# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 13:24:15 2022
#   Inital geometry file: a 137 line input string
#   Ligand name: 4-azanyl-7-methyl-2-[[5-methyl-1-[(3~{R})-oxolan-3-yl]pyrazol-4-yl]amino]-6-[(2~{R})-2-methylpyrrolidin-1-yl]pyrrolo[2,3-d]pyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CCCN1c2n(C)c3nc(Nc4cnn([C@@H]5CCOC5)c4C)nc(N)c3c2C#N
#
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
 U0K  U0K  4-azanyl-7-methyl-2-[[5-methyl-1-[(3~{R})-oxolan-3-yl]pyrazol-4-yl]amino]-6-[(2~{R})-2-methylpyrrolidin-1-yl]pyrrolo[2,3-d]pyrimidine-5-carbonitrile  ligand  58  31  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_U0K
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
 U0K  C1   C  CH3   0  -0.662   5.6110   -5.7991  13.3042
 U0K  N1   N  NT    0  -0.540   4.6585   -7.3633  14.9770
 U0K  O1   O  O2    0  -0.494  -4.9991   -6.4886  20.0358
 U0K  C2   C  CH1   0  -0.076   5.7928   -7.0860  14.0861
 U0K  N2   N  NS    0  -0.286   7.6681   -5.2164  16.5593
 U0K  C3   C  CH2   0  -0.456   5.8364   -8.3375  13.2166
 U0K  N3   N  NH2   0  -0.838   5.5350   -3.4120  19.0070
 U0K  C4   C  CH2   0  -0.471   5.4130   -9.4401  14.1749
 U0K  N4   N  N     0  -0.527   3.3281   -3.7952  19.4802
 U0K  C5   C  CH2   0  -0.284   4.2825   -8.7859  14.9600
 U0K  N5   N  NH1   0  -0.765   1.1346   -4.0426  20.0101
 U0K  C6   C  CR5   0   0.642   4.3652   -6.5602  16.0263
 U0K  N6   N  NR5   0  -0.325  -2.1949   -5.0684  20.5766
 U0K  C7   C  CR5   0  -0.165   5.1554   -5.6572  16.7373
 U0K  N7   N  N     0  -0.279  -2.1462   -5.3243  19.2747
 U0K  C8   C  CSP   0  -0.054   6.5323   -5.4389  16.6103
 U0K  N8   N  N     0  -0.518   1.9634   -5.3477  18.2928
 U0K  C9   C  CR56  0  -0.070   4.3021   -5.0529  17.7303
 U0K  N9   N  NR5   0  -0.576   3.0938   -6.5231  16.5497
 U0K  C10  C  CR6   0   0.424   4.4009   -4.0878  18.7491
 U0K  C11  C  CR6   0   0.566   2.1753   -4.4237  19.2205
 U0K  C12  C  CR5   0   0.026  -0.1656   -4.5352  19.9759
 U0K  C13  C  CR5   0   0.368  -1.0177   -4.6089  21.0635
 U0K  C14  C  CH3   0  -0.746  -0.7899   -4.2685  22.4923
 U0K  C15  C  CR15  0  -0.067  -0.9287   -4.9958  18.8869
 U0K  C16  C  CH1   0  -0.180  -3.3786   -5.3746  21.3584
 U0K  C17  C  CH2   0  -0.491  -3.4515   -6.8482  21.7629
 U0K  C18  C  CH2   0  -0.152  -4.1252   -7.4793  20.5535
 U0K  C19  C  CH2   0  -0.138  -4.6719   -5.2165  20.5637
 U0K  C20  C  CR56  0   0.528   3.0495   -5.6251  17.5833
 U0K  C21  C  CH3   0  -0.555   1.9220   -7.1554  15.9849
 U0K  H1   H  HCH3  0   0.237   5.5527   -4.9247  13.9529
 U0K  H2   H  HCH3  0   0.236   6.4571   -5.6515  12.6323
 U0K  H3   H  HCH3  0   0.227   4.7011   -5.8409  12.7043
 U0K  H4   H  HCH1  0   0.244   6.7275   -7.0391  14.6560
 U0K  H5   H  HCH2  0   0.253   6.8252   -8.4910  12.7858
 U0K  H6   H  HCH2  0   0.234   5.1210   -8.2498  12.3938
 U0K  H7   H  HNH2  0   0.395   5.5739   -2.8422  19.8352
 U0K  H8   H  HNH2  0   0.406   6.4163   -3.7153  18.6309
 U0K  H9   H  HCH2  0   0.253   5.0870  -10.3502  13.6727
 U0K  H10  H  HCH2  0   0.239   6.2382   -9.7002  14.8408
 U0K  H11  H  HCH2  0   0.238   3.3279   -8.9381  14.4517
 U0K  H12  H  HCH2  0   0.251   4.1896   -9.1806  15.9732
 U0K  H13  H  HNH1  0   0.398   1.3601   -3.3566  20.7122
 U0K  H14  H  HCH3  0   0.260  -1.3756   -3.4036  22.8098
 U0K  H15  H  HCH3  0   0.262  -1.0445   -5.0989  23.1525
 U0K  H16  H  HCH3  0   0.259   0.2594   -4.0324  22.6615
 U0K  H17  H  HCR5  0   0.263  -0.6331   -5.1045  17.8567
 U0K  H18  H  HCH1  0   0.294  -3.3712   -4.7133  22.2237
 U0K  H19  H  HCH2  0   0.254  -4.0783   -6.9413  22.6514
 U0K  H20  H  HCH2  0   0.265  -2.4766   -7.2794  21.9890
 U0K  H21  H  HCH2  0   0.228  -4.7014   -8.3697  20.8144
 U0K  H22  H  HCH2  0   0.205  -3.3852   -7.7673  19.7997
 U0K  H23  H  HCH2  0   0.232  -4.5785   -4.4815  19.7618
 U0K  H24  H  HCH2  0   0.225  -5.4634   -4.8773  21.2402
 U0K  H25  H  HCH3  0   0.282   1.0422   -6.6423  16.3627
 U0K  H26  H  HCH3  0   0.262   1.9388   -7.0682  14.9005
 U0K  H27  H  HCH3  0   0.259   1.8535   -8.2065  16.2598

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
 U0K  C3   C4   single    1.521  0.020  1.521
 U0K  C3   C2   single    1.525  0.020  1.525
 U0K  C1   C2   single    1.517  0.020  1.517
 U0K  C4   C5   single    1.524  0.020  1.524
 U0K  C2   N1   single    1.469  0.020  1.469
 U0K  C5   N1   single    1.472  0.020  1.472
 U0K  N1   C6   single    1.353  0.020  1.353
 U0K  C21  N9   single    1.446  0.020  1.446
 U0K  C6   N9   aromatic  1.375  0.020  1.375
 U0K  C6   C7   aromatic  1.395  0.020  1.395
 U0K  N2   C8   triple    1.158  0.020  1.158
 U0K  N9   C20  aromatic  1.370  0.020  1.370
 U0K  C8   C7   single    1.400  0.020  1.400
 U0K  C7   C9   aromatic  1.442  0.020  1.442
 U0K  C20  C9   aromatic  1.385  0.020  1.385
 U0K  C20  N8   aromatic  1.327  0.020  1.327
 U0K  C9   C10  aromatic  1.407  0.020  1.407
 U0K  N8   C11  aromatic  1.326  0.020  1.326
 U0K  C10  N3   single    1.345  0.020  1.345
 U0K  C10  N4   aromatic  1.331  0.020  1.331
 U0K  C15  N7   aromatic  1.319  0.020  1.319
 U0K  C15  C12  aromatic  1.407  0.020  1.407
 U0K  C11  N4   aromatic  1.338  0.020  1.338
 U0K  C11  N5   single    1.361  0.020  1.361
 U0K  N7   N6   aromatic  1.328  0.020  1.328
 U0K  O1   C18  single    1.419  0.020  1.419
 U0K  O1   C19  single    1.416  0.020  1.416
 U0K  N5   C12  single    1.391  0.020  1.391
 U0K  C12  C13  aromatic  1.384  0.020  1.384
 U0K  C18  C17  single    1.521  0.020  1.521
 U0K  N6   C13  aromatic  1.354  0.020  1.354
 U0K  N6   C16  single    1.451  0.020  1.451
 U0K  C19  C16  single    1.526  0.020  1.526
 U0K  C13  C14  single    1.486  0.020  1.486
 U0K  C16  C17  single    1.530  0.020  1.530
 U0K  C1   H1   single    0.970  0.020  1.090
 U0K  C1   H2   single    0.970  0.020  1.090
 U0K  C1   H3   single    0.970  0.020  1.090
 U0K  C2   H4   single    0.970  0.020  1.090
 U0K  C3   H5   single    0.970  0.020  1.090
 U0K  C3   H6   single    0.970  0.020  1.090
 U0K  N3   H7   single    0.890  0.020  1.040
 U0K  N3   H8   single    0.890  0.020  1.040
 U0K  C4   H9   single    0.970  0.020  1.090
 U0K  C4   H10  single    0.970  0.020  1.090
 U0K  C5   H11  single    0.970  0.020  1.090
 U0K  C5   H12  single    0.970  0.020  1.090
 U0K  N5   H13  single    0.860  0.020  1.020
 U0K  C14  H14  single    0.970  0.020  1.090
 U0K  C14  H15  single    0.970  0.020  1.090
 U0K  C14  H16  single    0.970  0.020  1.090
 U0K  C15  H17  single    0.930  0.020  1.080
 U0K  C16  H18  single    0.970  0.020  1.090
 U0K  C17  H19  single    0.970  0.020  1.090
 U0K  C17  H20  single    0.970  0.020  1.090
 U0K  C18  H21  single    0.970  0.020  1.090
 U0K  C18  H22  single    0.970  0.020  1.090
 U0K  C19  H23  single    0.970  0.020  1.090
 U0K  C19  H24  single    0.970  0.020  1.090
 U0K  C21  H25  single    0.970  0.020  1.090
 U0K  C21  H26  single    0.970  0.020  1.090
 U0K  C21  H27  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
 U0K  H3   C1   H2   108.27  3.000
 U0K  H3   C1   H1   108.26  3.000
 U0K  H2   C1   H1   107.43  3.000
 U0K  H3   C1   C2   110.55  3.000
 U0K  H2   C1   C2   109.85  3.000
 U0K  H1   C1   C2   112.35  3.000
 U0K  C6   N1   C5   121.82  3.000
 U0K  C6   N1   C2   121.71  3.000
 U0K  C5   N1   C2   111.89  3.000
 U0K  C19  O1   C18  110.43  3.000
 U0K  H4   C2   C3   107.90  3.000
 U0K  H4   C2   N1   110.57  3.000
 U0K  C3   C2   N1   102.30  3.000
 U0K  H4   C2   C1   109.51  3.000
 U0K  N1   C2   C1   112.35  3.000
 U0K  C3   C2   C1   113.95  3.000
 U0K  H6   C3   H5   107.90  3.000
 U0K  H6   C3   C4   110.49  3.000
 U0K  H5   C3   C4   113.56  3.000
 U0K  H6   C3   C2   110.15  3.000
 U0K  H5   C3   C2   111.54  3.000
 U0K  C4   C3   C2   103.17  3.000
 U0K  H8   N3   H7   116.42  3.000
 U0K  H8   N3   C10  121.06  3.000
 U0K  H7   N3   C10  118.36  3.000
 U0K  H10  C4   H9   107.96  3.000
 U0K  H10  C4   C5   110.41  3.000
 U0K  H9   C4   C5   111.97  3.000
 U0K  H10  C4   C3   110.28  3.000
 U0K  H9   C4   C3   113.49  3.000
 U0K  C5   C4   C3   102.70  3.000
 U0K  C11  N4   C10  118.98  3.000
 U0K  H12  C5   H11  107.90  3.000
 U0K  H12  C5   C4   112.72  3.000
 U0K  H11  C5   C4   110.41  3.000
 U0K  H12  C5   N1   111.14  3.000
 U0K  H11  C5   N1   111.31  3.000
 U0K  C4   C5   N1   103.38  3.000
 U0K  H13  N5   C12  117.88  3.000
 U0K  H13  N5   C11  115.09  3.000
 U0K  C12  N5   C11  126.98  3.000
 U0K  N9   C6   C7   108.19  3.000
 U0K  C7   C6   N1   131.04  3.000
 U0K  N9   C6   N1   120.75  3.000
 U0K  C16  N6   C13  125.94  3.000
 U0K  C16  N6   N7   121.16  3.000
 U0K  C13  N6   N7   112.71  3.000
 U0K  C9   C7   C8   125.39  3.000
 U0K  C9   C7   C6   106.69  3.000
 U0K  C8   C7   C6   127.73  3.000
 U0K  C15  N7   N6   105.91  3.000
 U0K  C7   C8   N2   180.00  3.000
 U0K  C20  N8   C11  112.89  3.000
 U0K  C20  C9   C10  115.08  3.000
 U0K  C10  C9   C7   138.13  3.000
 U0K  C20  C9   C7   106.79  3.000
 U0K  C21  N9   C20  123.71  3.000
 U0K  C20  N9   C6   109.55  3.000
 U0K  C21  N9   C6   126.06  3.000
 U0K  C9   C10  N4   119.48  3.000
 U0K  N4   C10  N3   117.64  3.000
 U0K  C9   C10  N3   122.87  3.000
 U0K  N8   C11  N5   118.60  3.000
 U0K  N5   C11  N4   114.49  3.000
 U0K  N8   C11  N4   126.90  3.000
 U0K  C15  C12  C13  104.88  3.000
 U0K  C13  C12  N5   125.12  3.000
 U0K  C15  C12  N5   129.93  3.000
 U0K  C14  C13  C12  130.47  3.000
 U0K  C14  C13  N6   123.82  3.000
 U0K  C12  C13  N6   105.71  3.000
 U0K  H16  C14  H15  107.21  3.000
 U0K  H16  C14  H14  107.46  3.000
 U0K  H15  C14  H14  107.56  3.000
 U0K  H16  C14  C13  110.29  3.000
 U0K  H15  C14  C13  111.81  3.000
 U0K  H14  C14  C13  112.26  3.000
 U0K  H17  C15  C12  128.63  3.000
 U0K  H17  C15  N7   120.61  3.000
 U0K  C12  C15  N7   110.76  3.000
 U0K  H18  C16  C19  110.89  3.000
 U0K  H18  C16  C17  112.04  3.000
 U0K  C19  C16  C17  101.37  3.000
 U0K  H18  C16  N6   107.12  3.000
 U0K  C17  C16  N6   112.62  3.000
 U0K  C19  C16  N6   112.88  3.000
 U0K  H20  C17  H19  108.13  3.000
 U0K  H20  C17  C18  113.39  3.000
 U0K  H19  C17  C18  110.94  3.000
 U0K  H20  C17  C16  113.16  3.000
 U0K  H19  C17  C16  108.95  3.000
 U0K  C18  C17  C16  102.15  3.000
 U0K  H22  C18  H21  107.86  3.000
 U0K  H22  C18  C17  110.92  3.000
 U0K  H21  C18  C17  112.45  3.000
 U0K  H22  C18  O1   110.41  3.000
 U0K  H21  C18  O1   109.35  3.000
 U0K  C17  C18  O1   105.86  3.000
 U0K  H24  C19  H23  107.89  3.000
 U0K  H24  C19  C16  108.84  3.000
 U0K  H23  C19  C16  112.32  3.000
 U0K  H24  C19  O1   109.98  3.000
 U0K  H23  C19  O1   110.54  3.000
 U0K  C16  C19  O1   107.27  3.000
 U0K  N9   C20  C9   108.77  3.000
 U0K  C9   C20  N8   126.67  3.000
 U0K  N9   C20  N8   124.54  3.000
 U0K  H27  C21  H26  109.27  3.000
 U0K  H27  C21  H25  108.50  3.000
 U0K  H26  C21  H25  108.74  3.000
 U0K  H27  C21  N9   111.99  3.000
 U0K  H26  C21  N9   109.97  3.000
 U0K  H25  C21  N9   108.29  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
 U0K  CONST_01  C7   C9   C10  N4    180.00   0.0  0
 U0K  CONST_02  C20  C9   C10  N4      0.00   0.0  0
 U0K  CONST_03  C20  N8   C11  N4      0.00   0.0  0
 U0K  CONST_04  C9   C20  N9   C6      0.00   0.0  0
 U0K  CONST_05  N8   C20  N9   C6    180.00   0.0  0
 U0K  CONST_06  C20  C9   C7   C6      0.00   0.0  0
 U0K  CONST_07  C10  C9   C7   C6    180.00   0.0  0
 U0K  CONST_08  C12  C15  N7   N6      0.00   0.0  0
 U0K  CONST_09  C15  C12  C13  N6      0.00   0.0  0
 U0K  CONST_10  C20  N9   C6   C7      0.00   0.0  0
 U0K  CONST_11  N9   C20  C9   C7      0.00   0.0  0
 U0K  CONST_12  N8   C20  C9   C7    180.00   0.0  0
 U0K  CONST_13  C13  C12  C15  N7      0.00   0.0  0
 U0K  CONST_14  C12  C13  N6   N7      0.00   0.0  0
 U0K  CONST_15  C10  C9   C20  N8      0.00   0.0  0
 U0K  CONST_16  C10  N4   C11  N8      0.00   0.0  0
 U0K  CONST_17  N9   C6   C7   C9      0.00   0.0  0
 U0K  CONST_18  C11  N8   C20  C9      0.00   0.0  0
 U0K  CONST_19  C11  N4   C10  C9      0.00   0.0  0
 U0K  CONST_20  C10  C9   C20  N9    180.00   0.0  0
 U0K  CONST_21  C11  N8   C20  N9    180.00   0.0  0
 U0K  CONST_22  C15  N7   N6   C13     0.00   0.0  0
 U0K  CONST_23  C20  N9   C6   N1    180.00   0.0  0
 U0K  CONST_24  C9   C7   C6   N1    180.00   0.0  0
 U0K  CONST_25  C16  N6   C13  C12   180.00   0.0  0
 U0K  CONST_26  C16  N6   N7   C15   180.00   0.0  0
 U0K  CONST_27  C21  N9   C6   N1      0.00   0.0  0
 U0K  CONST_28  C8   C7   C6   N1      0.00   0.0  0
 U0K  CONST_29  C7   C9   C10  N3      0.00   0.0  0
 U0K  CONST_30  C20  C9   C10  N3    180.00   0.0  0
 U0K  CONST_31  C11  N4   C10  N3    180.00   0.0  0
 U0K  CONST_32  C20  N8   C11  N5    180.00   0.0  0
 U0K  CONST_33  C10  N4   C11  N5    180.00   0.0  0
 U0K  CONST_34  N7   C15  C12  N5    180.00   0.0  0
 U0K  CONST_35  N6   C13  C12  N5    180.00   0.0  0
 U0K  CONST_36  C21  N9   C6   C7    180.00   0.0  0
 U0K  CONST_37  C14  C13  N6   N7    180.00   0.0  0
 U0K  CONST_38  N9   C6   C7   C8    180.00   0.0  0
 U0K  CONST_39  C20  C9   C7   C8    180.00   0.0  0
 U0K  CONST_40  C10  C9   C7   C8      0.00   0.0  0
 U0K  CONST_41  C21  N9   C20  N8      0.00   0.0  0
 U0K  CONST_42  C21  N9   C20  C9    180.00   0.0  0
 U0K  CONST_43  C15  C12  C13  C14   180.00   0.0  0
 U0K  CONST_44  C16  N6   C13  C14     0.00   0.0  0
 U0K  CONST_45  H17  C15  N7   N6    180.00   0.0  0
 U0K  CONST_46  H7   N3   C10  N4      0.00   0.0  0
 U0K  CONST_47  H8   N3   C10  N4    180.00   0.0  0
 U0K  Var_01    C3   C4   C5   N1    -30.76  30.0  1
 U0K  Var_02    C16  C17  C18  O1    -32.04  30.0  1
 U0K  Var_03    C5   C4   C3   C2     40.94  30.0  1
 U0K  Var_04    C4   C5   N1   C2      9.39  30.0  1
 U0K  Var_05    N9   C6   N1   C2    156.58  30.0  2
 U0K  Var_06    C12  N5   C11  N4   -179.14  30.0  2
 U0K  Var_07    C15  C12  N5   C11   -33.29  30.0  2
 U0K  Var_08    H23  C19  O1   C18   129.90  30.0  1
 U0K  Var_09    H25  C21  N9   C6   -157.47  30.0  2
 U0K  Var_10    H14  C14  C13  N6    -66.72  30.0  2

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
 U0K  chir_01  C2   C3  C1   N1   negativ
 U0K  chir_02  C16  N6  C19  C17  negativ

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
 U0K  plan-1  N3   0.020
 U0K  plan-1  C10  0.020
 U0K  plan-1  H7   0.020
 U0K  plan-1  H8   0.020
 U0K  plan-2  N5   0.020
 U0K  plan-2  N6   0.020
 U0K  plan-2  N7   0.020
 U0K  plan-2  C12  0.020
 U0K  plan-2  C13  0.020
 U0K  plan-2  C14  0.020
 U0K  plan-2  C15  0.020
 U0K  plan-2  C16  0.020
 U0K  plan-2  H17  0.020
 U0K  plan-3  N1   0.020
 U0K  plan-3  N2   0.020
 U0K  plan-3  N3   0.020
 U0K  plan-3  N4   0.020
 U0K  plan-3  N5   0.020
 U0K  plan-3  C6   0.020
 U0K  plan-3  C7   0.020
 U0K  plan-3  C8   0.020
 U0K  plan-3  N8   0.020
 U0K  plan-3  C9   0.020
 U0K  plan-3  N9   0.020
 U0K  plan-3  C10  0.020
 U0K  plan-3  C11  0.020
 U0K  plan-3  C20  0.020
 U0K  plan-3  C21  0.020

