# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 16:31:41 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: ~{N},9-dimethylpurin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1ncnc2n(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
 OYK  OYK  ~{N},9-dimethylpurin-6-amine  ligand  21  12  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OYK
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
 OYK  N12  N  N     0  -0.454  -24.1061  27.5324  -23.3158
 OYK  C01  C  CH3   0  -0.527  -22.8366  30.2946  -23.1046
 OYK  C03  C  CR15  0   0.100  -21.1233  28.9751  -24.3920
 OYK  C05  C  CR56  0   0.475  -22.9204  27.8912  -23.8109
 OYK  C06  C  CR56  0   0.004  -22.0430  27.0842  -24.5184
 OYK  C07  C  CR6   0   0.490  -22.4568  25.7536  -24.7331
 OYK  C09  C  CH3   0  -0.513  -22.1066  23.5050  -25.6372
 OYK  C11  C  CR16  0   0.036  -24.3804  26.2680  -23.5771
 OYK  N02  N  NR5   0  -0.485  -22.3126  29.1072  -23.7389
 OYK  N04  N  N     0  -0.451  -20.9197  27.7816  -24.8740
 OYK  N08  N  NH1   0  -0.643  -21.7125  24.8724  -25.4046
 OYK  N10  N  N     0  -0.488  -23.6425  25.3790  -24.2414
 OYK  H1   H  HCH3  0   0.262  -22.9806  30.1284  -22.0389
 OYK  H2   H  HCH3  0   0.268  -22.1283  31.1071  -23.2412
 OYK  H3   H  HCH3  0   0.262  -23.7869  30.5775  -23.5524
 OYK  H4   H  HCR5  0   0.289  -20.4423  29.8095  -24.4793
 OYK  H5   H  HCH3  0   0.251  -21.3275  23.0211  -26.2190
 OYK  H6   H  HCH3  0   0.236  -22.2315  22.9532  -24.7044
 OYK  H7   H  HCH3  0   0.237  -23.0415  23.4435  -26.1952
 OYK  H8   H  HCR6  0   0.246  -25.3296  25.8971  -23.2041
 OYK  H9   H  HNH1  0   0.405  -20.8210  25.1825  -25.7526

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
 OYK  C09  N08  single    1.442  0.020  1.442
 OYK  N08  C07  single    1.335  0.020  1.335
 OYK  N04  C06  aromatic  1.369  0.020  1.369
 OYK  N04  C03  aromatic  1.303  0.020  1.303
 OYK  C07  C06  aromatic  1.410  0.020  1.410
 OYK  C07  N10  aromatic  1.337  0.020  1.337
 OYK  C06  C05  aromatic  1.386  0.020  1.386
 OYK  C03  N02  aromatic  1.363  0.020  1.363
 OYK  N10  C11  aromatic  1.333  0.020  1.333
 OYK  N02  C05  aromatic  1.361  0.020  1.361
 OYK  N02  C01  single    1.445  0.020  1.445
 OYK  C05  N12  aromatic  1.334  0.020  1.334
 OYK  C11  N12  aromatic  1.320  0.020  1.320
 OYK  C01  H1   single    0.970  0.020  1.090
 OYK  C01  H2   single    0.970  0.020  1.090
 OYK  C01  H3   single    0.970  0.020  1.090
 OYK  C03  H4   single    0.930  0.020  1.080
 OYK  C09  H5   single    0.970  0.020  1.090
 OYK  C09  H6   single    0.970  0.020  1.090
 OYK  C09  H7   single    0.970  0.020  1.090
 OYK  C11  H8   single    0.930  0.020  1.080
 OYK  N08  H9   single    0.860  0.020  1.020

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
 OYK  C11  N12  C05  111.64  3.000
 OYK  H3   C01  H2   108.86  3.000
 OYK  H3   C01  H1   109.10  3.000
 OYK  H2   C01  H1   108.88  3.000
 OYK  H3   C01  N02  110.48  3.000
 OYK  H2   C01  N02  108.84  3.000
 OYK  H1   C01  N02  110.64  3.000
 OYK  H4   C03  N04  125.37  3.000
 OYK  H4   C03  N02  120.91  3.000
 OYK  N04  C03  N02  113.72  3.000
 OYK  N02  C05  C06  105.33  3.000
 OYK  N02  C05  N12  128.13  3.000
 OYK  C06  C05  N12  126.54  3.000
 OYK  N04  C06  C07  133.00  3.000
 OYK  C07  C06  C05  116.19  3.000
 OYK  N04  C06  C05  110.81  3.000
 OYK  N10  C07  N08  119.63  3.000
 OYK  N10  C07  C06  117.95  3.000
 OYK  N08  C07  C06  122.42  3.000
 OYK  H7   C09  H6   108.11  3.000
 OYK  H7   C09  H5   108.41  3.000
 OYK  H6   C09  H5   108.35  3.000
 OYK  H7   C09  N08  111.73  3.000
 OYK  H6   C09  N08  111.90  3.000
 OYK  H5   C09  N08  108.23  3.000
 OYK  H8   C11  N10  115.32  3.000
 OYK  H8   C11  N12  116.17  3.000
 OYK  N10  C11  N12  128.51  3.000
 OYK  C05  N02  C03  106.12  3.000
 OYK  C05  N02  C01  126.54  3.000
 OYK  C03  N02  C01  127.34  3.000
 OYK  C06  N04  C03  104.02  3.000
 OYK  H9   N08  C09  118.60  3.000
 OYK  H9   N08  C07  117.69  3.000
 OYK  C09  N08  C07  123.70  3.000
 OYK  C11  N10  C07  119.17  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
 OYK  CONST_01  N04  C06  C05  N12   180.00   0.0  0
 OYK  CONST_02  C07  C06  C05  N12     0.00   0.0  0
 OYK  CONST_03  C03  N02  C05  N12   180.00   0.0  0
 OYK  CONST_04  C07  N10  C11  N12     0.00   0.0  0
 OYK  CONST_05  C07  C06  N04  C03   180.00   0.0  0
 OYK  CONST_06  C05  C06  N04  C03     0.00   0.0  0
 OYK  CONST_07  C06  C05  N02  C03     0.00   0.0  0
 OYK  CONST_08  N10  C07  C06  C05     0.00   0.0  0
 OYK  CONST_09  N04  C03  N02  C05     0.00   0.0  0
 OYK  CONST_10  N10  C11  N12  C05     0.00   0.0  0
 OYK  CONST_11  N02  C03  N04  C06     0.00   0.0  0
 OYK  CONST_12  C11  N10  C07  C06     0.00   0.0  0
 OYK  CONST_13  C11  N12  C05  C06     0.00   0.0  0
 OYK  CONST_14  N02  C05  C06  C07   180.00   0.0  0
 OYK  CONST_15  N02  C05  N12  C11   180.00   0.0  0
 OYK  CONST_16  N04  C06  C05  N02     0.00   0.0  0
 OYK  CONST_17  N10  C07  C06  N04   180.00   0.0  0
 OYK  CONST_18  C01  N02  C05  N12     0.00   0.0  0
 OYK  CONST_19  N04  C03  N02  C01   180.00   0.0  0
 OYK  CONST_20  C06  C05  N02  C01   180.00   0.0  0
 OYK  CONST_21  N08  C07  C06  C05   180.00   0.0  0
 OYK  CONST_22  N08  C07  N10  C11   180.00   0.0  0
 OYK  CONST_23  N08  C07  C06  N04     0.00   0.0  0
 OYK  CONST_24  H4   C03  N02  C05   180.00   0.0  0
 OYK  CONST_25  H8   C11  N12  C05   180.00   0.0  0
 OYK  CONST_26  C09  N08  C07  C06   180.00   0.0  0
 OYK  CONST_27  N10  C07  N08  C09     0.00   0.0  0
 OYK  CONST_28  H9   N08  C07  C06     0.00   0.0  0
 OYK  Var_01    H1   C01  N02  C03  -118.59  30.0  2
 OYK  Var_02    H5   C09  N08  C07   179.07  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
 OYK  plan-1  N12  0.020
 OYK  plan-1  C01  0.020
 OYK  plan-1  C03  0.020
 OYK  plan-1  C05  0.020
 OYK  plan-1  C06  0.020
 OYK  plan-1  C07  0.020
 OYK  plan-1  C11  0.020
 OYK  plan-1  N02  0.020
 OYK  plan-1  N04  0.020
 OYK  plan-1  N08  0.020
 OYK  plan-1  N10  0.020
 OYK  plan-1  H4   0.020
 OYK  plan-1  H8   0.020
 OYK  plan-2  C07  0.020
 OYK  plan-2  C09  0.020
 OYK  plan-2  N08  0.020
 OYK  plan-2  H9   0.020

