# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 28 23:33:07 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: ~{N},3-dimethyl-1~{H}-pyrazolo[4,3-d]pyrimidin-7-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1ncnc2c(C)n[nH]c12
#
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
 5ZK  5ZK  "~{N},3-dimethyl-1~{H}-pyrazolo[4,3-d]pyrimidin-7-amine"  ligand  21  12  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5ZK
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
 5ZK  N12  N  N     0  -0.484   9.9208  -28.2836  4.0238
 5ZK  C01  C  CH3   0  -0.513   8.4098  -29.9721  5.6249
 5ZK  C03  C  CR6   0   0.537   8.7970  -27.8151  4.5485
 5ZK  C04  C  CR56  0   0.259   8.4549  -26.4709  4.2473
 5ZK  C07  C  CR5   0   0.169   8.7085  -24.4614  3.3179
 5ZK  C08  C  CH3   0  -0.734   9.2020  -23.2848  2.5548
 5ZK  C09  C  CR56  0   0.055   9.3103  -25.7439  3.4282
 5ZK  C11  C  CR16  0   0.017  10.6712  -27.4878  3.2451
 5ZK  N02  N  NH1   0  -0.646   8.0502  -28.6075  5.3228
 5ZK  N05  N  NR15  0  -0.534   7.4394  -25.6400  4.5704
 5ZK  N06  N  N     0  -0.235   7.5931  -24.4398  4.0156
 5ZK  N10  N  N     0  -0.442  10.4496  -26.2445  2.9035
 5ZK  H1   H  HCH3  0   0.253   7.6462  -30.3864  6.2766
 5ZK  H2   H  HCH3  0   0.239   8.4653  -30.5853  4.7246
 5ZK  H3   H  HCH3  0   0.240   9.3710  -30.0313  6.1362
 5ZK  H4   H  HCH3  0   0.251   8.5450  -22.4283  2.6940
 5ZK  H5   H  HCH3  0   0.247  10.2050  -23.0013  2.8757
 5ZK  H6   H  HCH3  0   0.248   9.2557  -23.5019  1.4871
 5ZK  H7   H  HCR6  0   0.241  11.5736  -27.9486  2.8559
 5ZK  H8   H  HNH1  0   0.411   7.1909  -28.2517  5.7047
 5ZK  H9   H  HNR5  0   0.422   6.6380  -25.8172  5.1542

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
 5ZK  C08  C07  single    1.487  0.020  1.487
 5ZK  N10  C11  aromatic  1.308  0.020  1.308
 5ZK  N10  C09  aromatic  1.351  0.020  1.351
 5ZK  C11  N12  aromatic  1.343  0.020  1.343
 5ZK  C07  C09  aromatic  1.421  0.020  1.421
 5ZK  C07  N06  aromatic  1.316  0.020  1.316
 5ZK  C09  C04  aromatic  1.390  0.020  1.390
 5ZK  N06  N05  aromatic  1.331  0.020  1.331
 5ZK  N12  C03  aromatic  1.326  0.020  1.326
 5ZK  C04  C03  aromatic  1.419  0.020  1.419
 5ZK  C04  N05  aromatic  1.351  0.020  1.351
 5ZK  C03  N02  single    1.336  0.020  1.336
 5ZK  N02  C01  single    1.443  0.020  1.443
 5ZK  C01  H1   single    0.970  0.020  1.090
 5ZK  C01  H2   single    0.970  0.020  1.090
 5ZK  C01  H3   single    0.970  0.020  1.090
 5ZK  C08  H4   single    0.970  0.020  1.090
 5ZK  C08  H5   single    0.970  0.020  1.090
 5ZK  C08  H6   single    0.970  0.020  1.090
 5ZK  C11  H7   single    0.930  0.020  1.080
 5ZK  N02  H8   single    0.860  0.020  1.020
 5ZK  N05  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
 5ZK  C11  N12  C03  119.59  3.000
 5ZK  H3   C01  H2   108.16  3.000
 5ZK  H3   C01  H1   108.53  3.000
 5ZK  H2   C01  H1   108.46  3.000
 5ZK  H3   C01  N02  111.66  3.000
 5ZK  H2   C01  N02  111.82  3.000
 5ZK  H1   C01  N02  108.13  3.000
 5ZK  N02  C03  C04  123.35  3.000
 5ZK  N02  C03  N12  119.58  3.000
 5ZK  C04  C03  N12  117.07  3.000
 5ZK  N05  C04  C09  106.37  3.000
 5ZK  N05  C04  C03  135.46  3.000
 5ZK  C09  C04  C03  118.17  3.000
 5ZK  N06  C07  C09  109.43  3.000
 5ZK  N06  C07  C08  122.72  3.000
 5ZK  C09  C07  C08  127.84  3.000
 5ZK  H6   C08  H5   107.12  3.000
 5ZK  H6   C08  H4   108.15  3.000
 5ZK  H5   C08  H4   108.24  3.000
 5ZK  H6   C08  C07  111.17  3.000
 5ZK  H5   C08  C07  111.10  3.000
 5ZK  H4   C08  C07  110.90  3.000
 5ZK  N10  C09  C07  131.43  3.000
 5ZK  C07  C09  C04  104.90  3.000
 5ZK  N10  C09  C04  123.67  3.000
 5ZK  H7   C11  N10  116.79  3.000
 5ZK  H7   C11  N12  114.90  3.000
 5ZK  N10  C11  N12  128.32  3.000
 5ZK  H8   N02  C03  119.21  3.000
 5ZK  H8   N02  C01  117.91  3.000
 5ZK  C03  N02  C01  122.87  3.000
 5ZK  H9   N05  N06  119.48  3.000
 5ZK  H9   N05  C04  128.93  3.000
 5ZK  N06  N05  C04  111.59  3.000
 5ZK  N05  N06  C07  107.70  3.000
 5ZK  C11  N10  C09  113.19  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
 5ZK  CONST_01  C09  N10  C11  N12     0.00   0.0  0
 5ZK  CONST_02  C09  C04  C03  N12     0.00   0.0  0
 5ZK  CONST_03  N05  C04  C03  N12   180.00   0.0  0
 5ZK  CONST_04  N10  C11  N12  C03     0.00   0.0  0
 5ZK  CONST_05  N10  C09  C04  C03     0.00   0.0  0
 5ZK  CONST_06  C07  C09  C04  C03   180.00   0.0  0
 5ZK  CONST_07  N06  N05  C04  C03   180.00   0.0  0
 5ZK  CONST_08  C11  N10  C09  C04     0.00   0.0  0
 5ZK  CONST_09  N06  C07  C09  C04     0.00   0.0  0
 5ZK  CONST_10  C11  N12  C03  C04     0.00   0.0  0
 5ZK  CONST_11  C07  N06  N05  C04     0.00   0.0  0
 5ZK  CONST_12  C11  N10  C09  C07   180.00   0.0  0
 5ZK  CONST_13  N05  C04  C09  C07     0.00   0.0  0
 5ZK  CONST_14  N05  N06  C07  C09     0.00   0.0  0
 5ZK  CONST_15  N06  N05  C04  C09     0.00   0.0  0
 5ZK  CONST_16  N10  C09  C04  N05   180.00   0.0  0
 5ZK  CONST_17  N10  C09  C07  N06   180.00   0.0  0
 5ZK  CONST_18  C08  C07  C09  C04   180.00   0.0  0
 5ZK  CONST_19  N10  C09  C07  C08     0.00   0.0  0
 5ZK  CONST_20  N05  N06  C07  C08   180.00   0.0  0
 5ZK  CONST_21  N02  C03  C04  C09   180.00   0.0  0
 5ZK  CONST_22  N02  C03  N12  C11   180.00   0.0  0
 5ZK  CONST_23  N05  C04  C03  N02     0.00   0.0  0
 5ZK  CONST_24  H7   C11  N12  C03   180.00   0.0  0
 5ZK  CONST_25  H9   N05  C04  C03     0.00   0.0  0
 5ZK  CONST_26  H9   N05  N06  C07   180.00   0.0  0
 5ZK  CONST_27  H7   C11  N10  C09   180.00   0.0  0
 5ZK  CONST_28  H9   N05  C04  C09   180.00   0.0  0
 5ZK  CONST_29  C01  N02  C03  N12     0.00   0.0  0
 5ZK  CONST_30  C04  C03  N02  C01   180.00   0.0  0
 5ZK  CONST_31  H8   N02  C03  N12   180.00   0.0  0
 5ZK  CONST_32  H8   N02  C03  C04     0.00   0.0  0
 5ZK  Var_01    H4   C08  C07  C09  -177.67  30.0  2
 5ZK  Var_02    H5   C08  C07  C09   -57.25  30.0  2
 5ZK  Var_03    H6   C08  C07  C09    61.96  30.0  2
 5ZK  Var_04    H4   C08  C07  N06     2.33  30.0  2
 5ZK  Var_05    H5   C08  C07  N06   122.76  30.0  2
 5ZK  Var_06    H6   C08  C07  N06  -118.04  30.0  2
 5ZK  Var_07    H1   C01  N02  C03   179.42  30.0  3
 5ZK  Var_08    H2   C01  N02  C03   -61.25  30.0  3
 5ZK  Var_09    H3   C01  N02  C03    60.10  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
 5ZK  plan-1  N12  0.020
 5ZK  plan-1  C03  0.020
 5ZK  plan-1  C04  0.020
 5ZK  plan-1  C07  0.020
 5ZK  plan-1  C08  0.020
 5ZK  plan-1  C09  0.020
 5ZK  plan-1  C11  0.020
 5ZK  plan-1  N02  0.020
 5ZK  plan-1  N05  0.020
 5ZK  plan-1  N06  0.020
 5ZK  plan-1  N10  0.020
 5ZK  plan-1  H7   0.020
 5ZK  plan-1  H9   0.020
 5ZK  plan-2  C01  0.020
 5ZK  plan-2  C03  0.020
 5ZK  plan-2  N02  0.020
 5ZK  plan-2  H8   0.020

