# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 10:30:44 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 2-[1-[4,4-bis(fluoranyl)cyclohexyl]piperidin-4-yl]-6-fluoranyl-3-oxidanylidene-1H-isoindole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(F)cc2CN(C3CCN(CC3)C4CCC(F)(F)CC4)C(=O)c12
#
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
 D7N  D7N  2-[1-[4,4-bis(fluoranyl)cyclohexyl]piperidin-4-yl]-6-fluoranyl-3-oxidanylidene-1H-isoindole-4-carboxamide  ligand  52  28  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D7N
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
 D7N  C25   C  CH2   0  -0.497  -4.7502  -0.4660  -1.2268
 D7N  C24   C  CH2   0  -0.558  -6.2629  -0.5791  -1.0453
 D7N  C23   C  CT    0   0.762  -6.7729   0.3533   0.0236
 D7N  F26   F  F     0  -0.357  -8.1221   0.1712   0.2017
 D7N  F27   F  F     0  -0.359  -6.6492   1.6549  -0.4053
 D7N  C22   C  CH2   0  -0.562  -6.0458   0.1825   1.3326
 D7N  C21   C  CH2   0  -0.465  -4.5385   0.3046   1.1332
 D7N  C20   C  CH1   0  -0.011  -4.0047  -0.6872   0.0913
 D7N  N16   N  NT    0  -0.437  -2.5522  -0.5322  -0.0259
 D7N  C15   C  CH2   0  -0.300  -1.8747  -1.1370   1.1119
 D7N  C14   C  CH2   0  -0.433  -0.3956  -0.7855   1.1416
 D7N  C17   C  CH2   0  -0.295  -1.9664  -1.0284  -1.2614
 D7N  C18   C  CH2   0  -0.429  -0.4869  -0.6749  -1.3483
 D7N  C13   C  CH1   0  -0.067   0.2693  -1.2375  -0.1521
 D7N  N10   N  NR5   0  -0.532   1.6951  -0.9579  -0.1911
 D7N  C9    C  CH2   0  -0.278   2.6604  -2.0380  -0.1938
 D7N  C11   C  CR5   0   0.565   2.2627   0.2707  -0.1635
 D7N  O12   O  O     0  -0.484   1.6908   1.3472  -0.1087
 D7N  C7    C  CR56  0  -0.081   3.7251   0.0458  -0.1906
 D7N  C8    C  CR56  0   0.103   3.9674  -1.3165  -0.1830
 D7N  C3    C  CR16  0  -0.489   5.2541  -1.8223  -0.1604
 D7N  C2    C  CR6   0   0.567   6.2765  -0.8928  -0.1289
 D7N  F5    F  F     0  -0.307   7.5398  -1.3329  -0.1012
 D7N  C1    C  CR16  0  -0.437   6.0642   0.4798  -0.1264
 D7N  C4    C  CR6   0  -0.057   4.7649   0.9647  -0.1667
 D7N  C6    C  C     0   0.443   4.5239   2.4447  -0.2742
 D7N  O28   O  O     0  -0.464   4.1627   2.9407  -1.3268
 D7N  N19   N  NH2   0  -0.782   4.7843   3.1310   0.8420
 D7N  H251  H  HCH2  0   0.258  -4.4632  -1.2083  -1.9718
 D7N  H252  H  HCH2  0   0.236  -4.4883   0.5141  -1.6373
 D7N  H241  H  HCH2  0   0.268  -6.7729  -0.3805  -1.9908
 D7N  H242  H  HCH2  0   0.252  -6.5161  -1.6000  -0.7483
 D7N  H20   H  HCH1  0   0.193  -4.2475  -1.7119   0.4324
 D7N  H221  H  HCH2  0   0.267  -6.4005   0.9157   2.0607
 D7N  H222  H  HCH2  0   0.251  -6.2876  -0.8084   1.7270
 D7N  H211  H  HCH2  0   0.231  -4.2786   1.3166   0.8114
 D7N  H212  H  HCH2  0   0.251  -4.0593   0.1537   2.1007
 D7N  H151  H  HCH2  0   0.246  -2.3285  -0.7915   2.0403
 D7N  H152  H  HCH2  0   0.193  -1.9927  -2.2358   1.1009
 D7N  H171  H  HCH2  0   0.188  -2.0877  -2.1218  -1.3647
 D7N  H172  H  HCH2  0   0.250  -2.4635  -0.5736  -2.1163
 D7N  H141  H  HCH2  0   0.235  -0.2799   0.2920   1.2689
 D7N  H142  H  HCH2  0   0.238   0.0763  -1.2723   1.9984
 D7N  H13   H  HCH1  0   0.248   0.1884  -2.3286  -0.1991
 D7N  H181  H  HCH2  0   0.239  -0.0766  -1.0803  -2.2760
 D7N  H182  H  HCH2  0   0.235  -0.3787   0.4102  -1.3869
 D7N  H91   H  HCH2  0   0.279   2.5423  -2.6790   0.6851
 D7N  H92   H  HCH2  0   0.280   2.5511  -2.6711  -1.0792
 D7N  H3    H  HCR6  0   0.287   5.4620  -2.8844  -0.1619
 D7N  H1    H  HCR6  0   0.293   6.9119   1.1527  -0.1039
 D7N  H191  H  HNH2  0   0.416   5.0494   2.6711   1.6960
 D7N  H192  H  HNH2  0   0.409   4.6734   4.1325   0.8675

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
 D7N  C25  C24   single    1.528  0.020  1.528
 D7N  C25  C20   single    1.530  0.020  1.530
 D7N  C24  C23   single    1.507  0.020  1.507
 D7N  C23  F26   single    1.373  0.020  1.373
 D7N  C23  F27   single    1.376  0.020  1.376
 D7N  C23  C22   single    1.507  0.020  1.507
 D7N  C22  C21   single    1.525  0.020  1.525
 D7N  C21  C20   single    1.534  0.020  1.534
 D7N  C20  N16   single    1.465  0.020  1.465
 D7N  N16  C15   single    1.456  0.020  1.456
 D7N  N16  C17   single    1.455  0.020  1.455
 D7N  C15  C14   single    1.520  0.020  1.520
 D7N  C14  C13   single    1.523  0.020  1.523
 D7N  C17  C18   single    1.524  0.020  1.524
 D7N  C18  C13   single    1.523  0.020  1.523
 D7N  C13  N10   single    1.453  0.020  1.453
 D7N  N10  C9    single    1.449  0.020  1.449
 D7N  N10  C11   single    1.354  0.020  1.354
 D7N  C9   C8    single    1.493  0.020  1.493
 D7N  C11  O12   double    1.220  0.020  1.220
 D7N  C11  C7    single    1.480  0.020  1.480
 D7N  C7   C8    aromatic  1.384  0.020  1.384
 D7N  C7   C4    aromatic  1.388  0.020  1.388
 D7N  C8   C3    aromatic  1.383  0.020  1.383
 D7N  C3   C2    aromatic  1.382  0.020  1.382
 D7N  C2   F5    single    1.338  0.020  1.338
 D7N  C2   C1    aromatic  1.389  0.020  1.389
 D7N  C1   C4    aromatic  1.387  0.020  1.387
 D7N  C4   C6    single    1.503  0.020  1.503
 D7N  C6   O28   double    1.218  0.020  1.218
 D7N  C6   N19   single    1.336  0.020  1.336
 D7N  C25  H251  single    0.970  0.020  1.090
 D7N  C25  H252  single    0.970  0.020  1.090
 D7N  C24  H241  single    0.970  0.020  1.090
 D7N  C24  H242  single    0.970  0.020  1.090
 D7N  C20  H20   single    0.970  0.020  1.090
 D7N  C22  H221  single    0.970  0.020  1.090
 D7N  C22  H222  single    0.970  0.020  1.090
 D7N  C21  H211  single    0.970  0.020  1.090
 D7N  C21  H212  single    0.970  0.020  1.090
 D7N  C15  H151  single    0.970  0.020  1.090
 D7N  C15  H152  single    0.970  0.020  1.090
 D7N  C17  H171  single    0.970  0.020  1.090
 D7N  C17  H172  single    0.970  0.020  1.090
 D7N  C14  H141  single    0.970  0.020  1.090
 D7N  C14  H142  single    0.970  0.020  1.090
 D7N  C13  H13   single    0.970  0.020  1.090
 D7N  C18  H181  single    0.970  0.020  1.090
 D7N  C18  H182  single    0.970  0.020  1.090
 D7N  C9   H91   single    0.970  0.020  1.090
 D7N  C9   H92   single    0.970  0.020  1.090
 D7N  C3   H3    single    0.930  0.020  1.080
 D7N  C1   H1    single    0.930  0.020  1.080
 D7N  N19  H191  single    0.860  0.020  1.020
 D7N  N19  H192  single    0.860  0.020  1.020

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
 D7N  H252  C25  H251  106.89  3.000
 D7N  H252  C25  C20   109.63  3.000
 D7N  H251  C25  C20   111.22  3.000
 D7N  H252  C25  C24   110.35  3.000
 D7N  H251  C25  C24   106.94  3.000
 D7N  C20   C25  C24   111.67  3.000
 D7N  H242  C24  H241  107.27  3.000
 D7N  H242  C24  C23   107.86  3.000
 D7N  H241  C24  C23   110.08  3.000
 D7N  H242  C24  C25   109.32  3.000
 D7N  H241  C24  C25   110.24  3.000
 D7N  C23   C24  C25   111.93  3.000
 D7N  C22   C23  F27   109.55  3.000
 D7N  C22   C23  F26   110.27  3.000
 D7N  F27   C23  F26   104.72  3.000
 D7N  C22   C23  C24   112.50  3.000
 D7N  F27   C23  C24   109.49  3.000
 D7N  F26   C23  C24   110.02  3.000
 D7N  H222  C22  H221  107.22  3.000
 D7N  H222  C22  C21   109.77  3.000
 D7N  H221  C22  C21   110.75  3.000
 D7N  H222  C22  C23   108.01  3.000
 D7N  H221  C22  C23   110.25  3.000
 D7N  C21   C22  C23   110.74  3.000
 D7N  H212  C21  H211  106.55  3.000
 D7N  H212  C21  C20   111.12  3.000
 D7N  H211  C21  C20   108.41  3.000
 D7N  H212  C21  C22   107.89  3.000
 D7N  H211  C21  C22   110.33  3.000
 D7N  C20   C21  C22   112.38  3.000
 D7N  H20   C20  N16   109.87  3.000
 D7N  H20   C20  C21   108.23  3.000
 D7N  N16   C20  C21   109.31  3.000
 D7N  H20   C20  C25   107.01  3.000
 D7N  N16   C20  C25   113.49  3.000
 D7N  C21   C20  C25   108.78  3.000
 D7N  C17   N16  C15   109.55  3.000
 D7N  C17   N16  C20   115.53  3.000
 D7N  C15   N16  C20   110.78  3.000
 D7N  H152  C15  H151  106.21  3.000
 D7N  H152  C15  C14   109.51  3.000
 D7N  H151  C15  C14   108.38  3.000
 D7N  H152  C15  N16   110.82  3.000
 D7N  H151  C15  N16   109.90  3.000
 D7N  C14   C15  N16   111.84  3.000
 D7N  H142  C14  H141  107.62  3.000
 D7N  H142  C14  C13   110.20  3.000
 D7N  H141  C14  C13   110.23  3.000
 D7N  H142  C14  C15   109.42  3.000
 D7N  H141  C14  C15   109.49  3.000
 D7N  C13   C14  C15   109.84  3.000
 D7N  H172  C17  H171  106.85  3.000
 D7N  H172  C17  C18   107.56  3.000
 D7N  H171  C17  C18   109.32  3.000
 D7N  H172  C17  N16   109.91  3.000
 D7N  H171  C17  N16   111.89  3.000
 D7N  C18   C17  N16   111.12  3.000
 D7N  H182  C18  H181  107.56  3.000
 D7N  H182  C18  C13   110.24  3.000
 D7N  H181  C18  C13   110.08  3.000
 D7N  H182  C18  C17   109.21  3.000
 D7N  H181  C18  C17   109.09  3.000
 D7N  C13   C18  C17   110.59  3.000
 D7N  H13   C13  N10   105.25  3.000
 D7N  H13   C13  C18   107.32  3.000
 D7N  N10   C13  C18   113.27  3.000
 D7N  H13   C13  C14   107.45  3.000
 D7N  N10   C13  C14   113.20  3.000
 D7N  C18   C13  C14   109.92  3.000
 D7N  C11   N10  C9    113.41  3.000
 D7N  C11   N10  C13   125.83  3.000
 D7N  C9    N10  C13   120.68  3.000
 D7N  H92   C9   H91   107.48  3.000
 D7N  H92   C9   C8    111.90  3.000
 D7N  H91   C9   C8    111.83  3.000
 D7N  H92   C9   N10   111.50  3.000
 D7N  H91   C9   N10   111.30  3.000
 D7N  C8    C9   N10   102.89  3.000
 D7N  C7    C11  O12   126.73  3.000
 D7N  C7    C11  N10   106.02  3.000
 D7N  O12   C11  N10   127.24  3.000
 D7N  C4    C7   C8    121.37  3.000
 D7N  C4    C7   C11   129.74  3.000
 D7N  C8    C7   C11   108.82  3.000
 D7N  C3    C8   C7    121.55  3.000
 D7N  C3    C8   C9    129.64  3.000
 D7N  C7    C8   C9    108.81  3.000
 D7N  H3    C3   C2    121.19  3.000
 D7N  H3    C3   C8    122.53  3.000
 D7N  C2    C3   C8    116.28  3.000
 D7N  C1    C2   F5    117.99  3.000
 D7N  C1    C2   C3    123.47  3.000
 D7N  F5    C2   C3    118.54  3.000
 D7N  H1    C1   C4    121.11  3.000
 D7N  H1    C1   C2    119.64  3.000
 D7N  C4    C1   C2    119.25  3.000
 D7N  C6    C4   C1    119.76  3.000
 D7N  C6    C4   C7    122.04  3.000
 D7N  C1    C4   C7    118.07  3.000
 D7N  N19   C6   O28   124.78  3.000
 D7N  N19   C6   C4    114.51  3.000
 D7N  O28   C6   C4    120.67  3.000
 D7N  H192  N19  H191  117.52  3.000
 D7N  H192  N19  C6    120.67  3.000
 D7N  H191  N19  C6    121.74  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
 D7N  CONST_01  C2    C3   C8   C7      0.00   0.0  0
 D7N  CONST_02  C2    C1   C4   C7      0.00   0.0  0
 D7N  CONST_03  C1    C4   C7   C8      0.00   0.0  0
 D7N  CONST_04  C1    C2   C3   C8      0.00   0.0  0
 D7N  CONST_05  C4    C7   C8   C3      0.00   0.0  0
 D7N  CONST_06  C4    C1   C2   C3      0.00   0.0  0
 D7N  CONST_07  C7    C11  N10  C13   180.00   0.0  0
 D7N  CONST_08  C7    C11  N10  C9      0.00   0.0  0
 D7N  CONST_09  C6    C4   C7   C11     0.00   0.0  0
 D7N  CONST_10  C6    C4   C7   C8    180.00   0.0  0
 D7N  CONST_11  F5    C2   C3   C8    180.00   0.0  0
 D7N  CONST_12  C6    C4   C1   C2    180.00   0.0  0
 D7N  CONST_13  C4    C1   C2   F5    180.00   0.0  0
 D7N  CONST_14  O12   C11  N10  C13     0.00   0.0  0
 D7N  CONST_15  O12   C11  N10  C9    180.00   0.0  0
 D7N  CONST_16  H3    C3   C8   C9      0.00   0.0  0
 D7N  CONST_17  H1    C1   C4   C7    180.00   0.0  0
 D7N  CONST_18  H191  N19  C6   C4      0.00   0.0  0
 D7N  CONST_19  H192  N19  C6   C4    180.00   0.0  0
 D7N  Var_01    C22   C23  C24  C25   -53.57  30.0  1
 D7N  Var_02    C21   C22  C23  C24    53.58  30.0  1
 D7N  Var_03    C20   C25  C24  C23    55.00  30.0  1
 D7N  Var_04    C20   C21  C22  C23   -56.00  30.0  1
 D7N  Var_05    C14   C15  N16  C20  -170.14  30.0  1
 D7N  Var_06    C18   C17  N16  C20   173.46  30.0  1
 D7N  Var_07    C13   C14  C15  N16   -57.93  30.0  1
 D7N  Var_08    C13   C18  C17  N16    57.61  30.0  1
 D7N  Var_09    H91   C9   N10  C13   -57.92  30.0  1
 D7N  Var_10    O28   C6   C4   C7    -70.95  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
 D7N  chir_01  C20  C25  C21  N16  positiv
 D7N  chir_02  C13  N10  C18  C14  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
 D7N  plan-1  C4    0.020
 D7N  plan-1  C6    0.020
 D7N  plan-1  O28   0.020
 D7N  plan-1  N19   0.020
 D7N  plan-1  H191  0.020
 D7N  plan-1  H192  0.020
 D7N  plan-2  C13   0.020
 D7N  plan-2  N10   0.020
 D7N  plan-2  C9    0.020
 D7N  plan-2  C11   0.020
 D7N  plan-2  O12   0.020
 D7N  plan-2  C7    0.020
 D7N  plan-2  C8    0.020
 D7N  plan-2  C3    0.020
 D7N  plan-2  C2    0.020
 D7N  plan-2  F5    0.020
 D7N  plan-2  C1    0.020
 D7N  plan-2  C4    0.020
 D7N  plan-2  C6    0.020
 D7N  plan-2  H3    0.020
 D7N  plan-2  H1    0.020

