# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 11:40:30 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: (3S,5R)-5-[(2R,3R)-1,3-dihydroxybutan-2-yl]-3-({(3R)-1-[(1E)-ethanimidoyl]pyrrolidin-3-yl}sulfanyl)-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@@H](CO)[C@H]1C[C@H](S[C@@H]2CCN(C2)C(C)=N)[C@H](N1)C(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
 E0Y  E0Y  (3S,5R)-5-[(2R,3R)-1,3-dihydroxybutan-2-yl]-3-({(3R)-1-[(1E)-ethanimidoyl]pyrrolidin-3-yl}sulfanyl)-L-proline  L-peptide  49  23  .  2019-03-22  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_E0Y
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
 E0Y  O    O  O      0  -0.611  26.6695  -10.5644  -24.3020
 E0Y  C11  C  CH2    0  -0.240  30.4905  -11.2133  -24.1070
 E0Y  OXT  O  OC    -1  -0.589  27.3233  -12.5863  -23.6188
 E0Y  CA   C  CH1    0  -0.159  27.5641  -10.7174  -22.1291
 E0Y  N    N  NH1    0  -0.618  26.3687  -10.5034  -21.3224
 E0Y  CD   C  CH1    0  -0.028  26.8564  -10.1056  -20.0123
 E0Y  C6   C  CH1    0  -0.294  25.7635  -10.0611  -18.9423
 E0Y  C7   C  CH2    0  -0.152  24.7389   -8.9575  -19.2083
 E0Y  O14  O  OH1    0  -0.668  23.8739   -9.3485  -20.2560
 E0Y  CB   C  CH1    0  -0.364  28.4325  -11.5466  -21.1825
 E0Y  CG   C  CH2    0  -0.450  27.9613  -11.1431  -19.7688
 E0Y  C10  C  CH1    0  -0.402  30.6365  -12.1099  -22.8838
 E0Y  C13  C  CH2    0  -0.290  32.7734  -11.1046  -23.3358
 E0Y  C14  C  CH2    0  -0.477  32.1321  -12.4205  -22.9044
 E0Y  C16  C  CH3    0  -0.750  30.7731   -8.7609  -25.5640
 E0Y  C    C  C      0   0.410  27.1617  -11.3594  -23.4753
 E0Y  C8   C  CH1    0   0.046  26.3616   -9.9266  -17.5341
 E0Y  C9   C  CH3    0  -0.707  27.0762   -8.6046  -17.2819
 E0Y  N12  N  NT     0  -0.457  31.7313  -10.4565  -24.1147
 E0Y  N15  N  N      0  -0.699  33.0286   -8.6100  -24.7617
 E0Y  O8   O  OH1    0  -0.669  25.3030  -10.1255  -16.6133
 E0Y  S2   S  S2     0  -0.032  30.2219  -11.2678  -21.3225
 E0Y  H2   H  HCH2   0   0.236  30.3875  -11.8336  -25.0064
 E0Y  HA   H  HCH1   0   0.190  28.0850   -9.7657  -22.3355
 E0Y  H    H  HNH1   0   0.341  25.7590   -9.8088  -21.7327
 E0Y  HD2  H  HCH1   0   0.194  27.3337   -9.1103  -20.0580
 E0Y  H8   H  HCH1   0   0.228  25.2417  -11.0268  -18.9669
 E0Y  H9   H  HCH2   0   0.189  25.2663   -8.0273  -19.4614
 E0Y  H10  H  HCH2   0   0.208  24.1673   -8.7582  -18.2950
 E0Y  H11  H  HOH1   0   0.449  23.2764   -8.6167  -20.4343
 E0Y  HB2  H  HCH1   0   0.270  28.2547  -12.6075  -21.3573
 E0Y  HG2  H  HCH2   0   0.244  27.5657  -12.0184  -19.2489
 E0Y  HG3  H  HCH2   0   0.242  28.7635  -10.7409  -19.1476
 E0Y  H15  H  HCH1   0   0.292  30.0178  -13.0029  -22.9605
 E0Y  H16  H  HCH2   0   0.245  33.6757  -11.2722  -23.9304
 E0Y  H17  H  HCH2   0   0.238  33.0605  -10.4917  -22.4739
 E0Y  H18  H  HCH2   0   0.261  32.3173  -13.1905  -23.6563
 E0Y  H19  H  HCH2   0   0.263  32.5167  -12.7867  -21.9537
 E0Y  H20  H  HCH3   0   0.250  30.4081   -9.4975  -26.2813
 E0Y  H21  H  HCH3   0   0.253  29.9337   -8.4984  -24.9172
 E0Y  H22  H  HCH3   0   0.256  31.0783   -7.8696  -26.1052
 E0Y  H23  H  HCH1   0   0.217  27.0997  -10.7304  -17.4107
 E0Y  H24  H  HCH3   0   0.235  27.5148   -8.5945  -16.2818
 E0Y  H25  H  HCH3   0   0.232  27.8905   -8.4531  -17.9907
 E0Y  H26  H  HCH3   0   0.230  26.3998   -7.7519  -17.3568
 E0Y  H27  H  H      0   0.322  33.7430   -9.0512  -24.1906
 E0Y  H28  H  HOH1   0   0.445  25.6588  -10.0334  -15.7241
 E0Y  C15  C  C      0   0.412  31.9368   -9.2862  -24.7698
 E0Y  H1   H  HCH2   0   0.261  29.6214  -10.5614  -24.0561

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
 E0Y  C16  C15  single  1.504  0.020  1.504
 E0Y  C15  N15  double  1.284  0.020  1.284
 E0Y  C15  N12  single  1.357  0.020  1.357
 E0Y  N12  C11  single  1.453  0.020  1.453
 E0Y  N12  C13  single  1.453  0.020  1.453
 E0Y  C11  C10  single  1.524  0.020  1.524
 E0Y  O    C    deloc   1.231  0.020  1.231
 E0Y  C13  C14  single  1.526  0.020  1.526
 E0Y  OXT  C    deloc   1.246  0.020  1.246
 E0Y  C    CA   single  1.525  0.021  1.525
 E0Y  C14  C10  single  1.528  0.020  1.528
 E0Y  C10  S2   single  1.822  0.020  1.822
 E0Y  CA   CB   single  1.530  0.020  1.530
 E0Y  CA   N    single  1.466  0.015  1.466
 E0Y  S2   CB   single  1.816  0.020  1.816
 E0Y  CB   CG   single  1.544  0.020  1.544
 E0Y  N    CD   single  1.473  0.014  1.473
 E0Y  O14  C7   single  1.414  0.020  1.414
 E0Y  CG   CD   single  1.535  0.020  1.535
 E0Y  CD   C6   single  1.530  0.020  1.530
 E0Y  C7   C6   single  1.529  0.020  1.529
 E0Y  C6   C8   single  1.536  0.020  1.536
 E0Y  C8   O8   single  1.417  0.020  1.417
 E0Y  C8   C9   single  1.524  0.020  1.524
 E0Y  C11  H1   single  0.970  0.020  1.090
 E0Y  C11  H2   single  0.970  0.020  1.090
 E0Y  CA   HA   single  0.970  0.020  0.970
 E0Y  N    H    single  0.860  0.020  1.020
 E0Y  CD   HD2  single  0.970  0.020  1.090
 E0Y  C6   H8   single  0.970  0.020  1.090
 E0Y  C7   H9   single  0.970  0.020  1.090
 E0Y  C7   H10  single  0.970  0.020  1.090
 E0Y  O14  H11  single  0.850  0.020  0.980
 E0Y  CB   HB2  single  0.970  0.020  1.090
 E0Y  CG   HG2  single  0.970  0.020  1.090
 E0Y  CG   HG3  single  0.970  0.020  1.090
 E0Y  C10  H15  single  0.970  0.020  1.090
 E0Y  C13  H16  single  0.970  0.020  1.090
 E0Y  C13  H17  single  0.970  0.020  1.090
 E0Y  C14  H18  single  0.970  0.020  1.090
 E0Y  C14  H19  single  0.970  0.020  1.090
 E0Y  C16  H20  single  0.970  0.020  1.090
 E0Y  C16  H21  single  0.970  0.020  1.090
 E0Y  C16  H22  single  0.970  0.020  1.090
 E0Y  C8   H23  single  0.970  0.020  1.090
 E0Y  C9   H24  single  0.970  0.020  1.090
 E0Y  C9   H25  single  0.970  0.020  1.090
 E0Y  C9   H26  single  0.970  0.020  1.090
 E0Y  N15  H27  single  0.890  0.020  1.040
 E0Y  O8   H28  single  0.850  0.020  0.980

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
 E0Y  H2   C11  H1   107.59  3.000
 E0Y  H2   C11  N12  111.73  3.000
 E0Y  H1   C11  N12  111.74  3.000
 E0Y  H2   C11  C10  109.53  3.000
 E0Y  H1   C11  C10  113.06  3.000
 E0Y  N12  C11  C10  103.23  3.000
 E0Y  HA   CA   C    109.00  3.000
 E0Y  HA   CA   CB   109.00  3.000
 E0Y  C    CA   CB   110.10  1.900
 E0Y  HA   CA   N    110.00  3.000
 E0Y  CB   CA   N    103.00  1.100
 E0Y  C    CA   N    112.10  2.500
 E0Y  H    N    CD   112.34  3.000
 E0Y  H    N    CA   111.76  3.000
 E0Y  CD   N    CA   105.29  3.000
 E0Y  HD2  CD   CG   107.73  3.000
 E0Y  HD2  CD   C6   108.13  3.000
 E0Y  CG   CD   C6   115.01  3.000
 E0Y  HD2  CD   N    110.75  3.000
 E0Y  C6   CD   N    113.49  3.000
 E0Y  CG   CD   N    103.20  1.500
 E0Y  H8   C6   C8   106.42  3.000
 E0Y  H8   C6   C7   108.20  3.000
 E0Y  C8   C6   C7   110.93  3.000
 E0Y  H8   C6   CD   107.35  3.000
 E0Y  C8   C6   CD   111.44  3.000
 E0Y  C7   C6   CD   112.21  3.000
 E0Y  H10  C7   H9   106.77  3.000
 E0Y  H10  C7   O14  110.41  3.000
 E0Y  H9   C7   O14  110.92  3.000
 E0Y  H10  C7   C6   109.62  3.000
 E0Y  H9   C7   C6   109.23  3.000
 E0Y  O14  C7   C6   109.83  3.000
 E0Y  H11  O14  C7   107.89  3.000
 E0Y  HB2  CB   S2   107.33  3.000
 E0Y  HB2  CB   CG   110.58  3.000
 E0Y  S2   CB   CG   109.34  3.000
 E0Y  HB2  CB   CA   109.63  3.000
 E0Y  CG   CB   CA   104.58  3.000
 E0Y  S2   CB   CA   115.38  3.000
 E0Y  HG3  CG   HG2  106.90  3.000
 E0Y  HG3  CG   CB   113.15  3.000
 E0Y  HG2  CG   CB   109.69  3.000
 E0Y  HG3  CG   CD   111.74  3.000
 E0Y  HG2  CG   CD   110.88  3.000
 E0Y  CB   CG   CD   104.54  3.000
 E0Y  H15  C10  S2   108.07  3.000
 E0Y  H15  C10  C14  112.86  3.000
 E0Y  S2   C10  C14  109.17  3.000
 E0Y  H15  C10  C11  111.81  3.000
 E0Y  S2   C10  C11  113.22  3.000
 E0Y  C14  C10  C11  101.69  3.000
 E0Y  H17  C13  H16  107.29  3.000
 E0Y  H17  C13  N12  111.09  3.000
 E0Y  H16  C13  N12  111.63  3.000
 E0Y  H17  C13  C14  111.71  3.000
 E0Y  H16  C13  C14  111.61  3.000
 E0Y  N12  C13  C14  103.57  3.000
 E0Y  H19  C14  H18  107.70  3.000
 E0Y  H19  C14  C13  112.86  3.000
 E0Y  H18  C14  C13  110.01  3.000
 E0Y  H19  C14  C10  113.72  3.000
 E0Y  H18  C14  C10  108.58  3.000
 E0Y  C13  C14  C10  103.88  3.000
 E0Y  H22  C16  H21  108.29  3.000
 E0Y  H22  C16  H20  108.68  3.000
 E0Y  H21  C16  H20  107.14  3.000
 E0Y  H22  C16  C15  109.41  3.000
 E0Y  H21  C16  C15  111.48  3.000
 E0Y  H20  C16  C15  111.74  3.000
 E0Y  CA   C    OXT  118.42  3.000
 E0Y  CA   C    O    119.00  3.000
 E0Y  OXT  C    O    127.03  3.000
 E0Y  H23  C8   O8   109.04  3.000
 E0Y  H23  C8   C9   107.53  3.000
 E0Y  O8   C8   C9   111.38  3.000
 E0Y  H23  C8   C6   107.50  3.000
 E0Y  C9   C8   C6   114.23  3.000
 E0Y  O8   C8   C6   107.02  3.000
 E0Y  H26  C9   H25  108.05  3.000
 E0Y  H26  C9   H24  107.73  3.000
 E0Y  H25  C9   H24  107.11  3.000
 E0Y  H26  C9   C8   112.08  3.000
 E0Y  H25  C9   C8   111.30  3.000
 E0Y  H24  C9   C8   110.36  3.000
 E0Y  C15  N12  C13  122.33  3.000
 E0Y  C13  N12  C11  112.15  3.000
 E0Y  C15  N12  C11  125.52  3.000
 E0Y  H27  N15  C15  111.89  3.000
 E0Y  H28  O8   C8   108.11  3.000
 E0Y  C10  S2   CB   102.67  3.000
 E0Y  N15  C15  N12  125.44  3.000
 E0Y  N12  C15  C16  116.05  3.000
 E0Y  N15  C15  C16  118.52  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
 E0Y  CONST_01  C16  C15  N12  C11    0.00   0.0  0
 E0Y  CONST_02  N15  C15  N12  C11  180.00   0.0  0
 E0Y  CONST_03  C16  C15  N12  C13  180.00   0.0  0
 E0Y  CONST_04  N15  C15  N12  C13    0.00   0.0  0
 E0Y  CONST_05  H27  N15  C15  N12    0.00   0.0  0
 E0Y  Var_01    C14  C13  N12  C11    4.35  30.0  1
 E0Y  Var_02    C13  N12  C11  C10   19.94  30.0  1
 E0Y  Var_03    N12  C13  C14  C10  -26.89  30.0  1
 E0Y  Var_04    H20  C16  C15  N12  -55.05  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
 E0Y  chir_01  CA   C   CB   N    positiv
 E0Y  chir_02  CD   N   CG   C6   positiv
 E0Y  chir_03  C6   CD  C7   C8   positiv
 E0Y  chir_04  CB   S2  CG   CA   negativ
 E0Y  chir_05  C10  S2  C11  C14  negativ
 E0Y  chir_06  C8   O8  C9   C6   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
 E0Y  plan-1  C11  0.020
 E0Y  plan-1  C13  0.020
 E0Y  plan-1  C16  0.020
 E0Y  plan-1  N12  0.020
 E0Y  plan-1  N15  0.020
 E0Y  plan-1  H27  0.020
 E0Y  plan-1  C15  0.020
 E0Y  plan-2  O    0.020
 E0Y  plan-2  OXT  0.020
 E0Y  plan-2  CA   0.020
 E0Y  plan-2  C    0.020

