# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 21:32:49 2022
#   Inital geometry file: a 137 line input string
#   Ligand name: 4-azanyl-7-methyl-2-[[5-methyl-1-[(3~{S})-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
 U0T  U0T  4-azanyl-7-methyl-2-[[5-methyl-1-[(3~{S})-oxolan-3-yl]pyrazol-4-yl]amino]-6-[(2~{R})-2-methylpyrrolidin-1-yl]pyrrolo[2,3-d]pyrimidine-5-carbonitrile  ligand  58  31  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_U0T
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
 U0T  C1   C  CH3   0  -0.663   5.5930   -5.7637  13.3126
 U0T  N1   N  NT    0  -0.540   4.6410   -7.3676  14.9493
 U0T  O1   O  O2    0  -0.487  -3.9106   -7.5697  21.0776
 U0T  C2   C  CH1   0  -0.076   5.7764   -7.0664  14.0677
 U0T  N2   N  NS    0  -0.286   7.6271   -5.2211  16.5712
 U0T  C3   C  CH2   0  -0.456   5.8253   -8.2980  13.1707
 U0T  N3   N  NH2   0  -0.839   5.4723   -3.4655  19.0336
 U0T  C4   C  CH2   0  -0.471   5.4086   -9.4237  14.1048
 U0T  N4   N  N     0  -0.529   3.2678   -3.8741  19.4972
 U0T  C5   C  CH2   0  -0.284   4.2762   -8.7928  14.9064
 U0T  N5   N  NH1   0  -0.765   1.0777   -4.1433  20.0198
 U0T  C6   C  CR5   0   0.643   4.3373   -6.5849  16.0108
 U0T  N6   N  NR5   0  -0.319  -2.2766   -5.0814  20.5852
 U0T  C7   C  CR5   0  -0.166   5.1175   -5.6847  16.7360
 U0T  N7   N  N     0  -0.277  -2.1812   -5.5108  19.3347
 U0T  C8   C  CSP   0  -0.054   6.4930   -5.4533  16.6157
 U0T  N8   N  N     0  -0.521   1.9198   -5.4262  18.2897
 U0T  C9   C  CR56  0  -0.072   4.2568   -5.1023  17.7355
 U0T  N9   N  NR5   0  -0.576   3.0650   -6.5685  16.5333
 U0T  C10  C  CR6   0   0.424   4.3447   -4.1482  18.7657
 U0T  C11  C  CR6   0   0.570   2.1208   -4.5097  19.2274
 U0T  C12  C  CR5   0   0.034  -0.2226   -4.6334  19.9944
 U0T  C13  C  CR5   0   0.352  -1.1155   -4.5589  21.0494
 U0T  C14  C  CH3   0  -0.745  -0.9479   -4.0298  22.4292
 U0T  C15  C  CR15  0  -0.079  -0.9477   -5.2395  18.9504
 U0T  C16  C  CH1   0  -0.142  -3.4819   -5.2952  21.3648
 U0T  C17  C  CH2   0  -0.519  -4.7323   -5.4190  20.4990
 U0T  C18  C  CH2   0  -0.148  -4.8304   -6.9223  20.2082
 U0T  C19  C  CH2   0  -0.159  -3.4835   -6.6551  22.0582
 U0T  C20  C  CR56  0   0.531   3.0103   -5.6846  17.5789
 U0T  C21  C  CH3   0  -0.558   1.8998   -7.2049  15.9592
 U0T  H1   H  HCH3  0   0.237   5.5375   -4.9018  13.9779
 U0T  H2   H  HCH3  0   0.237   6.4374   -5.6040  12.6413
 U0T  H3   H  HCH3  0   0.227   4.6813   -5.7931  12.7145
 U0T  H4   H  HCH1  0   0.244   6.7098   -7.0290  14.6406
 U0T  H5   H  HCH2  0   0.253   6.8140   -8.4365  12.7346
 U0T  H6   H  HCH2  0   0.234   5.1077   -8.1953  12.3517
 U0T  H7   H  HNH2  0   0.395   5.5042   -2.9024  19.8667
 U0T  H8   H  HNH2  0   0.406   6.3566   -3.7560  18.6545
 U0T  H9   H  HCH2  0   0.253   5.0854  -10.3236  13.5827
 U0T  H10  H  HCH2  0   0.239   6.2362   -9.6960  14.7628
 U0T  H11  H  HCH2  0   0.238   3.3212   -8.9427  14.3983
 U0T  H12  H  HCH2  0   0.251   4.1894   -9.2074  15.9121
 U0T  H13  H  HNH1  0   0.399   1.3031   -3.4534  20.7181
 U0T  H14  H  HCH3  0   0.260  -1.5607   -3.1442  22.6081
 U0T  H15  H  HCH3  0   0.262  -1.2141   -4.7713  23.1842
 U0T  H16  H  HCH3  0   0.259   0.0886   -3.7506  22.6099
 U0T  H17  H  HCR5  0   0.269  -0.6154   -5.4859  17.9566
 U0T  H18  H  HCH1  0   0.286  -3.5633   -4.4782  22.0809
 U0T  H19  H  HCH2  0   0.267  -4.6896   -4.8128  19.5963
 U0T  H20  H  HCH2  0   0.266  -5.5869   -5.0796  21.0846
 U0T  H21  H  HCH2  0   0.213  -5.8461   -7.2920  20.3812
 U0T  H22  H  HCH2  0   0.220  -4.5552   -7.1558  19.1786
 U0T  H23  H  HCH2  0   0.212  -4.1703   -6.6198  22.9148
 U0T  H24  H  HCH2  0   0.243  -2.5001   -6.9551  22.4255
 U0T  H25  H  HCH3  0   0.286   1.0145   -6.7110  16.3494
 U0T  H26  H  HCH3  0   0.263   1.9121   -7.0963  14.8766
 U0T  H27  H  HCH3  0   0.259   1.8462   -8.2618  16.2140

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
 U0T  C3   C4   single    1.521  0.020  1.521
 U0T  C3   C2   single    1.524  0.020  1.524
 U0T  C1   C2   single    1.517  0.020  1.517
 U0T  C4   C5   single    1.524  0.020  1.524
 U0T  C2   N1   single    1.469  0.020  1.469
 U0T  C5   N1   single    1.472  0.020  1.472
 U0T  N1   C6   single    1.353  0.020  1.353
 U0T  C21  N9   single    1.446  0.020  1.446
 U0T  C6   N9   aromatic  1.376  0.020  1.376
 U0T  C6   C7   aromatic  1.395  0.020  1.395
 U0T  N9   C20  aromatic  1.370  0.020  1.370
 U0T  N2   C8   triple    1.159  0.020  1.159
 U0T  C8   C7   single    1.400  0.020  1.400
 U0T  C7   C9   aromatic  1.442  0.020  1.442
 U0T  C20  C9   aromatic  1.385  0.020  1.385
 U0T  C20  N8   aromatic  1.327  0.020  1.327
 U0T  C9   C10  aromatic  1.407  0.020  1.407
 U0T  N8   C11  aromatic  1.327  0.020  1.327
 U0T  C10  N3   single    1.345  0.020  1.345
 U0T  C10  N4   aromatic  1.330  0.020  1.330
 U0T  C15  N7   aromatic  1.320  0.020  1.320
 U0T  C15  C12  aromatic  1.408  0.020  1.408
 U0T  C11  N4   aromatic  1.339  0.020  1.339
 U0T  C11  N5   single    1.360  0.020  1.360
 U0T  N7   N6   aromatic  1.326  0.020  1.326
 U0T  N5   C12  single    1.390  0.020  1.390
 U0T  C12  C13  aromatic  1.384  0.020  1.384
 U0T  C18  C17  single    1.534  0.020  1.534
 U0T  C18  O1   single    1.422  0.020  1.422
 U0T  C17  C16  single    1.526  0.020  1.526
 U0T  N6   C13  aromatic  1.355  0.020  1.355
 U0T  N6   C16  single    1.451  0.020  1.451
 U0T  C13  C14  single    1.487  0.020  1.487
 U0T  O1   C19  single    1.407  0.020  1.407
 U0T  C16  C19  single    1.526  0.020  1.526
 U0T  C1   H1   single    0.970  0.020  1.090
 U0T  C1   H2   single    0.970  0.020  1.090
 U0T  C1   H3   single    0.970  0.020  1.090
 U0T  C2   H4   single    0.970  0.020  1.090
 U0T  C3   H5   single    0.970  0.020  1.090
 U0T  C3   H6   single    0.970  0.020  1.090
 U0T  N3   H7   single    0.890  0.020  1.040
 U0T  N3   H8   single    0.890  0.020  1.040
 U0T  C4   H9   single    0.970  0.020  1.090
 U0T  C4   H10  single    0.970  0.020  1.090
 U0T  C5   H11  single    0.970  0.020  1.090
 U0T  C5   H12  single    0.970  0.020  1.090
 U0T  N5   H13  single    0.860  0.020  1.020
 U0T  C14  H14  single    0.970  0.020  1.090
 U0T  C14  H15  single    0.970  0.020  1.090
 U0T  C14  H16  single    0.970  0.020  1.090
 U0T  C15  H17  single    0.930  0.020  1.080
 U0T  C16  H18  single    0.970  0.020  1.090
 U0T  C17  H19  single    0.970  0.020  1.090
 U0T  C17  H20  single    0.970  0.020  1.090
 U0T  C18  H21  single    0.970  0.020  1.090
 U0T  C18  H22  single    0.970  0.020  1.090
 U0T  C19  H23  single    0.970  0.020  1.090
 U0T  C19  H24  single    0.970  0.020  1.090
 U0T  C21  H25  single    0.970  0.020  1.090
 U0T  C21  H26  single    0.970  0.020  1.090
 U0T  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
 U0T  H3   C1   H2   108.28  3.000
 U0T  H3   C1   H1   108.27  3.000
 U0T  H2   C1   H1   107.42  3.000
 U0T  H3   C1   C2   110.54  3.000
 U0T  H2   C1   C2   109.79  3.000
 U0T  H1   C1   C2   112.41  3.000
 U0T  C6   N1   C5   121.82  3.000
 U0T  C6   N1   C2   121.72  3.000
 U0T  C5   N1   C2   111.88  3.000
 U0T  C19  O1   C18  109.06  3.000
 U0T  H4   C2   C3   107.93  3.000
 U0T  H4   C2   N1   110.59  3.000
 U0T  C3   C2   N1   102.26  3.000
 U0T  H4   C2   C1   109.51  3.000
 U0T  N1   C2   C1   112.43  3.000
 U0T  C3   C2   C1   113.88  3.000
 U0T  H6   C3   H5   107.92  3.000
 U0T  H6   C3   C4   110.46  3.000
 U0T  H5   C3   C4   113.60  3.000
 U0T  H6   C3   C2   110.10  3.000
 U0T  H5   C3   C2   111.55  3.000
 U0T  C4   C3   C2   103.17  3.000
 U0T  H8   N3   H7   116.50  3.000
 U0T  H8   N3   C10  121.05  3.000
 U0T  H7   N3   C10  118.39  3.000
 U0T  H10  C4   H9   107.91  3.000
 U0T  H10  C4   C5   110.45  3.000
 U0T  H9   C4   C5   111.94  3.000
 U0T  H10  C4   C3   110.31  3.000
 U0T  H9   C4   C3   113.48  3.000
 U0T  C5   C4   C3   102.72  3.000
 U0T  C11  N4   C10  119.01  3.000
 U0T  H12  C5   H11  107.88  3.000
 U0T  H12  C5   C4   112.74  3.000
 U0T  H11  C5   C4   110.38  3.000
 U0T  H12  C5   N1   111.14  3.000
 U0T  H11  C5   N1   111.30  3.000
 U0T  C4   C5   N1   103.42  3.000
 U0T  H13  N5   C12  117.62  3.000
 U0T  H13  N5   C11  114.63  3.000
 U0T  C12  N5   C11  127.72  3.000
 U0T  N9   C6   C7   108.19  3.000
 U0T  C7   C6   N1   130.96  3.000
 U0T  N9   C6   N1   120.83  3.000
 U0T  C16  N6   C13  125.75  3.000
 U0T  C16  N6   N7   121.25  3.000
 U0T  C13  N6   N7   112.73  3.000
 U0T  C9   C7   C8   125.40  3.000
 U0T  C9   C7   C6   106.69  3.000
 U0T  C8   C7   C6   127.71  3.000
 U0T  C15  N7   N6   105.98  3.000
 U0T  C7   C8   N2   180.00  3.000
 U0T  C20  N8   C11  112.87  3.000
 U0T  C20  C9   C10  115.11  3.000
 U0T  C10  C9   C7   138.09  3.000
 U0T  C20  C9   C7   106.80  3.000
 U0T  C21  N9   C20  123.68  3.000
 U0T  C20  N9   C6   109.54  3.000
 U0T  C21  N9   C6   126.09  3.000
 U0T  C9   C10  N4   119.45  3.000
 U0T  N4   C10  N3   117.68  3.000
 U0T  C9   C10  N3   122.85  3.000
 U0T  N8   C11  N5   118.80  3.000
 U0T  N5   C11  N4   114.31  3.000
 U0T  N8   C11  N4   126.89  3.000
 U0T  C15  C12  C13  104.84  3.000
 U0T  C13  C12  N5   124.79  3.000
 U0T  C15  C12  N5   130.32  3.000
 U0T  C14  C13  C12  130.81  3.000
 U0T  C14  C13  N6   123.47  3.000
 U0T  C12  C13  N6   105.71  3.000
 U0T  H16  C14  H15  106.96  3.000
 U0T  H16  C14  H14  107.41  3.000
 U0T  H15  C14  H14  107.52  3.000
 U0T  H16  C14  C13  110.64  3.000
 U0T  H15  C14  C13  111.88  3.000
 U0T  H14  C14  C13  112.17  3.000
 U0T  H17  C15  C12  128.60  3.000
 U0T  H17  C15  N7   120.68  3.000
 U0T  C12  C15  N7   110.72  3.000
 U0T  H18  C16  C19  111.68  3.000
 U0T  H18  C16  C17  111.87  3.000
 U0T  C19  C16  C17  100.64  3.000
 U0T  H18  C16  N6   107.74  3.000
 U0T  C19  C16  N6   112.09  3.000
 U0T  C17  C16  N6   112.81  3.000
 U0T  H20  C17  H19  107.63  3.000
 U0T  H20  C17  C18  110.90  3.000
 U0T  H19  C17  C18  113.02  3.000
 U0T  H20  C17  C16  108.20  3.000
 U0T  H19  C17  C16  113.17  3.000
 U0T  C18  C17  C16  103.85  3.000
 U0T  H22  C18  H21  108.11  3.000
 U0T  H22  C18  C17  111.87  3.000
 U0T  H21  C18  C17  111.12  3.000
 U0T  H22  C18  O1   108.45  3.000
 U0T  H21  C18  O1   110.48  3.000
 U0T  C17  C18  O1   106.79  3.000
 U0T  H24  C19  H23  108.04  3.000
 U0T  H24  C19  C16  113.37  3.000
 U0T  H23  C19  C16  109.04  3.000
 U0T  H24  C19  O1   109.22  3.000
 U0T  H23  C19  O1   112.00  3.000
 U0T  C16  C19  O1   105.23  3.000
 U0T  N9   C20  C9   108.77  3.000
 U0T  C9   C20  N8   126.67  3.000
 U0T  N9   C20  N8   124.54  3.000
 U0T  H27  C21  H26  109.29  3.000
 U0T  H27  C21  H25  108.50  3.000
 U0T  H26  C21  H25  108.74  3.000
 U0T  H27  C21  N9   111.96  3.000
 U0T  H26  C21  N9   109.99  3.000
 U0T  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
 U0T  CONST_01  C7   C9   C10  N4    180.00   0.0  0
 U0T  CONST_02  C20  C9   C10  N4      0.00   0.0  0
 U0T  CONST_03  C20  N8   C11  N4      0.00   0.0  0
 U0T  CONST_04  C9   C20  N9   C6      0.00   0.0  0
 U0T  CONST_05  N8   C20  N9   C6    180.00   0.0  0
 U0T  CONST_06  C20  C9   C7   C6      0.00   0.0  0
 U0T  CONST_07  C10  C9   C7   C6    180.00   0.0  0
 U0T  CONST_08  C12  C15  N7   N6      0.00   0.0  0
 U0T  CONST_09  C15  C12  C13  N6      0.00   0.0  0
 U0T  CONST_10  C20  N9   C6   C7      0.00   0.0  0
 U0T  CONST_11  N9   C20  C9   C7      0.00   0.0  0
 U0T  CONST_12  N8   C20  C9   C7    180.00   0.0  0
 U0T  CONST_13  C13  C12  C15  N7      0.00   0.0  0
 U0T  CONST_14  C12  C13  N6   N7      0.00   0.0  0
 U0T  CONST_15  C10  C9   C20  N8      0.00   0.0  0
 U0T  CONST_16  C10  N4   C11  N8      0.00   0.0  0
 U0T  CONST_17  N9   C6   C7   C9      0.00   0.0  0
 U0T  CONST_18  C11  N8   C20  C9      0.00   0.0  0
 U0T  CONST_19  C11  N4   C10  C9      0.00   0.0  0
 U0T  CONST_20  C10  C9   C20  N9    180.00   0.0  0
 U0T  CONST_21  C11  N8   C20  N9    180.00   0.0  0
 U0T  CONST_22  C15  N7   N6   C13     0.00   0.0  0
 U0T  CONST_23  C20  N9   C6   N1    180.00   0.0  0
 U0T  CONST_24  C9   C7   C6   N1    180.00   0.0  0
 U0T  CONST_25  C16  N6   C13  C12   180.00   0.0  0
 U0T  CONST_26  C16  N6   N7   C15   180.00   0.0  0
 U0T  CONST_27  C21  N9   C6   N1      0.00   0.0  0
 U0T  CONST_28  C8   C7   C6   N1      0.00   0.0  0
 U0T  CONST_29  C7   C9   C10  N3      0.00   0.0  0
 U0T  CONST_30  C20  C9   C10  N3    180.00   0.0  0
 U0T  CONST_31  C11  N4   C10  N3    180.00   0.0  0
 U0T  CONST_32  C20  N8   C11  N5    180.00   0.0  0
 U0T  CONST_33  C10  N4   C11  N5    180.00   0.0  0
 U0T  CONST_34  N7   C15  C12  N5    180.00   0.0  0
 U0T  CONST_35  N6   C13  C12  N5    180.00   0.0  0
 U0T  CONST_36  C21  N9   C6   C7    180.00   0.0  0
 U0T  CONST_37  C14  C13  N6   N7    180.00   0.0  0
 U0T  CONST_38  N9   C6   C7   C8    180.00   0.0  0
 U0T  CONST_39  C20  C9   C7   C8    180.00   0.0  0
 U0T  CONST_40  C10  C9   C7   C8      0.00   0.0  0
 U0T  CONST_41  C21  N9   C20  N8      0.00   0.0  0
 U0T  CONST_42  C21  N9   C20  C9    180.00   0.0  0
 U0T  CONST_43  C15  C12  C13  C14   180.00   0.0  0
 U0T  CONST_44  C16  N6   C13  C14     0.00   0.0  0
 U0T  CONST_45  H17  C15  N7   N6    180.00   0.0  0
 U0T  CONST_46  H7   N3   C10  N4      0.00   0.0  0
 U0T  CONST_47  H8   N3   C10  N4    180.00   0.0  0
 U0T  Var_01    C3   C4   C5   N1    -30.47  30.0  1
 U0T  Var_02    C16  C17  C18  O1     11.94  30.0  1
 U0T  Var_03    C5   C4   C3   C2     40.90  30.0  1
 U0T  Var_04    C4   C5   N1   C2      8.94  30.0  1
 U0T  Var_05    N9   C6   N1   C2    156.76  30.0  2
 U0T  Var_06    C12  N5   C11  N4   -179.07  30.0  2
 U0T  Var_07    C15  C12  N5   C11   -24.48  30.0  2
 U0T  Var_08    H23  C19  O1   C18    85.77  30.0  1
 U0T  Var_09    H25  C21  N9   C6   -157.89  30.0  2
 U0T  Var_10    H14  C14  C13  N6    -65.52  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
 U0T  chir_01  C2   C3   C1  N1   negativ
 U0T  chir_02  C16  C17  N6  C19  positiv

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
 U0T  plan-1  N5   0.020
 U0T  plan-1  N6   0.020
 U0T  plan-1  N7   0.020
 U0T  plan-1  C12  0.020
 U0T  plan-1  C13  0.020
 U0T  plan-1  C14  0.020
 U0T  plan-1  C15  0.020
 U0T  plan-1  C16  0.020
 U0T  plan-1  H17  0.020
 U0T  plan-2  N3   0.020
 U0T  plan-2  C10  0.020
 U0T  plan-2  H7   0.020
 U0T  plan-2  H8   0.020
 U0T  plan-3  N1   0.020
 U0T  plan-3  N2   0.020
 U0T  plan-3  N3   0.020
 U0T  plan-3  N4   0.020
 U0T  plan-3  N5   0.020
 U0T  plan-3  C6   0.020
 U0T  plan-3  C7   0.020
 U0T  plan-3  C8   0.020
 U0T  plan-3  N8   0.020
 U0T  plan-3  C9   0.020
 U0T  plan-3  N9   0.020
 U0T  plan-3  C10  0.020
 U0T  plan-3  C11  0.020
 U0T  plan-3  C20  0.020
 U0T  plan-3  C21  0.020

