# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 19:22:21 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  55  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  -0.657   2.1234   0.1484  -2.8692
 6XU  C02  C  CR6   0  -0.024   1.8183  -0.0768  -1.3861
 6XU  C03  C  CR6   0  -0.159   0.5298  -0.8869  -1.2098
 6XU  C04  C  CR6   0   0.381  -0.6396  -0.2389  -1.0470
 6XU  N05  N  NR16  0  -0.718  -0.6380   1.1294  -0.9233
 6XU  C06  C  CR6   0   0.448   0.5409   1.7597  -0.6427
 6XU  N07  N  N     0  -0.404   1.6937   1.2505  -0.7831
 6XU  C08  C  CR5   0  -0.017   0.4279   3.1219  -0.1162
 6XU  N09  N  N     0  -0.383  -0.6934   3.7256   0.1173
 6XU  C10  C  CR15  0  -0.012  -0.4765   4.9784   0.6031
 6XU  C11  C  CR15  0  -0.500   0.8320   5.3271   0.7392
 6XU  S12  S  S2    0   0.283   1.8386   4.0393   0.2378
 6XU  C13  C  CH2   0  -0.392  -2.0270  -0.8209  -1.0310
 6XU  N14  N  NR5   0  -0.466  -2.7344  -0.3823   0.1476
 6XU  C15  C  CH2   0  -0.365  -2.3558  -1.0260   1.3981
 6XU  C16  C  CR5   0   0.724  -3.6783  -1.4688   1.9927
 6XU  C17  C  CH2   0  -0.584  -4.6861  -0.4756   1.4650
 6XU  C18  C  CR15  0  -0.196  -4.1725  -0.2700   0.0358
 6XU  C19  C  C     0   0.564  -4.5818   1.0742  -0.5307
 6XU  O20  O  O     0  -0.424  -3.8199   1.9440  -0.8680
 6XU  O21  O  OH1   0  -0.588  -5.8993   1.1724  -0.6117
 6XU  F22  F  F     0  -0.349  -3.9953  -2.7257   1.5492
 6XU  F23  F  F     0  -0.333  -3.6560  -1.5520   3.3474
 6XU  C24  C  C     0   0.529   0.5996  -2.3607  -1.2114
 6XU  O25  O  O     0  -0.449  -0.0625  -3.1037  -0.5211
 6XU  O26  O  O2    0  -0.444   1.5198  -2.8043  -2.0569
 6XU  C27  C  CH3   0  -0.419   1.8231  -4.1962  -2.0402
 6XU  C28  C  CR6   0   0.157   2.9531  -0.7634  -0.6301
 6XU  C29  C  CR16  0  -0.305   4.1458  -1.1544  -1.2247
 6XU  C30  C  CR16  0  -0.397   5.1525  -1.7636  -0.4859
 6XU  C31  C  CR6   0   0.510   4.9481  -1.9794   0.8611
 6XU  C32  C  CR16  0  -0.402   3.7765  -1.6052   1.4905
 6XU  C33  C  CR16  0  -0.265   2.7873  -0.9967   0.7337
 6XU  F34  F  F     0  -0.318   5.9164  -2.5706   1.5824
 6XU  H1   H  HCH3  0   0.244   2.3107  -0.7850  -3.3960
 6XU  H2   H  HCH3  0   0.246   1.2723   0.6370  -3.3439
 6XU  H3   H  HCH3  0   0.237   2.9918   0.7985  -2.9883
 6XU  H4   H  HNR6  0   0.422  -1.5118   1.5841  -0.6800
 6XU  H5   H  HCR5  0   0.278  -1.3145   5.6139   0.8494
 6XU  H6   H  HCR5  0   0.315   1.2387   6.2569   1.1034
 6XU  H7   H  HCH2  0   0.284  -2.5389  -0.4248  -1.9129
 6XU  H8   H  HCH2  0   0.268  -2.0079  -1.9058  -1.1420
 6XU  H10  H  HCH2  0   0.270  -1.6795  -1.8690   1.2394
 6XU  H11  H  HCH2  0   0.257  -1.8601  -0.3271   2.0784
 6XU  H12  H  HCH2  0   0.299  -5.7118  -0.8369   1.5072
 6XU  H13  H  HCH2  0   0.288  -4.6147   0.4445   2.0492
 6XU  H14  H  HCR5  0   0.288  -4.6068  -1.0444  -0.6140
 6XU  H15  H  HOH1  0   0.488  -6.1551   2.0381  -0.9649
 6XU  H16  H  HCH3  0   0.250   2.6302  -4.3336  -2.7537
 6XU  H17  H  HCH3  0   0.235   2.1566  -4.5181  -1.0535
 6XU  H18  H  HCH3  0   0.239   0.9664  -4.7978  -2.3435
 6XU  H19  H  HCR6  0   0.259   4.3133  -0.9966  -2.2812
 6XU  H20  H  HCR6  0   0.277   6.0780  -2.0689  -0.9566
 6XU  H21  H  HCR6  0   0.276   3.6377  -1.7829   2.5488
 6XU  H22  H  HCR6  0   0.258   1.8675  -0.7001   1.2234

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    1.357  0.020  1.357
 6XU  C10  C11  aromatic  1.361  0.020  1.361
 6XU  C10  N09  aromatic  1.361  0.020  1.361
 6XU  C17  C16  single    1.510  0.020  1.510
 6XU  C17  C18  single    1.532  0.020  1.532
 6XU  O20  C19  double    1.205  0.020  1.205
 6XU  F22  C16  single    1.370  0.020  1.370
 6XU  C16  C15  single    1.516  0.020  1.516
 6XU  C11  S12  aromatic  1.710  0.020  1.710
 6XU  C19  O21  single    1.324  0.020  1.324
 6XU  C19  C18  single    1.515  0.020  1.515
 6XU  N09  C08  aromatic  1.295  0.020  1.295
 6XU  C18  N14  single    1.447  0.020  1.447
 6XU  C15  N14  single    1.456  0.020  1.456
 6XU  N14  C13  single    1.443  0.020  1.443
 6XU  C08  S12  aromatic  1.720  0.020  1.720
 6XU  C08  C06  single    1.465  0.020  1.465
 6XU  N05  C06  single    1.366  0.020  1.366
 6XU  N05  C04  single    1.374  0.020  1.374
 6XU  C06  N07  double    1.268  0.020  1.268
 6XU  C13  C04  single    1.505  0.020  1.505
 6XU  C04  C03  double    1.347  0.020  1.347
 6XU  N07  C02  single    1.463  0.020  1.463
 6XU  C03  C02  single    1.532  0.020  1.532
 6XU  C03  C24  single    1.475  0.020  1.475
 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    1.211  0.020  1.211
 6XU  C24  O26  single    1.326  0.020  1.326
 6XU  C28  C29  aromatic  1.389  0.020  1.389
 6XU  C31  F34  single    1.344  0.020  1.344
 6XU  C31  C30  aromatic  1.379  0.020  1.379
 6XU  O26  C27  single    1.425  0.020  1.425
 6XU  C29  C30  aromatic  1.389  0.020  1.389
 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    0.890  0.020  1.040
 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  O21  H15  single    0.850  0.020  0.980
 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   107.86  3.000
 6XU  H3   C01  H1   108.74  3.000
 6XU  H2   C01  H1   107.94  3.000
 6XU  H3   C01  C02  110.61  3.000
 6XU  H2   C01  C02  109.40  3.000
 6XU  H1   C01  C02  112.16  3.000
 6XU  C28  C02  N07  105.50  3.000
 6XU  C28  C02  C03  109.29  3.000
 6XU  N07  C02  C03  111.14  3.000
 6XU  C28  C02  C01  113.43  3.000
 6XU  C03  C02  C01  110.91  3.000
 6XU  N07  C02  C01  106.43  3.000
 6XU  C24  C03  C04  121.45  3.000
 6XU  C24  C03  C02  119.22  3.000
 6XU  C04  C03  C02  119.32  3.000
 6XU  C13  C04  N05  112.66  3.000
 6XU  C13  C04  C03  128.01  3.000
 6XU  N05  C04  C03  119.28  3.000
 6XU  H4   N05  C06  119.16  3.000
 6XU  H4   N05  C04  117.83  3.000
 6XU  C06  N05  C04  118.62  3.000
 6XU  C08  C06  N07  118.90  3.000
 6XU  N07  C06  N05  125.21  3.000
 6XU  C08  C06  N05  115.87  3.000
 6XU  C06  N07  C02  119.16  3.000
 6XU  S12  C08  N09  115.12  3.000
 6XU  S12  C08  C06  120.46  3.000
 6XU  N09  C08  C06  124.42  3.000
 6XU  C10  N09  C08  110.83  3.000
 6XU  H5   C10  C11  124.92  3.000
 6XU  H5   C10  N09  119.95  3.000
 6XU  C11  C10  N09  115.13  3.000
 6XU  H6   C11  S12  121.77  3.000
 6XU  H6   C11  C10  128.12  3.000
 6XU  S12  C11  C10  110.11  3.000
 6XU  C11  S12  C08   88.81  3.000
 6XU  H8   C13  H7   106.63  3.000
 6XU  H8   C13  N14  113.21  3.000
 6XU  H7   C13  N14  108.60  3.000
 6XU  H8   C13  C04  111.56  3.000
 6XU  H7   C13  C04  106.43  3.000
 6XU  N14  C13  C04  110.07  3.000
 6XU  C18  N14  C15  111.04  3.000
 6XU  C15  N14  C13  116.07  3.000
 6XU  C18  N14  C13  116.60  3.000
 6XU  H11  C15  H10  107.63  3.000
 6XU  H11  C15  C16  109.75  3.000
 6XU  H10  C15  C16  111.81  3.000
 6XU  H11  C15  N14  111.67  3.000
 6XU  H10  C15  N14  112.17  3.000
 6XU  C16  C15  N14  103.83  3.000
 6XU  F23  C16  F22  105.70  3.000
 6XU  F22  C16  C17  109.62  3.000
 6XU  F23  C16  C17  113.58  3.000
 6XU  F22  C16  C15  110.05  3.000
 6XU  C17  C16  C15  104.66  3.000
 6XU  F23  C16  C15  113.27  3.000
 6XU  H13  C17  H12  108.69  3.000
 6XU  H13  C17  C18  111.34  3.000
 6XU  H12  C17  C18  113.36  3.000
 6XU  H13  C17  C16  108.87  3.000
 6XU  H12  C17  C16  113.40  3.000
 6XU  C18  C17  C16  100.98  3.000
 6XU  H14  C18  C19  107.27  3.000
 6XU  H14  C18  C17  108.91  3.000
 6XU  C19  C18  C17  112.16  3.000
 6XU  H14  C18  N14  112.54  3.000
 6XU  C19  C18  N14  111.49  3.000
 6XU  C17  C18  N14  104.52  3.000
 6XU  O21  C19  O20  123.98  3.000
 6XU  O21  C19  C18  110.96  3.000
 6XU  O20  C19  C18  125.06  3.000
 6XU  H15  O21  C19  110.56  3.000
 6XU  O26  C24  O25  122.51  3.000
 6XU  O26  C24  C03  111.57  3.000
 6XU  O25  C24  C03  125.90  3.000
 6XU  C27  O26  C24  117.85  3.000
 6XU  H18  C27  H17  109.23  3.000
 6XU  H18  C27  H16  109.37  3.000
 6XU  H17  C27  H16  109.26  3.000
 6XU  H18  C27  O26  111.64  3.000
 6XU  H17  C27  O26  111.35  3.000
 6XU  H16  C27  O26  105.91  3.000
 6XU  C33  C28  C29  118.29  3.000
 6XU  C29  C28  C02  123.57  3.000
 6XU  C33  C28  C02  118.13  3.000
 6XU  H19  C29  C30  118.12  3.000
 6XU  H19  C29  C28  120.68  3.000
 6XU  C30  C29  C28  121.20  3.000
 6XU  H20  C30  C31  120.48  3.000
 6XU  H20  C30  C29  120.80  3.000
 6XU  C31  C30  C29  118.72  3.000
 6XU  F34  C31  C32  119.05  3.000
 6XU  F34  C31  C30  119.07  3.000
 6XU  C32  C31  C30  121.88  3.000
 6XU  H21  C32  C33  120.96  3.000
 6XU  H21  C32  C31  120.65  3.000
 6XU  C33  C32  C31  118.38  3.000
 6XU  H22  C33  C32  118.64  3.000
 6XU  H22  C33  C28  119.84  3.000
 6XU  C32  C33  C28  121.53  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  CONST_29  H15  O21  C19  C18   180.00   0.0  0
 6XU  Var_01    N05  C04  C03  C02    -5.75  30.0  1
 6XU  Var_02    C06  N05  C04  C03   -15.77  30.0  1
 6XU  Var_03    N09  C08  C06  N05     1.61  30.0  1
 6XU  Var_04    C17  C16  C15  N14   -28.62  30.0  1
 6XU  Var_05    C18  C17  C16  C15    38.29  30.0  1
 6XU  Var_06    C18  N14  C15  C16     6.80  30.0  1
 6XU  Var_07    N14  C13  C04  C03   128.37  30.0  2
 6XU  Var_08    O25  C24  C03  C02   142.84  30.0  2
 6XU  Var_09    H16  C27  O26  C24  -176.69  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-4  H15  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

