# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 20:37:02 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 8-methyl-9-pent-4-ynyl-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc2c(N)ncnc2n1CCCC#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
 JY2  JY2  8-methyl-9-pent-4-ynyl-purin-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_JY2
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
 JY2  C2   C  CR16  0   0.034   1.9868   2.2037   0.3831
 JY2  C4   C  CR56  0   0.479   0.8685   0.3143   0.4049
 JY2  C5   C  CR56  0   0.002   1.9361  -0.3946  -0.1221
 JY2  C6   C  CR6   0   0.435   3.0999   0.3447  -0.3914
 JY2  C8   C  CR5   0   0.437   0.3795  -1.8088   0.1488
 JY2  N1   N  N     0  -0.474   3.0881   1.6560  -0.1245
 JY2  CAA  C  CSP1  0  -0.558  -5.4738   1.0928  -1.4649
 JY2  CAB  C  CH3   0  -0.767  -0.4254  -3.0545   0.1810
 JY2  CAD  C  CSP   0   0.286  -4.7244   0.7631  -0.5843
 JY2  CAF  C  CH2   0  -0.583  -3.8011   0.3578   0.4668
 JY2  CAG  C  CH2   0  -0.440  -2.3939   0.0869  -0.0690
 JY2  N3   N  N     0  -0.458   0.8394   1.6170   0.6771
 JY2  N6   N  NH2   0  -0.819   4.2143  -0.2114  -0.8809
 JY2  N7   N  N     0  -0.470   1.6112  -1.7171  -0.2742
 JY2  N9   N  NR5   0  -0.529  -0.1210  -0.6058   0.5814
 JY2  H1   H  HCR6  0   0.248   2.0432   3.2699   0.5761
 JY2  H2   H  H     0   0.278  -6.1394   1.3885  -2.2429
 JY2  H3   H  HCH3  0   0.264  -1.3124  -2.9778  -0.4511
 JY2  H4   H  HCH3  0   0.275   0.1775  -3.8835  -0.1802
 JY2  H5   H  HCH3  0   0.267  -0.7615  -3.2897   1.1919
 JY2  H6   H  HCH2  0   0.276  -3.7645   1.1377   1.2323
 JY2  H7   H  HCH2  0   0.275  -4.1918  -0.5378   0.9575
 JY2  H8   H  HCH2  0   0.249  -2.4355  -0.6962  -0.8295
 JY2  H9   H  HCH2  0   0.254  -2.0058   0.9852  -0.5534
 JY2  H10  H  HCH2  0   0.276  -1.3896   0.4585   1.8090
 JY2  H11  H  HCH2  0   0.274  -1.8334  -1.2195   1.5643
 JY2  H12  H  HNH2  0   0.400   4.9765   0.3765  -1.1717
 JY2  H13  H  HNH2  0   0.407   4.2065  -1.1610  -1.2099
 JY2  CAH  C  CH2   0  -0.317  -1.4591  -0.3292   1.0581

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
 JY2  N6   C6   single    1.338  0.020  1.338
 JY2  C6   N1   aromatic  1.338  0.020  1.338
 JY2  C6   C5   aromatic  1.405  0.020  1.405
 JY2  N7   C5   aromatic  1.370  0.020  1.370
 JY2  N7   C8   aromatic  1.306  0.020  1.306
 JY2  N1   C2   aromatic  1.331  0.020  1.331
 JY2  C5   C4   aromatic  1.386  0.020  1.386
 JY2  CAG  CAF  single    1.530  0.020  1.530
 JY2  CAG  CAH  single    1.522  0.020  1.522
 JY2  C8   CAB  single    1.483  0.020  1.483
 JY2  C8   N9   aromatic  1.373  0.020  1.373
 JY2  C2   N3   aromatic  1.322  0.020  1.322
 JY2  CAF  CAD  single    1.457  0.020  1.457
 JY2  C4   N3   aromatic  1.331  0.020  1.331
 JY2  C4   N9   aromatic  1.363  0.020  1.363
 JY2  N9   CAH  single    1.447  0.020  1.447
 JY2  CAD  CAA  triple    1.202  0.020  1.202
 JY2  C2   H1   single    0.929  0.020  1.085
 JY2  CAA  H2   single    0.913  0.020  1.066
 JY2  CAB  H3   single    0.939  0.020  1.096
 JY2  CAB  H4   single    0.939  0.020  1.096
 JY2  CAB  H5   single    0.939  0.020  1.096
 JY2  CAF  H6   single    0.939  0.020  1.096
 JY2  CAF  H7   single    0.939  0.020  1.096
 JY2  CAG  H8   single    0.939  0.020  1.096
 JY2  CAG  H9   single    0.939  0.020  1.096
 JY2  CAH  H10  single    0.939  0.020  1.096
 JY2  CAH  H11  single    0.939  0.020  1.096
 JY2  N6   H12  single    0.868  0.020  1.013
 JY2  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
 JY2  H1   C2   N3   116.21  3.000
 JY2  H1   C2   N1   115.43  3.000
 JY2  N3   C2   N1   128.36  3.000
 JY2  N9   C4   N3   128.20  3.000
 JY2  N9   C4   C5   105.27  3.000
 JY2  N3   C4   C5   126.53  3.000
 JY2  N7   C5   C6   133.08  3.000
 JY2  N7   C5   C4   110.69  3.000
 JY2  C6   C5   C4   116.23  3.000
 JY2  N6   C6   N1   119.18  3.000
 JY2  N1   C6   C5   118.04  3.000
 JY2  N6   C6   C5   122.77  3.000
 JY2  N9   C8   N7   112.61  3.000
 JY2  N9   C8   CAB  122.09  3.000
 JY2  N7   C8   CAB  125.31  3.000
 JY2  C6   N1   C2   119.12  3.000
 JY2  H2   CAA  CAD  180.00  3.000
 JY2  H5   CAB  H4   108.32  3.000
 JY2  H5   CAB  H3   107.53  3.000
 JY2  H4   CAB  H3   108.17  3.000
 JY2  H5   CAB  C8   111.61  3.000
 JY2  H4   CAB  C8   109.42  3.000
 JY2  H3   CAB  C8   111.67  3.000
 JY2  CAF  CAD  CAA  180.00  3.000
 JY2  H7   CAF  H6   106.38  3.000
 JY2  H7   CAF  CAG  109.92  3.000
 JY2  H6   CAF  CAG  109.92  3.000
 JY2  H7   CAF  CAD  108.98  3.000
 JY2  H6   CAF  CAD  109.14  3.000
 JY2  CAG  CAF  CAD  112.31  3.000
 JY2  H9   CAG  H8   107.13  3.000
 JY2  H9   CAG  CAH  109.57  3.000
 JY2  H8   CAG  CAH  110.05  3.000
 JY2  H9   CAG  CAF  109.68  3.000
 JY2  H8   CAG  CAF  109.61  3.000
 JY2  CAH  CAG  CAF  110.73  3.000
 JY2  C4   N3   C2   111.71  3.000
 JY2  H13  N6   H12  117.62  3.000
 JY2  H13  N6   C6   120.39  3.000
 JY2  H12  N6   C6   119.61  3.000
 JY2  C8   N7   C5   104.81  3.000
 JY2  CAH  N9   C8   127.47  3.000
 JY2  CAH  N9   C4   125.81  3.000
 JY2  C8   N9   C4   106.62  3.000
 JY2  H11  CAH  H10  106.97  3.000
 JY2  H11  CAH  N9   108.32  3.000
 JY2  H10  CAH  N9   107.81  3.000
 JY2  H11  CAH  CAG  110.86  3.000
 JY2  H10  CAH  CAG  110.58  3.000
 JY2  N9   CAH  CAG  112.10  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
 JY2  CONST_01  C5   C6   N1   C2      0.00   0.0  0
 JY2  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 JY2  CONST_03  N9   C4   N3   C2    180.00   0.0  0
 JY2  CONST_04  N1   C6   C5   C4      0.00   0.0  0
 JY2  CONST_05  C8   N7   C5   C4      0.00   0.0  0
 JY2  CONST_06  N1   C2   N3   C4      0.00   0.0  0
 JY2  CONST_07  N7   C8   N9   C4      0.00   0.0  0
 JY2  CONST_08  N9   C8   N7   C5      0.00   0.0  0
 JY2  CONST_09  C8   N9   C4   C5      0.00   0.0  0
 JY2  CONST_10  N3   C2   N1   C6      0.00   0.0  0
 JY2  CONST_11  C8   N7   C5   C6    180.00   0.0  0
 JY2  CONST_12  N3   C4   C5   C6      0.00   0.0  0
 JY2  CONST_13  N9   C4   C5   C6    180.00   0.0  0
 JY2  CONST_14  N3   C4   N9   C8    180.00   0.0  0
 JY2  CONST_15  N7   C5   C6   N1    180.00   0.0  0
 JY2  CONST_16  N7   C5   C4   N3    180.00   0.0  0
 JY2  CONST_17  N9   C4   C5   N7      0.00   0.0  0
 JY2  CONST_18  N6   C6   N1   C2    180.00   0.0  0
 JY2  CONST_19  N6   C6   C5   C4    180.00   0.0  0
 JY2  CONST_20  CAB  C8   N9   C4    180.00   0.0  0
 JY2  CONST_21  CAB  C8   N7   C5    180.00   0.0  0
 JY2  CONST_22  CAH  N9   C4   C5    180.00   0.0  0
 JY2  CONST_23  N7   C8   N9   CAH   180.00   0.0  0
 JY2  CONST_24  N3   C4   N9   CAH     0.00   0.0  0
 JY2  CONST_25  N7   C5   C6   N6      0.00   0.0  0
 JY2  CONST_26  H1   C2   N3   C4    180.00   0.0  0
 JY2  CONST_27  H12  N6   C6   C5    180.00   0.0  0
 JY2  CONST_28  H13  N6   C6   C5      0.00   0.0  0
 JY2  Var_01    CAG  CAH  N9   C4     85.83  30.0  2
 JY2  Var_02    H3   CAB  C8   N7   -118.38  30.0  2
 JY2  Var_03    N9   CAH  CAG  CAF   179.44  30.0  3
 JY2  Var_04    CAG  CAF  CAD  CAA    10.69  30.0  1
 JY2  Var_05    CAH  CAG  CAF  CAD   179.83  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
 JY2  plan-1  C2   0.020
 JY2  plan-1  C4   0.020
 JY2  plan-1  C5   0.020
 JY2  plan-1  C6   0.020
 JY2  plan-1  C8   0.020
 JY2  plan-1  N1   0.020
 JY2  plan-1  CAB  0.020
 JY2  plan-1  N3   0.020
 JY2  plan-1  N6   0.020
 JY2  plan-1  N7   0.020
 JY2  plan-1  N9   0.020
 JY2  plan-1  H1   0.020
 JY2  plan-1  CAH  0.020
 JY2  plan-2  C6   0.020
 JY2  plan-2  N6   0.020
 JY2  plan-2  H12  0.020
 JY2  plan-2  H13  0.020

