# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 09:58:44 2021
#   Inital geometry file: a 77 line input string
#   Ligand name: (3~{S})-1-[(2~{S})-2-methyl-3-sulfanyl-propanoyl]piperidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CS)C(=O)N1CCC[C@@H](C1)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
 EF9  EF9  '(3~{S})-1-[(2~{S})-2-methyl-3-sulfanyl-propanoyl]piperidine-3-carboxylic acid'  ligand  32  15  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EF9
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
 EF9  N1   N  NT    0  -0.480  30.7059  42.2306  26.7833
 EF9  C4   C  CH1   0  -0.332  28.3762  42.9493  26.9515
 EF9  C5   C  CH2   0  -0.455  28.4013  42.6031  28.4405
 EF9  C6   C  C     0   0.559  31.3197  41.5370  25.8005
 EF9  C7   C  CH1   0  -0.368  32.1740  40.3353  26.1822
 EF9  C8   C  CH2   0  -0.543  32.0359  39.2540  25.1232
 EF9  C10  C  C     0   0.502  27.7814  41.8999  26.0330
 EF9  C1   C  CH2   0  -0.465  29.4714  41.5718  28.7846
 EF9  C2   C  CH2   0  -0.272  30.8188  41.9894  28.2128
 EF9  C3   C  CH2   0  -0.288  29.7851  43.3084  26.4677
 EF9  C9   C  CH3   0  -0.652  33.6306  40.7799  26.3246
 EF9  O1   O  O     0  -0.492  31.2374  41.8668  24.6241
 EF9  O2   O  OH1   0  -0.388  27.1683  40.9104  26.6676
 EF9  O3   O  O     0  -0.599  27.8138  41.9818  24.8300
 EF9  S1   S  S2    0  -0.257  30.3290  38.6462  24.9375
 EF9  H1   H  HCH1  0   0.286  27.7506  43.8381  26.8104
 EF9  H2   H  HCH2  0   0.216  28.6248  43.5292  28.9798
 EF9  H3   H  HCH2  0   0.249  27.4199  42.2799  28.7872
 EF9  H4   H  HCH1  0   0.276  31.8485  39.8992  27.1260
 EF9  H5   H  HCH2  0   0.265  32.6799  38.4071  25.3601
 EF9  H6   H  HCH2  0   0.257  32.3324  39.6205  24.1418
 EF9  H7   H  HCH2  0   0.226  29.2031  40.5898  28.3877
 EF9  H8   H  HCH2  0   0.260  29.5558  41.4685  29.8679
 EF9  H9   H  HCH2  0   0.272  31.5768  41.2429  28.4306
 EF9  H10  H  HCH2  0   0.253  31.1526  42.9185  28.6871
 EF9  H11  H  HCH2  0   0.258  30.1106  44.2192  26.9777
 EF9  H12  H  HCH2  0   0.247  29.7967  43.5001  25.3998
 EF9  H13  H  HCH3  0   0.264  33.7441  41.5372  27.1020
 EF9  H14  H  HCH3  0   0.227  34.2651  39.9341  26.5911
 EF9  H15  H  HCH3  0   0.229  34.0041  41.2025  25.3908
 EF9  H16  H  HOH1  0   0.505  26.7854  40.2962  26.0230
 EF9  H17  H  HSH1  0   0.237  30.3391  37.7809  25.9574

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
 EF9  O1   C6   double  1.225  0.020  1.225
 EF9  S1   C8   single  1.821  0.020  1.821
 EF9  C8   C7   single  1.520  0.020  1.520
 EF9  O3   C10  double  1.206  0.020  1.206
 EF9  C6   C7   single  1.523  0.020  1.523
 EF9  C6   N1   single  1.351  0.020  1.351
 EF9  C9   C7   single  1.530  0.020  1.530
 EF9  C3   N1   single  1.452  0.020  1.452
 EF9  C3   C4   single  1.532  0.020  1.532
 EF9  C10  O2   single  1.326  0.020  1.326
 EF9  C10  C4   single  1.516  0.020  1.516
 EF9  N1   C2   single  1.454  0.020  1.454
 EF9  C4   C5   single  1.529  0.020  1.529
 EF9  C2   C1   single  1.522  0.020  1.522
 EF9  C5   C1   single  1.525  0.020  1.525
 EF9  C4   H1   single  0.970  0.020  1.090
 EF9  C5   H2   single  0.970  0.020  1.090
 EF9  C5   H3   single  0.970  0.020  1.090
 EF9  C7   H4   single  0.970  0.020  1.090
 EF9  C8   H5   single  0.970  0.020  1.090
 EF9  C8   H6   single  0.970  0.020  1.090
 EF9  C1   H7   single  0.970  0.020  1.090
 EF9  C1   H8   single  0.970  0.020  1.090
 EF9  C2   H9   single  0.970  0.020  1.090
 EF9  C2   H10  single  0.970  0.020  1.090
 EF9  C3   H11  single  0.970  0.020  1.090
 EF9  C3   H12  single  0.970  0.020  1.090
 EF9  C9   H13  single  0.970  0.020  1.090
 EF9  C9   H14  single  0.970  0.020  1.090
 EF9  C9   H15  single  0.970  0.020  1.090
 EF9  O2   H16  single  0.850  0.020  0.980
 EF9  S1   H17  single  1.200  0.020  1.300

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
 EF9  C3   N1   C2   112.71  3.000
 EF9  C2   N1   C6   126.51  3.000
 EF9  C3   N1   C6   120.74  3.000
 EF9  H1   C4   C3   107.11  3.000
 EF9  H1   C4   C10  105.03  3.000
 EF9  C3   C4   C10  109.37  3.000
 EF9  H1   C4   C5   108.57  3.000
 EF9  C10  C4   C5   116.09  3.000
 EF9  C3   C4   C5   110.21  3.000
 EF9  H3   C5   H2   106.14  3.000
 EF9  H3   C5   C1   111.07  3.000
 EF9  H2   C5   C1   108.52  3.000
 EF9  H3   C5   C4   111.23  3.000
 EF9  H2   C5   C4   106.95  3.000
 EF9  C1   C5   C4   112.60  3.000
 EF9  O1   C6   C7   119.41  3.000
 EF9  C7   C6   N1   118.54  3.000
 EF9  O1   C6   N1   122.02  3.000
 EF9  H4   C7   C9   108.67  3.000
 EF9  H4   C7   C8   106.96  3.000
 EF9  C9   C7   C8   110.99  3.000
 EF9  H4   C7   C6   111.44  3.000
 EF9  C9   C7   C6   109.15  3.000
 EF9  C8   C7   C6   109.62  3.000
 EF9  H6   C8   H5   107.25  3.000
 EF9  H6   C8   S1   106.00  3.000
 EF9  H5   C8   S1   108.46  3.000
 EF9  H6   C8   C7   111.34  3.000
 EF9  H5   C8   C7   110.34  3.000
 EF9  S1   C8   C7   113.18  3.000
 EF9  O3   C10  O2   122.72  3.000
 EF9  O2   C10  C4   114.08  3.000
 EF9  O3   C10  C4   123.14  3.000
 EF9  H8   C1   H7   107.12  3.000
 EF9  H8   C1   C2   109.30  3.000
 EF9  H7   C1   C2   109.12  3.000
 EF9  H8   C1   C5   110.00  3.000
 EF9  H7   C1   C5   110.69  3.000
 EF9  C2   C1   C5   110.53  3.000
 EF9  H10  C2   H9   106.47  3.000
 EF9  H10  C2   C1   109.87  3.000
 EF9  H9   C2   C1   110.73  3.000
 EF9  H10  C2   N1   107.98  3.000
 EF9  H9   C2   N1   111.43  3.000
 EF9  C1   C2   N1   110.25  3.000
 EF9  H12  C3   H11  107.98  3.000
 EF9  H12  C3   C4   111.22  3.000
 EF9  H11  C3   C4   108.76  3.000
 EF9  H12  C3   N1   109.77  3.000
 EF9  H11  C3   N1   109.15  3.000
 EF9  C4   C3   N1   109.90  3.000
 EF9  H15  C9   H14  108.08  3.000
 EF9  H15  C9   H13  107.78  3.000
 EF9  H14  C9   H13  107.68  3.000
 EF9  H15  C9   C7   111.03  3.000
 EF9  H14  C9   C7   110.57  3.000
 EF9  H13  C9   C7   111.54  3.000
 EF9  H16  O2   C10  109.72  3.000
 EF9  H17  S1   C8    97.53  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
 EF9  CONST_01  C3   N1  C6   C7  180.00   0.0  0
 EF9  CONST_02  C2   N1  C6   C7    0.00   0.0  0
 EF9  CONST_03  O1   C6  N1   C2  180.00   0.0  0
 EF9  CONST_04  O1   C6  N1   C3    0.00   0.0  0
 EF9  CONST_05  H16  O2  C10  C4  180.00   0.0  0
 EF9  Var_01    C5   C1  C2   N1  -54.54  30.0  1
 EF9  Var_02    C2   N1  C3   C4  -61.85  30.0  1
 EF9  Var_03    C2   C1  C5   C4   50.64  30.0  1
 EF9  Var_04    C3   N1  C2   C1   61.76  30.0  1

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
 EF9  chir_01  C4  C3  C10  C5  negativ
 EF9  chir_02  C7  C9  C6   C8  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
 EF9  plan-1  N1   0.020
 EF9  plan-1  C6   0.020
 EF9  plan-1  C7   0.020
 EF9  plan-1  C2   0.020
 EF9  plan-1  C3   0.020
 EF9  plan-1  O1   0.020
 EF9  plan-2  C4   0.020
 EF9  plan-2  C10  0.020
 EF9  plan-2  O2   0.020
 EF9  plan-2  O3   0.020
 EF9  plan-2  H16  0.020

