# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 11:08:02 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: 4-azanyl-7-(1-methylcyclopropyl)-~{N}-(5-methyl-1~{H}-pyrazol-3-yl)pyrrolo[2,3-d]pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]nc(NC(=O)c2cn(c3ncnc(N)c23)C4(C)CC4)c1
#
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
 HJ0  HJ0  "4-azanyl-7-(1-methylcyclopropyl)-~{N}-(5-methyl-1~{H}-pyrazol-3-yl)pyrrolo[2,3-d]pyrimidine-5-carboxamide"
  ligand  40  23  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HJ0
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
 HJ0  C2   C  C     0   0.494   7.6527  -0.6794  -2.5786
 HJ0  C4   C  CR5   0   0.475   9.4472  -2.3070  -2.9418
 HJ0  C5   C  CR15  0  -0.540   8.7962  -3.5566  -2.9576
 HJ0  C6   C  CR5   0   0.397   9.8183  -4.4673  -3.1312
 HJ0  C7   C  CH3   0  -0.731   9.7878  -5.9505  -3.2229
 HJ0  C11  C  CR15  0  -0.007   8.1510   1.7586  -3.0691
 HJ0  C15  C  CR16  0   0.039   4.5113   3.3030  -1.1741
 HJ0  C17  C  CR6   0   0.415   5.0409   1.0697  -1.2775
 HJ0  C19  C  CR56  0  -0.061   6.2216   1.4168  -1.9788
 HJ0  C21  C  CH3   0  -0.655   8.8445   4.9244  -2.1058
 HJ0  C23  C  CH2   0  -0.496   8.6608   4.3625  -4.6352
 HJ0  O1   O  O     0  -0.487   6.7739  -1.5216  -2.4258
 HJ0  N3   N  NH1   0  -0.734   8.9433  -1.0190  -2.8054
 HJ0  N8   N  NR15  0  -0.472  10.9488  -3.7482  -3.2051
 HJ0  N9   N  N     0  -0.323  10.7510  -2.4339  -3.0932
 HJ0  C10  C  CR5   0  -0.197   7.3751   0.7607  -2.5322
 HJ0  N12  N  NR5   0  -0.533   7.5591   2.9684  -2.8849
 HJ0  C13  C  CR56  0   0.509   6.3901   2.7844  -2.2036
 HJ0  N14  N  N     0  -0.458   5.5663   3.7592  -1.8180
 HJ0  N16  N  N     0  -0.471   4.2061   2.0418  -0.8914
 HJ0  C20  C  CT    0   0.133   8.1279   4.2403  -3.2417
 HJ0  C22  C  CH2   0  -0.472   7.3853   5.0516  -4.2538
 HJ0  H1   H  HCR5  0   0.268   7.7501  -3.7764  -2.8538
 HJ0  H2   H  HCH3  0   0.258  10.2141  -6.3023  -4.1629
 HJ0  H3   H  HCH3  0   0.258  10.3519  -6.4130  -2.4121
 HJ0  H4   H  HCH3  0   0.260   8.7621  -6.3067  -3.1641
 HJ0  H5   H  HCR5  0   0.312   9.0834   1.6990  -3.6096
 HJ0  H6   H  HCR6  0   0.245   3.7983   4.0461  -0.8310
 HJ0  H7   H  HCH3  0   0.240   8.1670   5.1139  -1.2728
 HJ0  H8   H  HCH3  0   0.238   9.6732   4.3145  -1.7432
 HJ0  H9   H  HCH3  0   0.237   9.2499   5.8812  -2.4332
 HJ0  H10  H  HCH2  0   0.267   8.5914   3.5059  -5.2933
 HJ0  H11  H  HCH2  0   0.265   9.5565   4.9559  -4.7657
 HJ0  H12  H  HNH1  0   0.415   9.6432  -0.2925  -2.8202
 HJ0  H13  H  HNR5  0   0.416  11.8856  -4.0974  -3.3313
 HJ0  H14  H  HNH2  0   0.391   3.8314  -0.3757  -0.5411
 HJ0  H15  H  HNH2  0   0.419   5.2520  -0.9486  -1.3693
 HJ0  H16  H  HCH2  0   0.262   7.3906   6.1264  -4.1253
 HJ0  H17  H  HCH2  0   0.264   6.4612   4.6513  -4.6495
 HJ0  N18  N  NH2   0  -0.837   4.7246  -0.1881  -0.9635

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
 HJ0  C23  C22  single    1.499  0.020  1.499
 HJ0  C23  C20  single    1.497  0.020  1.497
 HJ0  C22  C20  single    1.495  0.020  1.495
 HJ0  C7   C6   single    1.486  0.020  1.486
 HJ0  C20  N12  single    1.438  0.020  1.438
 HJ0  C20  C21  single    1.507  0.020  1.507
 HJ0  C6   C5   aromatic  1.380  0.020  1.380
 HJ0  C6   N8   aromatic  1.342  0.020  1.342
 HJ0  C5   C4   aromatic  1.409  0.020  1.409
 HJ0  C11  N12  aromatic  1.359  0.020  1.359
 HJ0  C11  C10  aromatic  1.373  0.020  1.373
 HJ0  N8   N9   aromatic  1.334  0.020  1.334
 HJ0  N12  C13  aromatic  1.365  0.020  1.365
 HJ0  C4   N3   single    1.390  0.020  1.390
 HJ0  C4   N9   aromatic  1.319  0.020  1.319
 HJ0  N3   C2   single    1.354  0.020  1.354
 HJ0  C2   C10  single    1.467  0.020  1.467
 HJ0  C2   O1   double    1.227  0.020  1.227
 HJ0  C10  C19  aromatic  1.438  0.020  1.438
 HJ0  C13  C19  aromatic  1.396  0.020  1.396
 HJ0  C13  N14  aromatic  1.333  0.020  1.333
 HJ0  C19  C17  aromatic  1.416  0.020  1.416
 HJ0  N14  C15  aromatic  1.317  0.020  1.317
 HJ0  C17  N16  aromatic  1.338  0.020  1.338
 HJ0  C17  N18  single    1.334  0.020  1.334
 HJ0  C15  N16  aromatic  1.328  0.020  1.328
 HJ0  C5   H1   single    0.930  0.020  1.080
 HJ0  C7   H2   single    0.970  0.020  1.090
 HJ0  C7   H3   single    0.970  0.020  1.090
 HJ0  C7   H4   single    0.970  0.020  1.090
 HJ0  C11  H5   single    0.930  0.020  1.080
 HJ0  C15  H6   single    0.930  0.020  1.080
 HJ0  C21  H7   single    0.970  0.020  1.090
 HJ0  C21  H8   single    0.970  0.020  1.090
 HJ0  C21  H9   single    0.970  0.020  1.090
 HJ0  C23  H10  single    0.970  0.020  1.090
 HJ0  C23  H11  single    0.970  0.020  1.090
 HJ0  N3   H12  single    0.860  0.020  1.020
 HJ0  N8   H13  single    0.860  0.020  1.020
 HJ0  N18  H14  single    0.860  0.020  1.020
 HJ0  N18  H15  single    0.860  0.020  1.020
 HJ0  C22  H16  single    0.970  0.020  1.090
 HJ0  C22  H17  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
 HJ0  C10  C2   N3   115.59  3.000
 HJ0  C10  C2   O1   122.30  3.000
 HJ0  N3   C2   O1   122.11  3.000
 HJ0  N9   C4   N3   117.32  3.000
 HJ0  N9   C4   C5   111.72  3.000
 HJ0  N3   C4   C5   130.96  3.000
 HJ0  H1   C5   C6   126.76  3.000
 HJ0  H1   C5   C4   129.08  3.000
 HJ0  C6   C5   C4   104.15  3.000
 HJ0  N8   C6   C7   123.28  3.000
 HJ0  N8   C6   C5   106.10  3.000
 HJ0  C7   C6   C5   130.63  3.000
 HJ0  H4   C7   H3   107.98  3.000
 HJ0  H4   C7   H2   108.04  3.000
 HJ0  H3   C7   H2   107.57  3.000
 HJ0  H4   C7   C6   110.06  3.000
 HJ0  H3   C7   C6   111.51  3.000
 HJ0  H2   C7   C6   111.54  3.000
 HJ0  H5   C11  N12  119.54  3.000
 HJ0  H5   C11  C10  130.07  3.000
 HJ0  N12  C11  C10  110.34  3.000
 HJ0  H6   C15  N16  115.59  3.000
 HJ0  H6   C15  N14  116.32  3.000
 HJ0  N16  C15  N14  128.09  3.000
 HJ0  N18  C17  N16  117.97  3.000
 HJ0  N18  C17  C19  123.03  3.000
 HJ0  N16  C17  C19  119.00  3.000
 HJ0  C13  C19  C10  106.75  3.000
 HJ0  C13  C19  C17  114.86  3.000
 HJ0  C10  C19  C17  138.37  3.000
 HJ0  H9   C21  H8   107.95  3.000
 HJ0  H9   C21  H7   107.95  3.000
 HJ0  H8   C21  H7   108.38  3.000
 HJ0  H9   C21  C20  110.42  3.000
 HJ0  H8   C21  C20  110.97  3.000
 HJ0  H7   C21  C20  111.06  3.000
 HJ0  H11  C23  H10  114.43  3.000
 HJ0  H11  C23  C22  118.87  3.000
 HJ0  H10  C23  C22  117.64  3.000
 HJ0  H11  C23  C20  116.85  3.000
 HJ0  H10  C23  C20  118.59  3.000
 HJ0  C22  C23  C20   59.85  3.000
 HJ0  H12  N3   C4   114.48  3.000
 HJ0  H12  N3   C2   118.90  3.000
 HJ0  C4   N3   C2   126.49  3.000
 HJ0  H13  N8   N9   119.34  3.000
 HJ0  H13  N8   C6   127.18  3.000
 HJ0  N9   N8   C6   113.48  3.000
 HJ0  N8   N9   C4   104.55  3.000
 HJ0  C19  C10  C11  105.80  3.000
 HJ0  C19  C10  C2   127.72  3.000
 HJ0  C11  C10  C2   126.43  3.000
 HJ0  C20  N12  C13  125.56  3.000
 HJ0  C13  N12  C11  108.69  3.000
 HJ0  C20  N12  C11  125.54  3.000
 HJ0  N14  C13  N12  125.08  3.000
 HJ0  N14  C13  C19  126.51  3.000
 HJ0  N12  C13  C19  108.41  3.000
 HJ0  C13  N14  C15  112.52  3.000
 HJ0  C17  N16  C15  119.02  3.000
 HJ0  C22  C20  N12  116.84  3.000
 HJ0  N12  C20  C23  116.36  3.000
 HJ0  C22  C20  C23   60.15  3.000
 HJ0  N12  C20  C21  113.73  3.000
 HJ0  C22  C20  C21  120.01  3.000
 HJ0  C23  C20  C21  119.69  3.000
 HJ0  H17  C22  H16  114.52  3.000
 HJ0  H17  C22  C20  118.11  3.000
 HJ0  H16  C22  C20  117.14  3.000
 HJ0  H17  C22  C23  117.61  3.000
 HJ0  H16  C22  C23  118.84  3.000
 HJ0  C20  C22  C23   60.00  3.000
 HJ0  H15  N18  H14  119.46  3.000
 HJ0  H15  N18  C17  119.42  3.000
 HJ0  H14  N18  C17  119.02  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
 HJ0  CONST_01  N8   C6   C5   C4      0.00   0.0  0
 HJ0  CONST_02  C6   N8   N9   C4      0.00   0.0  0
 HJ0  CONST_03  N9   N8   C6   C5      0.00   0.0  0
 HJ0  CONST_04  N8   N9   C4   C5      0.00   0.0  0
 HJ0  CONST_05  N9   C4   C5   C6      0.00   0.0  0
 HJ0  CONST_06  C19  C13  N12  C11     0.00   0.0  0
 HJ0  CONST_07  N14  C13  N12  C11   180.00   0.0  0
 HJ0  CONST_08  C13  C19  C10  C11     0.00   0.0  0
 HJ0  CONST_09  C17  C19  C10  C11   180.00   0.0  0
 HJ0  CONST_10  N12  C13  N14  C15   180.00   0.0  0
 HJ0  CONST_11  C19  C13  N14  C15     0.00   0.0  0
 HJ0  CONST_12  C19  C17  N16  C15     0.00   0.0  0
 HJ0  CONST_13  N12  C13  C19  C17   180.00   0.0  0
 HJ0  CONST_14  N14  C13  C19  C17     0.00   0.0  0
 HJ0  CONST_15  N14  C15  N16  C17     0.00   0.0  0
 HJ0  CONST_16  N12  C11  C10  C19     0.00   0.0  0
 HJ0  CONST_17  C13  N12  C11  C10     0.00   0.0  0
 HJ0  CONST_18  N12  C13  C19  C10     0.00   0.0  0
 HJ0  CONST_19  N14  C13  C19  C10   180.00   0.0  0
 HJ0  CONST_20  N16  C17  C19  C10   180.00   0.0  0
 HJ0  CONST_21  N16  C17  C19  C13     0.00   0.0  0
 HJ0  CONST_22  N16  C15  N14  C13     0.00   0.0  0
 HJ0  CONST_23  C20  N12  C13  C19   180.00   0.0  0
 HJ0  CONST_24  C20  N12  C11  C10   180.00   0.0  0
 HJ0  CONST_25  C20  N12  C13  N14     0.00   0.0  0
 HJ0  CONST_26  N12  C11  C10  C2    180.00   0.0  0
 HJ0  CONST_27  C13  C19  C10  C2    180.00   0.0  0
 HJ0  CONST_28  C17  C19  C10  C2      0.00   0.0  0
 HJ0  CONST_29  C7   C6   C5   C4    180.00   0.0  0
 HJ0  CONST_30  N3   C4   C5   C6    180.00   0.0  0
 HJ0  CONST_31  N9   N8   C6   C7    180.00   0.0  0
 HJ0  CONST_32  N18  C17  N16  C15   180.00   0.0  0
 HJ0  CONST_33  N8   N9   C4   N3    180.00   0.0  0
 HJ0  CONST_34  N18  C17  C19  C10     0.00   0.0  0
 HJ0  CONST_35  N18  C17  C19  C13   180.00   0.0  0
 HJ0  CONST_36  H13  N8   N9   C4    180.00   0.0  0
 HJ0  CONST_37  H13  N8   C6   C5    180.00   0.0  0
 HJ0  CONST_38  H6   C15  N16  C17   180.00   0.0  0
 HJ0  CONST_39  H5   C11  C10  C19   180.00   0.0  0
 HJ0  CONST_40  H1   C5   C6   N8    180.00   0.0  0
 HJ0  CONST_41  H1   C5   C4   N9    180.00   0.0  0
 HJ0  CONST_42  H5   C11  N12  C13   180.00   0.0  0
 HJ0  CONST_43  H6   C15  N14  C13   180.00   0.0  0
 HJ0  CONST_44  H5   C11  N12  C20     0.00   0.0  0
 HJ0  CONST_45  C10  C2   N3   C4    180.00   0.0  0
 HJ0  CONST_46  C5   C4   N3   C2      0.00   0.0  0
 HJ0  CONST_47  N9   C4   N3   C2    180.00   0.0  0
 HJ0  CONST_48  H12  N3   C4   C5    180.00   0.0  0
 HJ0  CONST_49  H14  N18  C17  C19   180.00   0.0  0
 HJ0  CONST_50  H15  N18  C17  C19     0.00   0.0  0
 HJ0  CONST_51  H12  N3   C4   N9      0.00   0.0  0
 HJ0  CONST_52  H14  N18  C17  N16     0.00   0.0  0
 HJ0  CONST_53  H15  N18  C17  N16   180.00   0.0  0
 HJ0  CONST_54  O1   C2   N3   C4      0.00   0.0  0
 HJ0  CONST_55  H12  N3   C2   C10     0.00   0.0  0
 HJ0  CONST_56  H12  N3   C2   O1    180.00   0.0  0
 HJ0  Var_01    C23  C20  N12  C11    50.21  30.0  3
 HJ0  Var_02    C22  C20  N12  C11   118.39  30.0  3
 HJ0  Var_03    N12  C20  C22  C23  -106.46  30.0  1
 HJ0  Var_04    C13  N12  C20  C23  -135.74  30.0  2
 HJ0  Var_05    C22  C20  N12  C13   -67.57  30.0  3
 HJ0  Var_06    C21  C20  N12  C11   -95.02  30.0  3
 HJ0  Var_07    C22  C23  C20  C21  -109.68  30.0  1
 HJ0  Var_08    C13  N12  C20  C21    79.02  30.0  2
 HJ0  Var_09    H16  C22  C20  C23  -109.27  30.0  1
 HJ0  Var_10    H17  C22  C20  C23   107.36  30.0  1
 HJ0  Var_11    H10  C23  C20  N12     0.14  30.0  1
 HJ0  Var_12    H11  C23  C20  N12  -143.37  30.0  1
 HJ0  Var_13    H16  C22  C20  N12   144.28  30.0  1
 HJ0  Var_14    H17  C22  C20  N12     0.91  30.0  1
 HJ0  Var_15    H10  C23  C22  C20   108.70  30.0  1
 HJ0  Var_16    H11  C23  C22  C20  -106.04  30.0  1
 HJ0  Var_17    N3   C2   C10  C11    20.81  30.0  2
 HJ0  Var_18    O1   C2   C10  C11  -159.00  30.0  2
 HJ0  Var_19    N3   C2   C10  C19  -162.29  30.0  2
 HJ0  Var_20    O1   C2   C10  C19    17.90  30.0  2
 HJ0  Var_21    H2   C7   C6   C5    121.79  30.0  2
 HJ0  Var_22    H3   C7   C6   C5   -117.93  30.0  2
 HJ0  Var_23    H4   C7   C6   C5      1.89  30.0  2
 HJ0  Var_24    H10  C23  C20  C21   143.20  30.0  1
 HJ0  Var_25    H11  C23  C20  C21    -0.30  30.0  1
 HJ0  Var_26    H16  C22  C20  C21    -0.13  30.0  1
 HJ0  Var_27    H17  C22  C20  C21  -143.50  30.0  1
 HJ0  Var_28    H7   C21  C20  C23   155.94  30.0  3
 HJ0  Var_29    H8   C21  C20  C23   -83.43  30.0  3
 HJ0  Var_30    H9   C21  C20  C23    36.23  30.0  3
 HJ0  Var_31    H2   C7   C6   N8    -58.58  30.0  2
 HJ0  Var_32    H3   C7   C6   N8     61.70  30.0  2
 HJ0  Var_33    H4   C7   C6   N8   -178.48  30.0  2
 HJ0  Var_34    H7   C21  C20  N12   -60.08  30.0  3
 HJ0  Var_35    H8   C21  C20  N12    60.54  30.0  3
 HJ0  Var_36    H9   C21  C20  N12  -179.80  30.0  3
 HJ0  Var_37    H7   C21  C20  C22    85.35  30.0  3
 HJ0  Var_38    H8   C21  C20  C22  -154.02  30.0  3
 HJ0  Var_39    H9   C21  C20  C22   -34.36  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 HJ0  chir_01  C20  C22  N12  C21  both

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
 HJ0  plan-1  C4   0.020
 HJ0  plan-1  C5   0.020
 HJ0  plan-1  C6   0.020
 HJ0  plan-1  C7   0.020
 HJ0  plan-1  N3   0.020
 HJ0  plan-1  N8   0.020
 HJ0  plan-1  N9   0.020
 HJ0  plan-1  H1   0.020
 HJ0  plan-1  H13  0.020
 HJ0  plan-2  C2   0.020
 HJ0  plan-2  C11  0.020
 HJ0  plan-2  C15  0.020
 HJ0  plan-2  C17  0.020
 HJ0  plan-2  C19  0.020
 HJ0  plan-2  C10  0.020
 HJ0  plan-2  N12  0.020
 HJ0  plan-2  C13  0.020
 HJ0  plan-2  N14  0.020
 HJ0  plan-2  N16  0.020
 HJ0  plan-2  C20  0.020
 HJ0  plan-2  H5   0.020
 HJ0  plan-2  H6   0.020
 HJ0  plan-2  N18  0.020
 HJ0  plan-3  C17  0.020
 HJ0  plan-3  H14  0.020
 HJ0  plan-3  H15  0.020
 HJ0  plan-3  N18  0.020
 HJ0  plan-4  C2   0.020
 HJ0  plan-4  C4   0.020
 HJ0  plan-4  O1   0.020
 HJ0  plan-4  N3   0.020
 HJ0  plan-4  C10  0.020
 HJ0  plan-4  H12  0.020

