# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 13:49:49 2021
#   Inital geometry file: a 138 line input string
#   Ligand name: ~{N}-pyridin-3-yl-4-[[3-[5-(trifluoromethyl)pyridin-2-yl]oxyphenyl]methyl]piperidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1ccc(Oc2cccc(CC3CCN(CC3)C(=O)Nc4cccnc4)c2)nc1
#
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
 H2R  H2R  ~{N}-pyridin-3-yl-4-[[3-[5-(trifluoromethyl)pyridin-2-yl]oxyphenyl]methyl]piperidine-1-carboxamide  ligand  56  33  .  2022-03-18  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_H2R
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
 H2R  C10  C  CR16  0  -0.238  77.3762  126.3476  62.4847
 H2R  C17  C  CR6   0  -0.321  78.5900  128.0386  69.0600
 H2R  C20  C  CT    0   1.065  78.5068  127.9609  70.5461
 H2R  C24  C  CR16  0  -0.359  79.6710  126.3354  64.0385
 H2R  C26  C  CH2   0  -0.366  83.1008  123.2914  60.2716
 H2R  C28  C  CR6   0   0.290  87.1708  123.2469  61.3076
 H2R  C02  C  C     0   0.715  85.1896  124.5839  60.7543
 H2R  C04  C  CH2   0  -0.318  83.0535  125.6961  60.4519
 H2R  C05  C  CH2   0  -0.417  82.1492  125.6271  61.6780
 H2R  C06  C  CH1   0  -0.239  81.3125  124.3478  61.6846
 H2R  C07  C  CH2   0  -0.506  80.4717  124.2061  62.9579
 H2R  C08  C  CR6   0   0.147  79.4620  125.3053  63.1281
 H2R  C09  C  CR16  0  -0.307  78.3027  125.3254  62.3526
 H2R  C11  C  CR16  0  -0.320  77.5818  127.3727  63.4004
 H2R  C12  C  CR6   0   0.311  78.7339  127.3501  64.1648
 H2R  C14  C  CR6   0   0.513  78.8151  128.1957  66.3625
 H2R  C16  C  CR16  0  -0.060  79.1312  129.1340  68.4082
 H2R  C18  C  CR16  0  -0.141  78.1369  126.9768  68.2804
 H2R  C19  C  CR16  0  -0.408  78.2423  127.0447  66.9090
 H2R  C25  C  CH2   0  -0.414  82.2134  123.1264  61.4987
 H2R  C29  C  CR16  0  -0.100  88.1837  124.0420  60.7626
 H2R  C31  C  CR16  0  -0.087  89.8142  122.9269  61.9142
 H2R  C32  C  CR16  0  -0.314  88.8905  122.0696  62.4900
 H2R  C33  C  CR16  0  -0.238  87.5508  122.2364  62.1862
 H2R  F21  F  F     0  -0.303  78.7862  129.1264  71.1358
 H2R  F22  F  F     0  -0.314  79.3621  127.0547  71.0437
 H2R  F23  F  F     0  -0.312  77.2854  127.5913  70.9554
 H2R  N03  N  NT    0  -0.477  83.8891  124.5087  60.3680
 H2R  N15  N  N     0  -0.427  79.2398  129.2080  67.0893
 H2R  N27  N  NH1   0  -0.790  85.8260  123.3778  60.9660
 H2R  N30  N  N     0  -0.397  89.4637  123.8874  61.0675
 H2R  O01  O  O     0  -0.521  85.7817  125.6465  60.8830
 H2R  O13  O  O2    0  -0.479  78.9730  128.3890  65.0412
 H2R  H1   H  HCR6  0   0.264  76.4802  126.3470  61.8780
 H2R  H2   H  HCR6  0   0.271  80.5635  126.3458  64.6539
 H2R  H3   H  HCH2  0   0.260  82.4779  123.3739  59.3757
 H2R  H4   H  HCH2  0   0.263  83.7292  122.4186  60.1031
 H2R  H5   H  HCH2  0   0.267  83.6767  126.5853  60.4734
 H2R  H6   H  HCH2  0   0.240  82.4461  125.7473  59.5428
 H2R  H7   H  HCH2  0   0.222  82.7670  125.6670  62.5823
 H2R  H8   H  HCH2  0   0.243  81.5043  126.5086  61.6942
 H2R  H9   H  HCH1  0   0.230  80.6285  124.3906  60.8267
 H2R  H10  H  HCH2  0   0.252  79.9540  123.2427  62.9286
 H2R  H11  H  HCH2  0   0.243  81.1366  124.1750  63.8260
 H2R  H12  H  HCR6  0   0.253  78.1250  124.5300  61.6384
 H2R  H13  H  HCR6  0   0.275  76.8622  128.1727  63.5150
 H2R  H14  H  HCR6  0   0.286  79.4966  129.9929  68.9575
 H2R  H15  H  HCR6  0   0.296  77.6970  126.0962  68.7302
 H2R  H16  H  HCR6  0   0.300  77.8859  126.2297  66.2962
 H2R  H17  H  HCH2  0   0.244  81.6078  122.2227  61.3946
 H2R  H18  H  HCH2  0   0.225  82.8430  122.9917  62.3854
 H2R  H19  H  HCR6  0   0.269  87.9523  124.8240  60.0525
 H2R  H20  H  HCR6  0   0.261  90.8710  122.8302  62.1351
 H2R  H21  H  HCR6  0   0.273  89.2105  121.2899  63.1675
 H2R  H22  H  HCR6  0   0.282  86.8036  121.5876  62.6275
 H2R  H23  H  HNH1  0   0.415  85.2631  122.5684  61.1708

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
 H2R  N30  C29  aromatic  1.325  0.020  1.325
 H2R  N30  C31  aromatic  1.328  0.020  1.328
 H2R  C29  C28  aromatic  1.398  0.020  1.398
 H2R  C31  C32  aromatic  1.386  0.020  1.386
 H2R  C26  N03  single    1.453  0.020  1.453
 H2R  C26  C25  single    1.523  0.020  1.523
 H2R  C28  N27  single    1.394  0.020  1.394
 H2R  C28  C33  aromatic  1.392  0.020  1.392
 H2R  N27  C02  single    1.380  0.020  1.380
 H2R  C32  C33  aromatic  1.384  0.020  1.384
 H2R  N03  C02  single    1.359  0.020  1.359
 H2R  N03  C04  single    1.454  0.020  1.454
 H2R  C02  O01  double    1.223  0.020  1.223
 H2R  C04  C05  single    1.525  0.020  1.525
 H2R  C25  C06  single    1.529  0.020  1.529
 H2R  C06  C05  single    1.529  0.020  1.529
 H2R  C06  C07  single    1.532  0.020  1.532
 H2R  C09  C10  aromatic  1.386  0.020  1.386
 H2R  C09  C08  aromatic  1.395  0.020  1.395
 H2R  C10  C11  aromatic  1.390  0.020  1.390
 H2R  C07  C08  single    1.502  0.020  1.502
 H2R  C08  C24  aromatic  1.391  0.020  1.391
 H2R  C11  C12  aromatic  1.383  0.020  1.383
 H2R  C24  C12  aromatic  1.387  0.020  1.387
 H2R  C12  O13  single    1.380  0.020  1.380
 H2R  O13  C14  single    1.345  0.020  1.345
 H2R  C14  C19  aromatic  1.397  0.020  1.397
 H2R  C14  N15  aromatic  1.317  0.020  1.317
 H2R  C19  C18  aromatic  1.377  0.020  1.377
 H2R  N15  C16  aromatic  1.325  0.020  1.325
 H2R  C18  C17  aromatic  1.393  0.020  1.393
 H2R  C16  C17  aromatic  1.385  0.020  1.385
 H2R  C17  C20  single    1.490  0.020  1.490
 H2R  C20  F23  single    1.340  0.020  1.340
 H2R  C20  F21  single    1.336  0.020  1.336
 H2R  C20  F22  single    1.342  0.020  1.342
 H2R  C10  H1   single    0.930  0.020  1.080
 H2R  C24  H2   single    0.930  0.020  1.080
 H2R  C26  H3   single    0.970  0.020  1.090
 H2R  C26  H4   single    0.970  0.020  1.090
 H2R  C04  H5   single    0.970  0.020  1.090
 H2R  C04  H6   single    0.970  0.020  1.090
 H2R  C05  H7   single    0.970  0.020  1.090
 H2R  C05  H8   single    0.970  0.020  1.090
 H2R  C06  H9   single    0.970  0.020  1.090
 H2R  C07  H10  single    0.970  0.020  1.090
 H2R  C07  H11  single    0.970  0.020  1.090
 H2R  C09  H12  single    0.930  0.020  1.080
 H2R  C11  H13  single    0.930  0.020  1.080
 H2R  C16  H14  single    0.930  0.020  1.080
 H2R  C18  H15  single    0.930  0.020  1.080
 H2R  C19  H16  single    0.930  0.020  1.080
 H2R  C25  H17  single    0.970  0.020  1.090
 H2R  C25  H18  single    0.970  0.020  1.090
 H2R  C29  H19  single    0.930  0.020  1.080
 H2R  C31  H20  single    0.930  0.020  1.080
 H2R  C32  H21  single    0.930  0.020  1.080
 H2R  C33  H22  single    0.930  0.020  1.080
 H2R  N27  H23  single    0.890  0.020  1.040

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
 H2R  H1   C10  C11  119.49  3.000
 H2R  H1   C10  C09  119.98  3.000
 H2R  C11  C10  C09  120.53  3.000
 H2R  C18  C17  C16  117.82  3.000
 H2R  C16  C17  C20  122.17  3.000
 H2R  C18  C17  C20  120.01  3.000
 H2R  F23  C20  F22  106.35  3.000
 H2R  F22  C20  F21  106.99  3.000
 H2R  F23  C20  F21  107.24  3.000
 H2R  F22  C20  C17  111.68  3.000
 H2R  F21  C20  C17  112.52  3.000
 H2R  F23  C20  C17  111.71  3.000
 H2R  H2   C24  C12  119.83  3.000
 H2R  H2   C24  C08  120.17  3.000
 H2R  C12  C24  C08  120.00  3.000
 H2R  H4   C26  H3   105.21  3.000
 H2R  H4   C26  N03  111.63  3.000
 H2R  H3   C26  N03  107.45  3.000
 H2R  H4   C26  C25  111.97  3.000
 H2R  H3   C26  C25  109.64  3.000
 H2R  N03  C26  C25  110.68  3.000
 H2R  N27  C28  C33  119.10  3.000
 H2R  C33  C28  C29  117.45  3.000
 H2R  N27  C28  C29  123.38  3.000
 H2R  O01  C02  N27  121.32  3.000
 H2R  O01  C02  N03  122.77  3.000
 H2R  N27  C02  N03  115.89  3.000
 H2R  H6   C04  H5   107.25  3.000
 H2R  H6   C04  N03  108.01  3.000
 H2R  H5   C04  N03  109.87  3.000
 H2R  H6   C04  C05  109.93  3.000
 H2R  H5   C04  C05  111.18  3.000
 H2R  N03  C04  C05  110.49  3.000
 H2R  H8   C05  H7   106.93  3.000
 H2R  H8   C05  C06  110.62  3.000
 H2R  H7   C05  C06  109.60  3.000
 H2R  H8   C05  C04  108.99  3.000
 H2R  H7   C05  C04  109.12  3.000
 H2R  C06  C05  C04  111.46  3.000
 H2R  H9   C06  C25  107.64  3.000
 H2R  H9   C06  C07  108.12  3.000
 H2R  C25  C06  C07  110.52  3.000
 H2R  H9   C06  C05  107.76  3.000
 H2R  C07  C06  C05  112.41  3.000
 H2R  C25  C06  C05  110.21  3.000
 H2R  H11  C07  H10  106.49  3.000
 H2R  H11  C07  C08  109.85  3.000
 H2R  H10  C07  C08  109.23  3.000
 H2R  H11  C07  C06  109.18  3.000
 H2R  H10  C07  C06  108.58  3.000
 H2R  C08  C07  C06  113.28  3.000
 H2R  C09  C08  C07  120.41  3.000
 H2R  C07  C08  C24  121.01  3.000
 H2R  C09  C08  C24  118.57  3.000
 H2R  H12  C09  C08  119.48  3.000
 H2R  H12  C09  C10  119.64  3.000
 H2R  C08  C09  C10  120.88  3.000
 H2R  H13  C11  C12  120.50  3.000
 H2R  H13  C11  C10  121.11  3.000
 H2R  C12  C11  C10  118.39  3.000
 H2R  O13  C12  C11  118.89  3.000
 H2R  O13  C12  C24  119.44  3.000
 H2R  C11  C12  C24  121.63  3.000
 H2R  O13  C14  N15  113.21  3.000
 H2R  N15  C14  C19  123.35  3.000
 H2R  O13  C14  C19  123.44  3.000
 H2R  H14  C16  N15  115.64  3.000
 H2R  H14  C16  C17  121.36  3.000
 H2R  N15  C16  C17  123.00  3.000
 H2R  H15  C18  C19  119.02  3.000
 H2R  H15  C18  C17  121.32  3.000
 H2R  C19  C18  C17  119.66  3.000
 H2R  H16  C19  C18  120.16  3.000
 H2R  H16  C19  C14  122.35  3.000
 H2R  C18  C19  C14  117.49  3.000
 H2R  H18  C25  H17  107.09  3.000
 H2R  H18  C25  C06  109.77  3.000
 H2R  H17  C25  C06  110.22  3.000
 H2R  H18  C25  C26  109.30  3.000
 H2R  H17  C25  C26  109.61  3.000
 H2R  C06  C25  C26  110.77  3.000
 H2R  H19  C29  N30  116.24  3.000
 H2R  H19  C29  C28  120.81  3.000
 H2R  N30  C29  C28  122.95  3.000
 H2R  H20  C31  N30  116.87  3.000
 H2R  H20  C31  C32  120.67  3.000
 H2R  N30  C31  C32  122.46  3.000
 H2R  H21  C32  C33  120.73  3.000
 H2R  H21  C32  C31  120.61  3.000
 H2R  C33  C32  C31  118.66  3.000
 H2R  H22  C33  C32  120.41  3.000
 H2R  H22  C33  C28  120.23  3.000
 H2R  C32  C33  C28  119.37  3.000
 H2R  C04  N03  C02  119.23  3.000
 H2R  C04  N03  C26  112.09  3.000
 H2R  C02  N03  C26  125.75  3.000
 H2R  C16  N15  C14  118.68  3.000
 H2R  H23  N27  C02  118.42  3.000
 H2R  H23  N27  C28  114.47  3.000
 H2R  C02  N27  C28  124.38  3.000
 H2R  C31  N30  C29  119.09  3.000
 H2R  C14  O13  C12  119.69  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
 H2R  CONST_01  C24  C08  C09  C10     0.00   0.0  0
 H2R  CONST_02  C24  C12  C11  C10     0.00   0.0  0
 H2R  CONST_03  C14  C19  C18  C17     0.00   0.0  0
 H2R  CONST_04  C14  N15  C16  C17     0.00   0.0  0
 H2R  CONST_05  C31  N30  C29  C28     0.00   0.0  0
 H2R  CONST_06  C31  C32  C33  C28     0.00   0.0  0
 H2R  CONST_07  C11  C10  C09  C08     0.00   0.0  0
 H2R  CONST_08  C11  C12  C24  C08     0.00   0.0  0
 H2R  CONST_09  C12  C11  C10  C09     0.00   0.0  0
 H2R  CONST_10  C12  C24  C08  C09     0.00   0.0  0
 H2R  CONST_11  C19  C14  N15  C16     0.00   0.0  0
 H2R  CONST_12  C19  C18  C17  C16     0.00   0.0  0
 H2R  CONST_13  N15  C14  C19  C18     0.00   0.0  0
 H2R  CONST_14  N15  C16  C17  C18     0.00   0.0  0
 H2R  CONST_15  C32  C31  N30  C29     0.00   0.0  0
 H2R  CONST_16  C32  C33  C28  C29     0.00   0.0  0
 H2R  CONST_17  N30  C29  C28  C33     0.00   0.0  0
 H2R  CONST_18  N30  C31  C32  C33     0.00   0.0  0
 H2R  CONST_19  C07  C08  C09  C10   180.00   0.0  0
 H2R  CONST_20  O13  C12  C11  C10   180.00   0.0  0
 H2R  CONST_21  C19  C18  C17  C20   180.00   0.0  0
 H2R  CONST_22  N15  C16  C17  C20   180.00   0.0  0
 H2R  CONST_23  C12  C24  C08  C07   180.00   0.0  0
 H2R  CONST_24  O13  C12  C24  C08   180.00   0.0  0
 H2R  CONST_25  O13  C14  N15  C16   180.00   0.0  0
 H2R  CONST_26  O13  C14  C19  C18   180.00   0.0  0
 H2R  CONST_27  N27  C28  C33  C32   180.00   0.0  0
 H2R  CONST_28  N30  C29  C28  N27   180.00   0.0  0
 H2R  CONST_29  H16  C19  C18  C17   180.00   0.0  0
 H2R  CONST_30  H12  C09  C08  C24   180.00   0.0  0
 H2R  CONST_31  H13  C11  C12  C24   180.00   0.0  0
 H2R  CONST_32  H21  C32  C33  C28   180.00   0.0  0
 H2R  CONST_33  H1   C10  C09  C08   180.00   0.0  0
 H2R  CONST_34  H2   C24  C08  C09   180.00   0.0  0
 H2R  CONST_35  H15  C18  C19  C14   180.00   0.0  0
 H2R  CONST_36  H14  C16  N15  C14   180.00   0.0  0
 H2R  CONST_37  H20  C31  N30  C29   180.00   0.0  0
 H2R  CONST_38  H22  C33  C28  C29   180.00   0.0  0
 H2R  CONST_39  H19  C29  N30  C31   180.00   0.0  0
 H2R  CONST_40  O01  C02  N03  C26   180.00   0.0  0
 H2R  CONST_42  N03  C02  N27  C28   180.00   0.0  0
 H2R  CONST_45  N27  C02  N03  C26     0.00   0.0  0
 H2R  CONST_48  O01  C02  N27  C28     0.00   0.0  0
 H2R  Var_01    C05  C04  N03  C26    59.71  30.0  1
 H2R  Var_02    C25  C26  N03  C04   -60.60  30.0  1
 H2R  Var_03    N03  C26  C25  C06    56.50  30.0  1
 H2R  Var_04    N03  C04  C05  C06   -55.27  30.0  1
 H2R  Var_05    C06  C07  C08  C24  -103.92  30.0  2
 H2R  Var_06    C19  C14  O13  C12    -9.07  30.0  2
 H2R  Var_07    F23  C20  C17  C16   131.51  30.0  2

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
 H2R  chir_01  C06  C25  C05  C07  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
 H2R  plan-1  C10  0.020
 H2R  plan-1  C24  0.020
 H2R  plan-1  C07  0.020
 H2R  plan-1  C08  0.020
 H2R  plan-1  C09  0.020
 H2R  plan-1  C11  0.020
 H2R  plan-1  C12  0.020
 H2R  plan-1  O13  0.020
 H2R  plan-1  H1   0.020
 H2R  plan-1  H2   0.020
 H2R  plan-1  H12  0.020
 H2R  plan-1  H13  0.020
 H2R  plan-2  C17  0.020
 H2R  plan-2  C20  0.020
 H2R  plan-2  C14  0.020
 H2R  plan-2  C16  0.020
 H2R  plan-2  C18  0.020
 H2R  plan-2  C19  0.020
 H2R  plan-2  N15  0.020
 H2R  plan-2  O13  0.020
 H2R  plan-2  H14  0.020
 H2R  plan-2  H15  0.020
 H2R  plan-2  H16  0.020
 H2R  plan-3  C28  0.020
 H2R  plan-3  C29  0.020
 H2R  plan-3  C31  0.020
 H2R  plan-3  C32  0.020
 H2R  plan-3  C33  0.020
 H2R  plan-3  N27  0.020
 H2R  plan-3  N30  0.020
 H2R  plan-3  H19  0.020
 H2R  plan-3  H20  0.020
 H2R  plan-3  H21  0.020
 H2R  plan-3  H22  0.020
 H2R  plan-4  C26  0.020
 H2R  plan-4  C28  0.020
 H2R  plan-4  C02  0.020
 H2R  plan-4  C04  0.020
 H2R  plan-4  N03  0.020
 H2R  plan-4  N27  0.020
 H2R  plan-4  O01  0.020
 H2R  plan-4  H23  0.020

