# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 07:22:20 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: 1-[3-[4-[2-[[4-chloranyl-5-(1-methylcyclopropyl)-2-oxidanyl-phenyl]amino]ethanoyl]piperazin-1-yl]azetidin-1-yl]prop-2-en-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(CC1)c2cc(NCC(=O)N3CCN(CC3)C4CN(C4)C(=O)C=C)c(O)cc2Cl
#
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
 5UT  5UT  1-[3-[4-[2-[[4-chloranyl-5-(1-methylcyclopropyl)-2-oxidanyl-phenyl]amino]ethanoyl]piperazin-1-yl]azetidin-1-yl]prop-2-en-1-one  ligand  59  30  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5UT
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
 5UT  C1   C   CT    0  -0.070   5.2308  -2.0011   0.5899
 5UT  C2   C   CR6   0   0.220   4.8362  -0.7466  -0.1197
 5UT  C3   C   CR6   0  -0.156   5.7372   0.0176  -0.8403
 5UT  C4   C   CR16  0  -0.326   5.3533   1.2052  -1.4584
 5UT  C5   C   CR6   0   0.265   4.0519   1.6502  -1.3566
 5UT  C6   C   CR6   0   0.336   3.1013   0.9127  -0.6192
 5UT  C10  C   CH2   0  -0.280  -2.6108  -0.8766   1.3497
 5UT  C11  C   C     0  -0.159  -4.9940  -0.9647   1.1780
 5UT  C14  C   C1    0  -0.322  -7.6023  -0.6648  -2.2435
 5UT  C18  C   CH2   0  -0.310  -2.6350   1.9619   1.2931
 5UT  C20  C   CH2   0  -0.489   4.3256  -3.1929   0.4788
 5UT  O2   O   O     0  -0.496  -0.3972   2.7533  -0.1473
 5UT  C8   C   C     0   0.550  -0.3704   1.6761   0.4338
 5UT  C7   C   CH2   0  -0.414   0.8680   0.7929   0.3549
 5UT  N    N   NH1   0  -0.693   1.8101   1.3695  -0.5543
 5UT  O    O   OH1   0  -0.636   3.6105   2.7891  -1.9358
 5UT  CL   CL  CL    0  -0.145   7.3967  -0.4777  -1.0005
 5UT  C19  C   CR16  0  -0.440   3.5263  -0.2698  -0.0200
 5UT  C21  C   CH2   0  -0.470   5.6468  -3.1845  -0.2312
 5UT  C    C   CH3   0  -0.648   5.9266  -1.7717   1.9142
 5UT  N1   N   NT    0  -0.459  -1.3903   1.2241   1.1827
 5UT  C17  C   CH2   0  -0.299  -3.7870   1.1216   0.7679
 5UT  N2   N   NT    0  -0.428  -3.8558  -0.1411   1.4837
 5UT  C9   C   CH2   0  -0.330  -1.4440  -0.0523   1.8692
 5UT  C16  C   C     0  -0.270  -6.3860  -0.3129   1.3347
 5UT  N3   N   N     0  -0.460  -6.6137  -0.5453  -0.0787
 5UT  C12  C   C     0  -0.282  -5.3593  -1.2482  -0.3126
 5UT  C13  C   C     0   0.505  -7.6878  -0.2569  -0.8180
 5UT  O1   O   O     0  -0.506  -8.6646   0.3123  -0.3391
 5UT  C15  C   C2    0  -0.471  -8.5976  -0.4315  -3.0919
 5UT  H1   H   HCR6  0   0.283   6.0750   1.7797  -2.0269
 5UT  H2   H   HCH2  0   0.252  -2.6733  -1.7956   1.9364
 5UT  H3   H   HCH2  0   0.211  -2.4069  -1.1659   0.3054
 5UT  H4   H   H     0   0.276  -4.9034  -1.8840   1.7570
 5UT  H5   H   H     0   0.273  -6.7010  -1.1597  -2.5859
 5UT  H7   H   HCH2  0   0.248  -2.8084   2.2093   2.3446
 5UT  H8   H   HCH2  0   0.271  -2.5668   2.8904   0.7339
 5UT  H9   H   HCH2  0   0.247   4.2138  -3.8231   1.3529
 5UT  H10  H   HCH2  0   0.247   3.4283  -3.1115  -0.1228
 5UT  H11  H   HCH2  0   0.263   1.2785   0.6801   1.3696
 5UT  H12  H   HCH2  0   0.265   0.5853  -0.2125   0.0241
 5UT  H13  H   HNH1  0   0.381   1.6555   2.3438  -0.7616
 5UT  H14  H   HOH1  0   0.479   4.3313   3.2428  -2.3865
 5UT  H15  H   HCR6  0   0.270   2.8242  -0.8621   0.5528
 5UT  H16  H   HCH2  0   0.245   5.6378  -3.0882  -1.3096
 5UT  H17  H   HCH2  0   0.246   6.4457  -3.8081   0.1516
 5UT  H18  H   HCH3  0   0.227   6.8458  -1.1984   1.7866
 5UT  H19  H   HCH3  0   0.228   5.2820  -1.2238   2.6040
 5UT  H20  H   HCH3  0   0.226   6.1925  -2.7192   2.3857
 5UT  H21  H   HCH2  0   0.257  -4.7086   1.6871   0.9110
 5UT  H22  H   HCH2  0   0.213  -3.6537   0.9861  -0.3168
 5UT  H24  H   HCH2  0   0.255  -1.5744   0.1308   2.9399
 5UT  H25  H   HCH2  0   0.279  -0.5212  -0.6138   1.7524
 5UT  H26  H   H     0   0.260  -7.0680  -0.8637   1.9856
 5UT  H27  H   H     0   0.252  -6.4013   0.7376   1.6301
 5UT  H28  H   H     0   0.253  -4.7110  -0.7881  -1.0619
 5UT  H29  H   H     0   0.260  -5.4835  -2.3049  -0.5558
 5UT  H30  H   H     0   0.257  -9.5076   0.0639  -2.7788
 5UT  H31  H   H     0   0.261  -8.5308  -0.7276  -4.1295

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
 5UT  C    C1   single    1.513  0.020  1.513
 5UT  CL   C3   single    1.739  0.020  1.739
 5UT  C20  C1   single    1.501  0.020  1.501
 5UT  C20  C21  single    1.500  0.020  1.500
 5UT  C1   C21  single    1.499  0.020  1.499
 5UT  C1   C2   single    1.494  0.020  1.494
 5UT  C3   C2   aromatic  1.384  0.020  1.384
 5UT  C3   C4   aromatic  1.393  0.020  1.393
 5UT  C2   C19  aromatic  1.398  0.020  1.398
 5UT  C4   C5   aromatic  1.379  0.020  1.379
 5UT  C19  C6   aromatic  1.392  0.020  1.392
 5UT  C9   C10  single    1.520  0.020  1.520
 5UT  C9   N1   single    1.450  0.020  1.450
 5UT  C10  N2   single    1.452  0.020  1.452
 5UT  C11  N2   single    1.438  0.020  1.438
 5UT  C11  C16  single    1.545  0.020  1.545
 5UT  C11  C12  single    1.561  0.020  1.561
 5UT  C5   C6   aromatic  1.411  0.020  1.411
 5UT  C5   O    single    1.352  0.020  1.352
 5UT  N2   C17  single    1.453  0.020  1.453
 5UT  C16  N3   single    1.450  0.020  1.450
 5UT  C6   N    single    1.371  0.020  1.371
 5UT  N1   C18  single    1.451  0.020  1.451
 5UT  N1   C8   single    1.344  0.020  1.344
 5UT  C7   N    single    1.431  0.020  1.431
 5UT  C7   C8   single    1.523  0.020  1.523
 5UT  C12  N3   single    1.457  0.020  1.457
 5UT  N3   C13  single    1.335  0.020  1.335
 5UT  C18  C17  single    1.520  0.020  1.520
 5UT  C8   O2   double    1.224  0.020  1.224
 5UT  O1   C13  double    1.228  0.020  1.228
 5UT  C13  C14  single    1.485  0.020  1.485
 5UT  C15  C14  double    1.328  0.020  1.328
 5UT  C4   H1   single    0.930  0.020  1.080
 5UT  C10  H2   single    0.970  0.020  1.090
 5UT  C10  H3   single    0.970  0.020  1.090
 5UT  C11  H4   single    0.970  0.020  1.090
 5UT  C14  H5   single    0.930  0.020  1.080
 5UT  C18  H7   single    0.970  0.020  1.090
 5UT  C18  H8   single    0.970  0.020  1.090
 5UT  C20  H9   single    0.970  0.020  1.090
 5UT  C20  H10  single    0.970  0.020  1.090
 5UT  C7   H11  single    0.970  0.020  1.090
 5UT  C7   H12  single    0.970  0.020  1.090
 5UT  N    H13  single    0.890  0.020  1.040
 5UT  O    H14  single    0.850  0.020  0.980
 5UT  C19  H15  single    0.930  0.020  1.080
 5UT  C21  H16  single    0.970  0.020  1.090
 5UT  C21  H17  single    0.970  0.020  1.090
 5UT  C    H18  single    0.970  0.020  1.090
 5UT  C    H19  single    0.970  0.020  1.090
 5UT  C    H20  single    0.970  0.020  1.090
 5UT  C17  H21  single    0.970  0.020  1.090
 5UT  C17  H22  single    0.970  0.020  1.090
 5UT  C9   H24  single    0.970  0.020  1.090
 5UT  C9   H25  single    0.970  0.020  1.090
 5UT  C16  H26  single    0.970  0.020  1.090
 5UT  C16  H27  single    0.970  0.020  1.090
 5UT  C12  H28  single    0.970  0.020  1.090
 5UT  C12  H29  single    0.970  0.020  1.090
 5UT  C15  H30  single    0.930  0.020  1.080
 5UT  C15  H31  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
 5UT  C    C1   C21  118.12  3.000
 5UT  C21  C1   C20   59.99  3.000
 5UT  C    C1   C20  117.54  3.000
 5UT  C21  C1   C2   118.42  3.000
 5UT  C20  C1   C2   118.18  3.000
 5UT  C    C1   C2   114.19  3.000
 5UT  C19  C2   C3   117.32  3.000
 5UT  C19  C2   C1   120.01  3.000
 5UT  C3   C2   C1   122.61  3.000
 5UT  CL   C3   C4   117.71  3.000
 5UT  C4   C3   C2   121.50  3.000
 5UT  CL   C3   C2   120.79  3.000
 5UT  H1   C4   C5   119.75  3.000
 5UT  H1   C4   C3   120.08  3.000
 5UT  C5   C4   C3   120.17  3.000
 5UT  O    C5   C6   116.37  3.000
 5UT  O    C5   C4   123.25  3.000
 5UT  C6   C5   C4   120.37  3.000
 5UT  C19  C6   N    123.38  3.000
 5UT  N    C6   C5   119.01  3.000
 5UT  C19  C6   C5   117.59  3.000
 5UT  H3   C10  H2   107.37  3.000
 5UT  H3   C10  C9   108.90  3.000
 5UT  H2   C10  C9   108.46  3.000
 5UT  H3   C10  N2   112.25  3.000
 5UT  H2   C10  N2   109.12  3.000
 5UT  C9   C10  N2   110.60  3.000
 5UT  H4   C11  C12  111.93  3.000
 5UT  H4   C11  C16  112.13  3.000
 5UT  C12  C11  C16   87.86  3.000
 5UT  H4   C11  N2   107.72  3.000
 5UT  C12  C11  N2   119.50  3.000
 5UT  C16  C11  N2   116.75  3.000
 5UT  H5   C14  C15  120.10  3.000
 5UT  H5   C14  C13  118.46  3.000
 5UT  C15  C14  C13  121.44  3.000
 5UT  H8   C18  H7   108.15  3.000
 5UT  H8   C18  C17  110.02  3.000
 5UT  H7   C18  C17  109.70  3.000
 5UT  H8   C18  N1   109.97  3.000
 5UT  H7   C18  N1   108.91  3.000
 5UT  C17  C18  N1   110.05  3.000
 5UT  H10  C20  H9   113.97  3.000
 5UT  H10  C20  C21  117.79  3.000
 5UT  H9   C20  C21  118.43  3.000
 5UT  H10  C20  C1   118.75  3.000
 5UT  H9   C20  C1   117.68  3.000
 5UT  C21  C20  C1    59.95  3.000
 5UT  N1   C8   C7   116.81  3.000
 5UT  C7   C8   O2   120.23  3.000
 5UT  N1   C8   O2   122.95  3.000
 5UT  H12  C7   H11  106.30  3.000
 5UT  H12  C7   N    110.36  3.000
 5UT  H11  C7   N    112.44  3.000
 5UT  H12  C7   C8   109.75  3.000
 5UT  H11  C7   C8   108.36  3.000
 5UT  N    C7   C8   109.55  3.000
 5UT  H13  N    C7   114.79  3.000
 5UT  H13  N    C6   117.17  3.000
 5UT  C7   N    C6   121.06  3.000
 5UT  H14  O    C5   110.66  3.000
 5UT  H15  C19  C6   119.63  3.000
 5UT  H15  C19  C2   117.32  3.000
 5UT  C6   C19  C2   123.05  3.000
 5UT  H17  C21  H16  114.16  3.000
 5UT  H17  C21  C20  118.63  3.000
 5UT  H16  C21  C20  117.69  3.000
 5UT  H17  C21  C1   117.74  3.000
 5UT  H16  C21  C1   118.22  3.000
 5UT  C20  C21  C1    60.05  3.000
 5UT  H20  C    H19  107.86  3.000
 5UT  H20  C    H18  107.55  3.000
 5UT  H19  C    H18  107.92  3.000
 5UT  H20  C    C1   111.01  3.000
 5UT  H19  C    C1   110.95  3.000
 5UT  H18  C    C1   111.39  3.000
 5UT  C9   N1   C8   126.01  3.000
 5UT  C8   N1   C18  121.50  3.000
 5UT  C9   N1   C18  112.31  3.000
 5UT  H22  C17  H21  107.18  3.000
 5UT  H22  C17  N2   112.58  3.000
 5UT  H21  C17  N2   110.24  3.000
 5UT  H22  C17  C18  108.46  3.000
 5UT  H21  C17  C18  107.97  3.000
 5UT  N2   C17  C18  110.25  3.000
 5UT  C17  N2   C11  115.50  3.000
 5UT  C17  N2   C10  110.74  3.000
 5UT  C11  N2   C10  111.65  3.000
 5UT  H25  C9   H24  107.04  3.000
 5UT  H25  C9   N1   111.87  3.000
 5UT  H24  C9   N1   108.69  3.000
 5UT  H25  C9   C10  109.57  3.000
 5UT  H24  C9   C10  109.49  3.000
 5UT  N1   C9   C10  110.12  3.000
 5UT  H27  C16  H26  108.39  3.000
 5UT  H27  C16  N3   114.57  3.000
 5UT  H26  C16  N3   113.71  3.000
 5UT  H27  C16  C11  116.49  3.000
 5UT  H26  C16  C11  114.23  3.000
 5UT  N3   C16  C11   88.57  3.000
 5UT  C13  N3   C12  135.06  3.000
 5UT  C13  N3   C16  129.13  3.000
 5UT  C12  N3   C16   95.66  3.000
 5UT  H29  C12  H28  108.81  3.000
 5UT  H29  C12  N3   113.89  3.000
 5UT  H28  C12  N3   114.70  3.000
 5UT  H29  C12  C11  114.54  3.000
 5UT  H28  C12  C11  116.08  3.000
 5UT  N3   C12  C11   87.74  3.000
 5UT  O1   C13  N3   121.61  3.000
 5UT  O1   C13  C14  123.20  3.000
 5UT  N3   C13  C14  115.19  3.000
 5UT  H31  C15  H30  117.05  3.000
 5UT  H31  C15  C14  121.23  3.000
 5UT  H30  C15  C14  121.71  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
 5UT  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 5UT  CONST_02  C5   C6   C19  C2      0.00   0.0  0
 5UT  CONST_03  C6   C19  C2   C3      0.00   0.0  0
 5UT  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 5UT  CONST_05  C19  C2   C3   C4      0.00   0.0  0
 5UT  CONST_06  C19  C6   C5   C4      0.00   0.0  0
 5UT  CONST_07  C4   C3   C2   C1    180.00   0.0  0
 5UT  CONST_08  C6   C19  C2   C1    180.00   0.0  0
 5UT  CONST_09  CL   C3   C2   C1      0.00   0.0  0
 5UT  CONST_10  N    C6   C19  C2    180.00   0.0  0
 5UT  CONST_11  O    C5   C4   C3    180.00   0.0  0
 5UT  CONST_12  N    C6   C5   C4    180.00   0.0  0
 5UT  CONST_13  CL   C3   C4   C5    180.00   0.0  0
 5UT  CONST_14  C19  C6   C5   O     180.00   0.0  0
 5UT  CONST_15  C19  C2   C3   CL    180.00   0.0  0
 5UT  CONST_16  H15  C19  C2   C1      0.00   0.0  0
 5UT  CONST_17  H1   C4   C3   C2    180.00   0.0  0
 5UT  CONST_18  C16  N3   C13  C14   180.00   0.0  0
 5UT  CONST_19  C12  N3   C13  C14     0.00   0.0  0
 5UT  CONST_20  C7   C8   N1   C18   180.00   0.0  0
 5UT  CONST_21  O2   C8   N1   C18     0.00   0.0  0
 5UT  CONST_22  C9   N1   C8   O2    180.00   0.0  0
 5UT  CONST_23  C9   N1   C8   C7      0.00   0.0  0
 5UT  CONST_24  O1   C13  N3   C16     0.00   0.0  0
 5UT  CONST_25  O1   C13  N3   C12   180.00   0.0  0
 5UT  CONST_26  C7   N    C6   C5    180.00   0.0  0
 5UT  CONST_27  C19  C6   N    C7      0.00   0.0  0
 5UT  Var_01    C21  C20  C1   C2    108.30  30.0  1
 5UT  Var_02    C20  C1   C2   C3   -136.46  30.0  2
 5UT  Var_03    C18  N1   C9   C10    55.88  30.0  1
 5UT  Var_04    C18  C17  N2   C10   -58.34  30.0  1
 5UT  Var_05    C9   C10  N2   C11  -171.79  30.0  1
 5UT  Var_06    C12  N3   C16  C11     3.31  30.0  1
 5UT  Var_07    N2   C10  C9   N1    -56.01  30.0  1
 5UT  Var_08    N2   C17  C18  N1     56.82  30.0  1
 5UT  Var_09    C9   N1   C18  C17   -56.37  30.0  1
 5UT  Var_10    H16  C21  C20  C1   -108.30  30.0  1
 5UT  Var_11    H18  C    C1   C2    -60.08  30.0  3
 5UT  Var_12    C8   C7   N    C6    167.67  30.0  2
 5UT  Var_13    N1   C8   C7   N     175.74  30.0  3
 5UT  Var_14    C15  C14  C13  N3   -179.62  30.0  2
 5UT  Var_15    H30  C15  C14  C13     0.01   0.0  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
 5UT  chir_02  C11  N2   C16  C12  negativ
 5UT  chir_03  C1   C20  C21  C2   both

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
 5UT  plan-1  C18  0.020
 5UT  plan-1  O2   0.020
 5UT  plan-1  C8   0.020
 5UT  plan-1  C7   0.020
 5UT  plan-1  N1   0.020
 5UT  plan-1  C9   0.020
 5UT  plan-2  C1   0.020
 5UT  plan-2  C2   0.020
 5UT  plan-2  C3   0.020
 5UT  plan-2  C4   0.020
 5UT  plan-2  C5   0.020
 5UT  plan-2  C6   0.020
 5UT  plan-2  N    0.020
 5UT  plan-2  O    0.020
 5UT  plan-2  CL   0.020
 5UT  plan-2  C19  0.020
 5UT  plan-2  H1   0.020
 5UT  plan-2  H15  0.020
 5UT  plan-3  C6   0.020
 5UT  plan-3  C7   0.020
 5UT  plan-3  N    0.020
 5UT  plan-3  H13  0.020
 5UT  plan-4  C14  0.020
 5UT  plan-4  C16  0.020
 5UT  plan-4  N3   0.020
 5UT  plan-4  C12  0.020
 5UT  plan-4  C13  0.020
 5UT  plan-4  O1   0.020
 5UT  plan-5  C14  0.020
 5UT  plan-5  C13  0.020
 5UT  plan-5  C15  0.020
 5UT  plan-5  H5   0.020
 5UT  plan-5  H30  0.020
 5UT  plan-5  H31  0.020

