# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 22:20:27 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: ~{N}-(3-aminocarbonyl-1-methyl-pyrazol-4-yl)-5-piperazin-1-yl-pyrazolo[1,5-a]pyrimidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(NC(=O)c2cnn3ccc(nc23)N4CCNCC4)c(n1)C(N)=O
#
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
 6YE  6YE  ~{N}-(3-aminocarbonyl-1-methyl-pyrazol-4-yl)-5-piperazin-1-yl-pyrazolo[1,5-a]pyrimidine-3-carboxamide  ligand  46  27  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6YE
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
 6YE  N01  N  NH1   0  -0.763   2.2457   0.2428   0.0439
 6YE  C02  C  C     0   0.507   0.9264   0.0099  -0.1985
 6YE  O03  O  O     0  -0.473   0.5057  -1.1084  -0.4606
 6YE  C04  C  CR5   0  -0.409   0.0727   1.1870  -0.1263
 6YE  C05  C  CR15  0  -0.042   0.4216   2.5506  -0.0141
 6YE  N06  N  N     0  -0.299  -0.6152   3.3539   0.0006
 6YE  N07  N  N     0  -0.393  -1.6729   2.5245  -0.0998
 6YE  C08  C  CR56  0   0.646  -1.3281   1.1982  -0.1833
 6YE  N09  N  N     0  -0.508  -2.2397   0.2398  -0.2793
 6YE  C10  C  CR6   0   0.565  -3.5231   0.5715  -0.2986
 6YE  C11  C  CR16  0  -0.454  -3.9243   1.9532  -0.2268
 6YE  C12  C  CR16  0   0.078  -2.9699   2.9024  -0.1259
 6YE  N13  N  NT    0  -0.504  -4.4266  -0.4186  -0.3956
 6YE  C14  C  CH2   0  -0.313  -5.8682  -0.2420  -0.3737
 6YE  C15  C  CH2   0  -0.288  -6.4713  -1.0223   0.7840
 6YE  N16  N  NH1   0  -0.601  -6.1042  -2.4198   0.6689
 6YE  C17  C  CH2   0  -0.295  -4.6626  -2.5820   0.7045
 6YE  C18  C  CH2   0  -0.319  -4.0355  -1.8194  -0.4515
 6YE  C19  C  CR5   0   0.121   3.2524  -0.7000  -0.0366
 6YE  C20  C  CR5   0   0.059   4.6231  -0.4327   0.1672
 6YE  N21  N  N     0  -0.281   5.3462  -1.5343   0.0056
 6YE  N22  N  NR5   0  -0.253   4.4915  -2.4800  -0.2948
 6YE  C23  C  CR15  0   0.010   3.2095  -2.0478  -0.3320
 6YE  C24  C  C     0   0.505   5.2269   0.8662   0.5058
 6YE  N25  N  NH2   0  -0.806   6.5571   0.8799   0.6305
 6YE  O26  O  O     0  -0.500   4.5185   1.8605   0.6646
 6YE  C27  C  CH3   0  -0.509   4.9389  -3.8422  -0.4759
 6YE  H1   H  HNH1  0   0.418   2.5664   1.1645   0.3039
 6YE  H2   H  HCR5  0   0.267   1.4109   2.9826   0.0459
 6YE  H3   H  HCR6  0   0.301  -4.9531   2.2705  -0.2512
 6YE  H4   H  HCR6  0   0.326  -3.1752   3.9611  -0.0644
 6YE  H5   H  HCH2  0   0.269  -6.1422   0.8040  -0.2857
 6YE  H6   H  HCH2  0   0.248  -6.2814  -0.6082  -1.3190
 6YE  H7   H  HCH2  0   0.202  -6.1337  -0.5637   1.7272
 6YE  H8   H  HCH2  0   0.245  -7.5576  -0.9263   0.7438
 6YE  H9   H  HNH1  0   0.360  -6.5265  -2.9458   1.4222
 6YE  H11  H  HCH2  0   0.202  -4.2133  -2.2262   1.6455
 6YE  H12  H  HCH2  0   0.243  -4.4140  -3.6399   0.6041
 6YE  H13  H  HCH2  0   0.241  -4.3861  -2.2396  -1.4002
 6YE  H14  H  HCH2  0   0.282  -2.9534  -1.8983  -0.4234
 6YE  H15  H  HCR5  0   0.302   2.3960  -2.7119  -0.5591
 6YE  H16  H  HNH2  0   0.412   7.1076   0.0535   0.4697
 6YE  H17  H  HNH2  0   0.407   7.0389   1.7350   0.8543
 6YE  H18  H  HCH3  0   0.265   5.0105  -4.3561   0.4815
 6YE  H19  H  HCH3  0   0.264   4.2332  -4.3690  -1.1116
 6YE  H20  H  HCH3  0   0.269   5.9136  -3.8363  -0.9550

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
 6YE  C12  C11  aromatic  1.350  0.020  1.350
 6YE  C12  N07  aromatic  1.351  0.020  1.351
 6YE  C11  C10  aromatic  1.440  0.020  1.440
 6YE  N06  N07  aromatic  1.348  0.020  1.348
 6YE  N06  C05  aromatic  1.312  0.020  1.312
 6YE  N07  C08  aromatic  1.373  0.020  1.373
 6YE  C14  C15  single    1.521  0.020  1.521
 6YE  C14  N13  single    1.453  0.020  1.453
 6YE  C05  C04  aromatic  1.412  0.020  1.412
 6YE  C10  N13  single    1.344  0.020  1.344
 6YE  C10  N09  aromatic  1.326  0.020  1.326
 6YE  C15  N16  single    1.449  0.020  1.449
 6YE  C08  N09  aromatic  1.326  0.020  1.326
 6YE  C08  C04  aromatic  1.402  0.020  1.402
 6YE  N13  C18  single    1.455  0.020  1.455
 6YE  C04  C02  single    1.456  0.020  1.456
 6YE  N16  C17  single    1.451  0.020  1.451
 6YE  C02  O03  double    1.223  0.020  1.223
 6YE  C02  N01  single    1.361  0.020  1.361
 6YE  C18  C17  single    1.520  0.020  1.520
 6YE  N01  C19  single    1.382  0.020  1.382
 6YE  O26  C24  double    1.231  0.020  1.231
 6YE  C19  C23  aromatic  1.380  0.020  1.380
 6YE  C19  C20  aromatic  1.411  0.020  1.411
 6YE  C24  C20  single    1.472  0.020  1.472
 6YE  C24  N25  single    1.336  0.020  1.336
 6YE  C23  N22  aromatic  1.353  0.020  1.353
 6YE  C20  N21  aromatic  1.328  0.020  1.328
 6YE  N22  N21  aromatic  1.310  0.020  1.310
 6YE  N22  C27  single    1.445  0.020  1.445
 6YE  N01  H1   single    0.860  0.020  1.020
 6YE  C05  H2   single    0.930  0.020  1.080
 6YE  C11  H3   single    0.930  0.020  1.080
 6YE  C12  H4   single    0.930  0.020  1.080
 6YE  C14  H5   single    0.970  0.020  1.090
 6YE  C14  H6   single    0.970  0.020  1.090
 6YE  C15  H7   single    0.970  0.020  1.090
 6YE  C15  H8   single    0.970  0.020  1.090
 6YE  N16  H9   single    0.890  0.020  1.040
 6YE  C17  H11  single    0.970  0.020  1.090
 6YE  C17  H12  single    0.970  0.020  1.090
 6YE  C18  H13  single    0.970  0.020  1.090
 6YE  C18  H14  single    0.970  0.020  1.090
 6YE  C23  H15  single    0.930  0.020  1.080
 6YE  N25  H16  single    0.860  0.020  1.020
 6YE  N25  H17  single    0.860  0.020  1.020
 6YE  C27  H18  single    0.970  0.020  1.090
 6YE  C27  H19  single    0.970  0.020  1.090
 6YE  C27  H20  single    0.970  0.020  1.090

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
 6YE  H1   N01  C19  113.98  3.000
 6YE  H1   N01  C02  120.64  3.000
 6YE  C19  N01  C02  125.38  3.000
 6YE  C04  C02  O03  123.24  3.000
 6YE  O03  C02  N01  121.85  3.000
 6YE  C04  C02  N01  114.90  3.000
 6YE  C08  C04  C05  104.03  3.000
 6YE  C08  C04  C02  126.18  3.000
 6YE  C05  C04  C02  129.78  3.000
 6YE  H2   C05  N06  118.55  3.000
 6YE  H2   C05  C04  128.05  3.000
 6YE  N06  C05  C04  113.39  3.000
 6YE  N07  N06  C05  104.04  3.000
 6YE  C12  N07  C08  120.67  3.000
 6YE  C08  N07  N06  113.70  3.000
 6YE  C12  N07  N06  125.63  3.000
 6YE  N09  C08  N07  122.00  3.000
 6YE  N09  C08  C04  133.15  3.000
 6YE  N07  C08  C04  104.85  3.000
 6YE  C10  N09  C08  119.06  3.000
 6YE  N13  C10  C11  121.54  3.000
 6YE  N13  C10  N09  117.88  3.000
 6YE  C11  C10  N09  120.59  3.000
 6YE  H3   C11  C12  118.03  3.000
 6YE  H3   C11  C10  123.19  3.000
 6YE  C12  C11  C10  118.77  3.000
 6YE  H4   C12  C11  124.00  3.000
 6YE  H4   C12  N07  117.10  3.000
 6YE  C11  C12  N07  118.91  3.000
 6YE  C18  N13  C14  112.60  3.000
 6YE  C18  N13  C10  122.09  3.000
 6YE  C14  N13  C10  125.21  3.000
 6YE  H6   C14  H5   107.29  3.000
 6YE  H6   C14  C15  109.63  3.000
 6YE  H5   C14  C15  109.44  3.000
 6YE  H6   C14  N13  108.72  3.000
 6YE  H5   C14  N13  111.66  3.000
 6YE  C15  C14  N13  110.04  3.000
 6YE  H8   C15  H7   107.45  3.000
 6YE  H8   C15  N16  109.51  3.000
 6YE  H7   C15  N16  113.05  3.000
 6YE  H8   C15  C14  108.76  3.000
 6YE  H7   C15  C14  108.46  3.000
 6YE  N16  C15  C14  109.50  3.000
 6YE  H9   N16  C17  109.79  3.000
 6YE  H9   N16  C15  109.67  3.000
 6YE  C17  N16  C15  110.94  3.000
 6YE  H12  C17  H11  107.38  3.000
 6YE  H12  C17  C18  108.80  3.000
 6YE  H11  C17  C18  108.62  3.000
 6YE  H12  C17  N16  109.42  3.000
 6YE  H11  C17  N16  112.95  3.000
 6YE  C18  C17  N16  109.57  3.000
 6YE  H14  C18  H13  108.28  3.000
 6YE  H14  C18  C17  110.80  3.000
 6YE  H13  C18  C17  109.52  3.000
 6YE  H14  C18  N13  109.69  3.000
 6YE  H13  C18  N13  108.46  3.000
 6YE  C17  C18  N13  110.04  3.000
 6YE  C23  C19  C20  104.24  3.000
 6YE  C20  C19  N01  124.75  3.000
 6YE  C23  C19  N01  131.00  3.000
 6YE  C24  C20  N21  122.47  3.000
 6YE  N21  C20  C19  110.75  3.000
 6YE  C24  C20  C19  126.78  3.000
 6YE  N22  N21  C20  105.76  3.000
 6YE  C27  N22  C23  126.21  3.000
 6YE  C27  N22  N21  120.49  3.000
 6YE  C23  N22  N21  113.20  3.000
 6YE  H15  C23  N22  121.71  3.000
 6YE  H15  C23  C19  132.24  3.000
 6YE  N22  C23  C19  106.05  3.000
 6YE  O26  C24  N25  123.54  3.000
 6YE  N25  C24  C20  116.04  3.000
 6YE  O26  C24  C20  120.42  3.000
 6YE  H17  N25  H16  118.13  3.000
 6YE  H17  N25  C24  120.40  3.000
 6YE  H16  N25  C24  121.43  3.000
 6YE  H20  C27  H19  109.12  3.000
 6YE  H20  C27  H18  109.35  3.000
 6YE  H19  C27  H18  109.18  3.000
 6YE  H20  C27  N22  109.14  3.000
 6YE  H19  C27  N22  109.23  3.000
 6YE  H18  C27  N22  110.79  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
 6YE  CONST_01  N07  N06  C05  C04     0.00   0.0  0
 6YE  CONST_02  C12  N07  C08  C04   180.00   0.0  0
 6YE  CONST_03  N06  N07  C08  C04     0.00   0.0  0
 6YE  CONST_04  C10  N09  C08  C04   180.00   0.0  0
 6YE  CONST_05  C12  N07  N06  C05   180.00   0.0  0
 6YE  CONST_06  C08  N07  N06  C05     0.00   0.0  0
 6YE  CONST_07  N07  C08  C04  C05     0.00   0.0  0
 6YE  CONST_08  N09  C08  C04  C05   180.00   0.0  0
 6YE  CONST_09  C11  C12  N07  N06   180.00   0.0  0
 6YE  CONST_10  N09  C08  N07  N06   180.00   0.0  0
 6YE  CONST_11  C08  C04  C05  N06     0.00   0.0  0
 6YE  CONST_12  C10  C11  C12  N07     0.00   0.0  0
 6YE  CONST_13  C10  N09  C08  N07     0.00   0.0  0
 6YE  CONST_14  C11  C12  N07  C08     0.00   0.0  0
 6YE  CONST_15  C11  C10  N09  C08     0.00   0.0  0
 6YE  CONST_16  C12  C11  C10  N09     0.00   0.0  0
 6YE  CONST_17  C12  N07  C08  N09     0.00   0.0  0
 6YE  CONST_18  N21  N22  C23  C19     0.00   0.0  0
 6YE  CONST_19  N22  N21  C20  C19     0.00   0.0  0
 6YE  CONST_20  N22  C23  C19  C20     0.00   0.0  0
 6YE  CONST_21  C23  N22  N21  C20     0.00   0.0  0
 6YE  CONST_22  C23  C19  C20  N21     0.00   0.0  0
 6YE  CONST_23  N13  C10  N09  C08   180.00   0.0  0
 6YE  CONST_24  N13  C10  C11  C12   180.00   0.0  0
 6YE  CONST_25  N22  C23  C19  N01   180.00   0.0  0
 6YE  CONST_26  N21  C20  C19  N01   180.00   0.0  0
 6YE  CONST_27  N06  C05  C04  C02   180.00   0.0  0
 6YE  CONST_28  N07  C08  C04  C02   180.00   0.0  0
 6YE  CONST_29  N09  C08  C04  C02     0.00   0.0  0
 6YE  CONST_30  C27  N22  C23  C19   180.00   0.0  0
 6YE  CONST_31  C27  N22  N21  C20   180.00   0.0  0
 6YE  CONST_32  C24  C20  N21  N22   180.00   0.0  0
 6YE  CONST_33  C24  C20  C19  C23   180.00   0.0  0
 6YE  CONST_34  H4   C12  N07  N06     0.00   0.0  0
 6YE  CONST_35  H3   C11  C12  N07   180.00   0.0  0
 6YE  CONST_36  H2   C05  N06  N07   180.00   0.0  0
 6YE  CONST_37  H15  C23  C19  C20   180.00   0.0  0
 6YE  CONST_38  C19  N01  C02  C04   180.00   0.0  0
 6YE  CONST_39  N25  C24  C20  C19   180.00   0.0  0
 6YE  CONST_40  C23  C19  N01  C02     0.00   0.0  0
 6YE  CONST_41  C20  C19  N01  C02   180.00   0.0  0
 6YE  CONST_42  H1   N01  C19  C20     0.00   0.0  0
 6YE  CONST_43  C19  N01  C02  O03     0.00   0.0  0
 6YE  CONST_44  H16  N25  C24  C20     0.00   0.0  0
 6YE  CONST_45  H17  N25  C24  C20   180.00   0.0  0
 6YE  Var_01    C14  N13  C10  N09   177.25  30.0  2
 6YE  Var_02    C15  C14  N13  C10  -120.72  30.0  1
 6YE  Var_03    C17  C18  N13  C10   121.00  30.0  1
 6YE  Var_04    N16  C15  C14  N13   -56.86  30.0  1
 6YE  Var_05    N16  C17  C18  N13    56.51  30.0  1
 6YE  Var_06    C17  N16  C15  C14    60.22  30.0  1
 6YE  Var_07    C18  C17  N16  C15   -60.10  30.0  1
 6YE  Var_08    C05  C04  C02  N01     9.12  30.0  2
 6YE  Var_09    H18  C27  N22  N21    84.02  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
 6YE  plan-1  C02  0.020
 6YE  plan-1  C04  0.020
 6YE  plan-1  C05  0.020
 6YE  plan-1  N06  0.020
 6YE  plan-1  N07  0.020
 6YE  plan-1  C08  0.020
 6YE  plan-1  N09  0.020
 6YE  plan-1  C10  0.020
 6YE  plan-1  C11  0.020
 6YE  plan-1  C12  0.020
 6YE  plan-1  N13  0.020
 6YE  plan-1  H2   0.020
 6YE  plan-1  H3   0.020
 6YE  plan-1  H4   0.020
 6YE  plan-2  N01  0.020
 6YE  plan-2  C19  0.020
 6YE  plan-2  C20  0.020
 6YE  plan-2  N21  0.020
 6YE  plan-2  N22  0.020
 6YE  plan-2  C23  0.020
 6YE  plan-2  C24  0.020
 6YE  plan-2  N25  0.020
 6YE  plan-2  O26  0.020
 6YE  plan-2  C27  0.020
 6YE  plan-2  H15  0.020
 6YE  plan-2  H16  0.020
 6YE  plan-2  H17  0.020
 6YE  plan-3  N01  0.020
 6YE  plan-3  C02  0.020
 6YE  plan-3  O03  0.020
 6YE  plan-3  C04  0.020
 6YE  plan-3  C19  0.020
 6YE  plan-3  H1   0.020

