# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 16:06:46 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: N-{[4-(4-phenyl-1,3-thiazol-2-yl)tetrahydro-2H-pyran-4-yl]methyl}-3-[5-(trifluoromethyl)-1,2,4-oxadiazol-3-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1onc(n1)c2cccc(c2)C(=O)NCC3(CCOCC3)c4scc(n4)c5ccccc5
#
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
 NU9  NU9  N-{[4-(4-phenyl-1,3-thiazol-2-yl)tetrahydro-2H-pyran-4-yl]methyl}-3-[5-(trifluoromethyl)-1,2,4-oxadiazol-3-yl]benzamide  ligand  57  36  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NU9
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
 NU9  F01   F  F     0  -0.295  -8.1414  -0.1539  -1.3688
 NU9  C02   C  CT    0   1.078  -7.6922  -0.0663  -0.1200
 NU9  F03   F  F     0  -0.286  -7.8132   1.1903   0.2807
 NU9  F04   F  F     0  -0.293  -8.4458  -0.8416   0.6489
 NU9  C05   C  CR5   0   0.277  -6.2512  -0.4865  -0.0506
 NU9  N06   N  N     0  -0.431  -5.2255   0.2689  -0.1685
 NU9  C07   C  CR5   0   0.349  -4.1988  -0.6300  -0.0592
 NU9  N08   N  N     0  -0.129  -4.6067  -1.8535   0.1145
 NU9  O09   O  O     0  -0.307  -5.9654  -1.7599   0.1208
 NU9  C10   C  CR6   0   0.015  -2.7910  -0.2472  -0.1233
 NU9  C11   C  CR16  0  -0.277  -2.4502   1.0748  -0.4032
 NU9  C12   C  CR16  0  -0.229  -1.1168   1.4443  -0.4691
 NU9  C13   C  CR16  0  -0.291  -0.1220   0.5077  -0.2364
 NU9  C14   C  CR6   0  -0.009  -0.4574  -0.8134   0.0566
 NU9  C15   C  CR16  0  -0.308  -1.7917  -1.1920   0.0917
 NU9  C16   C  C     0   0.519   0.5939  -1.8551   0.2803
 NU9  O17   O  O     0  -0.477   0.4282  -3.0096  -0.0856
 NU9  N18   N  NH1   0  -0.632   1.6981  -1.4119   0.9049
 NU9  C19   C  CH2   0  -0.272   2.9228  -2.1537   1.0415
 NU9  C20   C  CT    0  -0.208   4.0351  -1.6763   0.0702
 NU9  C21   C  CH2   0  -0.463   5.3126  -2.4900   0.3321
 NU9  C22   C  CH2   0  -0.183   5.1920  -3.9238  -0.1663
 NU9  O23   O  O2    0  -0.481   4.8450  -3.9805  -1.5299
 NU9  C24   C  CH2   0  -0.193   3.6115  -3.3444  -1.7844
 NU9  C25   C  CH2   0  -0.437   3.6381  -1.8741  -1.4004
 NU9  C26   C  CR5   0   0.094   4.2675  -0.2134   0.3328
 NU9  N27   N  N     0  -0.406   3.5635   0.7390  -0.1847
 NU9  C28   C  CR5   0   0.371   3.9227   1.9747   0.2836
 NU9  C29   C  CR15  0  -0.585   4.9437   1.9533   1.1883
 NU9  S30   S  S2    0   0.254   5.4582   0.3470   1.4600
 NU9  C31   C  CR6   0   0.059   3.2064   3.1620  -0.1998
 NU9  C32   C  CR16  0  -0.327   3.3078   4.3869   0.4621
 NU9  C33   C  CR16  0  -0.236   2.6203   5.4984   0.0010
 NU9  C34   C  CR16  0  -0.266   1.8116   5.4052  -1.1252
 NU9  C35   C  CR16  0  -0.237   1.7029   4.1910  -1.7897
 NU9  C36   C  CR16  0  -0.305   2.3960   3.0792  -1.3336
 NU9  H11   H  HCR6  0   0.273  -3.2236   1.8108  -0.5757
 NU9  H12   H  HCR6  0   0.270  -0.8504   2.4657  -0.7062
 NU9  H13   H  HCR6  0   0.281   0.9174   0.8048  -0.3157
 NU9  H15   H  HCR6  0   0.270  -2.0500  -2.2213   0.3045
 NU9  HN18  H  HNH1  0   0.409   1.7009  -0.4642   1.2445
 NU9  H19   H  HCH2  0   0.268   3.2831  -2.0558   2.0680
 NU9  H19A  H  HCH2  0   0.267   2.7065  -3.2081   0.8807
 NU9  H21   H  HCH2  0   0.256   6.1530  -2.0103  -0.1777
 NU9  H21A  H  HCH2  0   0.253   5.5535  -2.5125   1.3995
 NU9  H22   H  HCH2  0   0.247   6.1535  -4.4277  -0.0572
 NU9  H22A  H  HCH2  0   0.206   4.4684  -4.4863   0.4406
 NU9  H24   H  HCH2  0   0.243   3.4180  -3.4396  -2.8540
 NU9  H24A  H  HCH2  0   0.207   2.7951  -3.8622  -1.2633
 NU9  H25   H  HCH2  0   0.253   2.6668  -1.4254  -1.6126
 NU9  H25A  H  HCH2  0   0.249   4.3628  -1.3530  -2.0320
 NU9  H29   H  HCR5  0   0.306   5.4243   2.7810   1.6855
 NU9  H32   H  HCR6  0   0.251   3.9168   4.4745   1.3531
 NU9  H33   H  HCR6  0   0.260   2.7101   6.4390   0.5289
 NU9  H34   H  HCR6  0   0.259   1.2685   6.2716  -1.4794
 NU9  H35   H  HCR6  0   0.260   1.0771   4.1062  -2.6688
 NU9  H36   H  HCR6  0   0.258   2.3133   2.1391  -1.8631

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
 NU9  F01  C02   single    1.330  0.020  1.330
 NU9  C02  F03   single    1.324  0.020  1.324
 NU9  C02  F04   single    1.327  0.020  1.327
 NU9  C02  C05   single    1.503  0.020  1.503
 NU9  C05  N06   aromatic  1.279  0.020  1.279
 NU9  C05  O09   aromatic  1.316  0.020  1.316
 NU9  N06  C07   aromatic  1.369  0.020  1.369
 NU9  C07  N08   aromatic  1.301  0.020  1.301
 NU9  C07  C10   single    1.460  0.020  1.460
 NU9  N08  O09   aromatic  1.362  0.020  1.362
 NU9  C10  C11   aromatic  1.394  0.020  1.394
 NU9  C10  C15   aromatic  1.392  0.020  1.392
 NU9  C11  C12   aromatic  1.385  0.020  1.385
 NU9  C12  C13   aromatic  1.386  0.020  1.386
 NU9  C13  C14   aromatic  1.394  0.020  1.394
 NU9  C14  C15   aromatic  1.387  0.020  1.387
 NU9  C14  C16   single    1.497  0.020  1.497
 NU9  C16  O17   double    1.222  0.020  1.222
 NU9  C16  N18   single    1.344  0.020  1.344
 NU9  N18  C19   single    1.438  0.020  1.438
 NU9  C19  C20   single    1.552  0.020  1.552
 NU9  C20  C21   single    1.537  0.020  1.537
 NU9  C20  C25   single    1.536  0.020  1.536
 NU9  C20  C26   single    1.504  0.020  1.504
 NU9  C21  C22   single    1.523  0.020  1.523
 NU9  C22  O23   single    1.408  0.020  1.408
 NU9  O23  C24   single    1.411  0.020  1.411
 NU9  C24  C25   single    1.520  0.020  1.520
 NU9  C26  N27   aromatic  1.292  0.020  1.292
 NU9  C26  S30   aromatic  1.733  0.020  1.733
 NU9  N27  C28   aromatic  1.369  0.020  1.369
 NU9  C28  C29   aromatic  1.364  0.020  1.364
 NU9  C28  C31   single    1.468  0.020  1.468
 NU9  C29  S30   aromatic  1.708  0.020  1.708
 NU9  C31  C32   aromatic  1.396  0.020  1.396
 NU9  C31  C36   aromatic  1.396  0.020  1.396
 NU9  C32  C33   aromatic  1.386  0.020  1.386
 NU9  C33  C34   aromatic  1.390  0.020  1.390
 NU9  C34  C35   aromatic  1.388  0.020  1.388
 NU9  C35  C36   aromatic  1.387  0.020  1.387
 NU9  C11  H11   single    0.930  0.020  1.080
 NU9  C12  H12   single    0.930  0.020  1.080
 NU9  C13  H13   single    0.930  0.020  1.080
 NU9  C15  H15   single    0.930  0.020  1.080
 NU9  N18  HN18  single    0.860  0.020  1.020
 NU9  C19  H19   single    0.970  0.020  1.090
 NU9  C19  H19A  single    0.970  0.020  1.090
 NU9  C21  H21   single    0.970  0.020  1.090
 NU9  C21  H21A  single    0.970  0.020  1.090
 NU9  C22  H22   single    0.970  0.020  1.090
 NU9  C22  H22A  single    0.970  0.020  1.090
 NU9  C24  H24   single    0.970  0.020  1.090
 NU9  C24  H24A  single    0.970  0.020  1.090
 NU9  C25  H25   single    0.970  0.020  1.090
 NU9  C25  H25A  single    0.970  0.020  1.090
 NU9  C29  H29   single    0.930  0.020  1.080
 NU9  C32  H32   single    0.930  0.020  1.080
 NU9  C33  H33   single    0.930  0.020  1.080
 NU9  C34  H34   single    0.930  0.020  1.080
 NU9  C35  H35   single    0.930  0.020  1.080
 NU9  C36  H36   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
 NU9  C05   C02  F04  110.76  3.000
 NU9  C05   C02  F03  109.81  3.000
 NU9  F04   C02  F03  109.10  3.000
 NU9  C05   C02  F01  110.41  3.000
 NU9  F04   C02  F01  108.29  3.000
 NU9  F03   C02  F01  108.40  3.000
 NU9  O09   C05  N06  114.15  3.000
 NU9  O09   C05  C02  119.00  3.000
 NU9  N06   C05  C02  126.84  3.000
 NU9  C07   N06  C05  101.90  3.000
 NU9  C10   C07  N08  123.67  3.000
 NU9  C10   C07  N06  123.19  3.000
 NU9  N08   C07  N06  113.14  3.000
 NU9  O09   N08  C07  104.40  3.000
 NU9  N08   O09  C05  106.41  3.000
 NU9  C15   C10  C11  119.96  3.000
 NU9  C15   C10  C07  120.49  3.000
 NU9  C11   C10  C07  119.55  3.000
 NU9  H11   C11  C12  119.95  3.000
 NU9  H11   C11  C10  120.18  3.000
 NU9  C12   C11  C10  119.87  3.000
 NU9  H12   C12  C13  119.88  3.000
 NU9  H12   C12  C11  119.95  3.000
 NU9  C13   C12  C11  120.17  3.000
 NU9  H13   C13  C14  120.39  3.000
 NU9  H13   C13  C12  119.39  3.000
 NU9  C14   C13  C12  120.20  3.000
 NU9  C16   C14  C15  118.80  3.000
 NU9  C16   C14  C13  121.46  3.000
 NU9  C15   C14  C13  119.69  3.000
 NU9  H15   C15  C14  119.60  3.000
 NU9  H15   C15  C10  120.30  3.000
 NU9  C14   C15  C10  120.09  3.000
 NU9  N18   C16  O17  124.19  3.000
 NU9  N18   C16  C14  114.65  3.000
 NU9  O17   C16  C14  121.16  3.000
 NU9  HN18  N18  C19  116.81  3.000
 NU9  HN18  N18  C16  118.01  3.000
 NU9  C19   N18  C16  125.01  3.000
 NU9  H19A  C19  H19  106.93  3.000
 NU9  H19A  C19  C20  110.36  3.000
 NU9  H19   C19  C20  108.92  3.000
 NU9  H19A  C19  N18  108.44  3.000
 NU9  H19   C19  N18  108.90  3.000
 NU9  C20   C19  N18  113.10  3.000
 NU9  C26   C20  C25  109.41  3.000
 NU9  C26   C20  C21  110.89  3.000
 NU9  C25   C20  C21  108.05  3.000
 NU9  C26   C20  C19  107.49  3.000
 NU9  C25   C20  C19  111.98  3.000
 NU9  C21   C20  C19  109.04  3.000
 NU9  H21A  C21  H21  107.13  3.000
 NU9  H21A  C21  C22  108.50  3.000
 NU9  H21   C21  C22  108.73  3.000
 NU9  H21A  C21  C20  111.10  3.000
 NU9  H21   C21  C20  109.09  3.000
 NU9  C22   C21  C20  112.14  3.000
 NU9  H22A  C22  H22  106.77  3.000
 NU9  H22A  C22  O23  110.60  3.000
 NU9  H22   C22  O23  107.19  3.000
 NU9  H22A  C22  C21  110.68  3.000
 NU9  H22   C22  C21  109.41  3.000
 NU9  O23   C22  C21  111.98  3.000
 NU9  C24   O23  C22  111.84  3.000
 NU9  H24A  C24  H24  106.99  3.000
 NU9  H24A  C24  C25  110.44  3.000
 NU9  H24   C24  C25  109.58  3.000
 NU9  H24A  C24  O23  110.60  3.000
 NU9  H24   C24  O23  107.01  3.000
 NU9  C25   C24  O23  112.04  3.000
 NU9  H25A  C25  H25  106.36  3.000
 NU9  H25A  C25  C24  109.07  3.000
 NU9  H25   C25  C24  109.46  3.000
 NU9  H25A  C25  C20  108.69  3.000
 NU9  H25   C25  C20  111.31  3.000
 NU9  C24   C25  C20  111.78  3.000
 NU9  S30   C26  N27  113.36  3.000
 NU9  S30   C26  C20  122.29  3.000
 NU9  N27   C26  C20  124.23  3.000
 NU9  C28   N27  C26  112.65  3.000
 NU9  C31   C28  C29  126.58  3.000
 NU9  C31   C28  N27  119.28  3.000
 NU9  C29   C28  N27  114.14  3.000
 NU9  H29   C29  S30  120.93  3.000
 NU9  H29   C29  C28  128.84  3.000
 NU9  S30   C29  C28  110.21  3.000
 NU9  C29   S30  C26   89.64  3.000
 NU9  C36   C31  C32  118.64  3.000
 NU9  C36   C31  C28  120.17  3.000
 NU9  C32   C31  C28  121.20  3.000
 NU9  H32   C32  C33  119.20  3.000
 NU9  H32   C32  C31  120.13  3.000
 NU9  C33   C32  C31  120.66  3.000
 NU9  H33   C33  C34  120.12  3.000
 NU9  H33   C33  C32  119.58  3.000
 NU9  C34   C33  C32  120.30  3.000
 NU9  H34   C34  C35  120.28  3.000
 NU9  H34   C34  C33  120.24  3.000
 NU9  C35   C34  C33  119.48  3.000
 NU9  H35   C35  C36  119.55  3.000
 NU9  H35   C35  C34  120.16  3.000
 NU9  C36   C35  C34  120.29  3.000
 NU9  H36   C36  C35  119.81  3.000
 NU9  H36   C36  C31  119.56  3.000
 NU9  C35   C36  C31  120.63  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
 NU9  CONST_01  N08   C07  N06  C05     0.00   0.0  0
 NU9  CONST_02  C10   C07  N06  C05   180.00   0.0  0
 NU9  CONST_03  C07   N08  O09  C05     0.00   0.0  0
 NU9  CONST_04  N08   O09  C05  N06     0.00   0.0  0
 NU9  CONST_05  O09   N08  C07  N06     0.00   0.0  0
 NU9  CONST_06  C11   C10  C07  N06     0.00   0.0  0
 NU9  CONST_07  C15   C10  C07  N06   180.00   0.0  0
 NU9  CONST_08  O09   C05  N06  C07     0.00   0.0  0
 NU9  CONST_09  C12   C11  C10  C07   180.00   0.0  0
 NU9  CONST_10  C14   C15  C10  C07   180.00   0.0  0
 NU9  CONST_11  C11   C10  C07  N08   180.00   0.0  0
 NU9  CONST_12  C15   C10  C07  N08     0.00   0.0  0
 NU9  CONST_13  C10   C07  N08  O09   180.00   0.0  0
 NU9  CONST_14  C13   C12  C11  C10     0.00   0.0  0
 NU9  CONST_15  C13   C14  C15  C10     0.00   0.0  0
 NU9  CONST_16  C14   C15  C10  C11     0.00   0.0  0
 NU9  CONST_17  C14   C13  C12  C11     0.00   0.0  0
 NU9  CONST_18  C15   C10  C11  C12     0.00   0.0  0
 NU9  CONST_19  C15   C14  C13  C12     0.00   0.0  0
 NU9  CONST_20  C29   C28  N27  C26     0.00   0.0  0
 NU9  CONST_21  C31   C28  N27  C26   180.00   0.0  0
 NU9  CONST_22  C28   C29  S30  C26     0.00   0.0  0
 NU9  CONST_23  C29   S30  C26  N27     0.00   0.0  0
 NU9  CONST_24  S30   C29  C28  N27     0.00   0.0  0
 NU9  CONST_26  C36   C31  C28  N27     0.00   0.0  0
 NU9  CONST_27  S30   C26  N27  C28     0.00   0.0  0
 NU9  CONST_28  C33   C32  C31  C28   180.00   0.0  0
 NU9  CONST_29  C35   C36  C31  C28   180.00   0.0  0
 NU9  CONST_30  C32   C31  C28  C29     0.00   0.0  0
 NU9  CONST_31  C36   C31  C28  C29   180.00   0.0  0
 NU9  CONST_32  C31   C28  C29  S30   180.00   0.0  0
 NU9  CONST_33  C34   C33  C32  C31     0.00   0.0  0
 NU9  CONST_34  C34   C35  C36  C31     0.00   0.0  0
 NU9  CONST_35  C35   C36  C31  C32     0.00   0.0  0
 NU9  CONST_36  C35   C34  C33  C32     0.00   0.0  0
 NU9  CONST_37  C36   C31  C32  C33     0.00   0.0  0
 NU9  CONST_38  C36   C35  C34  C33     0.00   0.0  0
 NU9  CONST_39  C28   N27  C26  C20   180.00   0.0  0
 NU9  CONST_40  C29   S30  C26  C20   180.00   0.0  0
 NU9  CONST_41  C07   N06  C05  C02   180.00   0.0  0
 NU9  CONST_42  N08   O09  C05  C02   180.00   0.0  0
 NU9  CONST_43  C16   C14  C15  C10   180.00   0.0  0
 NU9  CONST_44  C16   C14  C13  C12   180.00   0.0  0
 NU9  CONST_45  H11   C11  C10  C07     0.00   0.0  0
 NU9  CONST_46  H15   C15  C10  C07     0.00   0.0  0
 NU9  CONST_47  H12   C12  C11  C10   180.00   0.0  0
 NU9  CONST_48  H13   C13  C12  C11   180.00   0.0  0
 NU9  CONST_49  H29   C29  S30  C26   180.00   0.0  0
 NU9  CONST_50  H32   C32  C31  C28     0.00   0.0  0
 NU9  CONST_51  H36   C36  C31  C28     0.00   0.0  0
 NU9  CONST_52  H33   C33  C32  C31   180.00   0.0  0
 NU9  CONST_53  H35   C35  C36  C31   180.00   0.0  0
 NU9  CONST_54  H34   C34  C33  C32   180.00   0.0  0
 NU9  CONST_55  C19   N18  C16  C14   180.00   0.0  0
 NU9  CONST_56  HN18  N18  C16  C14     0.00   0.0  0
 NU9  CONST_57  C19   N18  C16  O17     0.00   0.0  0
 NU9  Var_01    O23   C22  C21  C20    55.25  30.0  1
 NU9  Var_02    O23   C24  C25  C20   -56.13  30.0  1
 NU9  Var_03    C25   C24  O23  C22    60.21  30.0  1
 NU9  Var_04    N06   C05  C02  F01    91.06  30.0  2
 NU9  Var_05    O17   C16  C14  C13  -144.55  30.0  2
 NU9  Var_06    C20   C19  N18  C16   103.39  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
 NU9  chir_01  C20  C21  C25  C26  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
 NU9  plan-1  C02   0.020
 NU9  plan-1  C05   0.020
 NU9  plan-1  N06   0.020
 NU9  plan-1  C07   0.020
 NU9  plan-1  N08   0.020
 NU9  plan-1  O09   0.020
 NU9  plan-1  C10   0.020
 NU9  plan-2  C20   0.020
 NU9  plan-2  C26   0.020
 NU9  plan-2  N27   0.020
 NU9  plan-2  C28   0.020
 NU9  plan-2  C29   0.020
 NU9  plan-2  S30   0.020
 NU9  plan-2  C31   0.020
 NU9  plan-2  H29   0.020
 NU9  plan-3  C07   0.020
 NU9  plan-3  C10   0.020
 NU9  plan-3  C11   0.020
 NU9  plan-3  C12   0.020
 NU9  plan-3  C13   0.020
 NU9  plan-3  C14   0.020
 NU9  plan-3  C15   0.020
 NU9  plan-3  C16   0.020
 NU9  plan-3  H11   0.020
 NU9  plan-3  H12   0.020
 NU9  plan-3  H13   0.020
 NU9  plan-3  H15   0.020
 NU9  plan-4  C28   0.020
 NU9  plan-4  C31   0.020
 NU9  plan-4  C32   0.020
 NU9  plan-4  C33   0.020
 NU9  plan-4  C34   0.020
 NU9  plan-4  C35   0.020
 NU9  plan-4  C36   0.020
 NU9  plan-4  H32   0.020
 NU9  plan-4  H33   0.020
 NU9  plan-4  H34   0.020
 NU9  plan-4  H35   0.020
 NU9  plan-4  H36   0.020
 NU9  plan-5  C14   0.020
 NU9  plan-5  C16   0.020
 NU9  plan-5  O17   0.020
 NU9  plan-5  N18   0.020
 NU9  plan-5  C19   0.020
 NU9  plan-5  HN18  0.020

