# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 05:01:38 2021
#   Inital geometry file: a 102 line input string
#   Ligand name: 3-[(3~{S},4~{R})-3-methyl-7-(7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl)-1,7-diazaspiro[3.4]octan-1-yl]-3-oxidanylidene-propanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CN(C(=O)CC#N)[C@]12CCN(C2)c3ncnc4[nH]ccc34
#
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
 FHX  FHX  3-[(3~{S},4~{R})-3-methyl-7-(7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl)-1,7-diazaspiro[3.4]octan-1-yl]-3-oxidanylidene-propanenitrile  ligand  41  23  .  2022-07-25  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_FHX
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
 FHX  C1   C  C     0   0.215   7.4926  -0.8508  25.7299
 FHX  C3   C  C     0  -0.241   6.1214   0.8092  25.6808
 FHX  C4   C  C     0  -0.337   6.2658  -0.4254  26.5965
 FHX  N2   N  N     0  -0.509   7.3055   0.3645  24.9578
 FHX  C7   C  CR6   0   0.503   9.6086  -3.0082  27.7036
 FHX  C8   C  CR56  0  -0.085  10.6806  -2.3501  28.3526
 FHX  C9   C  CR56  0   0.470  11.3702  -3.1375  29.2897
 FHX  C11  C  CR15  0  -0.017  12.3441  -1.1408  29.2404
 FHX  C12  C  CR15  0  -0.438  11.3288  -1.0727  28.3338
 FHX  C13  C  CR16  0   0.035  10.1045  -4.9034  28.9099
 FHX  C15  C  CH2   0  -0.266   8.8348  -1.0262  26.4359
 FHX  C16  C  CH2   0  -0.486   7.3319  -2.1824  25.0085
 FHX  C17  C  CH2   0  -0.266   7.7801  -3.1715  26.0740
 FHX  C18  C  C     0   0.539   7.9489   0.8395  23.8937
 FHX  C20  C  CH2   0  -0.681   7.3606   2.1431  23.3637
 FHX  C21  C  CSP   0   0.144   8.1361   2.6452  22.2463
 FHX  C23  C  CH3   0  -0.683   6.4761  -0.1298  28.0647
 FHX  N10  N  NR15  0  -0.656  12.3626  -2.3847  29.8159
 FHX  N14  N  N     0  -0.455  11.1115  -4.4114  29.5999
 FHX  N22  N  NS    0  -0.261   8.7372   3.0609  21.3593
 FHX  N5   N  NT    0  -0.500   8.8149  -2.4311  26.7898
 FHX  N6   N  N     0  -0.497   9.3556  -4.2887  27.9998
 FHX  O19  O  O     0  -0.475   8.9171   0.3069  23.3780
 FHX  H1   H  H     0   0.257   6.2487   1.7719  26.1813
 FHX  H2   H  H     0   0.263   5.2174   0.8409  25.0700
 FHX  H3   H  H     0   0.270   5.4422  -1.1311  26.4776
 FHX  H4   H  HCR5  0   0.286  13.0659  -0.3932  29.5247
 FHX  H5   H  HCR5  0   0.258  11.0982  -0.2101  27.7321
 FHX  H6   H  HCR6  0   0.242   9.8460  -5.9394  29.1053
 FHX  H7   H  HCH2  0   0.265   9.6560  -0.7875  25.7529
 FHX  H8   H  HCH2  0   0.256   8.9284  -0.3883  27.3134
 FHX  H9   H  HCH2  0   0.262   6.3131  -2.3638  24.6670
 FHX  H10  H  HCH2  0   0.262   7.9989  -2.2221  24.1453
 FHX  H11  H  HCH2  0   0.240   6.9568  -3.4398  26.7430
 FHX  H12  H  HCH2  0   0.256   8.1749  -4.0955  25.6528
 FHX  H13  H  HCH2  0   0.345   7.3332   2.9057  24.1466
 FHX  H14  H  HCH2  0   0.348   6.3281   1.9926  23.0364
 FHX  H15  H  HCH3  0   0.252   5.5473   0.2302  28.5082
 FHX  H16  H  HCH3  0   0.240   6.7771  -1.0237  28.6125
 FHX  H17  H  HCH3  0   0.232   7.2336   0.6385  28.2260
 FHX  H18  H  HNR5  0   0.412  13.0212  -2.6989  30.5101

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
 FHX  N22  C21  triple    1.149  0.020  1.149
 FHX  C21  C20  single    1.450  0.020  1.450
 FHX  O19  C18  double    1.219  0.020  1.219
 FHX  C20  C18  single    1.525  0.020  1.525
 FHX  C18  N2   single    1.331  0.020  1.331
 FHX  N2   C1   single    1.452  0.020  1.452
 FHX  N2   C3   single    1.457  0.020  1.457
 FHX  C16  C1   single    1.523  0.020  1.523
 FHX  C16  C17  single    1.521  0.020  1.521
 FHX  C1   C15  single    1.527  0.020  1.527
 FHX  C1   C4   single    1.561  0.020  1.561
 FHX  C3   C4   single    1.544  0.020  1.544
 FHX  C17  N5   single    1.460  0.020  1.460
 FHX  C15  N5   single    1.449  0.020  1.449
 FHX  N5   C7   single    1.341  0.020  1.341
 FHX  C4   C23  single    1.512  0.020  1.512
 FHX  C7   N6   aromatic  1.339  0.020  1.339
 FHX  C7   C8   aromatic  1.415  0.020  1.415
 FHX  N6   C13  aromatic  1.329  0.020  1.329
 FHX  C8   C12  aromatic  1.433  0.020  1.433
 FHX  C8   C9   aromatic  1.405  0.020  1.405
 FHX  C12  C11  aromatic  1.363  0.020  1.363
 FHX  C13  N14  aromatic  1.316  0.020  1.316
 FHX  C9   N14  aromatic  1.336  0.020  1.336
 FHX  C9   N10  aromatic  1.352  0.020  1.352
 FHX  C11  N10  aromatic  1.371  0.020  1.371
 FHX  C3   H1   single    0.970  0.020  1.090
 FHX  C3   H2   single    0.970  0.020  1.090
 FHX  C4   H3   single    0.970  0.020  1.090
 FHX  C11  H4   single    0.930  0.020  1.080
 FHX  C12  H5   single    0.930  0.020  1.080
 FHX  C13  H6   single    0.930  0.020  1.080
 FHX  C15  H7   single    0.970  0.020  1.090
 FHX  C15  H8   single    0.970  0.020  1.090
 FHX  C16  H9   single    0.970  0.020  1.090
 FHX  C16  H10  single    0.970  0.020  1.090
 FHX  C17  H11  single    0.970  0.020  1.090
 FHX  C17  H12  single    0.970  0.020  1.090
 FHX  C20  H13  single    0.970  0.020  1.090
 FHX  C20  H14  single    0.970  0.020  1.090
 FHX  C23  H15  single    0.970  0.020  1.090
 FHX  C23  H16  single    0.970  0.020  1.090
 FHX  C23  H17  single    0.970  0.020  1.090
 FHX  N10  H18  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
 FHX  C16  C1   C15  102.20  3.000
 FHX  C15  C1   N2   117.09  3.000
 FHX  C16  C1   N2   117.80  3.000
 FHX  C15  C1   C4   117.74  3.000
 FHX  C16  C1   C4   114.73  3.000
 FHX  N2   C1   C4    88.04  3.000
 FHX  H2   C3   H1   109.10  3.000
 FHX  H2   C3   N2   113.85  3.000
 FHX  H1   C3   N2   113.68  3.000
 FHX  H2   C3   C4   115.63  3.000
 FHX  H1   C3   C4   114.97  3.000
 FHX  N2   C3   C4    88.52  3.000
 FHX  H3   C4   C23  109.71  3.000
 FHX  H3   C4   C3   112.46  3.000
 FHX  C23  C4   C3   115.63  3.000
 FHX  H3   C4   C1   110.88  3.000
 FHX  C23  C4   C1   118.87  3.000
 FHX  C3   C4   C1    87.83  3.000
 FHX  C18  N2   C3   132.89  3.000
 FHX  C3   N2   C1    95.53  3.000
 FHX  C18  N2   C1   131.42  3.000
 FHX  N6   C7   N5   116.79  3.000
 FHX  N6   C7   C8   119.11  3.000
 FHX  N5   C7   C8   124.11  3.000
 FHX  C12  C8   C9   106.64  3.000
 FHX  C9   C8   C7   114.65  3.000
 FHX  C12  C8   C7   138.70  3.000
 FHX  N14  C9   N10  125.62  3.000
 FHX  N10  C9   C8   107.93  3.000
 FHX  N14  C9   C8   126.45  3.000
 FHX  H4   C11  N10  120.65  3.000
 FHX  H4   C11  C12  129.79  3.000
 FHX  N10  C11  C12  109.55  3.000
 FHX  H5   C12  C11  124.85  3.000
 FHX  H5   C12  C8   128.66  3.000
 FHX  C11  C12  C8   106.49  3.000
 FHX  H6   C13  N6   115.50  3.000
 FHX  H6   C13  N14  116.40  3.000
 FHX  N6   C13  N14  128.11  3.000
 FHX  H8   C15  H7   108.10  3.000
 FHX  H8   C15  N5   111.86  3.000
 FHX  H7   C15  N5   111.97  3.000
 FHX  H8   C15  C1   112.39  3.000
 FHX  H7   C15  C1   110.25  3.000
 FHX  N5   C15  C1   102.25  3.000
 FHX  H10  C16  H9   108.51  3.000
 FHX  H10  C16  C17  110.50  3.000
 FHX  H9   C16  C17  112.75  3.000
 FHX  H10  C16  C1   109.99  3.000
 FHX  H9   C16  C1   113.11  3.000
 FHX  C17  C16  C1   101.86  3.000
 FHX  H12  C17  H11  107.52  3.000
 FHX  H12  C17  N5   111.27  3.000
 FHX  H11  C17  N5   110.97  3.000
 FHX  H12  C17  C16  112.79  3.000
 FHX  H11  C17  C16  111.47  3.000
 FHX  N5   C17  C16  102.86  3.000
 FHX  O19  C18  C20  122.17  3.000
 FHX  C20  C18  N2   113.35  3.000
 FHX  O19  C18  N2   124.47  3.000
 FHX  H14  C20  H13  106.66  3.000
 FHX  H14  C20  C21  108.78  3.000
 FHX  H13  C20  C21  108.89  3.000
 FHX  H14  C20  C18  110.52  3.000
 FHX  H13  C20  C18  110.92  3.000
 FHX  C21  C20  C18  110.95  3.000
 FHX  N22  C21  C20  180.00  3.000
 FHX  H17  C23  H16  108.14  3.000
 FHX  H17  C23  H15  107.38  3.000
 FHX  H16  C23  H15  107.53  3.000
 FHX  H17  C23  C4   112.20  3.000
 FHX  H16  C23  C4   111.46  3.000
 FHX  H15  C23  C4   109.94  3.000
 FHX  H18  N10  C11  125.55  3.000
 FHX  H18  N10  C9   125.06  3.000
 FHX  C11  N10  C9   109.39  3.000
 FHX  C13  N14  C9   112.50  3.000
 FHX  C17  N5   C15  112.44  3.000
 FHX  C15  N5   C7   125.14  3.000
 FHX  C17  N5   C7   122.37  3.000
 FHX  C13  N6   C7   119.17  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
 FHX  CONST_01  N14  C13  N6   C7      0.00   0.0  0
 FHX  CONST_02  C11  C12  C8   C7    180.00   0.0  0
 FHX  CONST_03  N14  C9   C8   C7      0.00   0.0  0
 FHX  CONST_04  N10  C9   C8   C7    180.00   0.0  0
 FHX  CONST_05  C13  N6   C7   C8      0.00   0.0  0
 FHX  CONST_06  N10  C11  C12  C8      0.00   0.0  0
 FHX  CONST_07  C13  N14  C9   C8      0.00   0.0  0
 FHX  CONST_08  C11  N10  C9   C8      0.00   0.0  0
 FHX  CONST_09  N6   C7   C8   C9      0.00   0.0  0
 FHX  CONST_10  C11  C12  C8   C9      0.00   0.0  0
 FHX  CONST_11  N6   C13  N14  C9      0.00   0.0  0
 FHX  CONST_12  C12  C11  N10  C9      0.00   0.0  0
 FHX  CONST_13  N14  C9   N10  C11   180.00   0.0  0
 FHX  CONST_14  N6   C7   C8   C12   180.00   0.0  0
 FHX  CONST_15  N14  C9   C8   C12   180.00   0.0  0
 FHX  CONST_16  N10  C9   C8   C12     0.00   0.0  0
 FHX  CONST_17  N10  C9   N14  C13   180.00   0.0  0
 FHX  CONST_18  N5   C7   C8   C9    180.00   0.0  0
 FHX  CONST_19  N5   C7   C8   C12     0.00   0.0  0
 FHX  CONST_20  N5   C7   N6   C13   180.00   0.0  0
 FHX  CONST_21  H6   C13  N6   C7    180.00   0.0  0
 FHX  CONST_22  H5   C12  C8   C7      0.00   0.0  0
 FHX  CONST_23  H4   C11  C12  C8    180.00   0.0  0
 FHX  CONST_24  H18  N10  C9   C8    180.00   0.0  0
 FHX  CONST_25  O19  C18  N2   C1      0.00   0.0  0
 FHX  CONST_26  C20  C18  N2   C1    180.00   0.0  0
 FHX  CONST_27  O19  C18  N2   C3    180.00   0.0  0
 FHX  CONST_28  C20  C18  N2   C3      0.00   0.0  0
 FHX  Var_01    C4   C3   N2   C1      2.16  30.0  1
 FHX  Var_02    N5   C17  C16  C1    -33.44  30.0  1
 FHX  Var_03    C17  N5   C15  C1     14.95  30.0  1
 FHX  Var_04    C16  C17  N5   C7   -170.59  30.0  1
 FHX  Var_05    C21  C20  C18  N2    177.35  30.0  1

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
 FHX  chir_01  C1  C16  C15  C4   positiv
 FHX  chir_02  C4  C1   C3   C23  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
 FHX  plan-1  C1   0.020
 FHX  plan-1  C3   0.020
 FHX  plan-1  N2   0.020
 FHX  plan-1  C18  0.020
 FHX  plan-1  C20  0.020
 FHX  plan-1  O19  0.020
 FHX  plan-2  C7   0.020
 FHX  plan-2  C8   0.020
 FHX  plan-2  C9   0.020
 FHX  plan-2  C11  0.020
 FHX  plan-2  C12  0.020
 FHX  plan-2  C13  0.020
 FHX  plan-2  N10  0.020
 FHX  plan-2  N14  0.020
 FHX  plan-2  N5   0.020
 FHX  plan-2  N6   0.020
 FHX  plan-2  H4   0.020
 FHX  plan-2  H5   0.020
 FHX  plan-2  H6   0.020
 FHX  plan-2  H18  0.020

