# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 22:15:17 2022
#   Inital geometry file: a 149 line input string
#   Ligand name: (4R,5S)-4-fluoro-1-[(4-fluorophenyl)sulfonyl]-5-methyl-N-({5-(trifluoromethyl)-2-[2-(trifluoromethyl)pyrimidin-5-yl]pyridin-4-yl}methyl)-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1[C@H](F)C[C@H](N1[S](=O)(=O)c2ccc(F)cc2)C(=O)NCc3cc(ncc3C(F)(F)F)c4cnc(nc4)C(F)(F)F
#
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
 LXY  LXY  (4R,5S)-4-fluoro-1-[(4-fluorophenyl)sulfonyl]-5-methyl-N-({5-(trifluoromethyl)-2-[2-(trifluoromethyl)pyrimidin-5-yl]pyridin-4-yl}methyl)-L-prolinamide  ligand  60  41  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LXY
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
 LXY  C1    C  CH3   0  -0.666  159.3709  140.7277  181.0921
 LXY  C13   C  CR6   0  -0.208  159.2019  141.8447  185.0622
 LXY  C14   C  CR16  0  -0.215  160.5558  141.6000  184.8598
 LXY  C15   C  CR16  0  -0.401  161.4949  142.3632  185.5324
 LXY  C16   C  CR6   0   0.556  161.0523  143.3480  186.3969
 LXY  C17   C  CR16  0  -0.398  159.7100  143.5989  186.6140
 LXY  C18   C  CR16  0  -0.214  158.7738  142.8367  185.9378
 LXY  C2    C  CH1   0  -0.117  158.8553  141.9679  181.7932
 LXY  C20   C  C     0   0.565  155.3748  142.3882  182.4190
 LXY  C23   C  CH2   0  -0.355  153.9979  140.7027  181.3342
 LXY  C24   C  CR6   0   0.225  153.3280  139.8944  182.4291
 LXY  C25   C  CR16  0  -0.367  154.0942  139.3887  183.4669
 LXY  C26   C  CR6   0   0.268  153.5063  138.6270  184.4686
 LXY  C28   C  CR16  0  -0.075  151.4619  138.8308  183.4969
 LXY  C29   C  CR6   0  -0.357  151.9637  139.5889  182.4442
 LXY  C30   C  CT    0   1.070  151.0286  140.0801  181.3807
 LXY  C34   C  CR6   0  -0.067  154.2982  138.0928  185.5913
 LXY  C35   C  CR16  0  -0.031  155.6744  137.8832  185.5266
 LXY  C37   C  CR6   0   0.138  155.6789  137.1469  187.6487
 LXY  C39   C  CR16  0  -0.004  153.6961  137.7647  186.8021
 LXY  C4    C  CH1   0   0.220  158.1794  142.9535  180.8426
 LXY  C40   C  CT    0   1.042  156.5001  136.6190  188.8055
 LXY  C6    C  CH2   0  -0.545  157.3469  143.8314  181.7470
 LXY  C7    C  CH1   0  -0.206  156.7881  142.8376  182.7713
 LXY  F19   F  F     0  -0.298  161.9527  144.0824  187.0521
 LXY  F31   F  F     0  -0.296  149.8145  139.5376  181.4832
 LXY  F32   F  F     0  -0.310  150.8657  141.4093  181.4384
 LXY  F33   F  F     0  -0.311  151.4777  139.7970  180.1507
 LXY  F41   F  F     0  -0.307  157.1893  135.5340  188.4438
 LXY  F42   F  F     0  -0.309  157.3872  137.5319  189.2133
 LXY  F43   F  F     0  -0.293  155.7432  136.2940  189.8465
 LXY  F44   F  F     0  -0.358  159.1198  143.6748  180.1321
 LXY  N22   N  NH1   0  -0.639  155.2701  141.2426  181.7248
 LXY  N27   N  N     0  -0.431  152.2046  138.3613  184.4830
 LXY  N36   N  N     0  -0.396  156.3639  137.4126  186.5533
 LXY  N38   N  N     0  -0.392  154.3842  137.2933  187.8329
 LXY  N9    N  N     0  -0.640  157.7554  141.7291  182.7474
 LXY  O11   O  OS    0  -0.635  156.7384  140.9790  184.8824
 LXY  O12   O  OS    0  -0.626  158.5758  139.6158  183.8460
 LXY  O21   O  O     0  -0.467  154.4212  143.0840  182.7207
 LXY  S10   S  S     0   1.404  158.0026  140.9097  184.1644
 LXY  H11   H  HCH3  0   0.255  159.9464  140.0847  181.7523
 LXY  H12   H  HCH3  0   0.238  158.5475  140.1502  180.6708
 LXY  H13   H  HCH3  0   0.244  160.0286  141.0311  180.2773
 LXY  H141  H  HCR6  0   0.303  160.8900  140.8187  184.1903
 LXY  H151  H  HCR6  0   0.298  162.5530  142.1887  185.3906
 LXY  H171  H  HCR6  0   0.298  159.3997  144.3713  187.3046
 LXY  H181  H  HCR6  0   0.298  157.7217  143.0163  186.1099
 LXY  H3    H  HCH1  0   0.271  159.6832  142.4938  182.2877
 LXY  H232  H  HCH2  0   0.274  153.3605  141.5193  181.0006
 LXY  H231  H  HCH2  0   0.305  154.1608  140.0534  180.4729
 LXY  H251  H  HCR6  0   0.273  155.1476  139.6149  183.5081
 LXY  H281  H  HCR6  0   0.287  150.4079  138.5890  183.5505
 LXY  H351  H  HCR6  0   0.283  156.2381  138.0781  184.6228
 LXY  H391  H  HCR6  0   0.289  152.6300  137.8946  186.9411
 LXY  H5    H  HCH1  0   0.227  157.5593  142.4161  180.1185
 LXY  H62   H  HCH2  0   0.281  157.9983  144.5443  182.2560
 LXY  H61   H  HCH2  0   0.292  156.5690  144.3890  181.2276
 LXY  H8    H  HCH1  0   0.311  156.7257  143.3213  183.7475
 LXY  H221  H  HNH1  0   0.419  156.0997  140.6921  181.5677

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
 LXY  F33  C30   single    1.340  0.020  1.340
 LXY  C1   C2    single    1.515  0.020  1.515
 LXY  F32  C30   single    1.340  0.020  1.340
 LXY  F31  C30   single    1.334  0.020  1.334
 LXY  C30  C29   single    1.499  0.020  1.499
 LXY  F44  C4    single    1.382  0.020  1.382
 LXY  C4   C2    single    1.527  0.020  1.527
 LXY  C4   C6    single    1.511  0.020  1.511
 LXY  C2   N9    single    1.476  0.020  1.476
 LXY  C23  N22   single    1.436  0.020  1.436
 LXY  C23  C24   single    1.517  0.020  1.517
 LXY  C29  C24   aromatic  1.398  0.020  1.398
 LXY  C29  C28   aromatic  1.391  0.020  1.391
 LXY  N22  C20   single    1.344  0.020  1.344
 LXY  O21  C20   double    1.218  0.020  1.218
 LXY  C6   C7    single    1.533  0.020  1.533
 LXY  C20  C7    single    1.524  0.020  1.524
 LXY  C24  C25   aromatic  1.386  0.020  1.386
 LXY  N9   C7    single    1.471  0.020  1.471
 LXY  N9   S10   single    1.655  0.020  1.655
 LXY  C28  N27   aromatic  1.321  0.020  1.321
 LXY  O12  S10   double    1.451  0.020  1.451
 LXY  C25  C26   aromatic  1.389  0.020  1.389
 LXY  S10  C13   single    1.766  0.020  1.766
 LXY  S10  O11   double    1.456  0.020  1.456
 LXY  N27  C26   aromatic  1.329  0.020  1.329
 LXY  C14  C13   aromatic  1.391  0.020  1.391
 LXY  C14  C15   aromatic  1.385  0.020  1.385
 LXY  C26  C34   single    1.474  0.020  1.474
 LXY  C13  C18   aromatic  1.391  0.020  1.391
 LXY  C15  C16   aromatic  1.383  0.020  1.383
 LXY  C34  C35   aromatic  1.394  0.020  1.394
 LXY  C34  C39   aromatic  1.391  0.020  1.391
 LXY  C18  C17   aromatic  1.384  0.020  1.384
 LXY  C16  C17   aromatic  1.383  0.020  1.383
 LXY  C16  F19   single    1.334  0.020  1.334
 LXY  C35  N36   aromatic  1.323  0.020  1.323
 LXY  C39  N38   aromatic  1.326  0.020  1.326
 LXY  N36  C37   aromatic  1.319  0.020  1.319
 LXY  N38  C37   aromatic  1.316  0.020  1.316
 LXY  C37  C40   single    1.514  0.020  1.514
 LXY  C40  F41   single    1.335  0.020  1.335
 LXY  C40  F42   single    1.337  0.020  1.337
 LXY  C40  F43   single    1.328  0.020  1.328
 LXY  C1   H11   single    0.970  0.020  1.090
 LXY  C1   H12   single    0.970  0.020  1.090
 LXY  C1   H13   single    0.970  0.020  1.090
 LXY  C14  H141  single    0.930  0.020  1.080
 LXY  C15  H151  single    0.930  0.020  1.080
 LXY  C17  H171  single    0.930  0.020  1.080
 LXY  C18  H181  single    0.930  0.020  1.080
 LXY  C2   H3    single    0.970  0.020  1.090
 LXY  C23  H232  single    0.970  0.020  1.090
 LXY  C23  H231  single    0.970  0.020  1.090
 LXY  C25  H251  single    0.930  0.020  1.080
 LXY  C28  H281  single    0.930  0.020  1.080
 LXY  C35  H351  single    0.930  0.020  1.080
 LXY  C39  H391  single    0.930  0.020  1.080
 LXY  C4   H5    single    0.970  0.020  1.090
 LXY  C6   H62   single    0.970  0.020  1.090
 LXY  C6   H61   single    0.970  0.020  1.090
 LXY  C7   H8    single    0.970  0.020  1.090
 LXY  N22  H221  single    0.860  0.020  1.020

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
 LXY  H13   C1   H12   108.31  3.000
 LXY  H13   C1   H11   107.41  3.000
 LXY  H12   C1   H11   108.74  3.000
 LXY  H13   C1   C2    108.86  3.000
 LXY  H12   C1   C2    110.82  3.000
 LXY  H11   C1   C2    112.55  3.000
 LXY  S10   C13  C18   119.26  3.000
 LXY  C18   C13  C14   121.12  3.000
 LXY  S10   C13  C14   119.60  3.000
 LXY  H141  C14  C15   119.29  3.000
 LXY  H141  C14  C13   121.19  3.000
 LXY  C15   C14  C13   119.52  3.000
 LXY  H151  C15  C16   120.65  3.000
 LXY  H151  C15  C14   120.72  3.000
 LXY  C16   C15  C14   118.63  3.000
 LXY  F19   C16  C17   118.57  3.000
 LXY  F19   C16  C15   118.88  3.000
 LXY  C17   C16  C15   122.55  3.000
 LXY  H171  C17  C18   120.75  3.000
 LXY  H171  C17  C16   120.55  3.000
 LXY  C18   C17  C16   118.69  3.000
 LXY  H181  C18  C17   119.28  3.000
 LXY  H181  C18  C13   121.22  3.000
 LXY  C17   C18  C13   119.50  3.000
 LXY  H3    C2   N9    110.38  3.000
 LXY  H3    C2   C4    107.75  3.000
 LXY  N9    C2   C4    100.20  3.000
 LXY  H3    C2   C1    110.11  3.000
 LXY  N9    C2   C1    114.86  3.000
 LXY  C4    C2   C1    113.01  3.000
 LXY  O21   C20  N22   123.63  3.000
 LXY  O21   C20  C7    120.00  3.000
 LXY  N22   C20  C7    116.30  3.000
 LXY  H231  C23  H232  106.98  3.000
 LXY  H231  C23  N22   107.83  3.000
 LXY  H232  C23  N22   108.67  3.000
 LXY  H231  C23  C24   108.58  3.000
 LXY  H232  C23  C24   111.25  3.000
 LXY  N22   C23  C24   113.28  3.000
 LXY  C29   C24  C25   116.86  3.000
 LXY  C25   C24  C23   119.40  3.000
 LXY  C29   C24  C23   123.72  3.000
 LXY  H251  C25  C26   120.06  3.000
 LXY  H251  C25  C24   119.50  3.000
 LXY  C26   C25  C24   120.41  3.000
 LXY  N27   C26  C34   116.46  3.000
 LXY  C34   C26  C25   121.38  3.000
 LXY  N27   C26  C25   122.15  3.000
 LXY  H281  C28  N27   115.53  3.000
 LXY  H281  C28  C29   120.69  3.000
 LXY  N27   C28  C29   123.77  3.000
 LXY  C30   C29  C28   119.37  3.000
 LXY  C28   C29  C24   118.64  3.000
 LXY  C30   C29  C24   121.97  3.000
 LXY  F33   C30  F32   106.85  3.000
 LXY  F32   C30  F31   106.82  3.000
 LXY  F33   C30  F31   106.84  3.000
 LXY  F31   C30  C29   112.34  3.000
 LXY  F32   C30  C29   111.73  3.000
 LXY  F33   C30  C29   111.91  3.000
 LXY  C39   C34  C35   115.61  3.000
 LXY  C39   C34  C26   121.04  3.000
 LXY  C35   C34  C26   123.35  3.000
 LXY  H351  C35  N36   116.12  3.000
 LXY  H351  C35  C34   121.72  3.000
 LXY  N36   C35  C34   122.15  3.000
 LXY  N38   C37  N36   127.22  3.000
 LXY  N38   C37  C40   117.75  3.000
 LXY  N36   C37  C40   115.04  3.000
 LXY  H391  C39  N38   116.98  3.000
 LXY  H391  C39  C34   120.63  3.000
 LXY  N38   C39  C34   122.39  3.000
 LXY  H5    C4   F44   107.56  3.000
 LXY  H5    C4   C6    111.67  3.000
 LXY  F44   C4   C6    112.31  3.000
 LXY  H5    C4   C2    110.23  3.000
 LXY  C6    C4   C2    104.26  3.000
 LXY  F44   C4   C2    110.84  3.000
 LXY  F43   C40  F42   107.85  3.000
 LXY  F43   C40  F41   107.92  3.000
 LXY  F42   C40  F41   107.17  3.000
 LXY  F43   C40  C37   112.04  3.000
 LXY  F42   C40  C37   110.79  3.000
 LXY  F41   C40  C37   110.87  3.000
 LXY  H61   C6   H62   108.31  3.000
 LXY  H61   C6   C7    112.98  3.000
 LXY  H62   C6   C7    109.23  3.000
 LXY  H61   C6   C4    113.94  3.000
 LXY  H62   C6   C4    109.26  3.000
 LXY  C7    C6   C4    102.96  3.000
 LXY  H8    C7   N9    112.71  3.000
 LXY  H8    C7   C6    109.35  3.000
 LXY  N9    C7   C6    103.77  3.000
 LXY  H8    C7   C20   106.52  3.000
 LXY  N9    C7   C20   112.56  3.000
 LXY  C6    C7   C20   112.00  3.000
 LXY  H221  N22  C23   118.77  3.000
 LXY  H221  N22  C20   118.82  3.000
 LXY  C23   N22  C20   122.02  3.000
 LXY  C28   N27  C26   118.15  3.000
 LXY  C37   N36  C35   116.45  3.000
 LXY  C39   N38  C37   116.19  3.000
 LXY  S10   N9   C7    117.20  3.000
 LXY  S10   N9   C2    121.49  3.000
 LXY  C7    N9   C2    112.25  3.000
 LXY  O12   S10  O11   119.60  3.000
 LXY  O11   S10  N9    105.60  3.000
 LXY  O12   S10  N9    108.22  3.000
 LXY  O11   S10  C13   108.29  3.000
 LXY  O12   S10  C13   108.39  3.000
 LXY  N9    S10  C13   105.93  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
 LXY  CONST_01  C16   C15  C14  C13    0.00   0.0  0
 LXY  CONST_02  C16   C17  C18  C13    0.00   0.0  0
 LXY  CONST_03  C17   C18  C13  C14    0.00   0.0  0
 LXY  CONST_04  C17   C16  C15  C14    0.00   0.0  0
 LXY  CONST_05  C18   C13  C14  C15    0.00   0.0  0
 LXY  CONST_06  C18   C17  C16  C15    0.00   0.0  0
 LXY  CONST_07  N27   C28  C29  C24    0.00   0.0  0
 LXY  CONST_08  N27   C26  C25  C24    0.00   0.0  0
 LXY  CONST_09  C34   C26  C25  C24  180.00   0.0  0
 LXY  CONST_10  C28   C29  C24  C25    0.00   0.0  0
 LXY  CONST_11  C28   N27  C26  C25    0.00   0.0  0
 LXY  CONST_14  C29   C24  C25  C26    0.00   0.0  0
 LXY  CONST_15  C29   C28  N27  C26    0.00   0.0  0
 LXY  CONST_16  N36   C35  C34  C26  180.00   0.0  0
 LXY  CONST_17  N38   C39  C34  C26  180.00   0.0  0
 LXY  CONST_18  C34   C26  N27  C28  180.00   0.0  0
 LXY  CONST_19  C37   N36  C35  C34    0.00   0.0  0
 LXY  CONST_20  C37   N38  C39  C34    0.00   0.0  0
 LXY  CONST_22  N38   C39  C34  C35    0.00   0.0  0
 LXY  CONST_23  N38   C37  N36  C35    0.00   0.0  0
 LXY  CONST_25  N36   C35  C34  C39    0.00   0.0  0
 LXY  CONST_26  N36   C37  N38  C39    0.00   0.0  0
 LXY  CONST_27  F19   C16  C15  C14  180.00   0.0  0
 LXY  CONST_28  S10   C13  C14  C15  180.00   0.0  0
 LXY  CONST_29  S10   C13  C18  C17  180.00   0.0  0
 LXY  CONST_30  F19   C16  C17  C18  180.00   0.0  0
 LXY  CONST_31  C28   C29  C24  C23  180.00   0.0  0
 LXY  CONST_32  C26   C25  C24  C23  180.00   0.0  0
 LXY  CONST_33  C30   C29  C24  C25  180.00   0.0  0
 LXY  CONST_34  N27   C28  C29  C30  180.00   0.0  0
 LXY  CONST_35  C40   C37  N36  C35  180.00   0.0  0
 LXY  CONST_36  C40   C37  N38  C39  180.00   0.0  0
 LXY  CONST_37  H151  C15  C14  C13  180.00   0.0  0
 LXY  CONST_38  H171  C17  C18  C13  180.00   0.0  0
 LXY  CONST_39  H181  C18  C13  C14  180.00   0.0  0
 LXY  CONST_40  H141  C14  C15  C16  180.00   0.0  0
 LXY  CONST_41  H281  C28  C29  C24  180.00   0.0  0
 LXY  CONST_42  H351  C35  C34  C26    0.00   0.0  0
 LXY  CONST_43  H391  C39  C34  C26    0.00   0.0  0
 LXY  CONST_44  H251  C25  C24  C29  180.00   0.0  0
 LXY  CONST_45  C7    C20  N22  C23  180.00   0.0  0
 LXY  CONST_46  H221  N22  C20  C7     0.00   0.0  0
 LXY  CONST_47  O21   C20  N22  C23    0.00   0.0  0
 LXY  Var_01    C2    N9   S10  C13   60.28  30.0  1
 LXY  Var_02    N9    S10  C13  C14  -88.10  30.0  2
 LXY  Var_03    F33   C30  C29  C24   51.65  30.0  3
 LXY  Var_04    N22   C23  C24  C25  -20.34  30.0  2
 LXY  Var_05    N36   C37  C40  F41  -55.45  30.0  3
 LXY  Var_06    C24   C23  N22  C20  -83.09  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
 LXY  chir_01  C2  C1   C4   N9  negativ
 LXY  chir_02  C4  F44  C2   C6  negativ
 LXY  chir_03  C7  N9   C20  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
 LXY  plan-1  C13   0.020
 LXY  plan-1  C14   0.020
 LXY  plan-1  C15   0.020
 LXY  plan-1  C16   0.020
 LXY  plan-1  C17   0.020
 LXY  plan-1  C18   0.020
 LXY  plan-1  F19   0.020
 LXY  plan-1  S10   0.020
 LXY  plan-1  H141  0.020
 LXY  plan-1  H151  0.020
 LXY  plan-1  H171  0.020
 LXY  plan-1  H181  0.020
 LXY  plan-2  C23   0.020
 LXY  plan-2  C24   0.020
 LXY  plan-2  C25   0.020
 LXY  plan-2  C26   0.020
 LXY  plan-2  C28   0.020
 LXY  plan-2  C29   0.020
 LXY  plan-2  C30   0.020
 LXY  plan-2  C34   0.020
 LXY  plan-2  N27   0.020
 LXY  plan-2  H251  0.020
 LXY  plan-2  H281  0.020
 LXY  plan-3  C26   0.020
 LXY  plan-3  C34   0.020
 LXY  plan-3  C35   0.020
 LXY  plan-3  C37   0.020
 LXY  plan-3  C39   0.020
 LXY  plan-3  C40   0.020
 LXY  plan-3  N36   0.020
 LXY  plan-3  N38   0.020
 LXY  plan-3  H351  0.020
 LXY  plan-3  H391  0.020
 LXY  plan-4  C20   0.020
 LXY  plan-4  C23   0.020
 LXY  plan-4  C7    0.020
 LXY  plan-4  N22   0.020
 LXY  plan-4  O21   0.020
 LXY  plan-4  H221  0.020

