# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 20:11:55 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: {(3S)-1-[5-(cyclohexylcarbamoyl)-6-(propylsulfanyl)pyridin-2-yl]piperidin-3-yl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCSc1nc(ccc1C(=O)NC2CCCCC2)N3CCC[C@H](C3)CC(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
 14M  14M  '{(3S)-1-[5-(cyclohexylcarbamoyl)-6-(propylsulfanyl)pyridin-2-yl]piperidin-3-yl}acetic acid'  ligand  61  29  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_14M
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
 14M  C1   C  C      0   0.412   5.0248   0.1570  -1.9023
 14M  C2   C  CH2    0  -0.583   3.9631   0.1533  -0.7891
 14M  C3   C  CH1    0  -0.225   4.5026   0.0288   0.6320
 14M  C7   C  CH2    0  -0.442   5.1882  -1.3158   0.8944
 14M  C8   C  CR6    0   0.562   1.2060  -0.7632   1.1564
 14M  C9   C  CR6    0   0.080  -0.3747   0.6616   0.2392
 14M  C10  C  CR6    0  -0.142  -1.3675  -0.3331   0.1834
 14M  C11  C  CR16   0  -0.163  -0.9594  -1.6035   0.6064
 14M  C12  C  CR16   0  -0.419   0.3019  -1.8481   1.0816
 14M  C13  C  C      0   0.530  -2.7230  -0.0557  -0.3307
 14M  C14  C  CH1    0  -0.054  -5.0572  -0.8384  -0.4822
 14M  C15  C  CH2    0  -0.440  -5.6362  -2.2261  -0.7427
 14M  C16  C  CH2    0  -0.436  -7.0895  -2.1419  -1.1985
 14M  C19  C  CH2    0  -0.426  -5.9138  -0.0654   0.5209
 14M  C20  C  CH2    0  -0.552   0.8812   3.1312   0.0274
 14M  C21  C  CH2    0  -0.429   0.7715   4.5816  -0.4255
 14M  C22  C  CH3    0  -0.658   2.0720   5.3342  -0.1772
 14M  S1   S  S2     0   0.059  -0.6872   2.2977  -0.3497
 14M  O1   O  O      0  -0.611   6.1675   0.5659  -1.6103
 14M  O2   O  OC    -1  -0.626   4.6448  -0.2160  -3.0322
 14M  O3   O  O      0  -0.500  -2.9535   0.9509  -0.9969
 14M  N1   N  NT     0  -0.482   2.4521  -0.8754   1.6662
 14M  N2   N  N      0  -0.488   0.8311   0.4441   0.7214
 14M  N3   N  NH1    0  -0.667  -3.6808  -0.9581  -0.0408
 14M  C4   C  CH2    0  -0.324   3.3974   0.2309   1.6707
 14M  C5   C  CH2    0  -0.323   3.0836  -2.1435   1.9836
 14M  C6   C  CH2    0  -0.436   4.1838  -2.4614   0.9761
 14M  C17  C  CH2    0  -0.432  -7.9448  -1.3672  -0.2016
 14M  C18  C  CH2    0  -0.439  -7.3653   0.0191   0.0581
 14M  H1   H  HCH2   0   0.240   3.4054   1.0956  -0.8652
 14M  H2   H  HCH2   0   0.212   3.2246  -0.6261  -0.9948
 14M  H3   H  HCH1   0   0.222   5.2357   0.8254   0.7849
 14M  H4   H  HCH2   0   0.236   5.9350  -1.5119   0.1235
 14M  H5   H  HCH2   0   0.216   5.7336  -1.2586   1.8433
 14M  H6   H  HCR6   0   0.256  -1.6382  -2.4446   0.5425
 14M  H7   H  HCR6   0   0.272   0.5694  -2.8493   1.3784
 14M  H8   H  HCH1   0   0.235  -5.0480  -0.2864  -1.4254
 14M  H9   H  HCH2   0   0.238  -5.0299  -2.7411  -1.4920
 14M  H10  H  HCH2   0   0.216  -5.5783  -2.8224   0.1757
 14M  H11  H  HCH2   0   0.214  -7.1321  -1.6484  -2.1751
 14M  H12  H  HCH2   0   0.232  -7.4894  -3.1480  -1.3440
 14M  H13  H  HCH2   0   0.211  -5.8685  -0.5702   1.4923
 14M  H14  H  HCH2   0   0.236  -5.4975   0.9346   0.6641
 14M  H15  H  HCH2   0   0.268   1.6957   2.6273  -0.4945
 14M  H16  H  HCH2   0   0.259   1.0908   3.0741   1.0959
 14M  H17  H  HCH2   0   0.230   0.5235   4.6211  -1.4895
 14M  H18  H  HCH2   0   0.230  -0.0473   5.0752   0.1039
 14M  H19  H  HCH3   0   0.222   2.3284   5.3415   0.8833
 14M  H20  H  HCH3   0   0.222   2.9024   4.8745  -0.7156
 14M  H21  H  HCH3   0   0.234   1.9942   6.3700  -0.5078
 14M  H23  H  HNH1   0   0.395  -3.4949  -1.6656   0.6515
 14M  H24  H  HCH2   0   0.239   3.8429   0.2765   2.6708
 14M  H25  H  HCH2   0   0.273   2.8665   1.1635   1.5038
 14M  H26  H  HCH2   0   0.239   3.5165  -2.0658   2.9867
 14M  H27  H  HCH2   0   0.264   2.3546  -2.9471   2.0267
 14M  H28  H  HCH2   0   0.225   3.7334  -2.6539  -0.0019
 14M  H29  H  HCH2   0   0.236   4.6826  -3.3854   1.2773
 14M  H30  H  HCH2   0   0.229  -8.9714  -1.2865  -0.5669
 14M  H31  H  HCH2   0   0.211  -7.9914  -1.9213   0.7421
 14M  H32  H  HCH2   0   0.231  -7.9628   0.5485   0.8038
 14M  H33  H  HCH2   0   0.213  -7.4181   0.6142  -0.8598

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
 14M  C7   C6   single    1.526  0.020  1.526
 14M  C7   C3   single    1.532  0.020  1.532
 14M  C2   C3   single    1.525  0.020  1.525
 14M  C2   C1   single    1.538  0.020  1.538
 14M  C6   C5   single    1.525  0.020  1.525
 14M  C3   C4   single    1.530  0.020  1.530
 14M  C1   O1   deloc     1.248  0.020  1.248
 14M  C1   O2   deloc     1.249  0.020  1.249
 14M  C5   N1   single    1.452  0.020  1.452
 14M  C4   N1   single    1.455  0.020  1.455
 14M  C22  C21  single    1.523  0.020  1.523
 14M  N1   C8   single    1.351  0.020  1.351
 14M  C21  C20  single    1.523  0.020  1.523
 14M  C8   N2   aromatic  1.337  0.020  1.337
 14M  C8   C12  aromatic  1.414  0.020  1.414
 14M  N2   C9   aromatic  1.317  0.020  1.317
 14M  C12  C11  aromatic  1.370  0.020  1.370
 14M  C20  S1   single    1.816  0.020  1.816
 14M  C9   S1   single    1.767  0.020  1.767
 14M  C9   C10  aromatic  1.406  0.020  1.406
 14M  C11  C10  aromatic  1.400  0.020  1.400
 14M  C10  C13  single    1.476  0.020  1.476
 14M  N3   C13  single    1.347  0.020  1.347
 14M  N3   C14  single    1.450  0.020  1.450
 14M  C19  C14  single    1.529  0.020  1.529
 14M  C19  C18  single    1.526  0.020  1.526
 14M  C15  C14  single    1.526  0.020  1.526
 14M  C15  C16  single    1.525  0.020  1.525
 14M  C13  O3   double    1.229  0.020  1.229
 14M  C17  C18  single    1.525  0.020  1.525
 14M  C17  C16  single    1.525  0.020  1.525
 14M  C2   H1   single    0.970  0.020  1.090
 14M  C2   H2   single    0.970  0.020  1.090
 14M  C3   H3   single    0.970  0.020  1.090
 14M  C7   H4   single    0.970  0.020  1.090
 14M  C7   H5   single    0.970  0.020  1.090
 14M  C11  H6   single    0.930  0.020  1.080
 14M  C12  H7   single    0.930  0.020  1.080
 14M  C14  H8   single    0.970  0.020  1.090
 14M  C15  H9   single    0.970  0.020  1.090
 14M  C15  H10  single    0.970  0.020  1.090
 14M  C16  H11  single    0.970  0.020  1.090
 14M  C16  H12  single    0.970  0.020  1.090
 14M  C19  H13  single    0.970  0.020  1.090
 14M  C19  H14  single    0.970  0.020  1.090
 14M  C20  H15  single    0.970  0.020  1.090
 14M  C20  H16  single    0.970  0.020  1.090
 14M  C21  H17  single    0.970  0.020  1.090
 14M  C21  H18  single    0.970  0.020  1.090
 14M  C22  H19  single    0.970  0.020  1.090
 14M  C22  H20  single    0.970  0.020  1.090
 14M  C22  H21  single    0.970  0.020  1.090
 14M  N3   H23  single    0.860  0.020  1.020
 14M  C4   H24  single    0.970  0.020  1.090
 14M  C4   H25  single    0.970  0.020  1.090
 14M  C5   H26  single    0.970  0.020  1.090
 14M  C5   H27  single    0.970  0.020  1.090
 14M  C6   H28  single    0.970  0.020  1.090
 14M  C6   H29  single    0.970  0.020  1.090
 14M  C17  H30  single    0.970  0.020  1.090
 14M  C17  H31  single    0.970  0.020  1.090
 14M  C18  H32  single    0.970  0.020  1.090
 14M  C18  H33  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
 14M  O2   C1   O1   126.01  3.000
 14M  O2   C1   C2   116.35  3.000
 14M  O1   C1   C2   117.60  3.000
 14M  H2   C2   H1   104.82  3.000
 14M  H2   C2   C3   110.86  3.000
 14M  H1   C2   C3   108.33  3.000
 14M  H2   C2   C1   109.37  3.000
 14M  H1   C2   C1   107.36  3.000
 14M  C3   C2   C1   115.49  3.000
 14M  H3   C3   C4   107.05  3.000
 14M  H3   C3   C7   108.39  3.000
 14M  C4   C3   C7   108.84  3.000
 14M  H3   C3   C2   107.93  3.000
 14M  C4   C3   C2   111.48  3.000
 14M  C7   C3   C2   112.93  3.000
 14M  H5   C7   H4   106.28  3.000
 14M  H5   C7   C6   108.69  3.000
 14M  H4   C7   C6   110.70  3.000
 14M  H5   C7   C3   108.98  3.000
 14M  H4   C7   C3   110.06  3.000
 14M  C6   C7   C3   111.94  3.000
 14M  N2   C8   N1   117.16  3.000
 14M  N2   C8   C12  119.75  3.000
 14M  N1   C8   C12  123.09  3.000
 14M  N2   C9   S1   115.91  3.000
 14M  S1   C9   C10  121.12  3.000
 14M  N2   C9   C10  122.96  3.000
 14M  C13  C10  C11  122.93  3.000
 14M  C13  C10  C9   121.95  3.000
 14M  C11  C10  C9   115.09  3.000
 14M  H6   C11  C12  117.33  3.000
 14M  H6   C11  C10  120.29  3.000
 14M  C12  C11  C10  122.36  3.000
 14M  H7   C12  C11  119.32  3.000
 14M  H7   C12  C8   122.63  3.000
 14M  C11  C12  C8   118.04  3.000
 14M  N3   C13  O3   122.12  3.000
 14M  O3   C13  C10  121.00  3.000
 14M  N3   C13  C10  116.87  3.000
 14M  H8   C14  N3   107.24  3.000
 14M  H8   C14  C19  108.39  3.000
 14M  N3   C14  C19  111.95  3.000
 14M  H8   C14  C15  108.37  3.000
 14M  C19  C14  C15  111.05  3.000
 14M  N3   C14  C15  109.69  3.000
 14M  H10  C15  H9   106.78  3.000
 14M  H10  C15  C16  109.30  3.000
 14M  H9   C15  C16  110.47  3.000
 14M  H10  C15  C14  109.35  3.000
 14M  H9   C15  C14  109.58  3.000
 14M  C16  C15  C14  111.24  3.000
 14M  H12  C16  H11  106.38  3.000
 14M  H12  C16  C17  110.47  3.000
 14M  H11  C16  C17  109.40  3.000
 14M  H12  C16  C15  109.74  3.000
 14M  H11  C16  C15  109.17  3.000
 14M  C17  C16  C15  111.54  3.000
 14M  H14  C19  H13  106.84  3.000
 14M  H14  C19  C18  110.58  3.000
 14M  H13  C19  C18  109.50  3.000
 14M  H14  C19  C14  109.58  3.000
 14M  H13  C19  C14  109.00  3.000
 14M  C18  C19  C14  111.23  3.000
 14M  H16  C20  H15  107.52  3.000
 14M  H16  C20  S1   110.21  3.000
 14M  H15  C20  S1   109.49  3.000
 14M  H16  C20  C21  110.79  3.000
 14M  H15  C20  C21  110.57  3.000
 14M  S1   C20  C21  108.25  3.000
 14M  H18  C21  H17  106.57  3.000
 14M  H18  C21  C22  109.73  3.000
 14M  H17  C21  C22  109.54  3.000
 14M  H18  C21  C20  109.88  3.000
 14M  H17  C21  C20  109.88  3.000
 14M  C22  C21  C20  111.14  3.000
 14M  H21  C22  H20  107.76  3.000
 14M  H21  C22  H19  107.76  3.000
 14M  H20  C22  H19  107.67  3.000
 14M  H21  C22  C21  111.05  3.000
 14M  H20  C22  C21  111.18  3.000
 14M  H19  C22  C21  111.25  3.000
 14M  C20  S1   C9   101.72  3.000
 14M  C5   N1   C4   112.39  3.000
 14M  C4   N1   C8   122.49  3.000
 14M  C5   N1   C8   123.80  3.000
 14M  C9   N2   C8   121.68  3.000
 14M  H23  N3   C14  116.25  3.000
 14M  H23  N3   C13  119.15  3.000
 14M  C14  N3   C13  123.64  3.000
 14M  H25  C4   H24  107.65  3.000
 14M  H25  C4   N1   109.56  3.000
 14M  H24  C4   N1   107.37  3.000
 14M  H25  C4   C3   111.23  3.000
 14M  H24  C4   C3   109.35  3.000
 14M  N1   C4   C3   111.51  3.000
 14M  H27  C5   H26  106.35  3.000
 14M  H27  C5   C6   110.87  3.000
 14M  H26  C5   C6   109.55  3.000
 14M  H27  C5   N1   111.29  3.000
 14M  H26  C5   N1   108.07  3.000
 14M  C6   C5   N1   110.57  3.000
 14M  H29  C6   H28  106.60  3.000
 14M  H29  C6   C5   108.88  3.000
 14M  H28  C6   C5   109.29  3.000
 14M  H29  C6   C7   110.44  3.000
 14M  H28  C6   C7   110.81  3.000
 14M  C5   C6   C7   110.71  3.000
 14M  H31  C17  H30  106.58  3.000
 14M  H31  C17  C18  109.22  3.000
 14M  H30  C17  C18  110.30  3.000
 14M  H31  C17  C16  109.27  3.000
 14M  H30  C17  C16  110.24  3.000
 14M  C18  C17  C16  111.10  3.000
 14M  H33  C18  H32  106.40  3.000
 14M  H33  C18  C17  109.44  3.000
 14M  H32  C18  C17  110.43  3.000
 14M  H33  C18  C19  109.28  3.000
 14M  H32  C18  C19  109.89  3.000
 14M  C17  C18  C19  111.28  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
 14M  CONST_01  C10  C9   N2   C8      0.00   0.0  0
 14M  CONST_02  C10  C11  C12  C8      0.00   0.0  0
 14M  CONST_03  C12  C8   N2   C9      0.00   0.0  0
 14M  CONST_04  C12  C11  C10  C9      0.00   0.0  0
 14M  CONST_05  N2   C8   C12  C11     0.00   0.0  0
 14M  CONST_06  N2   C9   C10  C11     0.00   0.0  0
 14M  CONST_07  N1   C8   N2   C9    180.00   0.0  0
 14M  CONST_08  N1   C8   C12  C11   180.00   0.0  0
 14M  CONST_09  S1   C9   N2   C8    180.00   0.0  0
 14M  CONST_10  S1   C9   C10  C11   180.00   0.0  0
 14M  CONST_11  C13  C10  C11  C12   180.00   0.0  0
 14M  CONST_12  N2   C9   C10  C13   180.00   0.0  0
 14M  CONST_13  H6   C11  C12  C8    180.00   0.0  0
 14M  CONST_14  H7   C12  C11  C10   180.00   0.0  0
 14M  CONST_15  C14  N3   C13  C10   180.00   0.0  0
 14M  CONST_16  O3   C13  N3   C14     0.00   0.0  0
 14M  CONST_17  H23  N3   C13  C10     0.00   0.0  0
 14M  Var_01    C5   C6   C7   C3    -52.79  30.0  1
 14M  Var_02    C5   N1   C4   C3     60.71  30.0  1
 14M  Var_03    N1   C5   C6   C7     54.74  30.0  1
 14M  Var_04    C6   C5   N1   C8    107.80  30.0  1
 14M  Var_05    C17  C18  C19  C14    55.67  30.0  1
 14M  Var_06    C17  C16  C15  C14   -55.28  30.0  1
 14M  Var_07    C18  C17  C16  C15    55.22  30.0  1
 14M  Var_08    C19  C18  C17  C16   -55.36  30.0  1
 14M  Var_09    N3   C13  C10  C9   -164.02  30.0  2
 14M  Var_10    N2   C9   S1   C20    -2.28  30.0  1
 14M  Var_11    O1   C1   C2   C3    -26.74  30.0  3
 14M  Var_12    C21  C20  S1   C9   -179.87  30.0  1
 14M  Var_13    S1   C20  C21  C22  -178.29  30.0  3
 14M  Var_14    H19  C22  C21  C20   -60.34  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
 14M  chir_01  C3   C7  C2   C4   negativ
 14M  chir_02  C14  N3  C19  C15  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
 14M  plan-1  C8   0.020
 14M  plan-1  C9   0.020
 14M  plan-1  C10  0.020
 14M  plan-1  C11  0.020
 14M  plan-1  C12  0.020
 14M  plan-1  C13  0.020
 14M  plan-1  S1   0.020
 14M  plan-1  N1   0.020
 14M  plan-1  N2   0.020
 14M  plan-1  H6   0.020
 14M  plan-1  H7   0.020
 14M  plan-2  C10  0.020
 14M  plan-2  C13  0.020
 14M  plan-2  C14  0.020
 14M  plan-2  O3   0.020
 14M  plan-2  N3   0.020
 14M  plan-2  H23  0.020
 14M  plan-3  C1   0.020
 14M  plan-3  C2   0.020
 14M  plan-3  O1   0.020
 14M  plan-3  O2   0.020

