# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 22:03:27 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (3R,4S)-1-{6-[3-(methylsulfonyl)phenyl]pyrimidin-4-yl}-4-(2,4,5-trifluorophenyl)pyrrolidin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)c1cccc(c1)c2cc(ncn2)N3C[C@H](N)[C@H](C3)c4cc(F)c(F)cc4F
#
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
 DLI  DLI  (3R,4S)-1-{6-[3-(methylsulfonyl)phenyl]pyrimidin-4-yl}-4-(2,4,5-trifluorophenyl)pyrrolidin-3-amine  ligand  50  31  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DLI
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
 DLI  C4    C  CR6   0   0.512   2.5950  -0.0747   2.8232
 DLI  C5    C  CR16  0  -0.554   3.8413  -0.0500   3.4243
 DLI  C6    C  CR6   0   0.403   4.6554  -1.1505   3.2804
 DLI  C7    C  CH1   0  -0.415   0.7636  -1.1559   1.4610
 DLI  C8    C  CH2   0  -0.241   0.7427  -1.4489  -0.0370
 DLI  C10   C  CH3   0  -0.790   3.6782   0.2746  -6.2586
 DLI  C17   C  CR16  0   0.055  -2.9704  -2.6395  -2.7090
 DLI  C20   C  CR16  0  -0.446  -0.4602  -1.8008  -2.6497
 DLI  C21   C  CR6   0   0.081  -0.5018  -1.6749  -5.1423
 DLI  C24   C  CR16  0  -0.227  -0.7278  -1.0872  -7.4789
 DLI  C26   C  CR6   0  -0.184   1.4377  -1.3756  -6.5254
 DLI  C1    C  CR6   0   0.413   4.2249  -2.2474   2.5528
 DLI  C2    C  CR16  0  -0.461   2.9811  -2.2475   1.9640
 DLI  C3    C  CR6   0  -0.007   2.1287  -1.1487   2.0810
 DLI  C9    C  CH1   0  -0.103  -0.1848  -2.2299   2.0322
 DLI  F10   F  F     0  -0.303   1.8181   1.0076   2.9746
 DLI  N11   N  NT    0  -0.512  -0.6048  -1.9492  -0.2522
 DLI  C12   C  CH2   0  -0.254  -1.2930  -2.2766   0.9841
 DLI  F13   F  F     0  -0.299   5.8663  -1.1675   3.8384
 DLI  C14   C  CR6   0   0.579  -1.1615  -2.0917  -1.4600
 DLI  F15   F  F     0  -0.305   5.0322  -3.3055   2.4299
 DLI  N16   N  N     0  -0.470  -2.4308  -2.5190  -1.5110
 DLI  N18   N  N     0  -0.465  -2.4091  -2.3907  -3.8766
 DLI  C19   C  CR6   0   0.279  -1.1352  -1.9704  -3.8379
 DLI  N22   N  NH2   0  -0.787  -0.7051  -2.0228   3.3588
 DLI  C23   C  CR16  0  -0.264  -1.2975  -1.3890  -6.2522
 DLI  C25   C  CR16  0  -0.239   0.6505  -1.0768  -7.6283
 DLI  C27   C  CR16  0  -0.305   0.8822  -1.6766  -5.2919
 DLI  S1    S  S     0   1.217   3.2066  -1.3829  -6.6950
 DLI  O2    O  OS    0  -0.666   3.7566  -2.2988  -5.6977
 DLI  O1    O  OS    0  -0.666   3.5292  -1.6010  -8.1031
 DLI  H5    H  HCR6  0   0.315   4.1694   0.8112   3.9918
 DLI  H7    H  HCH1  0   0.283   0.2882  -0.1847   1.6192
 DLI  H81   H  HCH2  0   0.268   0.9412  -0.5497  -0.6230
 DLI  H82   H  HCH2  0   0.251   1.4879  -2.2004  -0.3173
 DLI  H101  H  HCH3  0   0.297   3.3851   0.4733  -5.2305
 DLI  H102  H  HCH3  0   0.313   4.7611   0.3416  -6.3598
 DLI  H103  H  HCH3  0   0.297   3.1960   0.9773  -6.9342
 DLI  H17   H  HCR6  0   0.253  -3.9994  -2.9852  -2.7340
 DLI  H20   H  HCR6  0   0.282   0.5572  -1.4398  -2.6253
 DLI  H24   H  HCR6  0   0.277  -1.3607  -0.8609  -8.3260
 DLI  H2    H  HCR6  0   0.297   2.6763  -3.1233   1.4033
 DLI  H9    H  HCH1  0   0.255   0.3386  -3.1917   2.0248
 DLI  H121  H  HCH2  0   0.258  -1.7686  -3.2557   0.9334
 DLI  H122  H  HCH2  0   0.238  -2.0720  -1.5392   1.2083
 DLI  H221  H  HNH2  0   0.345  -1.0868  -1.0880   3.4447
 DLI  H222  H  HNH2  0   0.355   0.0356  -2.0970   4.0442
 DLI  H23   H  HCR6  0   0.271  -2.3734  -1.3976  -6.1469
 DLI  H25   H  HCR6  0   0.289   1.0936  -0.8446  -8.5871
 DLI  H27   H  HCR6  0   0.283   1.5236  -1.9313  -4.4585

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
 DLI  C4   F10   single    1.341  0.020  1.341
 DLI  C4   C5    aromatic  1.384  0.020  1.384
 DLI  C4   C3    aromatic  1.386  0.020  1.386
 DLI  C5   C6    aromatic  1.376  0.020  1.376
 DLI  C5   H5    single    0.930  0.020  1.080
 DLI  C6   F13   single    1.333  0.020  1.333
 DLI  C6   C1    aromatic  1.385  0.020  1.385
 DLI  C7   C8    single    1.527  0.020  1.527
 DLI  C7   C3    single    1.499  0.020  1.499
 DLI  C7   C9    single    1.543  0.020  1.543
 DLI  C7   H7    single    0.970  0.020  1.090
 DLI  C8   N11   single    1.453  0.020  1.453
 DLI  C8   H81   single    0.970  0.020  1.090
 DLI  C8   H82   single    0.970  0.020  1.090
 DLI  C10  S1    single    1.778  0.020  1.778
 DLI  C10  H101  single    0.970  0.020  1.090
 DLI  C10  H102  single    0.970  0.020  1.090
 DLI  C10  H103  single    0.970  0.020  1.090
 DLI  C17  N16   aromatic  1.319  0.020  1.319
 DLI  C17  N18   aromatic  1.319  0.020  1.319
 DLI  C17  H17   single    0.930  0.020  1.080
 DLI  C20  C14   aromatic  1.411  0.020  1.411
 DLI  C20  C19   aromatic  1.377  0.020  1.377
 DLI  C20  H20   single    0.930  0.020  1.080
 DLI  C21  C19   single    1.480  0.020  1.480
 DLI  C21  C27   aromatic  1.392  0.020  1.392
 DLI  C21  C23   aromatic  1.395  0.020  1.395
 DLI  C24  C23   aromatic  1.386  0.020  1.386
 DLI  C24  C25   aromatic  1.386  0.020  1.386
 DLI  C24  H24   single    0.930  0.020  1.080
 DLI  C26  C27   aromatic  1.386  0.020  1.386
 DLI  C26  S1    single    1.777  0.020  1.777
 DLI  C26  C25   aromatic  1.388  0.020  1.388
 DLI  C1   C2    aromatic  1.376  0.020  1.376
 DLI  C1   F15   single    1.337  0.020  1.337
 DLI  C2   C3    aromatic  1.396  0.020  1.396
 DLI  C2   H2    single    0.930  0.020  1.080
 DLI  C9   C12   single    1.526  0.020  1.526
 DLI  C9   N22   single    1.440  0.020  1.440
 DLI  C9   H9    single    0.970  0.020  1.090
 DLI  N11  C14   single    1.338  0.020  1.338
 DLI  N11  C12   single    1.452  0.020  1.452
 DLI  C12  H121  single    0.970  0.020  1.090
 DLI  C12  H122  single    0.970  0.020  1.090
 DLI  C14  N16   aromatic  1.340  0.020  1.340
 DLI  N18  C19   aromatic  1.342  0.020  1.342
 DLI  N22  H221  single    0.890  0.020  1.040
 DLI  N22  H222  single    0.890  0.020  1.040
 DLI  C23  H23   single    0.930  0.020  1.080
 DLI  C25  H25   single    0.930  0.020  1.080
 DLI  C27  H27   single    0.930  0.020  1.080
 DLI  S1   O2    double    1.461  0.020  1.461
 DLI  S1   O1    double    1.461  0.020  1.461

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
 DLI  F10   C4   C3    119.40  3.000
 DLI  C3    C4   C5    123.32  3.000
 DLI  F10   C4   C5    117.28  3.000
 DLI  H5    C5   C6    120.78  3.000
 DLI  H5    C5   C4    120.99  3.000
 DLI  C6    C5   C4    118.22  3.000
 DLI  F13   C6   C1    119.48  3.000
 DLI  C1    C6   C5    120.29  3.000
 DLI  F13   C6   C5    120.23  3.000
 DLI  H7    C7   C9    107.32  3.000
 DLI  H7    C7   C3    109.39  3.000
 DLI  C9    C7   C3    114.21  3.000
 DLI  H7    C7   C8    107.86  3.000
 DLI  C9    C7   C8    102.79  3.000
 DLI  C3    C7   C8    114.79  3.000
 DLI  H82   C8   H81   107.71  3.000
 DLI  H82   C8   N11   110.91  3.000
 DLI  H81   C8   N11   111.89  3.000
 DLI  H82   C8   C7    111.94  3.000
 DLI  H81   C8   C7    111.48  3.000
 DLI  N11   C8   C7    102.95  3.000
 DLI  H103  C10  H102  110.07  3.000
 DLI  H103  C10  H101  110.47  3.000
 DLI  H102  C10  H101  110.14  3.000
 DLI  H103  C10  S1    109.41  3.000
 DLI  H102  C10  S1    107.35  3.000
 DLI  H101  C10  S1    109.33  3.000
 DLI  H17   C17  N18   116.29  3.000
 DLI  H17   C17  N16   115.94  3.000
 DLI  N18   C17  N16   127.76  3.000
 DLI  H20   C20  C19   121.50  3.000
 DLI  H20   C20  C14   121.21  3.000
 DLI  C19   C20  C14   117.28  3.000
 DLI  C27   C21  C23   118.80  3.000
 DLI  C23   C21  C19   119.87  3.000
 DLI  C27   C21  C19   121.33  3.000
 DLI  H24   C24  C25   119.73  3.000
 DLI  H24   C24  C23   119.89  3.000
 DLI  C25   C24  C23   120.38  3.000
 DLI  S1    C26  C27   118.88  3.000
 DLI  S1    C26  C25   119.33  3.000
 DLI  C27   C26  C25   121.79  3.000
 DLI  F15   C1   C2    120.43  3.000
 DLI  F15   C1   C6    119.18  3.000
 DLI  C2    C1   C6    120.39  3.000
 DLI  H2    C2   C3    120.52  3.000
 DLI  H2    C2   C1    118.41  3.000
 DLI  C3    C2   C1    121.07  3.000
 DLI  C2    C3   C7    121.18  3.000
 DLI  C2    C3   C4    116.71  3.000
 DLI  C7    C3   C4    122.10  3.000
 DLI  H9    C9   N22   107.78  3.000
 DLI  H9    C9   C12   108.40  3.000
 DLI  N22   C9   C12   112.01  3.000
 DLI  H9    C9   C7    108.37  3.000
 DLI  N22   C9   C7    117.59  3.000
 DLI  C12   C9   C7    102.33  3.000
 DLI  C14   N11  C12   123.19  3.000
 DLI  C12   N11  C8    113.01  3.000
 DLI  C14   N11  C8    123.80  3.000
 DLI  H122  C12  H121  107.69  3.000
 DLI  H122  C12  N11   111.06  3.000
 DLI  H121  C12  N11   111.70  3.000
 DLI  H122  C12  C9    110.80  3.000
 DLI  H121  C12  C9    112.11  3.000
 DLI  N11   C12  C9    103.51  3.000
 DLI  N16   C14  N11   117.54  3.000
 DLI  N16   C14  C20   120.29  3.000
 DLI  N11   C14  C20   122.17  3.000
 DLI  C14   N16  C17   116.80  3.000
 DLI  C19   N18  C17   115.94  3.000
 DLI  N18   C19  C21   116.32  3.000
 DLI  N18   C19  C20   121.92  3.000
 DLI  C21   C19  C20   121.75  3.000
 DLI  H222  N22  H221  106.62  3.000
 DLI  H222  N22  C9    110.42  3.000
 DLI  H221  N22  C9    110.30  3.000
 DLI  H23   C23  C24   119.80  3.000
 DLI  H23   C23  C21   119.24  3.000
 DLI  C24   C23  C21   120.95  3.000
 DLI  H25   C25  C26   121.23  3.000
 DLI  H25   C25  C24   120.30  3.000
 DLI  C26   C25  C24   118.47  3.000
 DLI  H27   C27  C26   119.94  3.000
 DLI  H27   C27  C21   120.45  3.000
 DLI  C26   C27  C21   119.59  3.000
 DLI  O1    S1   O2    118.75  3.000
 DLI  O1    S1   C26   108.20  3.000
 DLI  O2    S1   C26   108.19  3.000
 DLI  O1    S1   C10   108.49  3.000
 DLI  O2    S1   C10   108.48  3.000
 DLI  C26   S1   C10   103.70  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
 DLI  CONST_01  C1    C6   C5   C4     0.00   0.0  0
 DLI  CONST_02  C1    C2   C3   C4     0.00   0.0  0
 DLI  CONST_03  C2    C3   C4   C5     0.00   0.0  0
 DLI  CONST_04  C2    C1   C6   C5     0.00   0.0  0
 DLI  CONST_05  C3    C4   C5   C6     0.00   0.0  0
 DLI  CONST_06  C3    C2   C1   C6     0.00   0.0  0
 DLI  CONST_07  C20   C14  N16  C17    0.00   0.0  0
 DLI  CONST_08  C20   C19  N18  C17    0.00   0.0  0
 DLI  CONST_09  C21   C19  N18  C17  180.00   0.0  0
 DLI  CONST_12  C14   C20  C19  C21  180.00   0.0  0
 DLI  CONST_13  C25   C26  C27  C21    0.00   0.0  0
 DLI  CONST_14  C25   C24  C23  C21    0.00   0.0  0
 DLI  CONST_15  C19   C21  C23  C24  180.00   0.0  0
 DLI  CONST_16  C27   C21  C23  C24    0.00   0.0  0
 DLI  CONST_17  C27   C26  C25  C24    0.00   0.0  0
 DLI  CONST_18  C19   C21  C27  C26  180.00   0.0  0
 DLI  CONST_19  C23   C21  C27  C26    0.00   0.0  0
 DLI  CONST_20  C23   C24  C25  C26    0.00   0.0  0
 DLI  CONST_21  N18   C19  C20  C14    0.00   0.0  0
 DLI  CONST_22  N18   C17  N16  C14    0.00   0.0  0
 DLI  CONST_23  C19   N18  C17  N16    0.00   0.0  0
 DLI  CONST_24  C19   C20  C14  N16    0.00   0.0  0
 DLI  CONST_27  C7    C3   C4   C5   180.00   0.0  0
 DLI  CONST_28  C1    C2   C3   C7   180.00   0.0  0
 DLI  CONST_29  N11   C14  N16  C17  180.00   0.0  0
 DLI  CONST_30  C19   C20  C14  N11  180.00   0.0  0
 DLI  CONST_31  F13   C6   C5   C4   180.00   0.0  0
 DLI  CONST_32  F15   C1   C6   C5   180.00   0.0  0
 DLI  CONST_33  F10   C4   C5   C6   180.00   0.0  0
 DLI  CONST_34  F10   C4   C3   C7     0.00   0.0  0
 DLI  CONST_35  S1    C26  C27  C21  180.00   0.0  0
 DLI  CONST_36  S1    C26  C25  C24  180.00   0.0  0
 DLI  CONST_37  F13   C6   C1   C2   180.00   0.0  0
 DLI  CONST_38  F10   C4   C3   C2   180.00   0.0  0
 DLI  CONST_39  F15   C1   C2   C3   180.00   0.0  0
 DLI  CONST_40  H2    C2   C3   C4   180.00   0.0  0
 DLI  CONST_41  H20   C20  C19  C21    0.00   0.0  0
 DLI  CONST_42  H24   C24  C23  C21  180.00   0.0  0
 DLI  CONST_43  H5    C5   C6   C1   180.00   0.0  0
 DLI  CONST_44  H17   C17  N16  C14  180.00   0.0  0
 DLI  CONST_45  H27   C27  C21  C19    0.00   0.0  0
 DLI  CONST_46  H23   C23  C21  C19    0.00   0.0  0
 DLI  CONST_47  H25   C25  C24  C23  180.00   0.0  0
 DLI  Var_01    C14   N11  C8   C7   166.55  30.0  1
 DLI  Var_02    C20   C14  N11  C8     1.97  30.0  2
 DLI  Var_03    C9    C12  N11  C8   -11.55  30.0  1
 DLI  Var_04    C27   C26  S1   C10  -88.39  30.0  2
 DLI  Var_05    H101  C10  S1   C26   61.49  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
 DLI  chir_01  C7  C8   C3  C9   positiv
 DLI  chir_02  C9  N22  C7  C12  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
 DLI  plan-1  C4   0.020
 DLI  plan-1  C5   0.020
 DLI  plan-1  C6   0.020
 DLI  plan-1  C7   0.020
 DLI  plan-1  C1   0.020
 DLI  plan-1  C2   0.020
 DLI  plan-1  C3   0.020
 DLI  plan-1  F10  0.020
 DLI  plan-1  F13  0.020
 DLI  plan-1  F15  0.020
 DLI  plan-1  H5   0.020
 DLI  plan-1  H2   0.020
 DLI  plan-2  C17  0.020
 DLI  plan-2  C20  0.020
 DLI  plan-2  C21  0.020
 DLI  plan-2  N11  0.020
 DLI  plan-2  C14  0.020
 DLI  plan-2  N16  0.020
 DLI  plan-2  N18  0.020
 DLI  plan-2  C19  0.020
 DLI  plan-2  H17  0.020
 DLI  plan-2  H20  0.020
 DLI  plan-3  C21  0.020
 DLI  plan-3  C24  0.020
 DLI  plan-3  C26  0.020
 DLI  plan-3  C19  0.020
 DLI  plan-3  C23  0.020
 DLI  plan-3  C25  0.020
 DLI  plan-3  C27  0.020
 DLI  plan-3  S1   0.020
 DLI  plan-3  H24  0.020
 DLI  plan-3  H23  0.020
 DLI  plan-3  H25  0.020
 DLI  plan-3  H27  0.020

