# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 14:01:31 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 4,6-difluoro-N-(spiro[5.5]undecan-3-yl)-1H-indole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cc(F)c2cc([nH]c2c1)C(=O)N[CH]3CC[C]4(CC[CH2]CC4)CC3
#
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
 J9E  J9E  4,6-difluoro-N-(spiro[5.5]undecan-3-yl)-1H-indole-2-carboxamide  ligand  49  25  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J9E
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
 J9E  C02  C  C     0   0.527  -0.4897  -1.1580  -0.2490
 J9E  C04  C  CH1   0  -0.045   1.8458  -0.4578  -0.5524
 J9E  C05  C  CH2   0  -0.452   2.4909   0.6371  -1.3916
 J9E  C06  C  CH2   0  -0.413   3.9729   0.3458  -1.6004
 J9E  C07  C  CT    0  -0.082   4.7687   0.1552  -0.3012
 J9E  C08  C  CH2   0  -0.415   4.8957   1.4971   0.4411
 J9E  C09  C  CH2   0  -0.434   5.8585   1.4535   1.6244
 J9E  C10  C  CH2   0  -0.428   7.2367   0.9542   1.2068
 J9E  C11  C  CH2   0  -0.436   7.1428  -0.3943   0.5022
 J9E  C12  C  CH2   0  -0.405   6.1763  -0.3317  -0.6753
 J9E  C13  C  CH2   0  -0.428   4.0559  -0.9055   0.5528
 J9E  C14  C  CH2   0  -0.432   2.5746  -0.6178   0.7783
 J9E  C15  C  CR5   0   0.215  -1.8987  -0.7204  -0.1557
 J9E  C16  C  CR15  0  -0.363  -2.9391  -1.4578   0.3346
 J9E  C17  C  CR56  0  -0.168  -4.1009  -0.6476   0.2117
 J9E  C18  C  CR6   0   0.522  -5.4515  -0.8104   0.5128
 J9E  C20  C  CR16  0  -0.591  -6.3691   0.1716   0.2438
 J9E  C21  C  CR6   0   0.528  -5.9123   1.3572  -0.3468
 J9E  C23  C  CR16  0  -0.479  -4.6028   1.6028  -0.6703
 J9E  C24  C  CR56  0   0.387  -3.7045   0.5743  -0.3729
 J9E  F19  F  F     0  -0.299  -5.8499  -1.9583   1.0706
 J9E  F22  F  F     0  -0.315  -6.8293   2.3017  -0.6060
 J9E  N03  N  NH1   0  -0.667   0.4288  -0.1874  -0.3853
 J9E  N25  N  NR15  0  -0.743  -2.3635   0.5070  -0.5705
 J9E  O01  O  O     0  -0.484  -0.2202  -2.3515  -0.2184
 J9E  H1   H  HCH1  0   0.236   1.9235  -1.4001  -1.1027
 J9E  H2   H  HCH2  0   0.242   1.9887   0.7038  -2.3599
 J9E  H3   H  HCH2  0   0.224   2.3550   1.6086  -0.9041
 J9E  H4   H  HCH2  0   0.218   4.0649  -0.5636  -2.2060
 J9E  H5   H  HCH2  0   0.227   4.4267   1.1489  -2.1889
 J9E  H6   H  HCH2  0   0.212   5.2556   2.2463  -0.2743
 J9E  H7   H  HCH2  0   0.228   3.9182   1.8496   0.7801
 J9E  H8   H  HCH2  0   0.226   5.9366   2.4514   2.0641
 J9E  H9   H  HCH2  0   0.212   5.4579   0.8090   2.4135
 J9E  H10  H  HCH2  0   0.204   7.6921   1.6830   0.5267
 J9E  H11  H  HCH2  0   0.224   7.8973   0.8877   2.0751
 J9E  H12  H  HCH2  0   0.225   8.1300  -0.7038   0.1493
 J9E  H13  H  HCH2  0   0.212   6.8249  -1.1610   1.2161
 J9E  H14  H  HCH2  0   0.219   6.1022  -1.3134  -1.1555
 J9E  H15  H  HCH2  0   0.211   6.5892   0.3484  -1.4308
 J9E  H16  H  HCH2  0   0.218   4.1497  -1.8740   0.0471
 J9E  H17  H  HCH2  0   0.235   4.5491  -1.0298   1.5198
 J9E  H18  H  HCH2  0   0.218   2.4450   0.2884   1.3784
 J9E  H19  H  HCH2  0   0.240   2.1244  -1.4339   1.3481
 J9E  H20  H  HCR5  0   0.268  -2.8716  -2.4511   0.7466
 J9E  H21  H  HCR6  0   0.299  -7.4179   0.0401   0.4747
 J9E  H22  H  HCR6  0   0.290  -4.2921   2.5336  -1.1252
 J9E  H23  H  HNH1  0   0.395   0.1689   0.7687  -0.1983
 J9E  H24  H  HNR5  0   0.417  -1.8319   1.2025  -1.0692

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
 J9E  F22  C21  single    1.342  0.020  1.342
 J9E  C20  C21  aromatic  1.401  0.020  1.401
 J9E  C20  C18  aromatic  1.371  0.020  1.371
 J9E  C21  C23  aromatic  1.371  0.020  1.371
 J9E  F19  C18  single    1.337  0.020  1.337
 J9E  C18  C17  aromatic  1.393  0.020  1.393
 J9E  C23  C24  aromatic  1.398  0.020  1.398
 J9E  C24  C17  aromatic  1.411  0.020  1.411
 J9E  C24  N25  aromatic  1.357  0.020  1.357
 J9E  C17  C16  aromatic  1.422  0.020  1.422
 J9E  N25  C15  aromatic  1.376  0.020  1.376
 J9E  C16  C15  aromatic  1.366  0.020  1.366
 J9E  C15  C02  single    1.478  0.020  1.478
 J9E  C02  O01  double    1.224  0.020  1.224
 J9E  C02  N03  single    1.343  0.020  1.343
 J9E  N03  C04  single    1.452  0.020  1.452
 J9E  C04  C05  single    1.523  0.020  1.523
 J9E  C04  C14  single    1.526  0.020  1.526
 J9E  C05  C06  single    1.525  0.020  1.525
 J9E  C14  C13  single    1.526  0.020  1.526
 J9E  C06  C07  single    1.535  0.020  1.535
 J9E  C13  C07  single    1.537  0.020  1.537
 J9E  C07  C08  single    1.539  0.020  1.539
 J9E  C07  C12  single    1.536  0.020  1.536
 J9E  C08  C09  single    1.526  0.020  1.526
 J9E  C12  C11  single    1.525  0.020  1.525
 J9E  C09  C10  single    1.524  0.020  1.524
 J9E  C11  C10  single    1.524  0.020  1.524
 J9E  C04  H1   single    0.970  0.020  1.090
 J9E  C05  H2   single    0.970  0.020  1.090
 J9E  C05  H3   single    0.970  0.020  1.090
 J9E  C06  H4   single    0.970  0.020  1.090
 J9E  C06  H5   single    0.970  0.020  1.090
 J9E  C08  H6   single    0.970  0.020  1.090
 J9E  C08  H7   single    0.970  0.020  1.090
 J9E  C09  H8   single    0.970  0.020  1.090
 J9E  C09  H9   single    0.970  0.020  1.090
 J9E  C10  H10  single    0.970  0.020  1.090
 J9E  C10  H11  single    0.970  0.020  1.090
 J9E  C11  H12  single    0.970  0.020  1.090
 J9E  C11  H13  single    0.970  0.020  1.090
 J9E  C12  H14  single    0.970  0.020  1.090
 J9E  C12  H15  single    0.970  0.020  1.090
 J9E  C13  H16  single    0.970  0.020  1.090
 J9E  C13  H17  single    0.970  0.020  1.090
 J9E  C14  H18  single    0.970  0.020  1.090
 J9E  C14  H19  single    0.970  0.020  1.090
 J9E  C16  H20  single    0.930  0.020  1.080
 J9E  C20  H21  single    0.930  0.020  1.080
 J9E  C23  H22  single    0.930  0.020  1.080
 J9E  N03  H23  single    0.860  0.020  1.020
 J9E  N25  H24  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
 J9E  O01  C02  N03  123.82  3.000
 J9E  N03  C02  C15  116.37  3.000
 J9E  O01  C02  C15  119.80  3.000
 J9E  H1   C04  N03  106.71  3.000
 J9E  H1   C04  C14  108.33  3.000
 J9E  N03  C04  C14  112.66  3.000
 J9E  H1   C04  C05  108.18  3.000
 J9E  C14  C04  C05  110.71  3.000
 J9E  N03  C04  C05  110.05  3.000
 J9E  H3   C05  H2   106.45  3.000
 J9E  H3   C05  C06  110.55  3.000
 J9E  H2   C05  C06  109.70  3.000
 J9E  H3   C05  C04  109.86  3.000
 J9E  H2   C05  C04  109.72  3.000
 J9E  C06  C05  C04  110.48  3.000
 J9E  H5   C06  H4   106.07  3.000
 J9E  H5   C06  C07  109.35  3.000
 J9E  H4   C06  C07  108.72  3.000
 J9E  H5   C06  C05  109.66  3.000
 J9E  H4   C06  C05  108.40  3.000
 J9E  C07  C06  C05  114.31  3.000
 J9E  C13  C07  C12  109.97  3.000
 J9E  C12  C07  C08  108.56  3.000
 J9E  C13  C07  C08  111.84  3.000
 J9E  C12  C07  C06  107.96  3.000
 J9E  C08  C07  C06  110.04  3.000
 J9E  C13  C07  C06  108.39  3.000
 J9E  H7   C08  H6   105.99  3.000
 J9E  H7   C08  C09  109.44  3.000
 J9E  H6   C08  C09  108.56  3.000
 J9E  H7   C08  C07  110.92  3.000
 J9E  H6   C08  C07  107.95  3.000
 J9E  C09  C08  C07  113.66  3.000
 J9E  H9   C09  H8   105.88  3.000
 J9E  H9   C09  C10  109.60  3.000
 J9E  H8   C09  C10  110.16  3.000
 J9E  H9   C09  C08  110.17  3.000
 J9E  H8   C09  C08  109.32  3.000
 J9E  C10  C09  C08  111.55  3.000
 J9E  H11  C10  H10  106.39  3.000
 J9E  H11  C10  C11  110.52  3.000
 J9E  H10  C10  C11  109.09  3.000
 J9E  H11  C10  C09  110.41  3.000
 J9E  H10  C10  C09  109.14  3.000
 J9E  C11  C10  C09  111.15  3.000
 J9E  H13  C11  H12  105.94  3.000
 J9E  H13  C11  C12  110.38  3.000
 J9E  H12  C11  C12  109.56  3.000
 J9E  H13  C11  C10  109.63  3.000
 J9E  H12  C11  C10  110.13  3.000
 J9E  C12  C11  C10  111.08  3.000
 J9E  H15  C12  H14  106.21  3.000
 J9E  H15  C12  C11  108.59  3.000
 J9E  H14  C12  C11  110.16  3.000
 J9E  H15  C12  C07  108.42  3.000
 J9E  H14  C12  C07  109.20  3.000
 J9E  C11  C12  C07  113.95  3.000
 J9E  H17  C13  H16  105.60  3.000
 J9E  H17  C13  C14  109.20  3.000
 J9E  H16  C13  C14  108.53  3.000
 J9E  H17  C13  C07  111.16  3.000
 J9E  H16  C13  C07  108.28  3.000
 J9E  C14  C13  C07  113.72  3.000
 J9E  H19  C14  H18  106.48  3.000
 J9E  H19  C14  C13  109.65  3.000
 J9E  H18  C14  C13  110.61  3.000
 J9E  H19  C14  C04  109.66  3.000
 J9E  H18  C14  C04  109.57  3.000
 J9E  C13  C14  C04  110.77  3.000
 J9E  N25  C15  C16  109.41  3.000
 J9E  C16  C15  C02  126.06  3.000
 J9E  N25  C15  C02  124.53  3.000
 J9E  H20  C16  C17  127.56  3.000
 J9E  H20  C16  C15  125.95  3.000
 J9E  C17  C16  C15  106.48  3.000
 J9E  C24  C17  C18  117.58  3.000
 J9E  C24  C17  C16  107.44  3.000
 J9E  C18  C17  C16  134.98  3.000
 J9E  F19  C18  C20  119.84  3.000
 J9E  F19  C18  C17  118.64  3.000
 J9E  C20  C18  C17  121.52  3.000
 J9E  H21  C20  C21  120.59  3.000
 J9E  H21  C20  C18  121.33  3.000
 J9E  C21  C20  C18  118.08  3.000
 J9E  F22  C21  C23  118.76  3.000
 J9E  C23  C21  C20  124.22  3.000
 J9E  F22  C21  C20  117.02  3.000
 J9E  H22  C23  C24  122.57  3.000
 J9E  H22  C23  C21  121.85  3.000
 J9E  C24  C23  C21  115.59  3.000
 J9E  N25  C24  C23  129.84  3.000
 J9E  N25  C24  C17  107.15  3.000
 J9E  C23  C24  C17  123.01  3.000
 J9E  H23  N03  C04  116.70  3.000
 J9E  H23  N03  C02  119.35  3.000
 J9E  C04  N03  C02  122.98  3.000
 J9E  H24  N25  C24  124.00  3.000
 J9E  H24  N25  C15  125.92  3.000
 J9E  C24  N25  C15  109.51  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
 J9E  CONST_01  C23  C24  N25  C15   180.00   0.0  0
 J9E  CONST_02  C17  C24  N25  C15     0.00   0.0  0
 J9E  CONST_03  C18  C17  C16  C15   180.00   0.0  0
 J9E  CONST_04  C24  C17  C16  C15     0.00   0.0  0
 J9E  CONST_05  C20  C18  C17  C16   180.00   0.0  0
 J9E  CONST_06  C23  C24  C17  C16   180.00   0.0  0
 J9E  CONST_07  N25  C24  C17  C16     0.00   0.0  0
 J9E  CONST_08  C24  N25  C15  C16     0.00   0.0  0
 J9E  CONST_09  C21  C20  C18  C17     0.00   0.0  0
 J9E  CONST_10  C21  C23  C24  C17     0.00   0.0  0
 J9E  CONST_11  N25  C15  C16  C17     0.00   0.0  0
 J9E  CONST_12  C23  C21  C20  C18     0.00   0.0  0
 J9E  CONST_13  C23  C24  C17  C18     0.00   0.0  0
 J9E  CONST_14  N25  C24  C17  C18   180.00   0.0  0
 J9E  CONST_15  C24  C23  C21  C20     0.00   0.0  0
 J9E  CONST_16  C24  C17  C18  C20     0.00   0.0  0
 J9E  CONST_17  N25  C24  C23  C21   180.00   0.0  0
 J9E  CONST_18  C24  N25  C15  C02   180.00   0.0  0
 J9E  CONST_19  C17  C16  C15  C02   180.00   0.0  0
 J9E  CONST_20  F19  C18  C17  C16     0.00   0.0  0
 J9E  CONST_21  F22  C21  C20  C18   180.00   0.0  0
 J9E  CONST_22  F19  C18  C20  C21   180.00   0.0  0
 J9E  CONST_23  F22  C21  C23  C24   180.00   0.0  0
 J9E  CONST_24  F19  C18  C17  C24   180.00   0.0  0
 J9E  CONST_25  H24  N25  C15  C16   180.00   0.0  0
 J9E  CONST_26  H21  C20  C18  C17   180.00   0.0  0
 J9E  CONST_27  H22  C23  C24  C17   180.00   0.0  0
 J9E  CONST_28  H20  C16  C17  C18     0.00   0.0  0
 J9E  CONST_29  C15  C02  N03  C04   180.00   0.0  0
 J9E  CONST_30  O01  C02  N03  C04     0.00   0.0  0
 J9E  CONST_31  H23  N03  C02  C15     0.00   0.0  0
 J9E  Var_01    C07  C06  C05  C04   -55.79  30.0  1
 J9E  Var_02    C07  C13  C14  C04    56.04  30.0  1
 J9E  Var_03    C13  C07  C06  C05    52.63  30.0  3
 J9E  Var_04    C14  C13  C07  C06   -52.53  30.0  3
 J9E  Var_05    C09  C08  C07  C06  -170.66  30.0  1
 J9E  Var_06    C11  C12  C07  C06   172.52  30.0  1
 J9E  Var_07    C10  C09  C08  C07    54.84  30.0  1
 J9E  Var_08    C10  C11  C12  C07   -55.53  30.0  1
 J9E  Var_09    C11  C10  C09  C08   -54.44  30.0  1
 J9E  Var_10    C12  C11  C10  C09    54.54  30.0  1
 J9E  Var_11    O01  C02  C15  C16    19.76  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
 J9E  chir_01  C04  N03  C05  C14  negativ

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
 J9E  plan-1  C02  0.020
 J9E  plan-1  C04  0.020
 J9E  plan-1  C15  0.020
 J9E  plan-1  N03  0.020
 J9E  plan-1  O01  0.020
 J9E  plan-1  H23  0.020
 J9E  plan-2  C02  0.020
 J9E  plan-2  C15  0.020
 J9E  plan-2  C16  0.020
 J9E  plan-2  C17  0.020
 J9E  plan-2  C18  0.020
 J9E  plan-2  C20  0.020
 J9E  plan-2  C21  0.020
 J9E  plan-2  C23  0.020
 J9E  plan-2  C24  0.020
 J9E  plan-2  F19  0.020
 J9E  plan-2  F22  0.020
 J9E  plan-2  N25  0.020
 J9E  plan-2  H20  0.020
 J9E  plan-2  H21  0.020
 J9E  plan-2  H22  0.020
 J9E  plan-2  H24  0.020

