# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 02:16:07 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 3-[[6-(cyclohexylmethoxy)-9~{H}-purin-2-yl]amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cccc(Nc2nc3[nH]cnc3c(OCC4CCCCC4)n2)c1
#
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
 NU6  NU6  3-[[6-(cyclohexylmethoxy)-9~{H}-purin-2-yl]amino]benzamide  ligand  49  27  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NU6
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
 NU6  O01  O  O     0  -0.482   6.6041   0.9256  -0.8559
 NU6  C02  C  C     0   0.494   6.2453  -0.0459  -0.2037
 NU6  N03  N  NH2   0  -0.815   7.1106  -0.9260   0.3190
 NU6  C04  C  CR6   0  -0.024   4.7925  -0.3117   0.0513
 NU6  C05  C  CR16  0  -0.313   4.3013  -1.5718   0.3894
 NU6  C06  C  CR16  0  -0.234   2.9400  -1.7303   0.5873
 NU6  C07  C  CR16  0  -0.320   2.0562  -0.6688   0.4597
 NU6  C08  C  CR6   0   0.397   2.5391   0.5961   0.1112
 NU6  N09  N  NH1   0  -0.775   1.7645   1.7373  -0.0407
 NU6  C10  C  CR6   0   0.600   0.4122   1.9283  -0.0427
 NU6  N11  N  N     0  -0.501   0.0321   3.1866  -0.2376
 NU6  C12  C  CR56  0   0.486  -1.2861   3.3248  -0.2381
 NU6  N13  N  NR15  0  -0.653  -2.0205   4.4532  -0.4113
 NU6  C14  C  CR15  0   0.098  -3.3348   4.0887  -0.3343
 NU6  N15  N  N     0  -0.437  -3.5060   2.8179  -0.1261
 NU6  C16  C  CR56  0  -0.056  -2.2305   2.3141  -0.0611
 NU6  C17  C  CR6   0   0.546  -1.6934   1.0384   0.1302
 NU6  O18  O  O2    0  -0.454  -2.5008   0.0131   0.2980
 NU6  C19  C  CH2   0  -0.152  -1.9332  -1.2950   0.4366
 NU6  C20  C  CH1   0  -0.281  -3.0529  -2.3144   0.4706
 NU6  C21  C  CH2   0  -0.416  -3.8976  -2.3049  -0.8042
 NU6  C22  C  CH2   0  -0.434  -4.9651  -3.3941  -0.7781
 NU6  C23  C  CH2   0  -0.428  -4.3575  -4.7726  -0.5429
 NU6  C24  C  CH2   0  -0.432  -3.5117  -4.7891   0.7259
 NU6  C25  C  CH2   0  -0.425  -2.4455  -3.7001   0.7011
 NU6  N26  N  N     0  -0.534  -0.3866   0.8717   0.1387
 NU6  C27  C  CR16  0  -0.390   3.9133   0.7505  -0.0960
 NU6  H1   H  HNH2  0   0.414   6.8311  -1.6617   0.9435
 NU6  H2   H  HNH2  0   0.406   8.0998  -0.7900   0.1878
 NU6  H3   H  HCR6  0   0.255   4.9521  -2.4316   0.4759
 NU6  H4   H  HCR6  0   0.262   2.5481  -2.7054   0.8457
 NU6  H5   H  HCR6  0   0.308   1.0033  -0.8251   0.6232
 NU6  H6   H  HNH1  0   0.410   2.2805   2.5835  -0.2291
 NU6  H7   H  HNR5  0   0.425  -1.6696   5.3859  -0.5661
 NU6  H8   H  HCR5  0   0.290  -4.1238   4.8167  -0.4441
 NU6  H10  H  HCH2  0   0.227  -1.2597  -1.4933  -0.4027
 NU6  H11  H  HCH2  0   0.240  -1.3421  -1.3397   1.3565
 NU6  H12  H  HCH1  0   0.227  -3.7051  -2.0879   1.3240
 NU6  H13  H  HCH2  0   0.234  -4.3675  -1.3290  -0.9435
 NU6  H14  H  HCH2  0   0.207  -3.2379  -2.4603  -1.6666
 NU6  H15  H  HCH2  0   0.210  -5.6841  -3.1775   0.0197
 NU6  H16  H  HCH2  0   0.228  -5.5307  -3.3825  -1.7131
 NU6  H17  H  HCH2  0   0.227  -5.1452  -5.5274  -0.4803
 NU6  H18  H  HCH2  0   0.208  -3.7339  -5.0464  -1.4008
 NU6  H19  H  HCH2  0   0.211  -4.1625  -4.6376   1.5938
 NU6  H20  H  HCH2  0   0.229  -3.0419  -5.7667   0.8569
 NU6  H21  H  HCH2  0   0.212  -1.7258  -3.9129  -0.0986
 NU6  H22  H  HCH2  0   0.232  -1.8785  -3.7083   1.6365
 NU6  H23  H  HCR6  0   0.271   4.3023   1.7225  -0.3747

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
 NU6  C14  N15  aromatic  1.299  0.020  1.299
 NU6  C14  N13  aromatic  1.366  0.020  1.366
 NU6  N15  C16  aromatic  1.373  0.020  1.373
 NU6  C22  C21  single    1.525  0.020  1.525
 NU6  C22  C23  single    1.525  0.020  1.525
 NU6  C21  C20  single    1.529  0.020  1.529
 NU6  N13  C12  aromatic  1.357  0.020  1.357
 NU6  C23  C24  single    1.525  0.020  1.525
 NU6  C16  C12  aromatic  1.395  0.020  1.395
 NU6  C16  C17  aromatic  1.397  0.020  1.397
 NU6  O18  C17  single    1.316  0.020  1.316
 NU6  O18  C19  single    1.433  0.020  1.433
 NU6  C12  N11  aromatic  1.325  0.020  1.325
 NU6  C17  N26  aromatic  1.317  0.020  1.317
 NU6  C20  C19  single    1.515  0.020  1.515
 NU6  C20  C25  single    1.530  0.020  1.530
 NU6  C24  C25  single    1.524  0.020  1.524
 NU6  N11  C10  aromatic  1.329  0.020  1.329
 NU6  N26  C10  aromatic  1.337  0.020  1.337
 NU6  C10  N09  single    1.366  0.020  1.366
 NU6  N09  C08  single    1.388  0.020  1.388
 NU6  N03  C02  single    1.340  0.020  1.340
 NU6  C27  C08  aromatic  1.398  0.020  1.398
 NU6  C27  C04  aromatic  1.387  0.020  1.387
 NU6  C08  C07  aromatic  1.398  0.020  1.398
 NU6  C02  C04  single    1.499  0.020  1.499
 NU6  C02  O01  double    1.224  0.020  1.224
 NU6  C04  C05  aromatic  1.394  0.020  1.394
 NU6  C07  C06  aromatic  1.387  0.020  1.387
 NU6  C05  C06  aromatic  1.385  0.020  1.385
 NU6  N03  H1   single    0.860  0.020  1.020
 NU6  N03  H2   single    0.860  0.020  1.020
 NU6  C05  H3   single    0.930  0.020  1.080
 NU6  C06  H4   single    0.930  0.020  1.080
 NU6  C07  H5   single    0.930  0.020  1.080
 NU6  N09  H6   single    0.860  0.020  1.020
 NU6  N13  H7   single    0.860  0.020  1.020
 NU6  C14  H8   single    0.930  0.020  1.080
 NU6  C19  H10  single    0.970  0.020  1.090
 NU6  C19  H11  single    0.970  0.020  1.090
 NU6  C20  H12  single    0.970  0.020  1.090
 NU6  C21  H13  single    0.970  0.020  1.090
 NU6  C21  H14  single    0.970  0.020  1.090
 NU6  C22  H15  single    0.970  0.020  1.090
 NU6  C22  H16  single    0.970  0.020  1.090
 NU6  C23  H17  single    0.970  0.020  1.090
 NU6  C23  H18  single    0.970  0.020  1.090
 NU6  C24  H19  single    0.970  0.020  1.090
 NU6  C24  H20  single    0.970  0.020  1.090
 NU6  C25  H21  single    0.970  0.020  1.090
 NU6  C25  H22  single    0.970  0.020  1.090
 NU6  C27  H23  single    0.930  0.020  1.080

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
 NU6  C04  C02  N03  116.30  3.000
 NU6  C04  C02  O01  121.04  3.000
 NU6  N03  C02  O01  122.67  3.000
 NU6  H2   N03  H1   116.94  3.000
 NU6  H2   N03  C02  119.65  3.000
 NU6  H1   N03  C02  122.93  3.000
 NU6  C27  C04  C05  119.66  3.000
 NU6  C05  C04  C02  122.89  3.000
 NU6  C27  C04  C02  117.43  3.000
 NU6  H3   C05  C06  119.27  3.000
 NU6  H3   C05  C04  121.73  3.000
 NU6  C06  C05  C04  118.98  3.000
 NU6  H4   C06  C07  118.73  3.000
 NU6  H4   C06  C05  119.56  3.000
 NU6  C07  C06  C05  121.71  3.000
 NU6  H5   C07  C08  120.46  3.000
 NU6  H5   C07  C06  119.86  3.000
 NU6  C08  C07  C06  119.68  3.000
 NU6  C27  C08  N09  116.21  3.000
 NU6  C27  C08  C07  118.44  3.000
 NU6  N09  C08  C07  125.35  3.000
 NU6  H6   N09  C10  112.89  3.000
 NU6  H6   N09  C08  115.14  3.000
 NU6  C10  N09  C08  131.90  3.000
 NU6  N26  C10  N11  126.68  3.000
 NU6  N26  C10  N09  118.74  3.000
 NU6  N11  C10  N09  114.57  3.000
 NU6  C12  N11  C10  112.53  3.000
 NU6  C16  C12  N13  104.61  3.000
 NU6  C16  C12  N11  126.72  3.000
 NU6  N13  C12  N11  128.66  3.000
 NU6  H7   N13  C14  126.17  3.000
 NU6  H7   N13  C12  126.88  3.000
 NU6  C14  N13  C12  106.95  3.000
 NU6  H8   C14  N15  125.44  3.000
 NU6  H8   C14  N13  121.18  3.000
 NU6  N15  C14  N13  113.38  3.000
 NU6  C16  N15  C14  104.13  3.000
 NU6  C17  C16  N15  134.32  3.000
 NU6  C17  C16  C12  114.75  3.000
 NU6  N15  C16  C12  110.93  3.000
 NU6  N26  C17  O18  120.61  3.000
 NU6  N26  C17  C16  119.85  3.000
 NU6  O18  C17  C16  119.54  3.000
 NU6  C19  O18  C17  118.73  3.000
 NU6  H11  C19  H10  107.76  3.000
 NU6  H11  C19  C20  110.67  3.000
 NU6  H10  C19  C20  110.51  3.000
 NU6  H11  C19  O18  109.42  3.000
 NU6  H10  C19  O18  109.57  3.000
 NU6  C20  C19  O18  108.89  3.000
 NU6  H12  C20  C25  107.79  3.000
 NU6  H12  C20  C21  108.58  3.000
 NU6  C25  C20  C21  110.51  3.000
 NU6  H12  C20  C19  108.53  3.000
 NU6  C25  C20  C19  108.62  3.000
 NU6  C21  C20  C19  112.67  3.000
 NU6  H14  C21  H13  106.56  3.000
 NU6  H14  C21  C22  109.46  3.000
 NU6  H13  C21  C22  109.83  3.000
 NU6  H14  C21  C20  108.80  3.000
 NU6  H13  C21  C20  110.46  3.000
 NU6  C22  C21  C20  111.59  3.000
 NU6  H16  C22  H15  106.34  3.000
 NU6  H16  C22  C23  110.36  3.000
 NU6  H15  C22  C23  109.14  3.000
 NU6  H16  C22  C21  109.88  3.000
 NU6  H15  C22  C21  109.30  3.000
 NU6  C23  C22  C21  111.68  3.000
 NU6  H18  C23  H17  106.42  3.000
 NU6  H18  C23  C24  109.46  3.000
 NU6  H17  C23  C24  110.16  3.000
 NU6  H18  C23  C22  109.39  3.000
 NU6  H17  C23  C22  110.25  3.000
 NU6  C24  C23  C22  111.05  3.000
 NU6  H20  C24  H19  106.52  3.000
 NU6  H20  C24  C25  109.90  3.000
 NU6  H19  C24  C25  109.25  3.000
 NU6  H20  C24  C23  110.36  3.000
 NU6  H19  C24  C23  109.16  3.000
 NU6  C25  C24  C23  111.51  3.000
 NU6  H22  C25  H21  106.38  3.000
 NU6  H22  C25  C24  110.08  3.000
 NU6  H21  C25  C24  109.41  3.000
 NU6  H22  C25  C20  109.96  3.000
 NU6  H21  C25  C20  109.05  3.000
 NU6  C24  C25  C20  111.82  3.000
 NU6  C17  N26  C10  119.45  3.000
 NU6  H23  C27  C08  119.34  3.000
 NU6  H23  C27  C04  119.14  3.000
 NU6  C08  C27  C04  121.52  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
 NU6  CONST_01  C07  C08  C27  C04     0.00   0.0  0
 NU6  CONST_02  C07  C06  C05  C04     0.00   0.0  0
 NU6  CONST_03  C08  C27  C04  C05     0.00   0.0  0
 NU6  CONST_04  C08  C07  C06  C05     0.00   0.0  0
 NU6  CONST_05  C27  C08  C07  C06     0.00   0.0  0
 NU6  CONST_06  C27  C04  C05  C06     0.00   0.0  0
 NU6  CONST_07  N13  C12  N11  C10   180.00   0.0  0
 NU6  CONST_08  C16  C12  N11  C10     0.00   0.0  0
 NU6  CONST_09  C16  C17  N26  C10     0.00   0.0  0
 NU6  CONST_10  C14  N13  C12  N11   180.00   0.0  0
 NU6  CONST_11  N15  C16  C12  N11   180.00   0.0  0
 NU6  CONST_12  C17  C16  C12  N11     0.00   0.0  0
 NU6  CONST_13  C17  N26  C10  N11     0.00   0.0  0
 NU6  CONST_14  N15  C14  N13  C12     0.00   0.0  0
 NU6  CONST_15  C14  N15  C16  C12     0.00   0.0  0
 NU6  CONST_16  N26  C17  C16  C12     0.00   0.0  0
 NU6  CONST_17  N26  C10  N11  C12     0.00   0.0  0
 NU6  CONST_18  C16  N15  C14  N13     0.00   0.0  0
 NU6  CONST_19  N15  C16  C12  N13     0.00   0.0  0
 NU6  CONST_20  C17  C16  C12  N13   180.00   0.0  0
 NU6  CONST_21  C17  C16  N15  C14   180.00   0.0  0
 NU6  CONST_22  C16  C12  N13  C14     0.00   0.0  0
 NU6  CONST_23  N26  C17  C16  N15   180.00   0.0  0
 NU6  CONST_24  C08  C27  C04  C02   180.00   0.0  0
 NU6  CONST_25  C06  C05  C04  C02   180.00   0.0  0
 NU6  CONST_26  N09  C08  C27  C04   180.00   0.0  0
 NU6  CONST_27  N09  C08  C07  C06   180.00   0.0  0
 NU6  CONST_28  C12  N11  C10  N09   180.00   0.0  0
 NU6  CONST_29  C17  N26  C10  N09   180.00   0.0  0
 NU6  CONST_30  O18  C17  N26  C10   180.00   0.0  0
 NU6  CONST_31  O18  C17  C16  C12   180.00   0.0  0
 NU6  CONST_32  O18  C17  C16  N15     0.00   0.0  0
 NU6  CONST_33  H4   C06  C05  C04   180.00   0.0  0
 NU6  CONST_34  H23  C27  C04  C05   180.00   0.0  0
 NU6  CONST_35  H5   C07  C06  C05   180.00   0.0  0
 NU6  CONST_36  H3   C05  C06  C07   180.00   0.0  0
 NU6  CONST_37  H7   N13  C12  N11     0.00   0.0  0
 NU6  CONST_38  H8   C14  N13  C12   180.00   0.0  0
 NU6  CONST_39  H1   N03  C02  C04     0.00   0.0  0
 NU6  CONST_40  H2   N03  C02  C04   180.00   0.0  0
 NU6  Var_01    C23  C22  C21  C20   -55.44  30.0  1
 NU6  Var_02    C23  C24  C25  C20    55.31  30.0  1
 NU6  Var_03    C24  C23  C22  C21    54.88  30.0  1
 NU6  Var_04    C25  C24  C23  C22   -54.72  30.0  1
 NU6  Var_05    C10  N09  C08  C07    -7.69  30.0  3
 NU6  Var_06    N11  C10  N09  C08  -179.15  30.0  2
 NU6  Var_07    C27  C04  C02  O01   -19.63  30.0  2
 NU6  Var_08    C20  C19  O18  C17  -174.13  30.0  3
 NU6  Var_09    N26  C17  O18  C19    -2.46  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
 NU6  chir_01  C20  C21  C19  C25  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
 NU6  plan-1  C02  0.020
 NU6  plan-1  C04  0.020
 NU6  plan-1  C05  0.020
 NU6  plan-1  C06  0.020
 NU6  plan-1  C07  0.020
 NU6  plan-1  C08  0.020
 NU6  plan-1  N09  0.020
 NU6  plan-1  C27  0.020
 NU6  plan-1  H3   0.020
 NU6  plan-1  H4   0.020
 NU6  plan-1  H5   0.020
 NU6  plan-1  H23  0.020
 NU6  plan-2  N09  0.020
 NU6  plan-2  C10  0.020
 NU6  plan-2  N11  0.020
 NU6  plan-2  C12  0.020
 NU6  plan-2  N13  0.020
 NU6  plan-2  C14  0.020
 NU6  plan-2  N15  0.020
 NU6  plan-2  C16  0.020
 NU6  plan-2  C17  0.020
 NU6  plan-2  O18  0.020
 NU6  plan-2  N26  0.020
 NU6  plan-2  H7   0.020
 NU6  plan-2  H8   0.020
 NU6  plan-3  O01  0.020
 NU6  plan-3  C02  0.020
 NU6  plan-3  N03  0.020
 NU6  plan-3  C04  0.020
 NU6  plan-3  H1   0.020
 NU6  plan-3  H2   0.020

