13  C12  N1   111.80  3.000
 D8D  C11  C12  N1   104.80  3.000
 D8D  O1   C13  O2   122.96  3.000
 D8D  O2   C13  C12  111.22  3.000
 D8D  O1   C13  C12  125.75  3.000
 D8D  H19  O2   C13  109.97  3.000
 D8D  H20  C2   C3   106.71  3.000
 D8D  H20  C2   C1   108.28  3.000
 D8D  C3   C2   C1   110.67  3.000
 D8D  H20  C2   N1   106.08  3.000
 D8D  C3   C2   N1   112.60  3.000
 D8D  C1   C2   N1   112.17  3.000
 D8D  N    C1   O    122.05  3.000
 D8D  O    C1   C2   122.13  3.000
 D8D  N    C1   C2   115.82  3.000
 D8D  H21  N    C    118.24  3.000
 D8D  H21  N    C1   119.19  3.000
 D8D  C    N    C1   122.56  3.000
 D8D  H24  C    H23  108.26  3.000
 D8D  H24  C    H22  108.37  3.000
 D8D  H23  C    H22  108.33  3.000
 D8D  H24  C    N    111.54  3.000
 D8D  H23  C    N    111.67  3.000
 D8D  H22  C    N    108.57  3.000
 D8D  H25  C3   C2   107.85  3.000
 D8D  H25  C3   C8   107.94  3.000
 D8D  C2   C3   C8   112.11  3.000
 D8D  H25  C3   C4   108.30  3.000
 D8D  C8   C3   C4   108.67  3.000
 D8D  C2   C3   C4   111.84  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  H19  O2   C13  C12  180.00   0.0  0
 D8D  CONST_02  C    N    C1   C2   180.00   0.0  0
 D8D  CONST_03  C    N    C1   O      0.00   0.0  0
 D8D  CONST_04  H21  N    C1   C2     0.00   0.0  0
 D8D  Var_01    C7   C6   C5   C4   -31.71  30.0  1
 D8D  Var_02    C8   C7   C6   C5    63.23  30.0  1
 D8D  Var_03    C3   C8   C7   C6   -26.66  30.0  1
 D8D  Var_04    C3   C4   C5   C6   -31.68  30.0  1
 D8D  Var_05    C11  C10  C9   N1    35.59  30.0  1
 D8D  Var_06    C12  C11  C10  C9   -38.63  30.0  1
 D8D  Var_07    C12  N1   C9   C10  -18.84  30.0  1
 D8D  Var_08    H22  C    N    C1   176.93  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
 D8D  plan-2  H19  0.020

