# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 07:31:55 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: 4-azanyl-7-methyl-2-[(1-methylpyrazol-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)c4)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
 U0Q  U0Q  4-azanyl-7-methyl-2-[(1-methylpyrazol-4-yl)amino]-6-[(2~{R})-2-methylpyrrolidin-1-yl]pyrrolo[2,3-d]pyrimidine-5-carbonitrile  ligand  47  26  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U0Q
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
 U0Q  C1   C  CH3   0  -0.662   5.4809  -4.3982  13.6759
 U0Q  C2   C  CH1   0  -0.077   5.6805  -5.6935  14.4392
 U0Q  C3   C  CH2   0  -0.456   5.7488  -6.9313  13.5523
 U0Q  C4   C  CH2   0  -0.471   5.3473  -8.0552  14.4954
 U0Q  C5   C  CH2   0  -0.284   4.2056  -7.4344  15.2921
 U0Q  N1   N  NT    0  -0.539   4.5477  -6.0028  15.3208
 U0Q  C6   C  CR5   0   0.641   4.2428  -5.2226  16.3845
 U0Q  C7   C  CR5   0  -0.163   5.0197  -4.3235  17.1142
 U0Q  C8   C  CSP   0  -0.054   6.3935  -4.0825  16.9926
 U0Q  N2   N  NS    0  -0.285   7.5259  -3.8425  16.9471
 U0Q  C9   C  CR56  0  -0.073   4.1587  -3.7537  18.1199
 U0Q  C10  C  CR6   0   0.425   4.2472  -2.8141  19.1635
 U0Q  N3   N  NH2   0  -0.838   5.3716  -2.1270  19.4342
 U0Q  N4   N  N     0  -0.528   3.1733  -2.5590  19.9056
 U0Q  C11  C  CR6   0   0.575   2.0288  -3.1975  19.6328
 U0Q  N5   N  NH1   0  -0.761   0.9929  -2.8557  20.4453
 U0Q  C12  C  CR5   0   0.080  -0.3106  -3.3254  20.4236
 U0Q  C13  C  CR15  0  -0.025  -1.3018  -2.9047  21.2892
 U0Q  N6   N  NR5   0  -0.249  -2.4179  -3.5835  20.9568
 U0Q  C14  C  CH3   0  -0.514  -3.7164  -3.4588  21.5752
 U0Q  N7   N  N     0  -0.281  -2.2232  -4.4076  19.9436
 U0Q  C15  C  CR15  0  -0.098  -0.9503  -4.2739  19.5999
 U0Q  N8   N  N     0  -0.524   1.8259  -4.0986  18.6810
 U0Q  C16  C  CR56  0   0.537   2.9145  -4.3411  17.9610
 U0Q  N9   N  NR5   0  -0.576   2.9711  -5.2147  16.9079
 U0Q  C17  C  CH3   0  -0.556   1.8101  -5.8572  16.3325
 U0Q  H1   H  HCH3  0   0.237   5.4080  -3.5342  14.3371
 U0Q  H2   H  HCH3  0   0.236   6.3260  -4.2283  13.0082
 U0Q  H3   H  HCH3  0   0.227   4.5728  -4.4447  13.0733
 U0Q  H4   H  HCH1  0   0.243   6.6125  -5.6400  15.0132
 U0Q  H5   H  HCH2  0   0.253   6.7405  -7.0589  13.1198
 U0Q  H6   H  HCH2  0   0.234   5.0317  -6.8464  12.7307
 U0Q  H7   H  HCH2  0   0.253   5.0376  -8.9638  13.9804
 U0Q  H8   H  HCH2  0   0.239   6.1781  -8.3098  15.1563
 U0Q  H9   H  HCH2  0   0.238   3.2519  -7.6047  14.7881
 U0Q  H10  H  HCH2  0   0.251   4.1283  -7.8399  16.3024
 U0Q  H11  H  HNH2  0   0.395   5.4059  -1.5841  20.2806
 U0Q  H12  H  HNH2  0   0.406   6.2559  -2.4112  19.0501
 U0Q  H13  H  HNH1  0   0.402   1.2156  -2.1660  21.1451
 U0Q  H14  H  HCR5  0   0.288  -1.2801  -2.1865  22.0936
 U0Q  H15  H  HCH3  0   0.265  -4.3853  -4.1757  21.1089
 U0Q  H16  H  HCH3  0   0.256  -3.6561  -3.6710  22.6413
 U0Q  H17  H  HCH3  0   0.255  -4.1168  -2.4558  21.4362
 U0Q  H18  H  HCR5  0   0.273  -0.5375  -4.8500  18.7909
 U0Q  H19  H  HCH3  0   0.284   0.9215  -5.3605  16.7117
 U0Q  H20  H  HCH3  0   0.264   1.8307  -5.7589  15.2491
 U0Q  H21  H  HCH3  0   0.259   1.7562  -6.9120  16.5963

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
 U0Q  C3   C4   single    1.521  0.020  1.521
 U0Q  C3   C2   single    1.524  0.020  1.524
 U0Q  C1   C2   single    1.517  0.020  1.517
 U0Q  C4   C5   single    1.524  0.020  1.524
 U0Q  C2   N1   single    1.468  0.020  1.468
 U0Q  C5   N1   single    1.472  0.020  1.472
 U0Q  N1   C6   single    1.354  0.020  1.354
 U0Q  C6   N9   aromatic  1.375  0.020  1.375
 U0Q  C6   C7   aromatic  1.394  0.020  1.394
 U0Q  C17  N9   single    1.446  0.020  1.446
 U0Q  N2   C8   triple    1.158  0.020  1.158
 U0Q  N9   C16  aromatic  1.369  0.020  1.369
 U0Q  C8   C7   single    1.400  0.020  1.400
 U0Q  C7   C9   aromatic  1.441  0.020  1.441
 U0Q  C16  C9   aromatic  1.385  0.020  1.385
 U0Q  C16  N8   aromatic  1.328  0.020  1.328
 U0Q  C9   C10  aromatic  1.407  0.020  1.407
 U0Q  N8   C11  aromatic  1.326  0.020  1.326
 U0Q  C10  N3   single    1.345  0.020  1.345
 U0Q  C10  N4   aromatic  1.330  0.020  1.330
 U0Q  C11  N4   aromatic  1.339  0.020  1.339
 U0Q  C11  N5   single    1.360  0.020  1.360
 U0Q  C15  N7   aromatic  1.325  0.020  1.325
 U0Q  C15  C12  aromatic  1.410  0.020  1.410
 U0Q  N7   N6   aromatic  1.321  0.020  1.321
 U0Q  C12  N5   single    1.386  0.020  1.386
 U0Q  C12  C13  aromatic  1.382  0.020  1.382
 U0Q  N6   C14  single    1.444  0.020  1.444
 U0Q  N6   C13  aromatic  1.348  0.020  1.348
 U0Q  C1   H1   single    0.970  0.020  1.090
 U0Q  C1   H2   single    0.970  0.020  1.090
 U0Q  C1   H3   single    0.970  0.020  1.090
 U0Q  C2   H4   single    0.970  0.020  1.090
 U0Q  C3   H5   single    0.970  0.020  1.090
 U0Q  C3   H6   single    0.970  0.020  1.090
 U0Q  C4   H7   single    0.970  0.020  1.090
 U0Q  C4   H8   single    0.970  0.020  1.090
 U0Q  C5   H9   single    0.970  0.020  1.090
 U0Q  C5   H10  single    0.970  0.020  1.090
 U0Q  N3   H11  single    0.890  0.020  1.040
 U0Q  N3   H12  single    0.890  0.020  1.040
 U0Q  N5   H13  single    0.860  0.020  1.020
 U0Q  C13  H14  single    0.930  0.020  1.080
 U0Q  C14  H15  single    0.970  0.020  1.090
 U0Q  C14  H16  single    0.970  0.020  1.090
 U0Q  C14  H17  single    0.970  0.020  1.090
 U0Q  C15  H18  single    0.930  0.020  1.080
 U0Q  C17  H19  single    0.970  0.020  1.090
 U0Q  C17  H20  single    0.970  0.020  1.090
 U0Q  C17  H21  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
 U0Q  H3   C1   H2   108.27  3.000
 U0Q  H3   C1   H1   108.25  3.000
 U0Q  H2   C1   H1   107.44  3.000
 U0Q  H3   C1   C2   110.56  3.000
 U0Q  H2   C1   C2   109.83  3.000
 U0Q  H1   C1   C2   112.36  3.000
 U0Q  H4   C2   N1   110.60  3.000
 U0Q  H4   C2   C3   107.83  3.000
 U0Q  N1   C2   C3   102.29  3.000
 U0Q  H4   C2   C1   109.50  3.000
 U0Q  N1   C2   C1   112.36  3.000
 U0Q  C3   C2   C1   113.99  3.000
 U0Q  H6   C3   H5   107.92  3.000
 U0Q  H6   C3   C4   110.49  3.000
 U0Q  H5   C3   C4   113.57  3.000
 U0Q  H6   C3   C2   110.16  3.000
 U0Q  H5   C3   C2   111.52  3.000
 U0Q  C4   C3   C2   103.14  3.000
 U0Q  H8   C4   H7   107.94  3.000
 U0Q  H8   C4   C5   110.40  3.000
 U0Q  H7   C4   C5   111.96  3.000
 U0Q  H8   C4   C3   110.29  3.000
 U0Q  H7   C4   C3   113.46  3.000
 U0Q  C5   C4   C3   102.76  3.000
 U0Q  H10  C5   H9   107.91  3.000
 U0Q  H10  C5   N1   111.08  3.000
 U0Q  H9   C5   N1   111.32  3.000
 U0Q  H10  C5   C4   112.68  3.000
 U0Q  H9   C5   C4   110.45  3.000
 U0Q  N1   C5   C4   103.43  3.000
 U0Q  C6   N1   C5   121.56  3.000
 U0Q  C6   N1   C2   121.60  3.000
 U0Q  C5   N1   C2   111.86  3.000
 U0Q  N9   C6   C7   108.20  3.000
 U0Q  C7   C6   N1   131.09  3.000
 U0Q  N9   C6   N1   120.70  3.000
 U0Q  C9   C7   C8   125.36  3.000
 U0Q  C9   C7   C6   106.69  3.000
 U0Q  C8   C7   C6   127.75  3.000
 U0Q  N2   C8   C7   180.00  3.000
 U0Q  C16  C9   C10  115.14  3.000
 U0Q  C10  C9   C7   138.07  3.000
 U0Q  C16  C9   C7   106.79  3.000
 U0Q  N4   C10  N3   117.69  3.000
 U0Q  N4   C10  C9   119.42  3.000
 U0Q  N3   C10  C9   122.88  3.000
 U0Q  H12  N3   H11  116.36  3.000
 U0Q  H12  N3   C10  120.94  3.000
 U0Q  H11  N3   C10  118.26  3.000
 U0Q  C11  N4   C10  119.02  3.000
 U0Q  N8   C11  N5   118.88  3.000
 U0Q  N5   C11  N4   114.18  3.000
 U0Q  N8   C11  N4   126.94  3.000
 U0Q  H13  N5   C12  116.80  3.000
 U0Q  H13  N5   C11  114.75  3.000
 U0Q  C12  N5   C11  128.45  3.000
 U0Q  C15  C12  C13  104.20  3.000
 U0Q  C13  C12  N5   124.19  3.000
 U0Q  C15  C12  N5   131.61  3.000
 U0Q  H14  C13  N6   122.40  3.000
 U0Q  H14  C13  C12  130.96  3.000
 U0Q  N6   C13  C12  106.63  3.000
 U0Q  N7   N6   C14  121.01  3.000
 U0Q  C14  N6   C13  126.56  3.000
 U0Q  N7   N6   C13  112.42  3.000
 U0Q  H17  C14  H16  108.96  3.000
 U0Q  H17  C14  H15  109.08  3.000
 U0Q  H16  C14  H15  109.03  3.000
 U0Q  H17  C14  N6   110.83  3.000
 U0Q  H16  C14  N6   110.66  3.000
 U0Q  H15  C14  N6   108.25  3.000
 U0Q  C15  N7   N6   106.12  3.000
 U0Q  H18  C15  N7   120.64  3.000
 U0Q  H18  C15  C12  128.73  3.000
 U0Q  N7   C15  C12  110.62  3.000
 U0Q  C16  N8   C11  112.82  3.000
 U0Q  N9   C16  N8   124.57  3.000
 U0Q  N8   C16  C9   126.66  3.000
 U0Q  N9   C16  C9   108.76  3.000
 U0Q  C17  N9   C16  123.79  3.000
 U0Q  C16  N9   C6   109.54  3.000
 U0Q  C17  N9   C6   126.04  3.000
 U0Q  H21  C17  H20  109.25  3.000
 U0Q  H21  C17  H19  108.54  3.000
 U0Q  H20  C17  H19  108.77  3.000
 U0Q  H21  C17  N9   111.95  3.000
 U0Q  H20  C17  N9   109.93  3.000
 U0Q  H19  C17  N9   108.34  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
 U0Q  CONST_01  C9   C16  N9   C6      0.00   0.0  0
 U0Q  CONST_02  N8   C16  N9   C6    180.00   0.0  0
 U0Q  CONST_03  C16  C9   C7   C6      0.00   0.0  0
 U0Q  CONST_04  C10  C9   C7   C6    180.00   0.0  0
 U0Q  CONST_05  C16  N9   C6   C7      0.00   0.0  0
 U0Q  CONST_06  N9   C16  C9   C7      0.00   0.0  0
 U0Q  CONST_07  N8   C16  C9   C7    180.00   0.0  0
 U0Q  CONST_08  N4   C10  C9   C7    180.00   0.0  0
 U0Q  CONST_09  N9   C6   C7   C9      0.00   0.0  0
 U0Q  CONST_10  C11  N8   C16  C9      0.00   0.0  0
 U0Q  CONST_11  C11  N4   C10  C9      0.00   0.0  0
 U0Q  CONST_12  N9   C16  C9   C10   180.00   0.0  0
 U0Q  CONST_13  N8   C16  C9   C10     0.00   0.0  0
 U0Q  CONST_14  N8   C11  N4   C10     0.00   0.0  0
 U0Q  CONST_15  C16  C9   C10  N4      0.00   0.0  0
 U0Q  CONST_16  C16  N8   C11  N4      0.00   0.0  0
 U0Q  CONST_17  N9   C16  N8   C11   180.00   0.0  0
 U0Q  CONST_18  N6   N7   C15  C12     0.00   0.0  0
 U0Q  CONST_19  N7   N6   C13  C12     0.00   0.0  0
 U0Q  CONST_20  N7   C15  C12  C13     0.00   0.0  0
 U0Q  CONST_21  C15  N7   N6   C13     0.00   0.0  0
 U0Q  CONST_22  C15  C12  C13  N6      0.00   0.0  0
 U0Q  CONST_23  C16  N9   C6   N1    180.00   0.0  0
 U0Q  CONST_24  C9   C7   C6   N1    180.00   0.0  0
 U0Q  CONST_25  C17  N9   C6   N1      0.00   0.0  0
 U0Q  CONST_26  C8   C7   C6   N1      0.00   0.0  0
 U0Q  CONST_27  C17  N9   C6   C7    180.00   0.0  0
 U0Q  CONST_28  N3   C10  C9   C7      0.00   0.0  0
 U0Q  CONST_29  N9   C6   C7   C8    180.00   0.0  0
 U0Q  CONST_30  C16  C9   C7   C8    180.00   0.0  0
 U0Q  CONST_31  C10  C9   C7   C8      0.00   0.0  0
 U0Q  CONST_32  C17  N9   C16  C9    180.00   0.0  0
 U0Q  CONST_33  N5   C11  N4   C10   180.00   0.0  0
 U0Q  CONST_34  C16  C9   C10  N3    180.00   0.0  0
 U0Q  CONST_35  C11  N4   C10  N3    180.00   0.0  0
 U0Q  CONST_36  C16  N8   C11  N5    180.00   0.0  0
 U0Q  CONST_37  N7   C15  C12  N5    180.00   0.0  0
 U0Q  CONST_38  N6   C13  C12  N5    180.00   0.0  0
 U0Q  CONST_39  C14  N6   C13  C12   180.00   0.0  0
 U0Q  CONST_40  C15  N7   N6   C14   180.00   0.0  0
 U0Q  CONST_41  C17  N9   C16  N8      0.00   0.0  0
 U0Q  CONST_42  H18  C15  C12  C13   180.00   0.0  0
 U0Q  CONST_43  H14  C13  N6   N7    180.00   0.0  0
 U0Q  CONST_44  H11  N3   C10  C9    180.00   0.0  0
 U0Q  CONST_45  H12  N3   C10  C9      0.00   0.0  0
 U0Q  Var_01    C5   C4   C3   C2     40.83  30.0  1
 U0Q  Var_02    C4   C5   N1   C2      8.72  30.0  1
 U0Q  Var_03    N9   C6   N1   C2    156.81  30.0  2
 U0Q  Var_04    N1   C5   C4   C3    -30.31  30.0  1
 U0Q  Var_05    C12  N5   C11  N4    179.74  30.0  2
 U0Q  Var_06    C15  C12  N5   C11     0.68  30.0  2
 U0Q  Var_07    H19  C17  N9   C6   -157.05  30.0  2
 U0Q  Var_08    H15  C14  N6   C13  -177.32  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
 U0Q  chir_01  C2  C3  C1  N1  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
 U0Q  plan-1  N5   0.020
 U0Q  plan-1  C12  0.020
 U0Q  plan-1  C13  0.020
 U0Q  plan-1  N6   0.020
 U0Q  plan-1  C14  0.020
 U0Q  plan-1  N7   0.020
 U0Q  plan-1  C15  0.020
 U0Q  plan-1  H14  0.020
 U0Q  plan-1  H18  0.020
 U0Q  plan-2  N1   0.020
 U0Q  plan-2  C6   0.020
 U0Q  plan-2  C7   0.020
 U0Q  plan-2  C8   0.020
 U0Q  plan-2  N2   0.020
 U0Q  plan-2  C9   0.020
 U0Q  plan-2  C10  0.020
 U0Q  plan-2  N3   0.020
 U0Q  plan-2  N4   0.020
 U0Q  plan-2  C11  0.020
 U0Q  plan-2  N5   0.020
 U0Q  plan-2  N8   0.020
 U0Q  plan-2  C16  0.020
 U0Q  plan-2  N9   0.020
 U0Q  plan-2  C17  0.020
 U0Q  plan-3  C10  0.020
 U0Q  plan-3  N3   0.020
 U0Q  plan-3  H11  0.020
 U0Q  plan-3  H12  0.020

