# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 16:54:17 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 6-ethyl-2,5-dimethyl-7-oxidanylidene-4~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC1=C(C)Nc2n(nc(C)c2C#N)C1=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
 6X9  6X9  6-ethyl-2,5-dimethyl-7-oxidanylidene-4~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile  ligand  28  16  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6X9
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
 6X9  C1   C  CR6   0   0.577   1.1040  -1.1296  -0.1986
 6X9  C3   C  CR56  0   0.788  -0.7422   0.4564  -0.0604
 6X9  C5   C  CR6   0   0.357   1.4595   1.2879  -0.2056
 6X9  C6   C  CR6   0  -0.182   1.9710   0.0252  -0.2569
 6X9  N2   N  N     0  -0.456  -0.2588  -0.8027  -0.1027
 6X9  C7   C  CR5   0  -0.317  -2.1201   0.3446   0.0396
 6X9  C8   C  CR5   0   0.364  -2.3562  -1.0595   0.0515
 6X9  C11  C  CH2   0  -0.502   3.4488  -0.2375  -0.3154
 6X9  C12  C  CH3   0  -0.656   4.0482  -0.5081   1.0636
 6X9  C13  C  CH3   0  -0.758   2.2961   2.5243  -0.2457
 6X9  C14  C  CH3   0  -0.740  -3.6777  -1.7271   0.1511
 6X9  C15  C  CSP   0  -0.026  -3.0608   1.3823   0.1152
 6X9  N4   N  NR16  0  -0.735   0.1123   1.4892  -0.1138
 6X9  N16  N  NS    0  -0.250  -3.8425   2.2304   0.1710
 6X9  N9   N  N     0  -0.294  -1.2379  -1.7309  -0.0342
 6X9  O10  O  O     0  -0.436   1.4480  -2.2921  -0.2253
 6X9  H2   H  HCH2  0   0.251   3.6350  -1.0924  -0.9672
 6X9  H3   H  HCH2  0   0.250   3.9632   0.6062  -0.7767
 6X9  H4   H  HCH3  0   0.234   5.1171  -0.7092   0.9870
 6X9  H5   H  HCH3  0   0.225   3.9166   0.3479   1.7266
 6X9  H6   H  HCH3  0   0.230   3.5805  -1.3718   1.5364
 6X9  H7   H  HCH3  0   0.275   1.6904   3.4258  -0.1767
 6X9  H8   H  HCH3  0   0.279   3.0087   2.5354   0.5781
 6X9  H9   H  HCH3  0   0.283   2.8652   2.5721  -1.1737
 6X9  H10  H  HCH3  0   0.264  -4.3239  -1.4335  -0.6765
 6X9  H11  H  HCH3  0   0.267  -3.5643  -2.8085   0.1348
 6X9  H12  H  HCH3  0   0.264  -4.1831  -1.4456   1.0752
 6X9  H1   H  HNR6  0   0.444  -0.2510   2.4306  -0.0722

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
 6X9  O10  C1   double    1.213  0.020  1.213
 6X9  C12  C11  single    1.528  0.020  1.528
 6X9  N9   N2   aromatic  1.351  0.020  1.351
 6X9  N9   C8   aromatic  1.307  0.020  1.307
 6X9  C1   N2   single    1.405  0.020  1.405
 6X9  C1   C6   single    1.445  0.020  1.445
 6X9  C14  C8   single    1.484  0.020  1.484
 6X9  N2   C3   aromatic  1.349  0.020  1.349
 6X9  C8   C7   aromatic  1.424  0.020  1.424
 6X9  C11  C6   single    1.502  0.020  1.502
 6X9  C6   C5   double    1.363  0.020  1.363
 6X9  C3   C7   aromatic  1.386  0.020  1.386
 6X9  C3   N4   single    1.342  0.020  1.342
 6X9  C7   C15  single    1.403  0.020  1.403
 6X9  C5   N4   single    1.365  0.020  1.365
 6X9  C5   C13  single    1.493  0.020  1.493
 6X9  C15  N16  triple    1.155  0.020  1.155
 6X9  C11  H2   single    0.970  0.020  1.090
 6X9  C11  H3   single    0.970  0.020  1.090
 6X9  C12  H4   single    0.970  0.020  1.090
 6X9  C12  H5   single    0.970  0.020  1.090
 6X9  C12  H6   single    0.970  0.020  1.090
 6X9  C13  H7   single    0.970  0.020  1.090
 6X9  C13  H8   single    0.970  0.020  1.090
 6X9  C13  H9   single    0.970  0.020  1.090
 6X9  C14  H10  single    0.970  0.020  1.090
 6X9  C14  H11  single    0.970  0.020  1.090
 6X9  C14  H12  single    0.970  0.020  1.090
 6X9  N4   H1   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
 6X9  O10  C1   N2   119.99  3.000
 6X9  N2   C1   C6   113.51  3.000
 6X9  O10  C1   C6   126.50  3.000
 6X9  N4   C3   C7   134.28  3.000
 6X9  N4   C3   N2   119.27  3.000
 6X9  C7   C3   N2   106.45  3.000
 6X9  N4   C5   C13  115.63  3.000
 6X9  C13  C5   C6   123.75  3.000
 6X9  N4   C5   C6   120.63  3.000
 6X9  C11  C6   C5   122.18  3.000
 6X9  C5   C6   C1   120.89  3.000
 6X9  C11  C6   C1   116.88  3.000
 6X9  N9   N2   C3   112.32  3.000
 6X9  C3   N2   C1   124.53  3.000
 6X9  N9   N2   C1   123.15  3.000
 6X9  C15  C7   C8   128.16  3.000
 6X9  C15  C7   C3   127.66  3.000
 6X9  C8   C7   C3   104.18  3.000
 6X9  N9   C8   C14  122.36  3.000
 6X9  C14  C8   C7   126.29  3.000
 6X9  N9   C8   C7   111.35  3.000
 6X9  H3   C11  H2   105.84  3.000
 6X9  H3   C11  C12  109.50  3.000
 6X9  H2   C11  C12  109.48  3.000
 6X9  H3   C11  C6   110.20  3.000
 6X9  H2   C11  C6   109.16  3.000
 6X9  C12  C11  C6   112.45  3.000
 6X9  H6   C12  H5   107.84  3.000
 6X9  H6   C12  H4   107.76  3.000
 6X9  H5   C12  H4   107.80  3.000
 6X9  H6   C12  C11  111.31  3.000
 6X9  H5   C12  C11  111.24  3.000
 6X9  H4   C12  C11  110.72  3.000
 6X9  H9   C13  H8   107.58  3.000
 6X9  H9   C13  H7   107.96  3.000
 6X9  H8   C13  H7   107.92  3.000
 6X9  H9   C13  C5   110.60  3.000
 6X9  H8   C13  C5   110.77  3.000
 6X9  H7   C13  C5   111.86  3.000
 6X9  H12  C14  H11  108.53  3.000
 6X9  H12  C14  H10  107.40  3.000
 6X9  H11  C14  H10  108.55  3.000
 6X9  H12  C14  C8   110.71  3.000
 6X9  H11  C14  C8   110.70  3.000
 6X9  H10  C14  C8   110.84  3.000
 6X9  N16  C15  C7   180.00  3.000
 6X9  H1   N4   C5   119.69  3.000
 6X9  H1   N4   C3   119.13  3.000
 6X9  C5   N4   C3   121.17  3.000
 6X9  C8   N9   N2   105.70  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
 6X9  CONST_01  C8   N9   N2   C3      0.00   0.0  0
 6X9  CONST_02  N9   C8   C7   C3      0.00   0.0  0
 6X9  CONST_03  C7   C8   N9   N2      0.00   0.0  0
 6X9  CONST_04  C8   C7   C3   N2      0.00   0.0  0
 6X9  CONST_05  N9   N2   C3   C7      0.00   0.0  0
 6X9  CONST_06  C14  C8   C7   C3    180.00   0.0  0
 6X9  CONST_07  C14  C8   N9   N2    180.00   0.0  0
 6X9  CONST_08  C15  C7   C3   N2    180.00   0.0  0
 6X9  CONST_09  N9   C8   C7   C15   180.00   0.0  0
 6X9  CONST_10  N4   C3   C7   C15     0.00   0.0  0
 6X9  Var_01    C12  C11  C6   C1    -81.97  30.0  2
 6X9  Var_02    H7   C13  C5   C6   -179.08  30.0  3
 6X9  Var_03    H10  C14  C8   C7     59.34  30.0  2
 6X9  Var_04    H4   C12  C11  C6    179.17  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
 6X9  plan-1  C1   0.020
 6X9  plan-1  C3   0.020
 6X9  plan-1  C5   0.020
 6X9  plan-1  C6   0.020
 6X9  plan-1  N2   0.020
 6X9  plan-1  C7   0.020
 6X9  plan-1  C8   0.020
 6X9  plan-1  C11  0.020
 6X9  plan-1  C13  0.020
 6X9  plan-1  C14  0.020
 6X9  plan-1  C15  0.020
 6X9  plan-1  N4   0.020
 6X9  plan-1  N16  0.020
 6X9  plan-1  N9   0.020
 6X9  plan-1  O10  0.020
 6X9  plan-1  H1   0.020

