# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 14:39:54 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: (2~{S})-4,4-bis(fluoranyl)-1-[[(4~{S})-4-(4-fluorophenyl)-5-methoxycarbonyl-4-methyl-2-(1,3-thiazol-2-yl)-1~{H}-pyrimidin-6-yl]methyl]pyrrolidine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)C1=C(CN2CC(F)(F)C[C@H]2C(O)=O)NC(=N[C@@]1(C)c3ccc(F)cc3)c4sccn4
#
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
 6XU  6XU  '(2~{S})-4,4-bis(fluoranyl)-1-[[(4~{S})-4-(4-fluorophenyl)-5-methoxycarbonyl-4-methyl-2-(1,3-thiazol-2-yl)-1~{H}-pyrimidin-6-yl]methyl]pyrrolidine-2-carboxylic acid'  ligand  54  34  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6XU
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
 6XU  C01  C  CH3    0  -0.658   2.0665   0.1872  -2.8487
 6XU  C02  C  CT     0  -0.018   1.7727  -0.0676  -1.3678
 6XU  C03  C  C      0  -0.170   0.5024  -0.9055  -1.1969
 6XU  C04  C  C      0   0.390  -0.6805  -0.2773  -1.0257
 6XU  N05  N  NH1    0  -0.746  -0.7132   1.0841  -0.8718
 6XU  C06  C  C      0   0.453   0.4533   1.7303  -0.5969
 6XU  N07  N  N      0  -0.418   1.6192   1.2452  -0.7431
 6XU  C08  C  C      0  -0.025   0.3508   3.0904  -0.0564
 6XU  N09  N  N      0  -0.371  -0.7505   3.7111   0.2169
 6XU  C10  C  C1     0  -0.019  -0.4973   4.9561   0.7068
 6XU  C11  C  C1     0  -0.502   0.8196   5.2838   0.8064
 6XU  S12  S  S2     0   0.269   1.7893   3.9847   0.2630
 6XU  C13  C  CH2    0  -0.394  -2.0601  -0.8863  -1.0242
 6XU  N14  N  NT     0  -0.463  -2.7635  -0.5324   0.1768
 6XU  C15  C  CH2    0  -0.334  -2.5377  -1.3731   1.3351
 6XU  C16  C  CT     0   0.714  -3.8579  -1.3092   2.0907
 6XU  C17  C  CH2    0  -0.574  -4.5910  -0.1138   1.5326
 6XU  C18  C  CH1    0  -0.183  -4.1492  -0.1268   0.0704
 6XU  C19  C  C      0   0.439  -4.3612   1.2479  -0.5904
 6XU  O20  O  O      0  -0.573  -3.3572   1.9274  -0.8986
 6XU  O21  O  OC    -1  -0.597  -5.5494   1.5751  -0.7457
 6XU  F22  F  F      0  -0.355  -4.5848  -2.4506   1.8614
 6XU  F23  F  F      0  -0.345  -3.6929  -1.2606   3.4427
 6XU  C24  C  C      0   0.526   0.5953  -2.3736  -1.2181
 6XU  O25  O  O      0  -0.455  -0.0739  -3.1432  -0.5633
 6XU  O26  O  O2     0  -0.448   1.5498  -2.7910  -2.0439
 6XU  C27  C  CH3    0  -0.417   1.8831  -4.1743  -2.0300
 6XU  C28  C  CR6    0   0.161   2.9300  -0.7366  -0.6294
 6XU  C29  C  CR16   0  -0.306   4.1271  -1.0934  -1.2364
 6XU  C30  C  CR16   0  -0.398   5.1539  -1.6874  -0.5127
 6XU  C31  C  CR6    0   0.508   4.9653  -1.9231   0.8332
 6XU  C32  C  CR16   0  -0.402   3.7907  -1.5822   1.4756
 6XU  C33  C  CR16   0  -0.266   2.7819  -0.9879   0.7333
 6XU  F34  F  F      0  -0.319   5.9530  -2.5006   1.5403
 6XU  H1   H  HCH3   0   0.240   2.2717  -0.7338  -3.3912
 6XU  H2   H  HCH3   0   0.244   1.2015   0.6631  -3.3114
 6XU  H3   H  HCH3   0   0.233   2.9192   0.8589  -2.9642
 6XU  H4   H  HNH1   0   0.455  -1.6422   1.5192  -0.7167
 6XU  H5   H  H      0   0.274  -1.3175   5.6022   0.9842
 6XU  H6   H  H      0   0.311   1.2504   6.2043   1.1670
 6XU  H7   H  HCH2   0   0.271  -2.5870  -0.4575  -1.8806
 6XU  H8   H  HCH2   0   0.255  -2.0197  -1.9633  -1.1924
 6XU  H10  H  HCH2   0   0.239  -2.2960  -2.4094   1.0732
 6XU  H11  H  HCH2   0   0.238  -1.7193  -0.9978   1.9582
 6XU  H12  H  HCH2   0   0.273  -5.6696  -0.1748   1.6673
 6XU  H13  H  HCH2   0   0.265  -4.2259   0.7891   2.0287
 6XU  H14  H  HCH1   0   0.221  -4.7628  -0.8581  -0.4820
 6XU  H16  H  HCH3   0   0.247   2.7112  -4.2887  -2.7236
 6XU  H17  H  HCH3   0   0.233   2.1996  -4.4981  -1.0380
 6XU  H18  H  HCH3   0   0.236   1.0490  -4.7939  -2.3592
 6XU  H19  H  HCR6   0   0.257   4.2826  -0.9197  -2.2923
 6XU  H20  H  HCR6   0   0.275   6.0825  -1.9655  -0.9941
 6XU  H21  H  HCR6   0   0.275   3.6646  -1.7740   2.5332
 6XU  H22  H  HCR6   0   0.256   1.8592  -0.7172   1.2321

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
 6XU  F23  C16  single    1.363  0.020  1.363
 6XU  C10  C11  aromatic  1.361  0.020  1.361
 6XU  C10  N09  aromatic  1.362  0.020  1.362
 6XU  C17  C16  single    1.509  0.020  1.509
 6XU  C17  C18  single    1.528  0.020  1.528
 6XU  O20  C19  deloc     1.251  0.020  1.251
 6XU  F22  C16  single    1.372  0.020  1.372
 6XU  C16  C15  single    1.522  0.020  1.522
 6XU  C11  S12  aromatic  1.710  0.020  1.710
 6XU  C19  O21  deloc     1.242  0.020  1.242
 6XU  C19  C18  single    1.540  0.020  1.540
 6XU  N09  C08  aromatic  1.293  0.020  1.293
 6XU  C18  N14  single    1.448  0.020  1.448
 6XU  C15  N14  single    1.449  0.020  1.449
 6XU  N14  C13  single    1.436  0.020  1.436
 6XU  C08  S12  aromatic  1.724  0.020  1.724
 6XU  C08  C06  single    1.467  0.020  1.467
 6XU  N05  C06  single    1.362  0.020  1.362
 6XU  N05  C04  single    1.370  0.020  1.370
 6XU  C06  N07  double    1.271  0.020  1.271
 6XU  C13  C04  single    1.508  0.020  1.508
 6XU  C04  C03  double    1.350  0.020  1.350
 6XU  N07  C02  single    1.462  0.020  1.462
 6XU  C03  C02  single    1.531  0.020  1.531
 6XU  C03  C24  single    1.471  0.020  1.471
 6XU  C33  C32  aromatic  1.386  0.020  1.386
 6XU  C33  C28  aromatic  1.394  0.020  1.394
 6XU  C02  C28  single    1.527  0.020  1.527
 6XU  C02  C01  single    1.531  0.020  1.531
 6XU  C32  C31  aromatic  1.382  0.020  1.382
 6XU  O25  C24  double    1.212  0.020  1.212
 6XU  C24  O26  single    1.329  0.020  1.329
 6XU  C28  C29  aromatic  1.389  0.020  1.389
 6XU  C31  F34  single    1.345  0.020  1.345
 6XU  C31  C30  aromatic  1.379  0.020  1.379
 6XU  O26  C27  single    1.423  0.020  1.423
 6XU  C29  C30  aromatic  1.390  0.020  1.390
 6XU  C01  H1   single    0.970  0.020  1.090
 6XU  C01  H2   single    0.970  0.020  1.090
 6XU  C01  H3   single    0.970  0.020  1.090
 6XU  N05  H4   single    0.860  0.020  1.020
 6XU  C10  H5   single    0.930  0.020  1.080
 6XU  C11  H6   single    0.930  0.020  1.080
 6XU  C13  H7   single    0.970  0.020  1.090
 6XU  C13  H8   single    0.970  0.020  1.090
 6XU  C15  H10  single    0.970  0.020  1.090
 6XU  C15  H11  single    0.970  0.020  1.090
 6XU  C17  H12  single    0.970  0.020  1.090
 6XU  C17  H13  single    0.970  0.020  1.090
 6XU  C18  H14  single    0.970  0.020  1.090
 6XU  C27  H16  single    0.970  0.020  1.090
 6XU  C27  H17  single    0.970  0.020  1.090
 6XU  C27  H18  single    0.970  0.020  1.090
 6XU  C29  H19  single    0.930  0.020  1.080
 6XU  C30  H20  single    0.930  0.020  1.080
 6XU  C32  H21  single    0.930  0.020  1.080
 6XU  C33  H22  single    0.930  0.020  1.080

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
 6XU  H3   C01  H2   107.83  3.000
 6XU  H3   C01  H1   108.71  3.000
 6XU  H2   C01  H1   107.91  3.000
 6XU  H3   C01  C02  110.77  3.000
 6XU  H2   C01  C02  109.32  3.000
 6XU  H1   C01  C02  112.17  3.000
 6XU  C28  C02  N07  105.45  3.000
 6XU  C28  C02  C03  109.57  3.000
 6XU  N07  C02  C03  110.89  3.000
 6XU  C28  C02  C01  113.27  3.000
 6XU  C03  C02  C01  110.99  3.000
 6XU  N07  C02  C01  106.50  3.000
 6XU  C24  C03  C04  121.43  3.000
 6XU  C24  C03  C02  119.48  3.000
 6XU  C04  C03  C02  119.10  3.000
 6XU  C13  C04  N05  112.29  3.000
 6XU  C13  C04  C03  127.85  3.000
 6XU  N05  C04  C03  119.82  3.000
 6XU  H4   N05  C06  122.55  3.000
 6XU  H4   N05  C04  117.04  3.000
 6XU  C06  N05  C04  118.28  3.000
 6XU  C08  C06  N07  117.40  3.000
 6XU  N07  C06  N05  125.55  3.000
 6XU  C08  C06  N05  117.03  3.000
 6XU  C06  N07  C02  119.22  3.000
 6XU  S12  C08  N09  114.99  3.000
 6XU  S12  C08  C06  119.40  3.000
 6XU  N09  C08  C06  125.61  3.000
 6XU  C10  N09  C08  110.88  3.000
 6XU  H5   C10  C11  124.88  3.000
 6XU  H5   C10  N09  119.87  3.000
 6XU  C11  C10  N09  115.25  3.000
 6XU  H6   C11  S12  121.89  3.000
 6XU  H6   C11  C10  128.08  3.000
 6XU  S12  C11  C10  110.04  3.000
 6XU  C11  S12  C08   88.84  3.000
 6XU  H8   C13  H7   106.52  3.000
 6XU  H8   C13  N14  112.98  3.000
 6XU  H7   C13  N14  108.81  3.000
 6XU  H8   C13  C04  111.39  3.000
 6XU  H7   C13  C04  106.36  3.000
 6XU  N14  C13  C04  110.45  3.000
 6XU  C18  N14  C15  111.75  3.000
 6XU  C15  N14  C13  116.69  3.000
 6XU  C18  N14  C13  118.45  3.000
 6XU  H11  C15  H10  107.18  3.000
 6XU  H11  C15  C16  110.57  3.000
 6XU  H10  C15  C16  110.46  3.000
 6XU  H11  C15  N14  111.87  3.000
 6XU  H10  C15  N14  113.07  3.000
 6XU  C16  C15  N14  103.72  3.000
 6XU  F23  C16  F22  105.04  3.000
 6XU  F22  C16  C17  109.86  3.000
 6XU  F23  C16  C17  113.41  3.000
 6XU  F22  C16  C15  109.96  3.000
 6XU  C17  C16  C15  105.72  3.000
 6XU  F23  C16  C15  112.88  3.000
 6XU  H13  C17  H12  108.73  3.000
 6XU  H13  C17  C18  110.17  3.000
 6XU  H12  C17  C18  113.86  3.000
 6XU  H13  C17  C16  108.92  3.000
 6XU  H12  C17  C16  113.02  3.000
 6XU  C18  C17  C16  101.93  3.000
 6XU  H14  C18  C19  107.48  3.000
 6XU  H14  C18  C17  108.91  3.000
 6XU  C19  C18  C17  111.31  3.000
 6XU  H14  C18  N14  112.55  3.000
 6XU  C19  C18  N14  114.42  3.000
 6XU  C17  C18  N14  102.06  3.000
 6XU  O21  C19  O20  126.43  3.000
 6XU  O21  C19  C18  114.87  3.000
 6XU  O20  C19  C18  118.69  3.000
 6XU  O26  C24  O25  122.19  3.000
 6XU  O26  C24  C03  111.56  3.000
 6XU  O25  C24  C03  126.23  3.000
 6XU  C27  O26  C24  117.86  3.000
 6XU  H18  C27  H17  109.15  3.000
 6XU  H18  C27  H16  109.31  3.000
 6XU  H17  C27  H16  109.17  3.000
 6XU  H18  C27  O26  111.74  3.000
 6XU  H17  C27  O26  111.44  3.000
 6XU  H16  C27  O26  105.94  3.000
 6XU  C33  C28  C29  118.21  3.000
 6XU  C29  C28  C02  123.67  3.000
 6XU  C33  C28  C02  118.12  3.000
 6XU  H19  C29  C30  118.10  3.000
 6XU  H19  C29  C28  120.63  3.000
 6XU  C30  C29  C28  121.27  3.000
 6XU  H20  C30  C31  120.49  3.000
 6XU  H20  C30  C29  120.81  3.000
 6XU  C31  C30  C29  118.70  3.000
 6XU  F34  C31  C32  119.07  3.000
 6XU  F34  C31  C30  119.07  3.000
 6XU  C32  C31  C30  121.86  3.000
 6XU  H21  C32  C33  120.96  3.000
 6XU  H21  C32  C31  120.65  3.000
 6XU  C33  C32  C31  118.39  3.000
 6XU  H22  C33  C32  118.71  3.000
 6XU  H22  C33  C28  119.72  3.000
 6XU  C32  C33  C28  121.57  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
 6XU  CONST_01  C11  C10  N09  C08     0.00   0.0  0
 6XU  CONST_02  C10  C11  S12  C08     0.00   0.0  0
 6XU  CONST_03  S12  C11  C10  N09     0.00   0.0  0
 6XU  CONST_04  C11  S12  C08  N09     0.00   0.0  0
 6XU  CONST_05  S12  C08  N09  C10     0.00   0.0  0
 6XU  CONST_06  C31  C32  C33  C28     0.00   0.0  0
 6XU  CONST_07  C31  C30  C29  C28     0.00   0.0  0
 6XU  CONST_08  C32  C33  C28  C29     0.00   0.0  0
 6XU  CONST_09  C32  C31  C30  C29     0.00   0.0  0
 6XU  CONST_10  C33  C32  C31  C30     0.00   0.0  0
 6XU  CONST_11  C33  C28  C29  C30     0.00   0.0  0
 6XU  CONST_12  C32  C33  C28  C02   180.00   0.0  0
 6XU  CONST_13  C30  C29  C28  C02   180.00   0.0  0
 6XU  CONST_14  C10  N09  C08  C06   180.00   0.0  0
 6XU  CONST_15  C11  S12  C08  C06   180.00   0.0  0
 6XU  CONST_16  C08  C06  N07  C02   180.00   0.0  0
 6XU  CONST_17  N05  C06  N07  C02     0.00   0.0  0
 6XU  CONST_20  F34  C31  C30  C29   180.00   0.0  0
 6XU  CONST_21  F34  C31  C32  C33   180.00   0.0  0
 6XU  CONST_22  H22  C33  C28  C02     0.00   0.0  0
 6XU  CONST_23  H19  C29  C28  C02     0.00   0.0  0
 6XU  CONST_24  H5   C10  N09  C08   180.00   0.0  0
 6XU  CONST_25  H6   C11  S12  C08   180.00   0.0  0
 6XU  CONST_26  H21  C32  C33  C28   180.00   0.0  0
 6XU  CONST_27  H20  C30  C29  C28   180.00   0.0  0
 6XU  CONST_28  H4   N05  C06  N07   180.00   0.0  0
 6XU  Var_01    N05  C04  C03  C02    -6.59  30.0  1
 6XU  Var_02    C06  N05  C04  C03   -14.50  30.0  1
 6XU  Var_03    N09  C08  C06  N05     2.14  30.0  2
 6XU  Var_04    C17  C16  C15  N14   -16.82  30.0  1
 6XU  Var_05    C18  C17  C16  C15    33.84  30.0  1
 6XU  Var_06    C18  N14  C15  C16    -8.17  30.0  1
 6XU  Var_07    N14  C13  C04  C03   126.05  30.0  2
 6XU  Var_08    O25  C24  C03  C02   144.96  30.0  2
 6XU  Var_09    H16  C27  O26  C24  -176.77  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
 6XU  chir_01  C02  C03  C28  N07  positiv
 6XU  chir_02  C18  N14  C17  C19  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
 6XU  plan-1  C06  0.020
 6XU  plan-1  C08  0.020
 6XU  plan-1  N09  0.020
 6XU  plan-1  C10  0.020
 6XU  plan-1  C11  0.020
 6XU  plan-1  S12  0.020
 6XU  plan-1  H5   0.020
 6XU  plan-1  H6   0.020
 6XU  plan-2  C02  0.020
 6XU  plan-2  C04  0.020
 6XU  plan-2  N05  0.020
 6XU  plan-2  C06  0.020
 6XU  plan-2  N07  0.020
 6XU  plan-2  C08  0.020
 6XU  plan-2  H4   0.020
 6XU  plan-3  C02  0.020
 6XU  plan-3  C28  0.020
 6XU  plan-3  C29  0.020
 6XU  plan-3  C30  0.020
 6XU  plan-3  C31  0.020
 6XU  plan-3  C32  0.020
 6XU  plan-3  C33  0.020
 6XU  plan-3  F34  0.020
 6XU  plan-3  H19  0.020
 6XU  plan-3  H20  0.020
 6XU  plan-3  H21  0.020
 6XU  plan-3  H22  0.020
 6XU  plan-4  C18  0.020
 6XU  plan-4  C19  0.020
 6XU  plan-4  O20  0.020
 6XU  plan-4  O21  0.020
 6XU  plan-5  C03  0.020
 6XU  plan-5  C24  0.020
 6XU  plan-5  O25  0.020
 6XU  plan-5  O26  0.020

