# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 10:42:02 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: [(2S,4S)-4-{4-[1-phenyl-3-(trifluoromethyl)-1H-pyrazol-5-yl]piperidin-1-yl}pyrrolidin-2-yl](1,3-thiazolidin-3-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cc([C@H]2CCN(CC2)[C@@H]3CN[C@@H](C3)C(=O)N4CCSC4)n(n1)c5ccccc5
#
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
 W94  W94  '[(2S,4S)-4-{4-[1-phenyl-3-(trifluoromethyl)-1H-pyrazol-5-yl]piperidin-1-yl}pyrrolidin-2-yl](1,3-thiazolidin-3-yl)methanone'  ligand  61  33  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_W94
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
 W94  C1    C  CR5   0   0.524   2.9570  -0.2318  -0.1155
 W94  C2    C  CR15  0  -0.568   3.3755  -1.5431  -0.0792
 W94  C3    C  CR5   0  -0.007   4.6864  -1.4783   0.4075
 W94  N4    N  N     0  -0.285   5.0624  -0.2430   0.6562
 W94  N5    N  NR5   0  -0.459   4.0071   0.5019   0.3423
 W94  C6    C  CR6   0   0.306   4.0959   1.9086   0.4983
 W94  C7    C  CR16  0  -0.275   3.1569   2.5839   1.2655
 W94  C8    C  CR16  0  -0.256   3.2553   3.9609   1.4072
 W94  C9    C  CR16  0  -0.245   4.2955   4.6526   0.8021
 W94  C10   C  CR16  0  -0.257   5.2388   3.9651   0.0487
 W94  C11   C  CR16  0  -0.266   5.1403   2.5912  -0.1111
 W94  C12   C  CT    0   1.071   5.6305  -2.6056   0.6141
 W94  F13   F  F     0  -0.317   6.2387  -2.9643  -0.5270
 W94  F14   F  F     0  -0.307   6.5904  -2.3033   1.4895
 W94  F15   F  F     0  -0.311   4.9928  -3.6924   1.0652
 W94  C16   C  CH1   0  -0.400   1.6551   0.3379  -0.5716
 W94  C17   C  CH2   0  -0.410   1.2972  -0.1251  -1.9852
 W94  C18   C  CH2   0  -0.285  -0.0499   0.4444  -2.4039
 W94  N19   N  NT    0  -0.432  -1.0903   0.0605  -1.4675
 W94  C20   C  CH2   0  -0.299  -0.7989   0.5537  -0.1338
 W94  C21   C  CH2   0  -0.412   0.5107  -0.0236   0.3790
 W94  C22   C  CH1   0  -0.076  -2.4235   0.3469  -1.9563
 W94  C23   C  CH2   0  -0.491  -3.5346  -0.4755  -1.2862
 W94  C24   C  CH1   0  -0.258  -4.8062   0.4032  -1.4528
 W94  N25   N  NH1   0  -0.574  -4.3975   1.6549  -2.0842
 W94  C26   C  CH2   0  -0.330  -2.9667   1.7831  -1.8537
 W94  C27   C  C     0   0.572  -5.4348   0.6798  -0.0934
 W94  N28   N  NT    0  -0.471  -6.2150  -0.2943   0.4222
 W94  C29   C  CH2   0  -0.241  -6.8392  -0.1173   1.7289
 W94  C30   C  CH2   0  -0.599  -7.8774  -1.2160   1.8680
 W94  S31   S  S2    0  -0.008  -7.1309  -2.6514   1.0497
 W94  C32   C  CH2   0  -0.406  -6.4972  -1.5559  -0.2448
 W94  O33   O  O     0  -0.489  -5.2214   1.7149   0.5192
 W94  H2    H  HCR5  0   0.283   2.8138  -2.4160  -0.3684
 W94  H7    H  HCR6  0   0.284   2.3621   2.0411   1.7599
 W94  H8    H  HCR6  0   0.269   2.5224   4.4893   2.0019
 W94  H9    H  HCR6  0   0.266   4.3739   5.7252   0.9200
 W94  H10   H  HCR6  0   0.268   6.0514   4.5000  -0.4242
 W94  H11   H  HCR6  0   0.275   5.8671   2.0528  -0.7047
 W94  H16   H  HCH1  0   0.262   1.7379   1.4292  -0.5990
 W94  H17   H  HCH2  0   0.245   2.0649   0.1938  -2.6934
 W94  H17A  H  HCH2  0   0.227   1.2521  -1.2172  -2.0206
 W94  H18   H  HCH2  0   0.195   0.0386   1.5405  -2.5024
 W94  H18A  H  HCH2  0   0.242  -0.3098   0.0622  -3.3935
 W94  H20   H  HCH2  0   0.198  -0.7280   1.6540  -0.1016
 W94  H20A  H  HCH2  0   0.243  -1.6050   0.2754   0.5476
 W94  H21   H  HCH2  0   0.232   0.4281  -1.1112   0.4580
 W94  H21A  H  HCH2  0   0.244   0.7065   0.3579   1.3840
 W94  H22   H  HCH1  0   0.243  -2.4236   0.0855  -3.0199
 W94  H23   H  HCH2  0   0.258  -3.6506  -1.4490  -1.7621
 W94  H23A  H  HCH2  0   0.249  -3.3057  -0.6659  -0.2353
 W94  H24   H  HCH1  0   0.282  -5.5345  -0.0908  -2.0995
 W94  HN25  H  HNH1  0   0.354  -4.5567   1.5677  -3.0797
 W94  H26   H  HCH2  0   0.229  -2.7925   2.1962  -0.8570
 W94  H26A  H  HCH2  0   0.240  -2.5188   2.4667  -2.5758
 W94  H29   H  HCH2  0   0.251  -6.0912  -0.1937   2.5211
 W94  H29A  H  HCH2  0   0.262  -7.3085   0.8642   1.7995
 W94  H30   H  HCH2  0   0.300  -8.0832  -1.4534   2.9096
 W94  H30A  H  HCH2  0   0.282  -8.8132  -0.9494   1.3762
 W94  H32   H  HCH2  0   0.286  -7.2403  -1.4337  -1.0361
 W94  H32A  H  HCH2  0   0.295  -5.6039  -2.0122  -0.6684

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
 W94  C1   C2    aromatic  1.377  0.020  1.377
 W94  C1   N5    aromatic  1.360  0.020  1.360
 W94  C1   C16   single    1.492  0.020  1.492
 W94  C2   C3    aromatic  1.400  0.020  1.400
 W94  C3   N4    aromatic  1.315  0.020  1.315
 W94  C3   C12   single    1.485  0.020  1.485
 W94  N4   N5    aromatic  1.329  0.020  1.329
 W94  N5   C6    single    1.418  0.020  1.418
 W94  C6   C7    aromatic  1.388  0.020  1.388
 W94  C6   C11   aromatic  1.388  0.020  1.388
 W94  C7   C8    aromatic  1.388  0.020  1.388
 W94  C8   C9    aromatic  1.388  0.020  1.388
 W94  C9   C10   aromatic  1.389  0.020  1.389
 W94  C10  C11   aromatic  1.387  0.020  1.387
 W94  C12  F13   single    1.342  0.020  1.342
 W94  C12  F14   single    1.334  0.020  1.334
 W94  C12  F15   single    1.338  0.020  1.338
 W94  C16  C17   single    1.530  0.020  1.530
 W94  C16  C21   single    1.531  0.020  1.531
 W94  C17  C18   single    1.521  0.020  1.521
 W94  C18  N19   single    1.452  0.020  1.452
 W94  N19  C20   single    1.451  0.020  1.451
 W94  N19  C22   single    1.449  0.020  1.449
 W94  C20  C21   single    1.520  0.020  1.520
 W94  C22  C23   single    1.536  0.020  1.536
 W94  C22  C26   single    1.539  0.020  1.539
 W94  C23  C24   single    1.555  0.020  1.555
 W94  C24  N25   single    1.460  0.020  1.460
 W94  C24  C27   single    1.523  0.020  1.523
 W94  N25  C26   single    1.455  0.020  1.455
 W94  C27  N28   single    1.350  0.020  1.350
 W94  C27  O33   double    1.222  0.020  1.222
 W94  N28  C29   single    1.459  0.020  1.459
 W94  N28  C32   single    1.455  0.020  1.455
 W94  C29  C30   single    1.518  0.020  1.518
 W94  C30  S31   single    1.813  0.020  1.813
 W94  S31  C32   single    1.810  0.020  1.810
 W94  C2   H2    single    0.930  0.020  1.080
 W94  C7   H7    single    0.930  0.020  1.080
 W94  C8   H8    single    0.930  0.020  1.080
 W94  C9   H9    single    0.930  0.020  1.080
 W94  C10  H10   single    0.930  0.020  1.080
 W94  C11  H11   single    0.930  0.020  1.080
 W94  C16  H16   single    0.970  0.020  1.090
 W94  C17  H17   single    0.970  0.020  1.090
 W94  C17  H17A  single    0.970  0.020  1.090
 W94  C18  H18   single    0.970  0.020  1.090
 W94  C18  H18A  single    0.970  0.020  1.090
 W94  C20  H20   single    0.970  0.020  1.090
 W94  C20  H20A  single    0.970  0.020  1.090
 W94  C21  H21   single    0.970  0.020  1.090
 W94  C21  H21A  single    0.970  0.020  1.090
 W94  C22  H22   single    0.970  0.020  1.090
 W94  C23  H23   single    0.970  0.020  1.090
 W94  C23  H23A  single    0.970  0.020  1.090
 W94  C24  H24   single    0.970  0.020  1.090
 W94  N25  HN25  single    0.890  0.020  1.040
 W94  C26  H26   single    0.970  0.020  1.090
 W94  C26  H26A  single    0.970  0.020  1.090
 W94  C29  H29   single    0.970  0.020  1.090
 W94  C29  H29A  single    0.970  0.020  1.090
 W94  C30  H30   single    0.970  0.020  1.090
 W94  C30  H30A  single    0.970  0.020  1.090
 W94  C32  H32   single    0.970  0.020  1.090
 W94  C32  H32A  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
 W94  C16   C1   N5   124.77  3.000
 W94  C16   C1   C2   129.54  3.000
 W94  N5    C1   C2   105.67  3.000
 W94  H2    C2   C3   128.24  3.000
 W94  H2    C2   C1   127.30  3.000
 W94  C3    C2   C1   104.46  3.000
 W94  C12   C3   N4   120.34  3.000
 W94  C12   C3   C2   127.49  3.000
 W94  N4    C3   C2   112.15  3.000
 W94  N5    N4   C3   104.76  3.000
 W94  C6    N5   N4   118.70  3.000
 W94  C6    N5   C1   128.34  3.000
 W94  N4    N5   C1   112.96  3.000
 W94  C11   C6   C7   120.82  3.000
 W94  C11   C6   N5   119.11  3.000
 W94  C7    C6   N5   120.07  3.000
 W94  H7    C7   C8   120.21  3.000
 W94  H7    C7   C6   120.36  3.000
 W94  C8    C7   C6   119.42  3.000
 W94  H8    C8   C9   120.26  3.000
 W94  H8    C8   C7   119.53  3.000
 W94  C9    C8   C7   120.21  3.000
 W94  H9    C9   C10  120.04  3.000
 W94  H9    C9   C8   120.05  3.000
 W94  C10   C9   C8   119.91  3.000
 W94  H10   C10  C11  119.53  3.000
 W94  H10   C10  C9   120.16  3.000
 W94  C11   C10  C9   120.30  3.000
 W94  H11   C11  C10  120.57  3.000
 W94  H11   C11  C6   120.10  3.000
 W94  C10   C11  C6   119.33  3.000
 W94  F15   C12  F14  107.80  3.000
 W94  F15   C12  F13  106.59  3.000
 W94  F14   C12  F13  107.01  3.000
 W94  F15   C12  C3   111.13  3.000
 W94  F14   C12  C3   112.13  3.000
 W94  F13   C12  C3   111.89  3.000
 W94  H16   C16  C21  107.91  3.000
 W94  H16   C16  C17  107.23  3.000
 W94  C21   C16  C17  109.11  3.000
 W94  H16   C16  C1   108.79  3.000
 W94  C21   C16  C1   111.85  3.000
 W94  C17   C16  C1   111.77  3.000
 W94  H17A  C17  H17  107.43  3.000
 W94  H17A  C17  C18  109.17  3.000
 W94  H17   C17  C18  109.55  3.000
 W94  H17A  C17  C16  109.98  3.000
 W94  H17   C17  C16  110.27  3.000
 W94  C18   C17  C16  110.38  3.000
 W94  H18A  C18  H18  106.60  3.000
 W94  H18A  C18  N19  108.75  3.000
 W94  H18   C18  N19  112.18  3.000
 W94  H18A  C18  C17  109.22  3.000
 W94  H18   C18  C17  108.98  3.000
 W94  N19   C18  C17  110.99  3.000
 W94  C22   N19  C20  115.32  3.000
 W94  C22   N19  C18  112.94  3.000
 W94  C20   N19  C18  111.04  3.000
 W94  H20A  C20  H20  106.47  3.000
 W94  H20A  C20  C21  109.19  3.000
 W94  H20   C20  C21  108.28  3.000
 W94  H20A  C20  N19  109.79  3.000
 W94  H20   C20  N19  112.25  3.000
 W94  C21   C20  N19  110.72  3.000
 W94  H21A  C21  H21  107.12  3.000
 W94  H21A  C21  C20  109.39  3.000
 W94  H21   C21  C20  109.69  3.000
 W94  H21A  C21  C16  110.77  3.000
 W94  H21   C21  C16  109.65  3.000
 W94  C20   C21  C16  110.17  3.000
 W94  H22   C22  C26  106.70  3.000
 W94  H22   C22  C23  107.20  3.000
 W94  C26   C22  C23  102.43  3.000
 W94  H22   C22  N19  106.30  3.000
 W94  C26   C22  N19  119.14  3.000
 W94  C23   C22  N19  114.37  3.000
 W94  H23A  C23  H23  106.66  3.000
 W94  H23A  C23  C24  111.90  3.000
 W94  H23   C23  C24  111.78  3.000
 W94  H23A  C23  C22  111.19  3.000
 W94  H23   C23  C22  111.39  3.000
 W94  C24   C23  C22  104.02  3.000
 W94  H24   C24  C27  109.60  3.000
 W94  H24   C24  N25  108.56  3.000
 W94  C27   C24  N25  110.23  3.000
 W94  H24   C24  C23  110.69  3.000
 W94  C27   C24  C23  110.16  3.000
 W94  N25   C24  C23  107.57  3.000
 W94  HN25  N25  C26  108.56  3.000
 W94  HN25  N25  C24  107.91  3.000
 W94  C26   N25  C24  106.40  3.000
 W94  H26A  C26  H26  107.54  3.000
 W94  H26A  C26  N25  110.75  3.000
 W94  H26   C26  N25  109.55  3.000
 W94  H26A  C26  C22  113.32  3.000
 W94  H26   C26  C22  110.93  3.000
 W94  N25   C26  C22  104.74  3.000
 W94  O33   C27  N28  121.38  3.000
 W94  O33   C27  C24  121.97  3.000
 W94  N28   C27  C24  116.63  3.000
 W94  C32   N28  C29  115.65  3.000
 W94  C32   N28  C27  124.24  3.000
 W94  C29   N28  C27  120.11  3.000
 W94  H29A  C29  H29  108.11  3.000
 W94  H29A  C29  C30  110.57  3.000
 W94  H29   C29  C30  110.56  3.000
 W94  H29A  C29  N28  110.57  3.000
 W94  H29   C29  N28  110.37  3.000
 W94  C30   C29  N28  106.67  3.000
 W94  H30A  C30  H30  108.83  3.000
 W94  H30A  C30  S31  110.09  3.000
 W94  H30   C30  S31  109.71  3.000
 W94  H30A  C30  C29  111.63  3.000
 W94  H30   C30  C29  112.02  3.000
 W94  S31   C30  C29  104.48  3.000
 W94  C32   S31  C30   89.30  3.000
 W94  H32A  C32  H32  108.86  3.000
 W94  H32A  C32  S31  108.16  3.000
 W94  H32   C32  S31  110.34  3.000
 W94  H32A  C32  N28  112.50  3.000
 W94  H32   C32  N28  111.53  3.000
 W94  S31   C32  N28  105.36  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
 W94  CONST_01  N4   C3   C2   C1     0.00   0.0  0
 W94  CONST_02  C3   N4   N5   C1     0.00   0.0  0
 W94  CONST_05  N4   N5   C1   C2     0.00   0.0  0
 W94  CONST_06  C6   N5   C1   C2   180.00   0.0  0
 W94  CONST_07  N5   N4   C3   C2     0.00   0.0  0
 W94  CONST_08  N5   C1   C2   C3     0.00   0.0  0
 W94  CONST_09  C6   N5   N4   C3   180.00   0.0  0
 W94  CONST_12  C8   C7   C6   N5   180.00   0.0  0
 W94  CONST_13  C10  C11  C6   N5   180.00   0.0  0
 W94  CONST_14  C9   C8   C7   C6     0.00   0.0  0
 W94  CONST_15  C9   C10  C11  C6     0.00   0.0  0
 W94  CONST_16  C10  C11  C6   C7     0.00   0.0  0
 W94  CONST_17  C10  C9   C8   C7     0.00   0.0  0
 W94  CONST_18  C11  C6   C7   C8     0.00   0.0  0
 W94  CONST_19  C11  C10  C9   C8     0.00   0.0  0
 W94  CONST_20  C16  C1   C2   C3   180.00   0.0  0
 W94  CONST_21  C16  C1   N5   N4   180.00   0.0  0
 W94  CONST_22  C16  C1   N5   C6     0.00   0.0  0
 W94  CONST_23  C12  C3   C2   C1   180.00   0.0  0
 W94  CONST_24  C12  C3   N4   N5   180.00   0.0  0
 W94  CONST_25  C29  N28  C27  C24  180.00   0.0  0
 W94  CONST_26  C32  N28  C27  C24    0.00   0.0  0
 W94  CONST_27  H2   C2   C3   N4   180.00   0.0  0
 W94  CONST_28  H7   C7   C6   N5     0.00   0.0  0
 W94  CONST_29  H11  C11  C6   N5     0.00   0.0  0
 W94  CONST_30  H8   C8   C7   C6   180.00   0.0  0
 W94  CONST_31  H10  C10  C11  C6   180.00   0.0  0
 W94  CONST_32  H9   C9   C8   C7   180.00   0.0  0
 W94  CONST_33  O33  C27  N28  C29    0.00   0.0  0
 W94  CONST_34  O33  C27  N28  C32  180.00   0.0  0
 W94  Var_01    N19  C18  C17  C16  -57.28  30.0  1
 W94  Var_02    N19  C20  C21  C16   58.24  30.0  1
 W94  Var_03    C20  N19  C18  C17   60.27  30.0  1
 W94  Var_04    C21  C20  N19  C18  -60.76  30.0  1
 W94  Var_05    C24  N25  C26  C22   36.68  30.0  1
 W94  Var_06    S31  C30  C29  N28   36.23  30.0  1
 W94  Var_07    S31  C32  N28  C29  -16.96  30.0  1
 W94  Var_08    C32  N28  C29  C30  -12.66  30.0  1
 W94  Var_09    F13  C12  C3   C2    81.37  30.0  2

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
 W94  chir_01  C16  C1   C17  C21  negativ
 W94  chir_02  C22  N19  C23  C26  negativ
 W94  chir_03  C24  N25  C23  C27  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
 W94  plan-1  C1   0.020
 W94  plan-1  C2   0.020
 W94  plan-1  C3   0.020
 W94  plan-1  N4   0.020
 W94  plan-1  N5   0.020
 W94  plan-1  C6   0.020
 W94  plan-1  C12  0.020
 W94  plan-1  C16  0.020
 W94  plan-1  H2   0.020
 W94  plan-2  C24  0.020
 W94  plan-2  C27  0.020
 W94  plan-2  N28  0.020
 W94  plan-2  C29  0.020
 W94  plan-2  C32  0.020
 W94  plan-2  O33  0.020
 W94  plan-3  N5   0.020
 W94  plan-3  C6   0.020
 W94  plan-3  C7   0.020
 W94  plan-3  C8   0.020
 W94  plan-3  C9   0.020
 W94  plan-3  C10  0.020
 W94  plan-3  C11  0.020
 W94  plan-3  H7   0.020
 W94  plan-3  H8   0.020
 W94  plan-3  H9   0.020
 W94  plan-3  H10  0.020
 W94  plan-3  H11  0.020

