# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 19:33:28 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 2-[4-[8-oxidanylidene-2-[(~{E})-(2-oxidanylidenepyridin-3-ylidene)amino]-7~{H}-purin-9-yl]cyclohexyl]ethanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1Nc2cnc(N=C3C=CC=NC3=O)nc2N1[C@@H]4CC[C@H](CC4)CC#N
#
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
 GYQ  GYQ  2-[4-[8-oxidanylidene-2-[(~{E})-(2-oxidanylidenepyridin-3-ylidene)amino]-7~{H}-purin-9-yl]cyclohexyl]ethanenitrile  ligand  44  27  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GYQ
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
 GYQ  C2   C  C     0   0.469  -4.6327  -2.1668  -0.6323
 GYQ  C4   C  C1    0  -0.001  -6.2730  -2.1165   0.9757
 GYQ  C5   C  C1    0  -0.317  -5.6207  -1.0695   1.7440
 GYQ  C6   C  C1    0  -0.138  -4.4719  -0.5356   1.3110
 GYQ  C7   C  C     0   0.050  -3.9009  -1.0333   0.0684
 GYQ  N10  N  N     0  -0.433  -2.6969   1.5577   0.2544
 GYQ  C11  C  CR16  0  -0.054  -1.9598   2.6315   0.5568
 GYQ  C12  C  CR56  0   0.247  -0.5926   2.5359   0.5314
 GYQ  N13  N  NR15  0  -0.751   0.4631   3.3713   0.7627
 GYQ  C17  C  CR56  0   0.517  -0.0466   1.2959   0.1630
 GYQ  C19  C  CR16  0  -0.086   2.2417   0.3410  -0.1510
 GYQ  C21  C  C     0  -0.435   3.1927   0.0068   0.9944
 GYQ  C23  C  CR16  0  -0.254   4.8440  -0.9098  -0.6836
 GYQ  O1   O  O     0  -0.361  -4.1891  -2.6488  -1.6436
 GYQ  N3   N  N     0  -0.427  -5.8355  -2.6383  -0.1103
 GYQ  N8   N  N     0  -0.373  -2.8260  -0.6528  -0.4987
 GYQ  C9   C  CR6   0   0.467  -2.0785   0.4397  -0.0880
 GYQ  C14  C  CR5   0   0.684   1.6516   2.7109   0.5535
 GYQ  O15  O  O     0  -0.469   2.7670   3.1696   0.6588
 GYQ  N16  N  NR5   0  -0.600   1.3101   1.4105   0.1924
 GYQ  N18  N  N     0  -0.440  -0.7566   0.2521  -0.1749
 GYQ  C22  C  C     0  -0.432   4.0802  -1.1733   0.6118
 GYQ  C25  C  CH2   0  -0.531   5.6945  -2.1164  -1.0995
 GYQ  C26  C  CSP   0   0.117   6.7250  -2.4388  -0.1250
 GYQ  N27  N  NS    0  -0.277   7.5342  -2.6861   0.6553
 GYQ  C28  C  C     0  -0.428   3.8785  -0.5563  -1.8126
 GYQ  C29  C  C     0  -0.437   2.9935   0.6296  -1.4459
 GYQ  H1   H  H     0   0.299  -7.2091  -2.5059   1.3645
 GYQ  H2   H  H     0   0.300  -6.0798  -0.7548   2.6706
 GYQ  H3   H  H     0   0.309  -3.9605   0.2270   1.8783
 GYQ  H4   H  HCR6  0   0.296  -2.4805   3.5457   0.8132
 GYQ  H5   H  HNR5  0   0.432   0.4123   4.3404   1.0369
 GYQ  H6   H  HCR6  0   0.267   1.6029  -0.5304  -0.3195
 GYQ  H7   H  H     0   0.239   3.8150   0.8715   1.2330
 GYQ  H8   H  H     0   0.249   2.6194  -0.2360   1.8916
 GYQ  H9   H  HCR6  0   0.250   5.5165  -0.0585  -0.5274
 GYQ  H10  H  H     0   0.250   4.7734  -1.3763   1.4318
 GYQ  H11  H  H     0   0.226   3.4649  -2.0722   0.4914
 GYQ  H12  H  HCH2  0   0.301   5.0670  -3.0017  -1.2318
 GYQ  H13  H  HCH2  0   0.313   6.1864  -1.9277  -2.0562
 GYQ  H14  H  H     0   0.248   4.4346  -0.3275  -2.7245
 GYQ  H15  H  H     0   0.227   3.2523  -1.4271  -2.0390
 GYQ  H16  H  H     0   0.250   2.2811   0.8244  -2.2504
 GYQ  H17  H  H     0   0.237   3.6091   1.5251  -1.3316

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
 GYQ  C11  N10  aromatic  1.337  0.020  1.337
 GYQ  C11  C12  aromatic  1.371  0.020  1.371
 GYQ  N10  C9   aromatic  1.323  0.020  1.323
 GYQ  C12  N13  single    1.366  0.020  1.366
 GYQ  C12  C17  aromatic  1.404  0.020  1.404
 GYQ  N13  C14  single    1.376  0.020  1.376
 GYQ  C9   N8   single    1.386  0.020  1.386
 GYQ  C9   N18  aromatic  1.338  0.020  1.338
 GYQ  N8   C7   double    1.273  0.020  1.273
 GYQ  O1   C2   double    1.205  0.020  1.205
 GYQ  C21  C22  single    1.525  0.020  1.525
 GYQ  C21  C19  single    1.526  0.020  1.526
 GYQ  C14  O15  double    1.211  0.020  1.211
 GYQ  C14  N16  single    1.392  0.020  1.392
 GYQ  C17  N18  aromatic  1.307  0.020  1.307
 GYQ  C17  N16  single    1.362  0.020  1.362
 GYQ  C7   C2   single    1.520  0.020  1.520
 GYQ  C7   C6   single    1.455  0.020  1.455
 GYQ  C2   N3   single    1.393  0.020  1.393
 GYQ  C22  C23  single    1.527  0.020  1.527
 GYQ  N16  C19  single    1.459  0.020  1.459
 GYQ  N27  C26  triple    1.151  0.020  1.151
 GYQ  C6   C5   double    1.339  0.020  1.339
 GYQ  N3   C4   double    1.282  0.020  1.282
 GYQ  C19  C29  single    1.525  0.020  1.525
 GYQ  C26  C25  single    1.455  0.020  1.455
 GYQ  C4   C5   single    1.453  0.020  1.453
 GYQ  C23  C25  single    1.534  0.020  1.534
 GYQ  C23  C28  single    1.527  0.020  1.527
 GYQ  C29  C28  single    1.525  0.020  1.525
 GYQ  C4   H1   single    0.930  0.020  1.080
 GYQ  C5   H2   single    0.930  0.020  1.080
 GYQ  C6   H3   single    0.930  0.020  1.080
 GYQ  C11  H4   single    0.930  0.020  1.080
 GYQ  N13  H5   single    0.860  0.020  1.020
 GYQ  C19  H6   single    0.970  0.020  1.090
 GYQ  C21  H7   single    0.970  0.020  1.090
 GYQ  C21  H8   single    0.970  0.020  1.090
 GYQ  C23  H9   single    0.970  0.020  1.090
 GYQ  C22  H10  single    0.970  0.020  1.090
 GYQ  C22  H11  single    0.970  0.020  1.090
 GYQ  C25  H12  single    0.970  0.020  1.090
 GYQ  C25  H13  single    0.970  0.020  1.090
 GYQ  C28  H14  single    0.970  0.020  1.090
 GYQ  C28  H15  single    0.970  0.020  1.090
 GYQ  C29  H16  single    0.970  0.020  1.090
 GYQ  C29  H17  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
 GYQ  N3   C2   O1   119.79  3.000
 GYQ  N3   C2   C7   119.68  3.000
 GYQ  O1   C2   C7   120.52  3.000
 GYQ  H1   C4   N3   116.85  3.000
 GYQ  H1   C4   C5   117.13  3.000
 GYQ  N3   C4   C5   126.01  3.000
 GYQ  H2   C5   C6   121.71  3.000
 GYQ  H2   C5   C4   118.18  3.000
 GYQ  C6   C5   C4   120.10  3.000
 GYQ  H3   C6   C7   120.30  3.000
 GYQ  H3   C6   C5   121.22  3.000
 GYQ  C7   C6   C5   118.45  3.000
 GYQ  N8   C7   C6   127.53  3.000
 GYQ  C6   C7   C2   117.37  3.000
 GYQ  N8   C7   C2   115.08  3.000
 GYQ  C9   N10  C11  118.66  3.000
 GYQ  H4   C11  C12  122.88  3.000
 GYQ  H4   C11  N10  117.81  3.000
 GYQ  C12  C11  N10  119.32  3.000
 GYQ  C17  C12  N13  106.50  3.000
 GYQ  C17  C12  C11  117.02  3.000
 GYQ  N13  C12  C11  136.47  3.000
 GYQ  H5   N13  C14  123.10  3.000
 GYQ  H5   N13  C12  126.50  3.000
 GYQ  C14  N13  C12  110.39  3.000
 GYQ  N18  C17  N16  127.88  3.000
 GYQ  N16  C17  C12  107.90  3.000
 GYQ  N18  C17  C12  124.19  3.000
 GYQ  H6   C19  C29  107.94  3.000
 GYQ  H6   C19  N16  104.32  3.000
 GYQ  C29  C19  N16  112.07  3.000
 GYQ  H6   C19  C21  107.77  3.000
 GYQ  C29  C19  C21  111.82  3.000
 GYQ  N16  C19  C21  112.44  3.000
 GYQ  H8   C21  H7   107.21  3.000
 GYQ  H8   C21  C22  109.85  3.000
 GYQ  H7   C21  C22  109.63  3.000
 GYQ  H8   C21  C19  109.77  3.000
 GYQ  H7   C21  C19  110.23  3.000
 GYQ  C22  C21  C19  110.10  3.000
 GYQ  H9   C23  C28  108.27  3.000
 GYQ  H9   C23  C25  108.03  3.000
 GYQ  C28  C23  C25  109.40  3.000
 GYQ  H9   C23  C22  108.67  3.000
 GYQ  C28  C23  C22  110.55  3.000
 GYQ  C25  C23  C22  111.82  3.000
 GYQ  C4   N3   C2   118.31  3.000
 GYQ  C9   N8   C7   123.97  3.000
 GYQ  N18  C9   N8   113.77  3.000
 GYQ  N18  C9   N10  126.67  3.000
 GYQ  N8   C9   N10  119.39  3.000
 GYQ  N16  C14  O15  127.05  3.000
 GYQ  N16  C14  N13  106.02  3.000
 GYQ  O15  C14  N13  126.93  3.000
 GYQ  C14  N16  C19  126.09  3.000
 GYQ  C19  N16  C17  124.69  3.000
 GYQ  C14  N16  C17  109.18  3.000
 GYQ  C9   N18  C17  114.08  3.000
 GYQ  H11  C22  H10  106.63  3.000
 GYQ  H11  C22  C23  109.22  3.000
 GYQ  H10  C22  C23  110.58  3.000
 GYQ  H11  C22  C21  109.60  3.000
 GYQ  H10  C22  C21  108.94  3.000
 GYQ  C23  C22  C21  111.74  3.000
 GYQ  H13  C25  H12  107.00  3.000
 GYQ  H13  C25  C26  107.82  3.000
 GYQ  H12  C25  C26  107.95  3.000
 GYQ  H13  C25  C23  110.58  3.000
 GYQ  H12  C25  C23  110.59  3.000
 GYQ  C26  C25  C23  112.68  3.000
 GYQ  N27  C26  C25  180.00  3.000
 GYQ  H15  C28  H14  106.55  3.000
 GYQ  H15  C28  C29  109.63  3.000
 GYQ  H14  C28  C29  109.47  3.000
 GYQ  H15  C28  C23  109.27  3.000
 GYQ  H14  C28  C23  110.11  3.000
 GYQ  C29  C28  C23  111.67  3.000
 GYQ  H17  C29  H16  107.36  3.000
 GYQ  H17  C29  C28  109.61  3.000
 GYQ  H16  C29  C28  109.89  3.000
 GYQ  H17  C29  C19  110.13  3.000
 GYQ  H16  C29  C19  109.74  3.000
 GYQ  C28  C29  C19  110.07  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
 GYQ  CONST_01  C17  C12  C11  N10     0.00   0.0  0
 GYQ  CONST_02  C17  N18  C9   N10     0.00   0.0  0
 GYQ  CONST_03  N18  C9   N10  C11     0.00   0.0  0
 GYQ  CONST_04  N18  C17  C12  C11     0.00   0.0  0
 GYQ  CONST_05  C9   N10  C11  C12     0.00   0.0  0
 GYQ  CONST_06  C9   N18  C17  C12     0.00   0.0  0
 GYQ  CONST_07  N16  C14  N13  C12     0.00   0.0  0
 GYQ  CONST_08  C14  N16  C17  C12     0.00   0.0  0
 GYQ  CONST_09  C19  N16  C17  C12   180.00   0.0  0
 GYQ  CONST_10  N16  C17  C12  N13     0.00   0.0  0
 GYQ  CONST_11  C17  N16  C14  N13     0.00   0.0  0
 GYQ  CONST_12  C19  N16  C14  N13   180.00   0.0  0
 GYQ  CONST_13  C14  N13  C12  C17     0.00   0.0  0
 GYQ  CONST_14  N8   C9   N10  C11   180.00   0.0  0
 GYQ  CONST_15  N8   C9   N18  C17   180.00   0.0  0
 GYQ  CONST_16  O15  C14  N13  C12   180.00   0.0  0
 GYQ  CONST_17  O15  C14  N16  C17   180.00   0.0  0
 GYQ  CONST_18  O15  C14  N16  C19     0.00   0.0  0
 GYQ  CONST_19  H4   C11  C12  N13     0.00   0.0  0
 GYQ  CONST_20  H5   N13  C12  C17   180.00   0.0  0
 GYQ  Var_01    C23  C22  C21  C19    55.80  30.0  1
 GYQ  Var_02    C23  C28  C29  C19   -56.11  30.0  1
 GYQ  Var_03    N10  C9   N8   C7    -42.63  30.0  1
 GYQ  Var_04    H12  C25  C26  N27  -107.62  30.0  3

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
 GYQ  chir_01  C19  C21  N16  C29  negativ
 GYQ  chir_02  C23  C28  C25  C22  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
 GYQ  plan-1  C2   0.020
 GYQ  plan-1  C4   0.020
 GYQ  plan-1  C5   0.020
 GYQ  plan-1  C6   0.020
 GYQ  plan-1  C7   0.020
 GYQ  plan-1  O1   0.020
 GYQ  plan-1  N3   0.020
 GYQ  plan-1  N8   0.020
 GYQ  plan-1  H1   0.020
 GYQ  plan-1  H2   0.020
 GYQ  plan-1  H3   0.020
 GYQ  plan-2  N10  0.020
 GYQ  plan-2  C11  0.020
 GYQ  plan-2  C12  0.020
 GYQ  plan-2  N13  0.020
 GYQ  plan-2  C17  0.020
 GYQ  plan-2  C19  0.020
 GYQ  plan-2  N8   0.020
 GYQ  plan-2  C9   0.020
 GYQ  plan-2  C14  0.020
 GYQ  plan-2  O15  0.020
 GYQ  plan-2  N16  0.020
 GYQ  plan-2  N18  0.020
 GYQ  plan-2  H4   0.020
 GYQ  plan-2  H5   0.020

