# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 21:02:33 2022
#   Inital geometry file: a 136 line input string
#   Ligand name: 3-[(~{E})-1-(3-cyclopentyloxy-4-methoxy-phenyl)ethylideneamino]oxy-1-morpholin-4-yl-propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1OC2CCCC2)\C(C)=N\OCCC(=O)N3CCOCC3
#
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
 T3K  T3K  3-[(~{E})-1-(3-cyclopentyloxy-4-methoxy-phenyl)ethylideneamino]oxy-1-morpholin-4-yl-propan-1-one  ligand  58  28  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T3K
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
 T3K  C13  C  C     0   0.549  26.2455  29.1484  28.4988
 T3K  C17  C  CH2   0  -0.184  28.2175  29.9223  25.5693
 T3K  C20  C  CH2   0  -0.324  25.9710  28.3679  26.2100
 T3K  C21  C  CR16  0  -0.421  31.1016  32.2322  28.1731
 T3K  C22  C  CR6   0   0.355  31.7739  33.2667  27.5545
 T3K  C24  C  CR15  0  -0.028  30.9170  34.9563  29.0269
 T3K  C26  C  CH2   0  -0.448  32.2684  36.8968  29.5345
 T3K  C28  C  CH2   0  -0.478  31.6670  34.6429  30.3183
 T3K  C01  C  CH3   0  -0.436  34.1324  33.8286  24.8431
 T3K  C03  C  CR6   0   0.289  32.6447  32.9833  26.4765
 T3K  C04  C  CR16  0  -0.367  32.8066  31.6720  26.0657
 T3K  C05  C  CR16  0  -0.329  32.1309  30.6363  26.7083
 T3K  C06  C  CR6   0   0.046  31.2728  30.9005  27.7627
 T3K  C07  C  C     0   0.205  30.5347  29.8105  28.4338
 T3K  C08  C  CH3   0  -0.768  30.9837  28.3954  28.2317
 T3K  C11  C  CH2   0  -0.169  27.7417  29.6593  30.4360
 T3K  C12  C  CH2   0  -0.603  26.6844  30.2093  29.4895
 T3K  C16  C  CH2   0  -0.322  27.1761  30.4361  26.5515
 T3K  C19  C  CH2   0  -0.185  27.0677  27.9352  25.2548
 T3K  C25  C  CH2   0  -0.452  30.8834  36.4761  29.0229
 T3K  C27  C  CH2   0  -0.442  32.7699  35.7106  30.3918
 T3K  N09  N  N     0  -0.141  29.5389  30.1740  29.1430
 T3K  N15  N  NT    0  -0.466  26.4917  29.3188  27.1805
 T3K  O10  O  O2    0  -0.393  28.8743  29.1522  29.7546
 T3K  O14  O  O     0  -0.504  25.6729  28.1530  28.9265
 T3K  O18  O  O2    0  -0.475  27.6665  29.0419  24.6199
 T3K  O23  O  O2    0  -0.477  31.6698  34.5670  27.8791
 T3K  H1   H  HCH2  0   0.244  28.6537  30.7638  25.0292
 T3K  H2   H  HCH2  0   0.212  29.0215  29.4259  26.1292
 T3K  H3   H  HCH2  0   0.269  25.5655  27.5008  26.7237
 T3K  H4   H  HCH2  0   0.244  25.1567  28.8398  25.6489
 T3K  H5   H  HCR6  0   0.276  30.4334  32.4304  28.9988
 T3K  H6   H  HCR5  0   0.248  29.9148  34.5174  28.9863
 T3K  H7   H  HCH2  0   0.231  32.9475  37.0830  28.7018
 T3K  H8   H  HCH2  0   0.231  32.2157  37.8229  30.1068
 T3K  H9   H  HCH2  0   0.240  30.9654  34.7560  31.1480
 T3K  H10  H  HCH2  0   0.252  32.0535  33.6242  30.3681
 T3K  H11  H  HCH3  0   0.259  34.5157  34.8045  24.5553
 T3K  H12  H  HCH3  0   0.228  34.9741  33.1862  25.1157
 T3K  H13  H  HCH3  0   0.228  33.6156  33.3867  23.9870
 T3K  H14  H  HCR6  0   0.282  33.4643  31.4289  25.2423
 T3K  H15  H  HCR6  0   0.256  32.2872  29.6261  26.3553
 T3K  H16  H  HCH3  0   0.275  30.5246  27.7089  28.9362
 T3K  H17  H  HCH3  0   0.263  30.7326  28.0539  27.2248
 T3K  H18  H  HCH3  0   0.259  32.0657  28.3207  28.3341
 T3K  H19  H  HCH2  0   0.237  28.0343  30.4321  31.1528
 T3K  H20  H  HCH2  0   0.244  27.3475  28.8110  30.9947
 T3K  H21  H  HCH2  0   0.281  25.8055  30.4607  30.0883
 T3K  H22  H  HCH2  0   0.265  27.0248  31.1399  29.0439
 T3K  H23  H  HCH2  0   0.264  27.6851  31.0558  27.2830
 T3K  H24  H  HCH2  0   0.246  26.4473  31.0646  26.0282
 T3K  H25  H  HCH2  0   0.242  26.6476  27.2969  24.4763
 T3K  H26  H  HCH2  0   0.207  27.8202  27.3506  25.8035
 T3K  H27  H  HCH2  0   0.244  30.6304  36.8902  28.0458
 T3K  H28  H  HCH2  0   0.237  30.1050  36.7954  29.7192
 T3K  H29  H  HCH2  0   0.232  32.9644  36.0040  31.4233
 T3K  H30  H  HCH2  0   0.231  33.7086  35.3204  29.9971
 T3K  O02  O  O2    0  -0.456  33.2596  34.0458  25.9318

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
 T3K  C01  O02  single    1.412  0.020  1.412
 T3K  C04  C05  aromatic  1.394  0.020  1.394
 T3K  C04  C03  aromatic  1.384  0.020  1.384
 T3K  C05  C06  aromatic  1.385  0.020  1.385
 T3K  C17  C16  single    1.521  0.020  1.521
 T3K  C17  O18  single    1.407  0.020  1.407
 T3K  O02  C03  single    1.343  0.020  1.343
 T3K  C16  N15  single    1.453  0.020  1.453
 T3K  C03  C22  aromatic  1.414  0.020  1.414
 T3K  O18  C19  single    1.409  0.020  1.409
 T3K  C06  C07  single    1.478  0.020  1.478
 T3K  C06  C21  aromatic  1.404  0.020  1.404
 T3K  C08  C07  single    1.498  0.020  1.498
 T3K  C07  N09  double    1.276  0.020  1.276
 T3K  C22  C21  aromatic  1.380  0.020  1.380
 T3K  C22  O23  single    1.344  0.020  1.344
 T3K  N15  C20  single    1.455  0.020  1.455
 T3K  N15  C13  single    1.352  0.020  1.352
 T3K  C12  C11  single    1.522  0.020  1.522
 T3K  C12  C13  single    1.516  0.020  1.516
 T3K  C19  C20  single    1.517  0.020  1.517
 T3K  N09  O10  single    1.364  0.020  1.364
 T3K  C11  O10  single    1.416  0.020  1.416
 T3K  C13  O14  double    1.225  0.020  1.225
 T3K  O23  C24  single    1.427  0.020  1.427
 T3K  C24  C25  single    1.520  0.020  1.520
 T3K  C24  C28  single    1.526  0.020  1.526
 T3K  C25  C26  single    1.535  0.020  1.535
 T3K  C28  C27  single    1.537  0.020  1.537
 T3K  C27  C26  single    1.547  0.020  1.547
 T3K  C17  H1   single    0.970  0.020  1.090
 T3K  C17  H2   single    0.970  0.020  1.090
 T3K  C20  H3   single    0.970  0.020  1.090
 T3K  C20  H4   single    0.970  0.020  1.090
 T3K  C21  H5   single    0.930  0.020  1.080
 T3K  C24  H6   single    0.970  0.020  1.090
 T3K  C26  H7   single    0.970  0.020  1.090
 T3K  C26  H8   single    0.970  0.020  1.090
 T3K  C28  H9   single    0.970  0.020  1.090
 T3K  C28  H10  single    0.970  0.020  1.090
 T3K  C01  H11  single    0.970  0.020  1.090
 T3K  C01  H12  single    0.970  0.020  1.090
 T3K  C01  H13  single    0.970  0.020  1.090
 T3K  C04  H14  single    0.930  0.020  1.080
 T3K  C05  H15  single    0.930  0.020  1.080
 T3K  C08  H16  single    0.970  0.020  1.090
 T3K  C08  H17  single    0.970  0.020  1.090
 T3K  C08  H18  single    0.970  0.020  1.090
 T3K  C11  H19  single    0.970  0.020  1.090
 T3K  C11  H20  single    0.970  0.020  1.090
 T3K  C12  H21  single    0.970  0.020  1.090
 T3K  C12  H22  single    0.970  0.020  1.090
 T3K  C16  H23  single    0.970  0.020  1.090
 T3K  C16  H24  single    0.970  0.020  1.090
 T3K  C19  H25  single    0.970  0.020  1.090
 T3K  C19  H26  single    0.970  0.020  1.090
 T3K  C25  H27  single    0.970  0.020  1.090
 T3K  C25  H28  single    0.970  0.020  1.090
 T3K  C27  H29  single    0.970  0.020  1.090
 T3K  C27  H30  single    0.970  0.020  1.090

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
 T3K  O14  C13  N15  121.86  3.000
 T3K  O14  C13  C12  118.39  3.000
 T3K  N15  C13  C12  119.75  3.000
 T3K  H2   C17  H1   107.96  3.000
 T3K  H2   C17  O18  110.35  3.000
 T3K  H1   C17  O18  107.76  3.000
 T3K  H2   C17  C16  108.94  3.000
 T3K  H1   C17  C16  109.46  3.000
 T3K  O18  C17  C16  112.27  3.000
 T3K  H4   C20  H3   107.97  3.000
 T3K  H4   C20  N15  109.03  3.000
 T3K  H3   C20  N15  109.86  3.000
 T3K  H4   C20  C19  109.73  3.000
 T3K  H3   C20  C19  109.87  3.000
 T3K  N15  C20  C19  110.34  3.000
 T3K  H5   C21  C06  118.21  3.000
 T3K  H5   C21  C22  120.42  3.000
 T3K  C06  C21  C22  121.37  3.000
 T3K  O23  C22  C03  115.18  3.000
 T3K  O23  C22  C21  125.39  3.000
 T3K  C03  C22  C21  119.43  3.000
 T3K  H6   C24  O23  110.11  3.000
 T3K  H6   C24  C25  112.36  3.000
 T3K  O23  C24  C25  106.40  3.000
 T3K  H6   C24  C28  113.51  3.000
 T3K  C25  C24  C28  102.61  3.000
 T3K  O23  C24  C28  111.43  3.000
 T3K  H8   C26  H7   106.62  3.000
 T3K  H8   C26  C27  112.10  3.000
 T3K  H7   C26  C27  110.62  3.000
 T3K  H8   C26  C25  111.36  3.000
 T3K  H7   C26  C25  110.74  3.000
 T3K  C27  C26  C25  105.48  3.000
 T3K  H10  C28  H9   106.83  3.000
 T3K  H10  C28  C27  113.10  3.000
 T3K  H9   C28  C27  110.65  3.000
 T3K  H10  C28  C24  113.87  3.000
 T3K  H9   C28  C24  107.81  3.000
 T3K  C27  C28  C24  104.51  3.000
 T3K  H13  C01  H12  108.76  3.000
 T3K  H13  C01  H11  108.80  3.000
 T3K  H12  C01  H11  108.78  3.000
 T3K  H13  C01  O02  111.94  3.000
 T3K  H12  C01  O02  111.96  3.000
 T3K  H11  C01  O02  106.49  3.000
 T3K  O02  C03  C04  125.15  3.000
 T3K  O02  C03  C22  115.62  3.000
 T3K  C04  C03  C22  119.22  3.000
 T3K  H14  C04  C05  118.62  3.000
 T3K  H14  C04  C03  120.68  3.000
 T3K  C05  C04  C03  120.71  3.000
 T3K  H15  C05  C06  121.08  3.000
 T3K  H15  C05  C04  118.27  3.000
 T3K  C06  C05  C04  120.65  3.000
 T3K  C07  C06  C05  120.97  3.000
 T3K  C07  C06  C21  120.40  3.000
 T3K  C05  C06  C21  118.62  3.000
 T3K  N09  C07  C08  125.32  3.000
 T3K  N09  C07  C06  115.61  3.000
 T3K  C08  C07  C06  119.07  3.000
 T3K  H18  C08  H17  107.07  3.000
 T3K  H18  C08  H16  108.40  3.000
 T3K  H17  C08  H16  107.65  3.000
 T3K  H18  C08  C07  110.47  3.000
 T3K  H17  C08  C07  110.53  3.000
 T3K  H16  C08  C07  112.52  3.000
 T3K  H20  C11  H19  108.11  3.000
 T3K  H20  C11  O10  104.91  3.000
 T3K  H19  C11  O10  110.75  3.000
 T3K  H20  C11  C12  110.42  3.000
 T3K  H19  C11  C12  109.76  3.000
 T3K  O10  C11  C12  112.70  3.000
 T3K  H22  C12  H21  106.24  3.000
 T3K  H22  C12  C11  110.30  3.000
 T3K  H21  C12  C11  107.52  3.000
 T3K  H22  C12  C13  114.96  3.000
 T3K  H21  C12  C13  106.63  3.000
 T3K  C11  C12  C13  110.77  3.000
 T3K  H24  C16  H23  107.84  3.000
 T3K  H24  C16  N15  109.54  3.000
 T3K  H23  C16  N15  111.60  3.000
 T3K  H24  C16  C17  109.92  3.000
 T3K  H23  C16  C17  107.88  3.000
 T3K  N15  C16  C17  110.02  3.000
 T3K  H26  C19  H25  107.97  3.000
 T3K  H26  C19  O18  110.58  3.000
 T3K  H25  C19  O18  107.55  3.000
 T3K  H26  C19  C20  109.40  3.000
 T3K  H25  C19  C20  109.74  3.000
 T3K  O18  C19  C20  111.51  3.000
 T3K  H28  C25  H27  107.14  3.000
 T3K  H28  C25  C26  110.51  3.000
 T3K  H27  C25  C26  113.81  3.000
 T3K  H28  C25  C24  107.84  3.000
 T3K  H27  C25  C24  112.77  3.000
 T3K  C26  C25  C24  104.67  3.000
 T3K  H30  C27  H29  106.57  3.000
 T3K  H30  C27  C28  110.60  3.000
 T3K  H29  C27  C28  111.12  3.000
 T3K  H30  C27  C26  110.66  3.000
 T3K  H29  C27  C26  112.08  3.000
 T3K  C28  C27  C26  105.88  3.000
 T3K  O10  N09  C07  114.60  3.000
 T3K  C16  N15  C20  112.47  3.000
 T3K  C20  N15  C13  120.19  3.000
 T3K  C16  N15  C13  127.21  3.000
 T3K  N09  O10  C11  109.71  3.000
 T3K  C19  O18  C17  110.71  3.000
 T3K  C24  O23  C22  119.93  3.000
 T3K  C03  O02  C01  118.29  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
 T3K  CONST_01  C04  C05  C06  C21     0.00   0.0  0
 T3K  CONST_02  C04  C03  C22  C21     0.00   0.0  0
 T3K  CONST_03  C05  C04  C03  C22     0.00   0.0  0
 T3K  CONST_04  C05  C06  C21  C22     0.00   0.0  0
 T3K  CONST_05  C06  C05  C04  C03     0.00   0.0  0
 T3K  CONST_06  C06  C21  C22  C03     0.00   0.0  0
 T3K  CONST_07  O02  C03  C22  C21   180.00   0.0  0
 T3K  CONST_08  C07  C06  C21  C22   180.00   0.0  0
 T3K  CONST_09  C07  C06  C05  C04   180.00   0.0  0
 T3K  CONST_10  O23  C22  C03  C04   180.00   0.0  0
 T3K  CONST_11  O02  C03  C04  C05   180.00   0.0  0
 T3K  CONST_12  O23  C22  C21  C06   180.00   0.0  0
 T3K  CONST_13  H15  C05  C06  C21   180.00   0.0  0
 T3K  CONST_14  H14  C04  C03  C22   180.00   0.0  0
 T3K  CONST_15  H5   C21  C22  C03   180.00   0.0  0
 T3K  CONST_16  C12  C13  N15  C20   180.00   0.0  0
 T3K  CONST_17  O14  C13  N15  C20     0.00   0.0  0
 T3K  CONST_18  C16  N15  C13  C12     0.00   0.0  0
 T3K  CONST_19  O14  C13  N15  C16   180.00   0.0  0
 T3K  Var_01    C20  N15  C16  C17   -51.77  30.0  1
 T3K  Var_02    C20  C19  O18  C17    58.87  30.0  1
 T3K  Var_03    C27  C26  C25  C24   -25.32  30.0  1
 T3K  Var_04    C26  C27  C28  C24    23.45  30.0  1
 T3K  Var_05    C25  C26  C27  C28     1.07  30.0  1
 T3K  Var_06    C19  C20  N15  C16    52.59  30.0  1
 T3K  Var_07    O18  C17  C16  N15    54.65  30.0  1
 T3K  Var_08    O18  C19  C20  N15   -55.65  30.0  1
 T3K  Var_09    C03  C22  O23  C24  -174.24  30.0  2
 T3K  Var_10    H1   C17  O18  C19  -179.23  30.0  1
 T3K  Var_11    C08  C07  C06  C21  -164.36  30.0  2
 T3K  Var_12    C04  C03  O02  C01     0.76  30.0  2
 T3K  Var_13    N15  C13  C12  C11  -115.51  30.0  3
 T3K  Var_14    H11  C01  O02  C03   179.81  30.0  3
 T3K  Var_15    H16  C08  C07  C06   166.92  30.0  3
 T3K  Var_16    O10  C11  C12  C13    56.96  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
 T3K  chir_01  C24  O23  C25  C28  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
 T3K  plan-1  C13  0.020
 T3K  plan-1  C20  0.020
 T3K  plan-1  C12  0.020
 T3K  plan-1  C16  0.020
 T3K  plan-1  N15  0.020
 T3K  plan-1  O14  0.020
 T3K  plan-2  C21  0.020
 T3K  plan-2  C22  0.020
 T3K  plan-2  C03  0.020
 T3K  plan-2  C04  0.020
 T3K  plan-2  C05  0.020
 T3K  plan-2  C06  0.020
 T3K  plan-2  C07  0.020
 T3K  plan-2  O23  0.020
 T3K  plan-2  H5   0.020
 T3K  plan-2  H14  0.020
 T3K  plan-2  H15  0.020
 T3K  plan-2  O02  0.020
 T3K  plan-3  C06  0.020
 T3K  plan-3  C07  0.020
 T3K  plan-3  C08  0.020
 T3K  plan-3  N09  0.020
 T3K  plan-3  O10  0.020

