# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 19:16:24 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: 9-ethyl-8-ethynyl-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCn1c(nc2c(N)ncnc12)C#C
#
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
 JYB  JYB  9-ethyl-8-ethynyl-purin-6-amine  ligand  23  14  .  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_JYB
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
 JYB  N12  N  N     0  -0.472  -2.9832  -0.3350   0.0016
 JYB  C13  C  CR6   0   0.446  -2.2529   0.7797   0.1045
 JYB  C01  C  CSP1  0  -0.503   3.6878   1.7979  -0.1080
 JYB  C02  C  CSP   0   0.249   2.5645   1.3690  -0.1023
 JYB  C03  C  CR5   0   0.343   1.2450   0.8540  -0.0956
 JYB  C05  C  CR56  0  -0.003  -0.8513   0.6595   0.0060
 JYB  C06  C  CR56  0   0.487  -0.3557  -0.6224  -0.1960
 JYB  C09  C  CH3   0  -0.661   2.4232  -2.0941   0.9329
 JYB  C11  C  CR16  0   0.042  -2.3676  -1.5002  -0.1891
 JYB  N04  N  N     0  -0.443   0.1601   1.5696   0.0664
 JYB  N07  N  NR5   0  -0.519   0.9937  -0.4834  -0.2686
 JYB  N10  N  N     0  -0.458  -1.0731  -1.7394  -0.2993
 JYB  N14  N  NH2   0  -0.813  -2.8633   1.9473   0.2999
 JYB  H1   H  H     0   0.292   4.6821   2.1837  -0.1137
 JYB  H2   H  HCH2  0   0.272   2.8068  -1.1709  -0.9856
 JYB  H3   H  HCH2  0   0.274   1.4970  -2.3368  -1.0041
 JYB  H4   H  HCH3  0   0.247   3.1478  -2.8926   0.7780
 JYB  H5   H  HCH3  0   0.236   2.8998  -1.3183   1.5317
 JYB  H6   H  HCH3  0   0.239   1.5866  -2.5018   1.4993
 JYB  H7   H  HCR6  0   0.253  -3.0210  -2.3629  -0.2637
 JYB  H8   H  HNH2  0   0.406  -3.8674   1.9956   0.3217
 JYB  H9   H  HNH2  0   0.414  -2.3444   2.8071   0.3396
 JYB  C08  C  CH2   0  -0.328   1.9650  -1.5539  -0.4098

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
 JYB  N14  C13  single    1.332  0.020  1.332
 JYB  C13  N12  aromatic  1.337  0.020  1.337
 JYB  C13  C05  aromatic  1.410  0.020  1.410
 JYB  N12  C11  aromatic  1.332  0.020  1.332
 JYB  N04  C05  aromatic  1.362  0.020  1.362
 JYB  N04  C03  aromatic  1.310  0.020  1.310
 JYB  C05  C06  aromatic  1.389  0.020  1.389
 JYB  C11  N10  aromatic  1.321  0.020  1.321
 JYB  C03  C02  single    1.416  0.020  1.416
 JYB  C03  N07  aromatic  1.372  0.020  1.372
 JYB  C06  N10  aromatic  1.332  0.020  1.332
 JYB  C06  N07  aromatic  1.358  0.020  1.358
 JYB  C02  C01  triple    1.202  0.020  1.202
 JYB  C09  C08  single    1.518  0.020  1.518
 JYB  N07  C08  single    1.452  0.020  1.452
 JYB  C01  H1   single    0.913  0.020  1.066
 JYB  C08  H2   single    0.939  0.020  1.096
 JYB  C08  H3   single    0.939  0.020  1.096
 JYB  C09  H4   single    0.939  0.020  1.096
 JYB  C09  H5   single    0.939  0.020  1.096
 JYB  C09  H6   single    0.939  0.020  1.096
 JYB  C11  H7   single    0.929  0.020  1.085
 JYB  N14  H8   single    0.868  0.020  1.013
 JYB  N14  H9   single    0.868  0.020  1.013

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
 JYB  C11  N12  C13  119.22  3.000
 JYB  N14  C13  C05  122.71  3.000
 JYB  C05  C13  N12  117.82  3.000
 JYB  N14  C13  N12  119.47  3.000
 JYB  H1   C01  C02  180.00  3.000
 JYB  C03  C02  C01  180.00  3.000
 JYB  N07  C03  N04  113.36  3.000
 JYB  N07  C03  C02  121.63  3.000
 JYB  N04  C03  C02  125.00  3.000
 JYB  N04  C05  C06  110.98  3.000
 JYB  C06  C05  C13  116.32  3.000
 JYB  N04  C05  C13  132.69  3.000
 JYB  N10  C06  N07  128.09  3.000
 JYB  N07  C06  C05  105.53  3.000
 JYB  N10  C06  C05  126.38  3.000
 JYB  H6   C09  H5   108.45  3.000
 JYB  H6   C09  H4   108.09  3.000
 JYB  H5   C09  H4   108.00  3.000
 JYB  H6   C09  C08  111.18  3.000
 JYB  H5   C09  C08  111.38  3.000
 JYB  H4   C09  C08  109.63  3.000
 JYB  H7   C11  N10  116.13  3.000
 JYB  H7   C11  N12  115.30  3.000
 JYB  N10  C11  N12  128.57  3.000
 JYB  C05  N04  C03  104.16  3.000
 JYB  C08  N07  C06  126.44  3.000
 JYB  C08  N07  C03  127.47  3.000
 JYB  C06  N07  C03  105.96  3.000
 JYB  C11  N10  C06  111.69  3.000
 JYB  H9   N14  H8   118.26  3.000
 JYB  H9   N14  C13  121.28  3.000
 JYB  H8   N14  C13  120.20  3.000
 JYB  H3   C08  H2   107.24  3.000
 JYB  H3   C08  N07  107.20  3.000
 JYB  H2   C08  N07  108.00  3.000
 JYB  H3   C08  C09  110.89  3.000
 JYB  H2   C08  C09  111.06  3.000
 JYB  N07  C08  C09  112.22  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
 JYB  CONST_01  N04  C05  C13  N12  180.00   0.0  0
 JYB  CONST_02  C06  C05  C13  N12    0.00   0.0  0
 JYB  CONST_03  C06  N10  C11  N12    0.00   0.0  0
 JYB  CONST_04  N10  C11  N12  C13    0.00   0.0  0
 JYB  CONST_05  C03  N04  C05  C13  180.00   0.0  0
 JYB  CONST_06  N10  C06  C05  C13    0.00   0.0  0
 JYB  CONST_07  N07  C06  C05  C13  180.00   0.0  0
 JYB  CONST_08  C06  C05  N04  C03    0.00   0.0  0
 JYB  CONST_09  C05  C06  N07  C03    0.00   0.0  0
 JYB  CONST_10  N10  C06  N07  C03  180.00   0.0  0
 JYB  CONST_11  C11  N12  C13  C05    0.00   0.0  0
 JYB  CONST_12  N07  C03  N04  C05    0.00   0.0  0
 JYB  CONST_13  C11  N10  C06  C05    0.00   0.0  0
 JYB  CONST_14  N04  C03  N07  C06    0.00   0.0  0
 JYB  CONST_15  N07  C06  N10  C11  180.00   0.0  0
 JYB  CONST_16  N10  C06  C05  N04  180.00   0.0  0
 JYB  CONST_17  N07  C06  C05  N04    0.00   0.0  0
 JYB  CONST_18  C05  N04  C03  C02  180.00   0.0  0
 JYB  CONST_19  C06  N07  C03  C02  180.00   0.0  0
 JYB  CONST_20  C08  N07  C06  C05  180.00   0.0  0
 JYB  CONST_21  N14  C13  C05  C06  180.00   0.0  0
 JYB  CONST_22  N04  C03  N07  C08  180.00   0.0  0
 JYB  CONST_23  N10  C06  N07  C08    0.00   0.0  0
 JYB  CONST_24  N14  C13  N12  C11  180.00   0.0  0
 JYB  CONST_25  N14  C13  C05  N04    0.00   0.0  0
 JYB  CONST_26  H7   C11  N12  C13  180.00   0.0  0
 JYB  CONST_27  H8   N14  C13  N12    0.00   0.0  0
 JYB  CONST_28  H9   N14  C13  N12  180.00   0.0  0
 JYB  Var_01    C09  C08  N07  C03   86.10  30.0  2
 JYB  Var_02    H4   C09  C08  N07  179.96  30.0  3

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
 JYB  plan-1  N12  0.020
 JYB  plan-1  C13  0.020
 JYB  plan-1  C01  0.020
 JYB  plan-1  C02  0.020
 JYB  plan-1  C03  0.020
 JYB  plan-1  C05  0.020
 JYB  plan-1  C06  0.020
 JYB  plan-1  C11  0.020
 JYB  plan-1  N04  0.020
 JYB  plan-1  N07  0.020
 JYB  plan-1  N10  0.020
 JYB  plan-1  N14  0.020
 JYB  plan-1  H7   0.020
 JYB  plan-1  C08  0.020
 JYB  plan-2  C13  0.020
 JYB  plan-2  N14  0.020
 JYB  plan-2  H8   0.020
 JYB  plan-2  H9   0.020

