# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:27:55 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 5,7-dimethylpyrazolo[1,5-a]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)n2nc(N)cc2n1
#
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
 XAZ  XAZ  5,7-dimethylpyrazolo[1,5-a]pyrimidin-2-amine  ligand  22  12  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XAZ
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
 XAZ  C1    C  CH3   0  -0.736   3.4771  -1.3052  -0.0273
 XAZ  C2    C  CR6   0   0.251   2.1166  -0.6843  -0.0017
 XAZ  C3    C  CR16  0  -0.448   1.9968   0.7258   0.0148
 XAZ  C4    C  CR6   0   0.426   0.7587   1.3082   0.0285
 XAZ  C5    C  CH3   0  -0.719   0.4991   2.7692   0.0463
 XAZ  N6    N  N     0  -0.401  -0.2978   0.4682   0.0252
 XAZ  N7    N  N     0  -0.363  -1.5861   0.8423   0.0324
 XAZ  C8    C  CR5   0   0.484  -2.2629  -0.3028   0.0271
 XAZ  N9    N  NH2   0  -0.850  -3.6292  -0.3005   0.0886
 XAZ  C10   C  CR15  0  -0.617  -1.4213  -1.4306   0.0131
 XAZ  C11   C  CR56  0   0.572  -0.1416  -0.9074   0.0104
 XAZ  N12   N  N     0  -0.468   1.0715  -1.4779  -0.0026
 XAZ  H11C  H  HCH3  0   0.255   4.0873  -0.9378   0.7989
 XAZ  H12C  H  HCH3  0   0.253   3.4125  -2.3888   0.0381
 XAZ  H13C  H  HCH3  0   0.257   3.9999  -1.0431  -0.9488
 XAZ  H3    H  HCR6  0   0.274   2.8773   1.3522   0.0177
 XAZ  H51C  H  HCH3  0   0.263   1.4375   3.3172   0.0516
 XAZ  H52C  H  HCH3  0   0.268  -0.0792   3.0724  -0.8275
 XAZ  H53C  H  HCH3  0   0.268  -0.0771   3.0515   0.9283
 XAZ  H91N  H  HNH2  0   0.379  -4.0706   0.5514  -0.2204
 XAZ  H92N  H  HNH2  0   0.386  -4.0784  -1.1185  -0.2892
 XAZ  H10   H  HCR5  0   0.267  -1.7030  -2.4702   0.0055

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
 XAZ  C1   C2    single    1.496  0.020  1.496
 XAZ  C2   C3    aromatic  1.415  0.020  1.415
 XAZ  C2   N12   aromatic  1.312  0.020  1.312
 XAZ  C3   C4    aromatic  1.368  0.020  1.368
 XAZ  C4   C5    single    1.484  0.020  1.484
 XAZ  C4   N6    aromatic  1.350  0.020  1.350
 XAZ  N6   N7    aromatic  1.342  0.020  1.342
 XAZ  N6   C11   aromatic  1.385  0.020  1.385
 XAZ  N7   C8    aromatic  1.330  0.020  1.330
 XAZ  C8   N9    single    1.368  0.020  1.368
 XAZ  C8   C10   aromatic  1.407  0.020  1.407
 XAZ  C10  C11   aromatic  1.383  0.020  1.383
 XAZ  C11  N12   aromatic  1.341  0.020  1.341
 XAZ  C1   H11C  single    0.970  0.020  1.090
 XAZ  C1   H12C  single    0.970  0.020  1.090
 XAZ  C1   H13C  single    0.970  0.020  1.090
 XAZ  C3   H3    single    0.930  0.020  1.080
 XAZ  C5   H51C  single    0.970  0.020  1.090
 XAZ  C5   H52C  single    0.970  0.020  1.090
 XAZ  C5   H53C  single    0.970  0.020  1.090
 XAZ  N9   H91N  single    0.890  0.020  1.040
 XAZ  N9   H92N  single    0.890  0.020  1.040
 XAZ  C10  H10   single    0.930  0.020  1.080

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
 XAZ  H13C  C1   H12C  108.57  3.000
 XAZ  H13C  C1   H11C  106.90  3.000
 XAZ  H12C  C1   H11C  108.86  3.000
 XAZ  H13C  C1   C2    110.51  3.000
 XAZ  H12C  C1   C2    111.01  3.000
 XAZ  H11C  C1   C2    110.86  3.000
 XAZ  N12   C2   C3    122.35  3.000
 XAZ  N12   C2   C1    118.26  3.000
 XAZ  C3    C2   C1    119.40  3.000
 XAZ  H3    C3   C4    119.38  3.000
 XAZ  H3    C3   C2    120.57  3.000
 XAZ  C4    C3   C2    120.05  3.000
 XAZ  N6    C4   C5    118.41  3.000
 XAZ  N6    C4   C3    116.32  3.000
 XAZ  C5    C4   C3    125.27  3.000
 XAZ  H53C  C5   H52C  107.20  3.000
 XAZ  H53C  C5   H51C  108.76  3.000
 XAZ  H52C  C5   H51C  108.76  3.000
 XAZ  H53C  C5   C4    110.91  3.000
 XAZ  H52C  C5   C4    110.90  3.000
 XAZ  H51C  C5   C4    110.21  3.000
 XAZ  C11   N6   N7    112.67  3.000
 XAZ  C11   N6   C4    122.01  3.000
 XAZ  N7    N6   C4    125.32  3.000
 XAZ  C8    N7   N6    104.39  3.000
 XAZ  C10   C8   N9    126.82  3.000
 XAZ  C10   C8   N7    112.68  3.000
 XAZ  N9    C8   N7    120.44  3.000
 XAZ  H92N  N9   H91N  112.10  3.000
 XAZ  H92N  N9   C8    115.31  3.000
 XAZ  H91N  N9   C8    115.16  3.000
 XAZ  H10   C10  C11   127.40  3.000
 XAZ  H10   C10  C8    128.11  3.000
 XAZ  C11   C10  C8    104.49  3.000
 XAZ  N12   C11  C10   132.57  3.000
 XAZ  N12   C11  N6    121.67  3.000
 XAZ  C10   C11  N6    105.76  3.000
 XAZ  C11   N12  C2    117.60  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
 XAZ  CONST_01  N6    C4   C3   C2    0.00   0.0  0
 XAZ  CONST_02  N6    C11  N12  C2    0.00   0.0  0
 XAZ  CONST_03  C10   C11  N12  C2  180.00   0.0  0
 XAZ  CONST_04  C11   N12  C2   C3    0.00   0.0  0
 XAZ  CONST_05  N7    N6   C4   C3  180.00   0.0  0
 XAZ  CONST_06  C11   N6   C4   C3    0.00   0.0  0
 XAZ  CONST_07  N12   C2   C3   C4    0.00   0.0  0
 XAZ  CONST_08  C8    N7   N6   C4  180.00   0.0  0
 XAZ  CONST_09  C10   C11  N6   C4  180.00   0.0  0
 XAZ  CONST_10  N12   C11  N6   C4    0.00   0.0  0
 XAZ  CONST_11  C10   C8   N7   N6    0.00   0.0  0
 XAZ  CONST_12  C8    C10  C11  N6    0.00   0.0  0
 XAZ  CONST_13  C10   C11  N6   N7    0.00   0.0  0
 XAZ  CONST_14  N12   C11  N6   N7  180.00   0.0  0
 XAZ  CONST_15  C11   C10  C8   N7    0.00   0.0  0
 XAZ  CONST_16  C11   N6   N7   C8    0.00   0.0  0
 XAZ  CONST_17  N12   C11  C10  C8  180.00   0.0  0
 XAZ  CONST_18  C4    C3   C2   C1  180.00   0.0  0
 XAZ  CONST_19  C11   N12  C2   C1  180.00   0.0  0
 XAZ  CONST_20  C5    C4   C3   C2  180.00   0.0  0
 XAZ  CONST_21  N7    N6   C4   C5    0.00   0.0  0
 XAZ  CONST_22  C11   N6   C4   C5  180.00   0.0  0
 XAZ  CONST_23  N9    C8   N7   N6  180.00   0.0  0
 XAZ  CONST_24  C11   C10  C8   N9  180.00   0.0  0
 XAZ  CONST_25  H3    C3   C4   N6  180.00   0.0  0
 XAZ  CONST_26  H10   C10  C11  N6  180.00   0.0  0
 XAZ  Var_01    H11C  C1   C2   C3   54.58  30.0  2
 XAZ  Var_02    H51C  C5   C4   C3   -0.26  30.0  2

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
 XAZ  plan-1  C1    0.020
 XAZ  plan-1  C2    0.020
 XAZ  plan-1  C3    0.020
 XAZ  plan-1  C4    0.020
 XAZ  plan-1  C5    0.020
 XAZ  plan-1  N6    0.020
 XAZ  plan-1  N7    0.020
 XAZ  plan-1  C8    0.020
 XAZ  plan-1  N9    0.020
 XAZ  plan-1  C10   0.020
 XAZ  plan-1  C11   0.020
 XAZ  plan-1  N12   0.020
 XAZ  plan-1  H3    0.020
 XAZ  plan-1  H10   0.020
 XAZ  plan-2  C8    0.020
 XAZ  plan-2  N9    0.020
 XAZ  plan-2  H91N  0.020
 XAZ  plan-2  H92N  0.020

