# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 18:49:44 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 9-hex-5-ynylpurin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(CCCCC#C)cnc12
#
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
 JXQ  JXQ  9-hex-5-ynylpurin-6-amine  ligand  29  16  .  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_JXQ
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
 JXQ  C5   C  CR56  0  -0.003   2.4390  -0.5547  -0.0390
 JXQ  C6   C  CR6   0   0.453   3.5302   0.2832  -0.3358
 JXQ  C2   C  CR16  0   0.036   2.1792   2.0698   0.1937
 JXQ  C4   C  CR56  0   0.480   1.2730   0.0777   0.3672
 JXQ  C8   C  CR15  0   0.106   1.0373  -2.0874   0.3132
 JXQ  C9B  C  CH2   0  -0.440  -1.8918  -0.3016  -0.1443
 JXQ  C9C  C  CH2   0  -0.430  -3.3385  -0.1509   0.3046
 JXQ  C9D  C  CH2   0  -0.575  -4.2323   0.3446  -0.8349
 JXQ  C9E  C  CSP   0   0.284  -5.6222   0.5047  -0.4277
 JXQ  C9F  C  CSP1  0  -0.565  -6.7628   0.6375  -0.0693
 JXQ  N1   N  N     0  -0.476   3.3599   1.6038  -0.2086
 JXQ  N3   N  N     0  -0.456   1.0893   1.3908   0.5023
 JXQ  N6   N  NH2   0  -0.818   4.7128  -0.1869  -0.7367
 JXQ  N7   N  N     0  -0.456   2.2714  -1.9141  -0.0657
 JXQ  N9   N  NR5   0  -0.496   0.3804  -0.9258   0.5944
 JXQ  H1   H  HCR6  0   0.249   2.1108   3.1498   0.2755
 JXQ  H2   H  HCR5  0   0.291   0.5443  -3.0435   0.4139
 JXQ  H3   H  HCH2  0   0.264  -1.0425  -0.0769   1.8329
 JXQ  H4   H  HCH2  0   0.269  -1.3405  -1.7447   1.3701
 JXQ  H5   H  HCH2  0   0.242  -1.5195   0.6559  -0.5185
 JXQ  H6   H  HCH2  0   0.238  -1.8291  -1.0148  -0.9712
 JXQ  H7   H  HCH2  0   0.239  -3.7180  -1.1087   0.6694
 JXQ  H8   H  HCH2  0   0.238  -3.3980   0.5516   1.1399
 JXQ  H9   H  HCH2  0   0.269  -3.8579   1.3015  -1.2098
 JXQ  H10  H  HCH2  0   0.269  -4.1861  -0.3546  -1.6746
 JXQ  H11  H  H     0   0.278  -7.7756   0.7525   0.2420
 JXQ  H12  H  HNH2  0   0.402   5.4667   0.4448  -0.9442
 JXQ  H13  H  HNH2  0   0.410   4.8761  -1.1734  -0.8297
 JXQ  C9A  C  CH2   0  -0.303  -1.0041  -0.7770   0.9970

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
 JXQ  N6   C6   single    1.334  0.020  1.334
 JXQ  C9D  C9C  single    1.531  0.020  1.531
 JXQ  C9D  C9E  single    1.457  0.020  1.457
 JXQ  C6   N1   aromatic  1.338  0.020  1.338
 JXQ  C6   C5   aromatic  1.407  0.020  1.407
 JXQ  N1   C2   aromatic  1.332  0.020  1.332
 JXQ  C9C  C9B  single    1.522  0.020  1.522
 JXQ  N7   C5   aromatic  1.370  0.020  1.370
 JXQ  N7   C8   aromatic  1.303  0.020  1.303
 JXQ  C5   C4   aromatic  1.387  0.020  1.387
 JXQ  C9E  C9F  triple    1.203  0.020  1.203
 JXQ  C2   N3   aromatic  1.321  0.020  1.321
 JXQ  C8   N9   aromatic  1.364  0.020  1.364
 JXQ  C4   N3   aromatic  1.333  0.020  1.333
 JXQ  C4   N9   aromatic  1.362  0.020  1.362
 JXQ  N9   C9A  single    1.449  0.020  1.449
 JXQ  C9B  C9A  single    1.522  0.020  1.522
 JXQ  C2   H1   single    0.929  0.020  1.085
 JXQ  C8   H2   single    0.929  0.020  1.085
 JXQ  C9A  H3   single    0.939  0.020  1.096
 JXQ  C9A  H4   single    0.939  0.020  1.096
 JXQ  C9B  H5   single    0.939  0.020  1.096
 JXQ  C9B  H6   single    0.939  0.020  1.096
 JXQ  C9C  H7   single    0.939  0.020  1.096
 JXQ  C9C  H8   single    0.939  0.020  1.096
 JXQ  C9D  H9   single    0.939  0.020  1.096
 JXQ  C9D  H10  single    0.939  0.020  1.096
 JXQ  C9F  H11  single    0.913  0.020  1.066
 JXQ  N6   H12  single    0.868  0.020  1.013
 JXQ  N6   H13  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
 JXQ  N7   C5   C4   110.80  3.000
 JXQ  C4   C5   C6   116.23  3.000
 JXQ  N7   C5   C6   132.96  3.000
 JXQ  N6   C6   N1   119.29  3.000
 JXQ  N1   C6   C5   117.97  3.000
 JXQ  N6   C6   C5   122.74  3.000
 JXQ  H1   C2   N3   116.24  3.000
 JXQ  H1   C2   N1   115.27  3.000
 JXQ  N3   C2   N1   128.50  3.000
 JXQ  N9   C4   N3   128.21  3.000
 JXQ  N9   C4   C5   105.30  3.000
 JXQ  N3   C4   C5   126.49  3.000
 JXQ  H2   C8   N9   120.98  3.000
 JXQ  H2   C8   N7   125.25  3.000
 JXQ  N9   C8   N7   113.77  3.000
 JXQ  H6   C9B  H5   107.02  3.000
 JXQ  H6   C9B  C9C  110.00  3.000
 JXQ  H5   C9B  C9C  109.74  3.000
 JXQ  H6   C9B  C9A  109.26  3.000
 JXQ  H5   C9B  C9A  109.36  3.000
 JXQ  C9C  C9B  C9A  111.35  3.000
 JXQ  H8   C9C  H7   106.82  3.000
 JXQ  H8   C9C  C9D  109.21  3.000
 JXQ  H7   C9C  C9D  109.23  3.000
 JXQ  H8   C9C  C9B  109.92  3.000
 JXQ  H7   C9C  C9B  109.98  3.000
 JXQ  C9D  C9C  C9B  111.56  3.000
 JXQ  H10  C9D  H9   106.36  3.000
 JXQ  H10  C9D  C9E  108.97  3.000
 JXQ  H9   C9D  C9E  109.04  3.000
 JXQ  H10  C9D  C9C  109.87  3.000
 JXQ  H9   C9D  C9C  109.79  3.000
 JXQ  C9E  C9D  C9C  112.62  3.000
 JXQ  C9F  C9E  C9D  180.00  3.000
 JXQ  H11  C9F  C9E  180.00  3.000
 JXQ  C2   N1   C6   119.15  3.000
 JXQ  C4   N3   C2   111.66  3.000
 JXQ  H13  N6   H12  118.44  3.000
 JXQ  H13  N6   C6   121.21  3.000
 JXQ  H12  N6   C6   120.35  3.000
 JXQ  C8   N7   C5   104.02  3.000
 JXQ  C9A  N9   C8   127.21  3.000
 JXQ  C9A  N9   C4   126.63  3.000
 JXQ  C8   N9   C4   106.11  3.000
 JXQ  H4   C9A  H3   107.25  3.000
 JXQ  H4   C9A  N9   107.37  3.000
 JXQ  H3   C9A  N9   108.20  3.000
 JXQ  H4   C9A  C9B  110.72  3.000
 JXQ  H3   C9A  C9B  110.71  3.000
 JXQ  N9   C9A  C9B  112.39  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
 JXQ  CONST_01  C2   N1   C6   C5      0.00   0.0  0
 JXQ  CONST_02  N9   C8   N7   C5      0.00   0.0  0
 JXQ  CONST_03  C2   N3   C4   C5      0.00   0.0  0
 JXQ  CONST_04  C8   N9   C4   C5      0.00   0.0  0
 JXQ  CONST_05  N3   C2   N1   C6      0.00   0.0  0
 JXQ  CONST_06  C8   N7   C5   C6    180.00   0.0  0
 JXQ  CONST_07  N3   C4   C5   C6      0.00   0.0  0
 JXQ  CONST_08  N9   C4   C5   C6    180.00   0.0  0
 JXQ  CONST_09  N9   C4   N3   C2    180.00   0.0  0
 JXQ  CONST_10  N1   C6   C5   C4      0.00   0.0  0
 JXQ  CONST_11  C8   N7   C5   C4      0.00   0.0  0
 JXQ  CONST_12  N1   C2   N3   C4      0.00   0.0  0
 JXQ  CONST_13  N7   C8   N9   C4      0.00   0.0  0
 JXQ  CONST_14  N3   C4   N9   C8    180.00   0.0  0
 JXQ  CONST_15  N7   C5   C6   N1    180.00   0.0  0
 JXQ  CONST_16  N7   C5   C4   N3    180.00   0.0  0
 JXQ  CONST_17  N9   C4   C5   N7      0.00   0.0  0
 JXQ  CONST_18  C9A  N9   C4   C5    180.00   0.0  0
 JXQ  CONST_19  N6   C6   N1   C2    180.00   0.0  0
 JXQ  CONST_20  N6   C6   C5   C4    180.00   0.0  0
 JXQ  CONST_21  N7   C8   N9   C9A   180.00   0.0  0
 JXQ  CONST_22  N3   C4   N9   C9A     0.00   0.0  0
 JXQ  CONST_23  N7   C5   C6   N6      0.00   0.0  0
 JXQ  CONST_24  H2   C8   N7   C5    180.00   0.0  0
 JXQ  CONST_25  H1   C2   N1   C6    180.00   0.0  0
 JXQ  CONST_26  H12  N6   C6   C5    180.00   0.0  0
 JXQ  CONST_27  H13  N6   C6   C5      0.00   0.0  0
 JXQ  Var_01    C9B  C9A  N9   C4     74.35  30.0  2
 JXQ  Var_02    N9   C9A  C9B  C9C  -179.89  30.0  3
 JXQ  Var_03    C9D  C9C  C9B  C9A   179.25  30.0  1
 JXQ  Var_04    C9E  C9D  C9C  C9B  -179.66  30.0  1

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
 JXQ  plan-1  C5   0.020
 JXQ  plan-1  C6   0.020
 JXQ  plan-1  C2   0.020
 JXQ  plan-1  C4   0.020
 JXQ  plan-1  C8   0.020
 JXQ  plan-1  N1   0.020
 JXQ  plan-1  N3   0.020
 JXQ  plan-1  N6   0.020
 JXQ  plan-1  N7   0.020
 JXQ  plan-1  N9   0.020
 JXQ  plan-1  H1   0.020
 JXQ  plan-1  H2   0.020
 JXQ  plan-1  C9A  0.020
 JXQ  plan-2  C6   0.020
 JXQ  plan-2  N6   0.020
 JXQ  plan-2  H12  0.020
 JXQ  plan-2  H13  0.020

