# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 11:36:35 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 3-[2-(4-fluoranylphenoxy)ethyl]-1,3-diazaspiro[4.5]decane-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(OCCN2C(=O)NC3(CCCCC3)C2=O)cc1
#
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
 7BJ  7BJ  3-[2-(4-fluoranylphenoxy)ethyl]-1,3-diazaspiro[4.5]decane-2,4-dione  ligand  41  22  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7BJ
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
 7BJ  C2   C  CR6   0   0.498  -4.6447  -1.2178  -0.5690
 7BJ  C3   C  CR16  0  -0.395  -4.5713   0.1193  -0.8914
 7BJ  C5   C  CR6   0   0.390  -2.4810   0.2656   0.3000
 7BJ  C7   C  CH2   0  -0.191  -1.1369   2.2299   0.3515
 7BJ  C8   C  CH2   0  -0.351   0.2387   2.6072   0.8638
 7BJ  C10  C  CR5   0   0.703   1.7982   1.7183  -0.8734
 7BJ  C13  C  CR5   0  -0.044   2.6156  -0.1859   0.1988
 7BJ  C14  C  CH2   0  -0.400   1.9869  -1.5547  -0.1056
 7BJ  C15  C  CH2   0  -0.451   2.8931  -2.3955  -0.9971
 7BJ  C16  C  CH2   0  -0.431   4.2786  -2.5603  -0.3821
 7BJ  C19  C  CR5   0   0.600   1.6957   0.6019   1.1168
 7BJ  C21  C  CR16  0  -0.329  -2.5780  -1.0914   0.6125
 7BJ  C22  C  CR16  0  -0.393  -3.6606  -1.8367   0.1813
 7BJ  F1   F  F     0  -0.322  -5.6980  -1.9415  -0.9926
 7BJ  C4   C  CR16  0  -0.364  -3.4837   0.8683  -0.4540
 7BJ  O6   O  O2    0  -0.470  -1.3949   0.9079   0.7747
 7BJ  N9   N  NR5   0  -0.546   1.2495   1.6805   0.4121
 7BJ  N12  N  NR15  0  -0.677   2.6352   0.6715  -0.9694
 7BJ  C17  C  CH2   0  -0.452   4.9093  -1.2077  -0.0659
 7BJ  C18  C  CH2   0  -0.401   4.0037  -0.3598   0.8206
 7BJ  O20  O  O     0  -0.437   1.4153   0.3213   2.2575
 7BJ  H23  H  HCR6  0   0.283  -5.3510   0.5878  -1.4772
 7BJ  H26  H  HCH2  0   0.245  -1.8736   2.9327   0.7561
 7BJ  H25  H  HCH2  0   0.236  -1.1693   2.3020  -0.7410
 7BJ  H27  H  HCH2  0   0.285   0.4853   3.6110   0.5206
 7BJ  H28  H  HCH2  0   0.280   0.2546   2.6210   1.9526
 7BJ  H31  H  HCH2  0   0.241   1.8212  -2.0722   0.8429
 7BJ  H30  H  HCH2  0   0.248   1.0065  -1.4139  -0.5685
 7BJ  H33  H  HCH2  0   0.246   2.4293  -3.3697  -1.1629
 7BJ  H32  H  HCH2  0   0.221   2.9817  -1.9316  -1.9854
 7BJ  H35  H  HCH2  0   0.218   4.2007  -3.1492   0.5380
 7BJ  H34  H  HCH2  0   0.237   4.9242  -3.1254  -1.0578
 7BJ  H40  H  HCR6  0   0.272  -1.7969  -1.5608   1.1967
 7BJ  H41  H  HCR6  0   0.282  -3.7342  -2.8885   0.4256
 7BJ  H24  H  HCR6  0   0.288  -3.4464   1.9182  -0.7099
 7BJ  H29  H  HNR5  0   0.413   3.0849   0.4363  -1.8396
 7BJ  H37  H  HCH2  0   0.245   5.8711  -1.3450   0.4322
 7BJ  H36  H  HCH2  0   0.221   5.1261  -0.6744  -0.9977
 7BJ  H38  H  HCH2  0   0.251   4.4498   0.6200   1.0058
 7BJ  H39  H  HCH2  0   0.239   3.8820  -0.8464   1.7921
 7BJ  O11  O  O     0  -0.485   1.5399   2.5643  -1.7027

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
 7BJ  F1   C2   single    1.346  0.020  1.346
 7BJ  C3   C2   aromatic  1.377  0.020  1.377
 7BJ  C3   C4   aromatic  1.391  0.020  1.391
 7BJ  C2   C22  aromatic  1.384  0.020  1.384
 7BJ  C4   C5   aromatic  1.392  0.020  1.392
 7BJ  C15  C14  single    1.524  0.020  1.524
 7BJ  C15  C16  single    1.525  0.020  1.525
 7BJ  C22  C21  aromatic  1.383  0.020  1.383
 7BJ  C14  C13  single    1.537  0.020  1.537
 7BJ  C5   C21  aromatic  1.396  0.020  1.396
 7BJ  C5   O6   single    1.348  0.020  1.348
 7BJ  C7   O6   single    1.412  0.020  1.412
 7BJ  C7   C8   single    1.516  0.020  1.516
 7BJ  C16  C17  single    1.526  0.020  1.526
 7BJ  N12  C13  single    1.449  0.020  1.449
 7BJ  N12  C10  single    1.344  0.020  1.344
 7BJ  O11  C10  double    1.212  0.020  1.212
 7BJ  C13  C19  single    1.520  0.020  1.520
 7BJ  C13  C18  single    1.531  0.020  1.531
 7BJ  C10  N9   single    1.398  0.020  1.398
 7BJ  C19  N9   single    1.363  0.020  1.363
 7BJ  C19  O20  double    1.208  0.020  1.208
 7BJ  N9   C8   single    1.444  0.020  1.444
 7BJ  C17  C18  single    1.525  0.020  1.525
 7BJ  C3   H23  single    0.930  0.020  1.080
 7BJ  C7   H26  single    0.970  0.020  1.090
 7BJ  C7   H25  single    0.970  0.020  1.090
 7BJ  C8   H27  single    0.970  0.020  1.090
 7BJ  C8   H28  single    0.970  0.020  1.090
 7BJ  C14  H31  single    0.970  0.020  1.090
 7BJ  C14  H30  single    0.970  0.020  1.090
 7BJ  C15  H33  single    0.970  0.020  1.090
 7BJ  C15  H32  single    0.970  0.020  1.090
 7BJ  C16  H35  single    0.970  0.020  1.090
 7BJ  C16  H34  single    0.970  0.020  1.090
 7BJ  C21  H40  single    0.930  0.020  1.080
 7BJ  C22  H41  single    0.930  0.020  1.080
 7BJ  C4   H24  single    0.930  0.020  1.080
 7BJ  N12  H29  single    0.860  0.020  1.020
 7BJ  C17  H37  single    0.970  0.020  1.090
 7BJ  C17  H36  single    0.970  0.020  1.090
 7BJ  C18  H38  single    0.970  0.020  1.090
 7BJ  C18  H39  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
 7BJ  F1   C2   C22  119.12  3.000
 7BJ  C22  C2   C3   121.55  3.000
 7BJ  F1   C2   C3   119.33  3.000
 7BJ  H23  C3   C4   120.03  3.000
 7BJ  H23  C3   C2   120.57  3.000
 7BJ  C4   C3   C2   119.39  3.000
 7BJ  O6   C5   C4   124.39  3.000
 7BJ  O6   C5   C21  116.13  3.000
 7BJ  C4   C5   C21  119.48  3.000
 7BJ  H25  C7   H26  107.83  3.000
 7BJ  H25  C7   O6   110.80  3.000
 7BJ  H26  C7   O6   111.53  3.000
 7BJ  H25  C7   C8   110.34  3.000
 7BJ  H26  C7   C8   109.02  3.000
 7BJ  O6   C7   C8   107.32  3.000
 7BJ  H28  C8   H27  107.46  3.000
 7BJ  H28  C8   N9   108.10  3.000
 7BJ  H27  C8   N9   109.54  3.000
 7BJ  H28  C8   C7   110.75  3.000
 7BJ  H27  C8   C7   109.18  3.000
 7BJ  N9   C8   C7   111.71  3.000
 7BJ  N12  C10  O11  128.86  3.000
 7BJ  O11  C10  N9   124.34  3.000
 7BJ  N12  C10  N9   106.80  3.000
 7BJ  C18  C13  N12  112.48  3.000
 7BJ  C18  C13  C19  111.24  3.000
 7BJ  N12  C13  C19  100.86  3.000
 7BJ  C18  C13  C14  110.50  3.000
 7BJ  C19  C13  C14  109.50  3.000
 7BJ  N12  C13  C14  111.89  3.000
 7BJ  H30  C14  H31  107.00  3.000
 7BJ  H30  C14  C15  110.89  3.000
 7BJ  H31  C14  C15  109.66  3.000
 7BJ  H30  C14  C13  109.64  3.000
 7BJ  H31  C14  C13  108.17  3.000
 7BJ  C15  C14  C13  111.35  3.000
 7BJ  H32  C15  H33  105.98  3.000
 7BJ  H32  C15  C16  109.65  3.000
 7BJ  H33  C15  C16  110.54  3.000
 7BJ  H32  C15  C14  110.01  3.000
 7BJ  H33  C15  C14  109.18  3.000
 7BJ  C16  C15  C14  111.34  3.000
 7BJ  H34  C16  H35  106.48  3.000
 7BJ  H34  C16  C17  110.04  3.000
 7BJ  H35  C16  C17  109.39  3.000
 7BJ  H34  C16  C15  110.09  3.000
 7BJ  H35  C16  C15  109.41  3.000
 7BJ  C17  C16  C15  111.31  3.000
 7BJ  O20  C19  N9   126.58  3.000
 7BJ  O20  C19  C13  126.20  3.000
 7BJ  N9   C19  C13  107.22  3.000
 7BJ  H40  C21  C22  119.96  3.000
 7BJ  H40  C21  C5   119.48  3.000
 7BJ  C22  C21  C5   120.56  3.000
 7BJ  H41  C22  C21  120.43  3.000
 7BJ  H41  C22  C2   120.58  3.000
 7BJ  C21  C22  C2   118.99  3.000
 7BJ  H24  C4   C5   121.59  3.000
 7BJ  H24  C4   C3   118.38  3.000
 7BJ  C5   C4   C3   120.03  3.000
 7BJ  C7   O6   C5   119.20  3.000
 7BJ  C19  N9   C10  111.60  3.000
 7BJ  C19  N9   C8   125.12  3.000
 7BJ  C10  N9   C8   123.02  3.000
 7BJ  H29  N12  C13  124.35  3.000
 7BJ  H29  N12  C10  121.44  3.000
 7BJ  C13  N12  C10  113.26  3.000
 7BJ  H36  C17  H37  105.96  3.000
 7BJ  H36  C17  C18  109.97  3.000
 7BJ  H37  C17  C18  109.14  3.000
 7BJ  H36  C17  C16  109.70  3.000
 7BJ  H37  C17  C16  110.32  3.000
 7BJ  C18  C17  C16  111.59  3.000
 7BJ  H39  C18  H38  107.10  3.000
 7BJ  H39  C18  C17  109.59  3.000
 7BJ  H38  C18  C17  110.78  3.000
 7BJ  H39  C18  C13  108.09  3.000
 7BJ  H38  C18  C13  109.71  3.000
 7BJ  C17  C18  C13  111.44  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
 7BJ  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 7BJ  CONST_02  C5   C21  C22  C2      0.00   0.0  0
 7BJ  CONST_03  C21  C22  C2   C3      0.00   0.0  0
 7BJ  CONST_04  C21  C5   C4   C3      0.00   0.0  0
 7BJ  CONST_05  C4   C3   C2   C22     0.00   0.0  0
 7BJ  CONST_06  C4   C5   C21  C22     0.00   0.0  0
 7BJ  CONST_07  C19  C13  N12  C10     0.00   0.0  0
 7BJ  CONST_08  C13  C19  N9   C10     0.00   0.0  0
 7BJ  CONST_09  N9   C10  N12  C13     0.00   0.0  0
 7BJ  CONST_10  N12  C10  N9   C19     0.00   0.0  0
 7BJ  CONST_11  N12  C13  C19  N9      0.00   0.0  0
 7BJ  CONST_12  O6   C5   C4   C3    180.00   0.0  0
 7BJ  CONST_13  F1   C2   C22  C21   180.00   0.0  0
 7BJ  CONST_14  O6   C5   C21  C22   180.00   0.0  0
 7BJ  CONST_15  C4   C3   C2   F1    180.00   0.0  0
 7BJ  CONST_16  N12  C10  N9   C8    180.00   0.0  0
 7BJ  CONST_17  C13  C19  N9   C8    180.00   0.0  0
 7BJ  CONST_18  O11  C10  N12  C13   180.00   0.0  0
 7BJ  CONST_19  O11  C10  N9   C19   180.00   0.0  0
 7BJ  CONST_20  H24  C4   C3   C2    180.00   0.0  0
 7BJ  CONST_21  H40  C21  C22  C2    180.00   0.0  0
 7BJ  CONST_22  H41  C22  C2   C3    180.00   0.0  0
 7BJ  CONST_23  H23  C3   C4   C5    180.00   0.0  0
 7BJ  CONST_24  H29  N12  C13  C19   180.00   0.0  0
 7BJ  CONST_25  O11  C10  N9   C8      0.00   0.0  0
 7BJ  Var_01    C14  C13  N12  C10   111.03  30.0  3
 7BJ  Var_02    C16  C15  C14  C13    55.79  30.0  1
 7BJ  Var_03    C16  C17  C18  C13   -55.29  30.0  1
 7BJ  Var_04    C17  C16  C15  C14   -55.07  30.0  1
 7BJ  Var_05    N9   C19  C13  C14  -114.23  30.0  3
 7BJ  Var_06    C17  C18  C13  C14    55.37  30.0  1
 7BJ  Var_07    N12  C13  C14  C15    70.47  30.0  1
 7BJ  Var_08    C18  C17  C16  C15    54.83  30.0  1
 7BJ  Var_09    C4   C5   O6   C7     -8.88  30.0  2
 7BJ  Var_10    C10  N9   C8   C7     78.94  30.0  2
 7BJ  Var_11    C8   C7   O6   C5   -171.22  30.0  1
 7BJ  Var_12    N9   C8   C7   O6     56.51  30.0  3

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
 7BJ  plan-1  C2   0.020
 7BJ  plan-1  C3   0.020
 7BJ  plan-1  C5   0.020
 7BJ  plan-1  C21  0.020
 7BJ  plan-1  C22  0.020
 7BJ  plan-1  F1   0.020
 7BJ  plan-1  C4   0.020
 7BJ  plan-1  O6   0.020
 7BJ  plan-1  H23  0.020
 7BJ  plan-1  H40  0.020
 7BJ  plan-1  H41  0.020
 7BJ  plan-1  H24  0.020
 7BJ  plan-2  C8   0.020
 7BJ  plan-2  C10  0.020
 7BJ  plan-2  C13  0.020
 7BJ  plan-2  C19  0.020
 7BJ  plan-2  N9   0.020
 7BJ  plan-2  N12  0.020
 7BJ  plan-2  O20  0.020
 7BJ  plan-2  H29  0.020
 7BJ  plan-2  O11  0.020

