# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 15:44:29 2022
#   Inital geometry file: a 63 line input string
#   Ligand name: ~{N}2,~{N}6,9-trimethylpurine-2,6-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1nc(NC)c2ncn(C)c2n1
#
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
 IF3  IF3  "~{N}2,~{N}6,9-trimethylpurine-2,6-diamine"
  ligand  26  14  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IF3
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
 IF3  C10  C  CH3   0  -0.506  18.5410  30.3411  6.3937
 IF3  C01  C  CH3   0  -0.513  18.2493  24.8328  3.3598
 IF3  C03  C  CR6   0   0.491  16.8554  26.8259  3.6597
 IF3  C04  C  CR56  0  -0.042  15.6711  27.5556  3.4119
 IF3  C05  C  CR56  0   0.497  15.5910  28.7931  4.0268
 IF3  C07  C  CR6   0   0.567  17.5724  28.5856  4.9740
 IF3  C12  C  CR15  0   0.081  13.8064  28.3602  2.8439
 IF3  N02  N  NH1   0  -0.648  17.0626  25.6161  3.1282
 IF3  N06  N  N     0  -0.526  16.5013  29.3611  4.8146
 IF3  N08  N  N     0  -0.544  17.7838  27.3640  4.4417
 IF3  N09  N  NH1   0  -0.650  18.5688  29.0553  5.7511
 IF3  N11  N  NR5   0  -0.492  14.3843  29.3004  3.6532
 IF3  N13  N  N     0  -0.450  14.5420  27.3010  2.6738
 IF3  H1   H  HCH3  0   0.245  19.4805  30.4789  6.9227
 IF3  H2   H  HCH3  0   0.226  18.4322  31.1565  5.6759
 IF3  H3   H  HCH3  0   0.226  17.7280  30.4242  7.1179
 IF3  H4   H  HCH3  0   0.249  18.1580  23.9027  2.8058
 IF3  H5   H  HCH3  0   0.234  19.1482  25.3479  3.0182
 IF3  H6   H  HCH3  0   0.233  18.3792  24.5916  4.4159
 IF3  H7   H  HCR5  0   0.280  12.8305  28.5244  2.4101
 IF3  H8   H  HCH3  0   0.257  14.4825  31.3895  3.7027
 IF3  H9   H  HCH3  0   0.264  12.8588  30.6994  3.5862
 IF3  H10  H  HCH3  0   0.257  13.7329  30.6399  5.1214
 IF3  H11  H  HNH1  0   0.402  16.3362  25.2306  2.5495
 IF3  H12  H  HNH1  0   0.388  19.3769  28.4684  5.8580
 IF3  C14  C  CH3   0  -0.526  13.8389  30.5788  4.0397

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
 IF3  N13  C12  aromatic  1.301  0.020  1.301
 IF3  N13  C04  aromatic  1.373  0.020  1.373
 IF3  C12  N11  aromatic  1.368  0.020  1.368
 IF3  N02  C01  single    1.441  0.020  1.441
 IF3  N02  C03  single    1.338  0.020  1.338
 IF3  C04  C03  aromatic  1.413  0.020  1.413
 IF3  C04  C05  aromatic  1.384  0.020  1.384
 IF3  C03  N08  aromatic  1.328  0.020  1.328
 IF3  N11  C05  aromatic  1.361  0.020  1.361
 IF3  N11  C14  single    1.443  0.020  1.443
 IF3  C05  N06  aromatic  1.331  0.020  1.331
 IF3  N08  C07  aromatic  1.349  0.020  1.349
 IF3  N06  C07  aromatic  1.332  0.020  1.332
 IF3  C07  N09  single    1.348  0.020  1.348
 IF3  N09  C10  single    1.438  0.020  1.438
 IF3  C10  H1   single    0.970  0.020  1.090
 IF3  C10  H2   single    0.970  0.020  1.090
 IF3  C10  H3   single    0.970  0.020  1.090
 IF3  C01  H4   single    0.970  0.020  1.090
 IF3  C01  H5   single    0.970  0.020  1.090
 IF3  C01  H6   single    0.970  0.020  1.090
 IF3  C12  H7   single    0.930  0.020  1.080
 IF3  C14  H8   single    0.970  0.020  1.090
 IF3  C14  H9   single    0.970  0.020  1.090
 IF3  C14  H10  single    0.970  0.020  1.090
 IF3  N02  H11  single    0.860  0.020  1.020
 IF3  N09  H12  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
 IF3  H3   C10  H2   107.76  3.000
 IF3  H3   C10  H1   108.12  3.000
 IF3  H2   C10  H1   108.15  3.000
 IF3  H3   C10  N09  112.26  3.000
 IF3  H2   C10  N09  112.09  3.000
 IF3  H1   C10  N09  108.31  3.000
 IF3  H6   C01  H5   108.03  3.000
 IF3  H6   C01  H4   108.32  3.000
 IF3  H5   C01  H4   108.29  3.000
 IF3  H6   C01  N02  111.96  3.000
 IF3  H5   C01  N02  111.82  3.000
 IF3  H4   C01  N02  108.31  3.000
 IF3  N08  C03  N02  119.49  3.000
 IF3  N08  C03  C04  118.69  3.000
 IF3  N02  C03  C04  121.82  3.000
 IF3  N13  C04  C05  110.91  3.000
 IF3  C05  C04  C03  115.62  3.000
 IF3  N13  C04  C03  133.47  3.000
 IF3  N11  C05  N06  127.56  3.000
 IF3  N06  C05  C04  127.21  3.000
 IF3  N11  C05  C04  105.22  3.000
 IF3  N09  C07  N08  115.29  3.000
 IF3  N09  C07  N06  117.41  3.000
 IF3  N08  C07  N06  127.30  3.000
 IF3  H7   C12  N13  125.59  3.000
 IF3  H7   C12  N11  120.96  3.000
 IF3  N13  C12  N11  113.45  3.000
 IF3  H11  N02  C03  117.62  3.000
 IF3  H11  N02  C01  118.63  3.000
 IF3  C03  N02  C01  123.74  3.000
 IF3  C07  N06  C05  111.86  3.000
 IF3  C07  N08  C03  119.33  3.000
 IF3  H12  N09  C07  116.90  3.000
 IF3  H12  N09  C10  119.38  3.000
 IF3  C07  N09  C10  123.71  3.000
 IF3  C14  N11  C12  127.42  3.000
 IF3  C14  N11  C05  126.28  3.000
 IF3  C12  N11  C05  106.29  3.000
 IF3  C12  N13  C04  104.11  3.000
 IF3  H10  C14  H9   108.71  3.000
 IF3  H10  C14  H8   108.87  3.000
 IF3  H9   C14  H8   108.75  3.000
 IF3  H10  C14  N11  110.66  3.000
 IF3  H9   C14  N11  109.11  3.000
 IF3  H8   C14  N11  110.70  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
 IF3  CONST_01  C12  N13  C04  C03   180.00   0.0  0
 IF3  CONST_02  N11  C05  C04  C03   180.00   0.0  0
 IF3  CONST_03  N06  C05  C04  C03     0.00   0.0  0
 IF3  CONST_04  N06  C07  N08  C03     0.00   0.0  0
 IF3  CONST_05  N11  C12  N13  C04     0.00   0.0  0
 IF3  CONST_06  C07  N08  C03  C04     0.00   0.0  0
 IF3  CONST_07  C12  N11  C05  C04     0.00   0.0  0
 IF3  CONST_08  C07  N06  C05  C04     0.00   0.0  0
 IF3  CONST_09  C12  N13  C04  C05     0.00   0.0  0
 IF3  CONST_10  N08  C03  C04  C05     0.00   0.0  0
 IF3  CONST_11  N13  C12  N11  C05     0.00   0.0  0
 IF3  CONST_12  N08  C07  N06  C05     0.00   0.0  0
 IF3  CONST_13  N11  C05  N06  C07   180.00   0.0  0
 IF3  CONST_14  N06  C05  N11  C12   180.00   0.0  0
 IF3  CONST_15  N13  C04  C05  N06   180.00   0.0  0
 IF3  CONST_16  N13  C04  C03  N08   180.00   0.0  0
 IF3  CONST_17  N13  C04  C05  N11     0.00   0.0  0
 IF3  CONST_18  N09  C07  N08  C03   180.00   0.0  0
 IF3  CONST_19  C14  N11  C05  C04   180.00   0.0  0
 IF3  CONST_20  N02  C03  C04  C05   180.00   0.0  0
 IF3  CONST_21  N09  C07  N06  C05   180.00   0.0  0
 IF3  CONST_22  N02  C03  N08  C07   180.00   0.0  0
 IF3  CONST_23  N13  C12  N11  C14   180.00   0.0  0
 IF3  CONST_24  N06  C05  N11  C14     0.00   0.0  0
 IF3  CONST_25  N13  C04  C03  N02     0.00   0.0  0
 IF3  CONST_26  H7   C12  N13  C04   180.00   0.0  0
 IF3  CONST_27  H7   C12  N11  C05   180.00   0.0  0
 IF3  CONST_28  N08  C07  N09  C10   180.00   0.0  0
 IF3  CONST_29  N06  C07  N09  C10     0.00   0.0  0
 IF3  CONST_30  C04  C03  N02  C01   180.00   0.0  0
 IF3  CONST_31  N08  C03  N02  C01     0.00   0.0  0
 IF3  CONST_32  H11  N02  C03  C04     0.00   0.0  0
 IF3  CONST_33  H12  N09  C07  N06   180.00   0.0  0
 IF3  CONST_34  H11  N02  C03  N08   180.00   0.0  0
 IF3  CONST_35  H12  N09  C07  N08     0.00   0.0  0
 IF3  Var_01    H8   C14  N11  C05    60.54  30.0  2
 IF3  Var_02    H9   C14  N11  C05  -179.81  30.0  2
 IF3  Var_03    H10  C14  N11  C05   -60.25  30.0  2
 IF3  Var_04    H8   C14  N11  C12  -119.29  30.0  2
 IF3  Var_05    H9   C14  N11  C12     0.36  30.0  2
 IF3  Var_06    H10  C14  N11  C12   119.92  30.0  2
 IF3  Var_07    H4   C01  N02  C03  -179.63  30.0  3
 IF3  Var_08    H5   C01  N02  C03   -60.39  30.0  3
 IF3  Var_09    H6   C01  N02  C03    61.00  30.0  3
 IF3  Var_10    H1   C10  N09  C07  -177.87  30.0  3
 IF3  Var_11    H2   C10  N09  C07   -58.64  30.0  3
 IF3  Var_12    H3   C10  N09  C07    62.82  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
 IF3  plan-1  C03  0.020
 IF3  plan-1  C04  0.020
 IF3  plan-1  C05  0.020
 IF3  plan-1  C07  0.020
 IF3  plan-1  C12  0.020
 IF3  plan-1  N02  0.020
 IF3  plan-1  N06  0.020
 IF3  plan-1  N08  0.020
 IF3  plan-1  N09  0.020
 IF3  plan-1  N11  0.020
 IF3  plan-1  N13  0.020
 IF3  plan-1  H7   0.020
 IF3  plan-1  C14  0.020
 IF3  plan-2  C01  0.020
 IF3  plan-2  C03  0.020
 IF3  plan-2  N02  0.020
 IF3  plan-2  H11  0.020
 IF3  plan-3  C10  0.020
 IF3  plan-3  C07  0.020
 IF3  plan-3  N09  0.020
 IF3  plan-3  H12  0.020

