# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 12:24:37 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: (2~{S})-1-[5-[4-[bis(fluoranyl)methoxy]-3-cyclopentyloxy-phenyl]pyrazol-1-yl]-3-morpholin-4-yl-propan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](CN1CCOCC1)Cn2nccc2c3ccc(OC(F)F)c(OC4CCCC4)c3
#
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
 D5N  D5N  (2~{S})-1-[5-[4-[bis(fluoranyl)methoxy]-3-cyclopentyloxy-phenyl]pyrazol-1-yl]-3-morpholin-4-yl-propan-2-ol  ligand  60  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_D5N
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
 D5N  C10  C  CR6   0   0.060   0.8741  -0.7899  -1.1053
 D5N  C11  C  CR16  0  -0.324   0.1025   0.3652  -1.1510
 D5N  C01  C  CH1   0   0.669   3.0333   3.6791  -1.3852
 D5N  O01  O  O2    0  -0.501   2.6282   2.9002  -0.3532
 D5N  C02  C  CR6   0   0.237   2.0434   1.6856  -0.6487
 D5N  C03  C  CR6   0   0.369   2.8441   0.5355  -0.6058
 D5N  O02  O  O2    0  -0.464   4.1385   0.7190  -0.3366
 D5N  C04  C  CH1   0  -0.020   5.0052  -0.4144  -0.2179
 D5N  C05  C  CH2   0  -0.475   4.7855  -1.1603   1.1122
 D5N  C06  C  CH2   0  -0.451   5.9259  -0.7122   2.0518
 D5N  C07  C  CH2   0  -0.446   6.5854   0.4789   1.3520
 D5N  C08  C  CH2   0  -0.457   6.4209   0.1357  -0.1247
 D5N  C09  C  CR16  0  -0.430   2.2394  -0.6978  -0.8296
 D5N  C12  C  CR16  0  -0.290   0.6928   1.5996  -0.9184
 D5N  C13  C  CR5   0   0.402   0.3113  -2.1227  -1.3492
 D5N  N01  N  NR5   0  -0.338  -0.7483  -2.6510  -0.6864
 D5N  N02  N  N     0  -0.267  -1.0125  -3.8962  -1.0728
 D5N  C14  C  CH2   0  -0.319  -1.5284  -2.0568   0.3747
 D5N  C15  C  CH1   0  -0.009  -2.8825  -1.5211  -0.0923
 D5N  O03  O  OH1   0  -0.643  -3.6885  -2.5150  -0.6626
 D5N  C16  C  CH2   0  -0.287  -3.5522  -0.8095   1.0826
 D5N  N03  N  NT    0  -0.417  -4.8869  -0.3394   0.7877
 D5N  C17  C  CH2   0  -0.302  -5.5637   0.1081   1.9918
 D5N  C18  C  CH2   0  -0.190  -6.9802   0.5386   1.6644
 D5N  O04  O  O2    0  -0.484  -6.9990   1.5602   0.6918
 D5N  C19  C  CH2   0  -0.184  -6.3397   1.1421  -0.4822
 D5N  C20  C  CH2   0  -0.314  -4.9097   0.7188  -0.2054
 D5N  C21  C  CR15  0  -0.076  -0.1218  -4.1776  -2.0044
 D5N  C22  C  CR15  0  -0.542   0.7459  -3.0996  -2.2208
 D5N  F01  F  F     0  -0.330   3.8104   2.9929  -2.2514
 D5N  F02  F  F     0  -0.335   1.9749   4.1117  -2.1155
 D5N  H12  H  HCR6  0   0.264  -0.9497   0.3211  -1.3957
 D5N  H01  H  HCH1  0   0.214   3.5763   4.5333  -0.9876
 D5N  H02  H  HCH1  0   0.255   4.8755  -1.0591  -1.0928
 D5N  H03  H  HCH2  0   0.251   3.8047  -0.9300   1.5318
 D5N  H04  H  HCH2  0   0.246   4.8049  -2.2385   0.9482
 D5N  H06  H  HCH2  0   0.236   5.5661  -0.4663   3.0508
 D5N  H05  H  HCH2  0   0.230   6.6542  -1.5180   2.1642
 D5N  H07  H  HCH2  0   0.226   6.0613   1.4079   1.5895
 D5N  H08  H  HCH2  0   0.235   7.6278   0.6142   1.6419
 D5N  H10  H  HCH2  0   0.238   7.1149  -0.6645  -0.3957
 D5N  H09  H  HCH2  0   0.247   6.5932   0.9653  -0.8115
 D5N  H11  H  HCR6  0   0.286   2.8174  -1.6103  -0.7809
 D5N  H13  H  HCR6  0   0.278   0.0876   2.4957  -0.9341
 D5N  H27  H  HCH2  0   0.277  -1.6695  -2.8142   1.1482
 D5N  H26  H  HCH2  0   0.271  -0.9419  -1.2523   0.8177
 D5N  H14  H  HCH1  0   0.237  -2.7035  -0.8030  -0.8977
 D5N  H15  H  HOH1  0   0.443  -3.9054  -3.1654   0.0139
 D5N  H16  H  HCH2  0   0.240  -3.6216  -1.5099   1.9226
 D5N  H17  H  HCH2  0   0.202  -2.8914   0.0097   1.4185
 D5N  H19  H  HCH2  0   0.243  -5.6023  -0.7114   2.7141
 D5N  H18  H  HCH2  0   0.196  -5.0283   0.9437   2.4762
 D5N  H21  H  HCH2  0   0.200  -7.5518  -0.3337   1.3160
 D5N  H20  H  HCH2  0   0.236  -7.4717   0.9267   2.5577
 D5N  H22  H  HCH2  0   0.200  -6.8785   0.3042  -0.9469
 D5N  H23  H  HCH2  0   0.237  -6.3530   1.9795  -1.1813
 D5N  H25  H  HCH2  0   0.197  -4.3198   1.5942   0.1207
 D5N  H24  H  HCH2  0   0.245  -4.4765   0.3699  -1.1445
 D5N  H28  H  HCR5  0   0.260  -0.1253  -5.1426  -2.4884
 D5N  H29  H  HCR5  0   0.268   1.5653  -3.0285  -2.9167

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
 D5N  C06  C07  single    1.531  0.020  1.531
 D5N  C06  C05  single    1.544  0.020  1.544
 D5N  C18  C17  single    1.516  0.020  1.516
 D5N  C18  O04  single    1.411  0.020  1.411
 D5N  C17  N03  single    1.452  0.020  1.452
 D5N  N03  C16  single    1.445  0.020  1.445
 D5N  N03  C20  single    1.451  0.020  1.451
 D5N  O03  C15  single    1.401  0.020  1.401
 D5N  C19  O04  single    1.410  0.020  1.410
 D5N  C19  C20  single    1.517  0.020  1.517
 D5N  C07  C08  single    1.525  0.020  1.525
 D5N  C05  C04  single    1.541  0.020  1.541
 D5N  C16  C15  single    1.528  0.020  1.528
 D5N  C15  C14  single    1.529  0.020  1.529
 D5N  C04  C08  single    1.522  0.020  1.522
 D5N  C04  O02  single    1.432  0.020  1.432
 D5N  N02  C21  aromatic  1.319  0.020  1.319
 D5N  N02  N01  aromatic  1.330  0.020  1.330
 D5N  C21  C22  aromatic  1.401  0.020  1.401
 D5N  C14  N01  single    1.445  0.020  1.445
 D5N  N01  C13  aromatic  1.357  0.020  1.357
 D5N  O02  C03  single    1.335  0.020  1.335
 D5N  C22  C13  aromatic  1.379  0.020  1.379
 D5N  C09  C03  aromatic  1.392  0.020  1.392
 D5N  C09  C10  aromatic  1.396  0.020  1.396
 D5N  C13  C10  single    1.467  0.020  1.467
 D5N  C03  C02  aromatic  1.402  0.020  1.402
 D5N  C10  C11  aromatic  1.390  0.020  1.390
 D5N  C02  O01  single    1.380  0.020  1.380
 D5N  C02  C12  aromatic  1.380  0.020  1.380
 D5N  O01  C01  single    1.355  0.020  1.355
 D5N  C11  C12  aromatic  1.388  0.020  1.388
 D5N  C01  F01  single    1.351  0.020  1.351
 D5N  C01  F02  single    1.357  0.020  1.357
 D5N  C11  H12  single    0.930  0.020  1.080
 D5N  C01  H01  single    0.970  0.020  1.090
 D5N  C04  H02  single    0.970  0.020  1.090
 D5N  C05  H03  single    0.970  0.020  1.090
 D5N  C05  H04  single    0.970  0.020  1.090
 D5N  C06  H06  single    0.970  0.020  1.090
 D5N  C06  H05  single    0.970  0.020  1.090
 D5N  C07  H07  single    0.970  0.020  1.090
 D5N  C07  H08  single    0.970  0.020  1.090
 D5N  C08  H10  single    0.970  0.020  1.090
 D5N  C08  H09  single    0.970  0.020  1.090
 D5N  C09  H11  single    0.930  0.020  1.080
 D5N  C12  H13  single    0.930  0.020  1.080
 D5N  C14  H27  single    0.970  0.020  1.090
 D5N  C14  H26  single    0.970  0.020  1.090
 D5N  C15  H14  single    0.970  0.020  1.090
 D5N  O03  H15  single    0.850  0.020  0.980
 D5N  C16  H16  single    0.970  0.020  1.090
 D5N  C16  H17  single    0.970  0.020  1.090
 D5N  C17  H19  single    0.970  0.020  1.090
 D5N  C17  H18  single    0.970  0.020  1.090
 D5N  C18  H21  single    0.970  0.020  1.090
 D5N  C18  H20  single    0.970  0.020  1.090
 D5N  C19  H22  single    0.970  0.020  1.090
 D5N  C19  H23  single    0.970  0.020  1.090
 D5N  C20  H25  single    0.970  0.020  1.090
 D5N  C20  H24  single    0.970  0.020  1.090
 D5N  C21  H28  single    0.930  0.020  1.080
 D5N  C22  H29  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
 D5N  C13  C10  C09  117.90  3.000
 D5N  C13  C10  C11  122.45  3.000
 D5N  C09  C10  C11  119.65  3.000
 D5N  H12  C11  C12  119.22  3.000
 D5N  H12  C11  C10  120.92  3.000
 D5N  C12  C11  C10  119.83  3.000
 D5N  H01  C01  F02  109.63  3.000
 D5N  H01  C01  F01  110.25  3.000
 D5N  F02  C01  F01  105.40  3.000
 D5N  H01  C01  O01  108.81  3.000
 D5N  F02  C01  O01  111.11  3.000
 D5N  F01  C01  O01  111.61  3.000
 D5N  C02  O01  C01  118.01  3.000
 D5N  C12  C02  C03  120.92  3.000
 D5N  C12  C02  O01  120.76  3.000
 D5N  C03  C02  O01  118.26  3.000
 D5N  C09  C03  O02  125.14  3.000
 D5N  C09  C03  C02  118.29  3.000
 D5N  O02  C03  C02  116.56  3.000
 D5N  C04  O02  C03  119.67  3.000
 D5N  H02  C04  C08  111.85  3.000
 D5N  H02  C04  C05  112.83  3.000
 D5N  C08  C04  C05  104.76  3.000
 D5N  H02  C04  O02  109.17  3.000
 D5N  C08  C04  O02  106.38  3.000
 D5N  C05  C04  O02  111.62  3.000
 D5N  H04  C05  H03  106.41  3.000
 D5N  H04  C05  C06  111.42  3.000
 D5N  H03  C05  C06  111.63  3.000
 D5N  H04  C05  C04  110.25  3.000
 D5N  H03  C05  C04  110.97  3.000
 D5N  C06  C05  C04  106.23  3.000
 D5N  H05  C06  H06  107.00  3.000
 D5N  H05  C06  C07  109.50  3.000
 D5N  H06  C06  C07  112.68  3.000
 D5N  H05  C06  C05  109.94  3.000
 D5N  H06  C06  C05  112.30  3.000
 D5N  C07  C06  C05  105.42  3.000
 D5N  H08  C07  H07  107.17  3.000
 D5N  H08  C07  C08  112.86  3.000
 D5N  H07  C07  C08  110.49  3.000
 D5N  H08  C07  C06  112.76  3.000
 D5N  H07  C07  C06  110.82  3.000
 D5N  C08  C07  C06  102.77  3.000
 D5N  H09  C08  H10  107.48  3.000
 D5N  H09  C08  C07  114.93  3.000
 D5N  H10  C08  C07  109.65  3.000
 D5N  H09  C08  C04  112.54  3.000
 D5N  H10  C08  C04  108.10  3.000
 D5N  C07  C08  C04  103.95  3.000
 D5N  H11  C09  C03  120.55  3.000
 D5N  H11  C09  C10  118.43  3.000
 D5N  C03  C09  C10  121.01  3.000
 D5N  H13  C12  C02  119.93  3.000
 D5N  H13  C12  C11  119.77  3.000
 D5N  C02  C12  C11  120.29  3.000
 D5N  C22  C13  N01  106.20  3.000
 D5N  C22  C13  C10  128.86  3.000
 D5N  N01  C13  C10  124.89  3.000
 D5N  C14  N01  N02  119.41  3.000
 D5N  C14  N01  C13  128.33  3.000
 D5N  N02  N01  C13  112.19  3.000
 D5N  C21  N02  N01  105.71  3.000
 D5N  H26  C14  H27  107.08  3.000
 D5N  H26  C14  C15  110.01  3.000
 D5N  H27  C14  C15  110.18  3.000
 D5N  H26  C14  N01  108.15  3.000
 D5N  H27  C14  N01  107.74  3.000
 D5N  C15  C14  N01  113.45  3.000
 D5N  H14  C15  C16  109.40  3.000
 D5N  H14  C15  O03  105.08  3.000
 D5N  C16  C15  O03  113.03  3.000
 D5N  H14  C15  C14  108.05  3.000
 D5N  C16  C15  C14  108.44  3.000
 D5N  O03  C15  C14  112.65  3.000
 D5N  H15  O03  C15  108.82  3.000
 D5N  H17  C16  H16  106.19  3.000
 D5N  H17  C16  N03  111.91  3.000
 D5N  H16  C16  N03  107.81  3.000
 D5N  H17  C16  C15  108.47  3.000
 D5N  H16  C16  C15  108.63  3.000
 D5N  N03  C16  C15  113.53  3.000
 D5N  C20  N03  C17  109.60  3.000
 D5N  C20  N03  C16  113.03  3.000
 D5N  C17  N03  C16  111.18  3.000
 D5N  H18  C17  H19  107.13  3.000
 D5N  H18  C17  C18  109.43  3.000
 D5N  H19  C17  C18  108.82  3.000
 D5N  H18  C17  N03  111.78  3.000
 D5N  H19  C17  N03  109.48  3.000
 D5N  C18  C17  N03  110.11  3.000
 D5N  H20  C18  H21  107.90  3.000
 D5N  H20  C18  O04  107.52  3.000
 D5N  H21  C18  O04  110.44  3.000
 D5N  H20  C18  C17  110.18  3.000
 D5N  H21  C18  C17  109.19  3.000
 D5N  O04  C18  C17  111.53  3.000
 D5N  C19  O04  C18  110.68  3.000
 D5N  H23  C19  H22  107.96  3.000
 D5N  H23  C19  C20  110.03  3.000
 D5N  H22  C19  C20  109.06  3.000
 D5N  H23  C19  O04  107.48  3.000
 D5N  H22  C19  O04  110.42  3.000
 D5N  C20  C19  O04  111.82  3.000
 D5N  H24  C20  H25  107.18  3.000
 D5N  H24  C20  C19  107.84  3.000
 D5N  H25  C20  C19  109.64  3.000
 D5N  H24  C20  N03  110.45  3.000
 D5N  H25  C20  N03  111.55  3.000
 D5N  C19  C20  N03  110.07  3.000
 D5N  H28  C21  C22  128.37  3.000
 D5N  H28  C21  N02  120.33  3.000
 D5N  C22  C21  N02  111.30  3.000
 D5N  H29  C22  C21  128.45  3.000
 D5N  H29  C22  C13  126.94  3.000
 D5N  C21  C22  C13  104.61  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
 D5N  CONST_01  C02  C03  C09  C10    0.00   0.0  0
 D5N  CONST_02  N02  N01  C13  C10  180.00   0.0  0
 D5N  CONST_03  C21  C22  C13  C10  180.00   0.0  0
 D5N  CONST_04  C02  C12  C11  C10    0.00   0.0  0
 D5N  CONST_05  C03  C09  C10  C11    0.00   0.0  0
 D5N  CONST_08  C03  C02  C12  C11    0.00   0.0  0
 D5N  CONST_09  C13  C10  C09  C03  180.00   0.0  0
 D5N  CONST_10  C12  C02  C03  C09    0.00   0.0  0
 D5N  CONST_13  C12  C11  C10  C09    0.00   0.0  0
 D5N  CONST_14  C13  C10  C11  C12  180.00   0.0  0
 D5N  CONST_15  C21  N02  N01  C13    0.00   0.0  0
 D5N  CONST_16  N02  C21  C22  C13    0.00   0.0  0
 D5N  CONST_17  C22  C21  N02  N01    0.00   0.0  0
 D5N  CONST_18  C21  C22  C13  N01    0.00   0.0  0
 D5N  CONST_19  C22  C13  N01  N02    0.00   0.0  0
 D5N  CONST_20  O02  C03  C09  C10  180.00   0.0  0
 D5N  CONST_21  C14  N01  C13  C10    0.00   0.0  0
 D5N  CONST_22  O01  C02  C12  C11  180.00   0.0  0
 D5N  CONST_23  C09  C03  C02  O01  180.00   0.0  0
 D5N  CONST_24  C12  C02  C03  O02  180.00   0.0  0
 D5N  CONST_25  C21  N02  N01  C14  180.00   0.0  0
 D5N  CONST_26  C22  C13  N01  C14  180.00   0.0  0
 D5N  CONST_27  H29  C22  C13  C10    0.00   0.0  0
 D5N  CONST_28  H13  C12  C11  C10  180.00   0.0  0
 D5N  CONST_29  H11  C09  C10  C11  180.00   0.0  0
 D5N  CONST_30  H12  C11  C12  C02  180.00   0.0  0
 D5N  CONST_31  H28  C21  C22  C13  180.00   0.0  0
 D5N  Var_01    C07  C06  C05  C04   11.48  30.0  1
 D5N  Var_02    C06  C07  C08  C04   41.64  30.0  1
 D5N  Var_03    C08  C07  C06  C05  -32.49  30.0  1
 D5N  Var_04    O04  C18  C17  N03  -57.56  30.0  1
 D5N  Var_05    O04  C19  C20  N03   57.09  30.0  1
 D5N  Var_06    C19  C20  N03  C17  -56.44  30.0  1
 D5N  Var_07    C20  N03  C17  C18   56.77  30.0  1
 D5N  Var_08    C20  C19  O04  C18  -57.10  30.0  1
 D5N  Var_09    C09  C03  O02  C04   -2.07  30.0  2
 D5N  Var_10    C03  C02  O01  C01   97.53  30.0  3
 D5N  Var_11    C15  C14  N01  C13  102.77  30.0  2
 D5N  Var_12    C17  N03  C16  C15  169.70  30.0  1
 D5N  Var_13    F01  C01  O01  C02  -51.27  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
 D5N  chir_01  C04  C05  C08  O02  positiv
 D5N  chir_02  C15  O03  C16  C14  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
 D5N  plan-1  C10  0.020
 D5N  plan-1  C13  0.020
 D5N  plan-1  N01  0.020
 D5N  plan-1  N02  0.020
 D5N  plan-1  C14  0.020
 D5N  plan-1  C21  0.020
 D5N  plan-1  C22  0.020
 D5N  plan-1  H28  0.020
 D5N  plan-1  H29  0.020
 D5N  plan-2  C10  0.020
 D5N  plan-2  C11  0.020
 D5N  plan-2  O01  0.020
 D5N  plan-2  C02  0.020
 D5N  plan-2  C03  0.020
 D5N  plan-2  O02  0.020
 D5N  plan-2  C09  0.020
 D5N  plan-2  C12  0.020
 D5N  plan-2  C13  0.020
 D5N  plan-2  H12  0.020
 D5N  plan-2  H11  0.020
 D5N  plan-2  H13  0.020

