# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 14:49:45 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: 4-azanyl-2-[(1,3-dimethylpyrazol-4-yl)amino]-7-methyl-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(Nc4cn(C)nc4C)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
 U0N  U0N  4-azanyl-2-[(1,3-dimethylpyrazol-4-yl)amino]-7-methyl-6-[(2~{R})-2-methylpyrrolidin-1-yl]pyrrolo[2,3-d]pyrimidine-5-carbonitrile  ligand  50  27  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U0N
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
 U0N  C1   C  CH3   0  -0.664   5.3078  -5.4291  13.4303
 U0N  N1   N  NT    0  -0.540   4.3943  -7.0993  15.0251
 U0N  C2   C  CH1   0  -0.077   5.5014  -6.7668  14.1192
 U0N  N2   N  NS    0  -0.285   7.4244  -4.9866  16.6032
 U0N  C3   C  CH2   0  -0.455   5.5024  -7.9546  13.1642
 U0N  N3   N  NH2   0  -0.837   5.3743  -3.3976  19.2592
 U0N  C4   C  CH2   0  -0.473   5.1189  -9.1210  14.0623
 U0N  N4   N  N     0  -0.529   3.1839  -3.8218  19.7759
 U0N  C5   C  CH2   0  -0.283   4.0300  -8.5233  14.9452
 U0N  N5   N  NH1   0  -0.762   1.0303  -4.1794  20.3985
 U0N  C6   C  CR5   0   0.643   4.1265  -6.3589  16.1255
 U0N  N6   N  NR5   0  -0.275  -2.1198  -5.7842  20.0881
 U0N  C7   C  CR5   0  -0.168   4.9281  -5.4816  16.8560
 U0N  N7   N  N     0  -0.293  -2.3687  -4.9829  21.1114
 U0N  C8   C  CSP   0  -0.053   6.2962  -5.2342  16.6907
 U0N  N8   N  N     0  -0.528   1.8019  -5.3389  18.5602
 U0N  C9   C  CR56  0  -0.073   4.1041  -4.9502  17.9127
 U0N  N9   N  NR5   0  -0.577   2.8763  -6.3767  16.6987
 U0N  C10  C  CR6   0   0.424   4.2272  -4.0421  18.9808
 U0N  C11  C  CR6   0   0.575   2.0380  -4.4704  19.5349
 U0N  C12  C  CR5   0   0.054  -0.2522  -4.7046  20.4141
 U0N  C13  C  CR15  0   0.007  -0.8565  -5.6612  19.6245
 U0N  C15  C  CR5   0   0.212  -1.2508  -4.3115  21.3326
 U0N  C16  C  CH3   0  -0.751  -1.1341  -3.2943  22.4141
 U0N  C17  C  CR56  0   0.538   2.8597  -5.5425  17.7848
 U0N  C18  C  CH3   0  -0.557   1.6908  -6.9963  16.1482
 U0N  H1   H  HCH3  0   0.238   5.2918  -4.5957  14.1327
 U0N  H2   H  HCH3  0   0.237   6.1273  -5.2526  12.7331
 U0N  H3   H  HCH3  0   0.227   4.3728  -5.4205  12.8685
 U0N  H4   H  HCH1  0   0.243   6.4547  -6.7652  14.6602
 U0N  H5   H  HCH2  0   0.253   6.4698  -8.0780  12.6789
 U0N  H6   H  HCH2  0   0.234   4.7489  -7.8075  12.3853
 U0N  H7   H  HNH2  0   0.395   5.3551  -2.6593  19.9423
 U0N  H8   H  HNH2  0   0.406   6.1279  -3.3734  18.5947
 U0N  H9   H  HCH2  0   0.254   4.7629  -9.9917  13.5128
 U0N  H10  H  HCH2  0   0.239   5.9740  -9.4318  14.6660
 U0N  H11  H  HCH2  0   0.238   3.0504  -8.6567  14.4817
 U0N  H12  H  HCH2  0   0.251   3.9962  -8.9773  15.9371
 U0N  H13  H  HNH1  0   0.404   1.2646  -3.5197  21.1229
 U0N  H14  H  HCR5  0   0.296  -0.4928  -6.2397  18.7953
 U0N  H15  H  HCH3  0   0.253  -4.0095  -6.1068  19.2539
 U0N  H16  H  HCH3  0   0.255  -2.7397  -7.2282  18.7474
 U0N  H17  H  HCH3  0   0.253  -3.4488  -7.3748  20.3602
 U0N  H18  H  HCH3  0   0.255  -2.0801  -3.1863  22.9415
 U0N  H19  H  HCH3  0   0.246  -0.3729  -3.5678  23.1479
 U0N  H20  H  HCH3  0   0.245  -0.8605  -2.3146  22.0168
 U0N  H21  H  HCH3  0   0.284   0.8205  -6.5169  16.5873
 U0N  H22  H  HCH3  0   0.264   1.6617  -6.8516  15.0702
 U0N  H23  H  HCH3  0   0.259   1.6473  -8.0611  16.3695
 U0N  C14  C  CH3   0  -0.504  -3.1403  -6.6706  19.5891

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
 U0N  C3   C4   single    1.521  0.020  1.521
 U0N  C3   C2   single    1.524  0.020  1.524
 U0N  C1   C2   single    1.517  0.020  1.517
 U0N  C4   C5   single    1.524  0.020  1.524
 U0N  C2   N1   single    1.469  0.020  1.469
 U0N  C5   N1   single    1.472  0.020  1.472
 U0N  N1   C6   single    1.353  0.020  1.353
 U0N  C18  N9   single    1.447  0.020  1.447
 U0N  C6   N9   aromatic  1.376  0.020  1.376
 U0N  C6   C7   aromatic  1.395  0.020  1.395
 U0N  N2   C8   triple    1.158  0.020  1.158
 U0N  N9   C17  aromatic  1.370  0.020  1.370
 U0N  C8   C7   single    1.400  0.020  1.400
 U0N  C7   C9   aromatic  1.442  0.020  1.442
 U0N  C17  C9   aromatic  1.384  0.020  1.384
 U0N  C17  N8   aromatic  1.327  0.020  1.327
 U0N  C9   C10  aromatic  1.407  0.020  1.407
 U0N  N8   C11  aromatic  1.327  0.020  1.327
 U0N  C10  N3   single    1.345  0.020  1.345
 U0N  C10  N4   aromatic  1.330  0.020  1.330
 U0N  C11  N4   aromatic  1.339  0.020  1.339
 U0N  C11  N5   single    1.359  0.020  1.359
 U0N  C13  N6   aromatic  1.351  0.020  1.351
 U0N  C13  C12  aromatic  1.380  0.020  1.380
 U0N  C14  N6   single    1.441  0.020  1.441
 U0N  N6   N7   aromatic  1.323  0.020  1.323
 U0N  N5   C12  single    1.386  0.020  1.386
 U0N  C12  C15  aromatic  1.413  0.020  1.413
 U0N  N7   C15  aromatic  1.323  0.020  1.323
 U0N  C15  C16  single    1.489  0.020  1.489
 U0N  C1   H1   single    0.970  0.020  1.090
 U0N  C1   H2   single    0.970  0.020  1.090
 U0N  C1   H3   single    0.970  0.020  1.090
 U0N  C2   H4   single    0.970  0.020  1.090
 U0N  C3   H5   single    0.970  0.020  1.090
 U0N  C3   H6   single    0.970  0.020  1.090
 U0N  N3   H7   single    0.890  0.020  1.040
 U0N  N3   H8   single    0.890  0.020  1.040
 U0N  C4   H9   single    0.970  0.020  1.090
 U0N  C4   H10  single    0.970  0.020  1.090
 U0N  C5   H11  single    0.970  0.020  1.090
 U0N  C5   H12  single    0.970  0.020  1.090
 U0N  N5   H13  single    0.860  0.020  1.020
 U0N  C13  H14  single    0.930  0.020  1.080
 U0N  C14  H15  single    0.970  0.020  1.090
 U0N  C14  H16  single    0.970  0.020  1.090
 U0N  C14  H17  single    0.970  0.020  1.090
 U0N  C16  H18  single    0.970  0.020  1.090
 U0N  C16  H19  single    0.970  0.020  1.090
 U0N  C16  H20  single    0.970  0.020  1.090
 U0N  C18  H21  single    0.970  0.020  1.090
 U0N  C18  H22  single    0.970  0.020  1.090
 U0N  C18  H23  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
 U0N  H3   C1   H2   108.28  3.000
 U0N  H3   C1   H1   108.26  3.000
 U0N  H2   C1   H1   107.41  3.000
 U0N  H3   C1   C2   110.50  3.000
 U0N  H2   C1   C2   109.70  3.000
 U0N  H1   C1   C2   112.55  3.000
 U0N  C6   N1   C5   121.64  3.000
 U0N  C6   N1   C2   121.80  3.000
 U0N  C5   N1   C2   111.84  3.000
 U0N  H4   C2   C3   108.05  3.000
 U0N  H4   C2   N1   110.58  3.000
 U0N  C3   C2   N1   102.15  3.000
 U0N  H4   C2   C1   109.50  3.000
 U0N  N1   C2   C1   112.55  3.000
 U0N  C3   C2   C1   113.75  3.000
 U0N  H6   C3   H5   108.05  3.000
 U0N  H6   C3   C4   110.48  3.000
 U0N  H5   C3   C4   113.58  3.000
 U0N  H6   C3   C2   109.94  3.000
 U0N  H5   C3   C2   111.59  3.000
 U0N  C4   C3   C2   103.15  3.000
 U0N  H8   N3   H7   116.46  3.000
 U0N  H8   N3   C10  120.95  3.000
 U0N  H7   N3   C10  118.42  3.000
 U0N  H10  C4   H9   107.90  3.000
 U0N  H10  C4   C5   110.54  3.000
 U0N  H9   C4   C5   111.85  3.000
 U0N  H10  C4   C3   110.31  3.000
 U0N  H9   C4   C3   113.42  3.000
 U0N  C5   C4   C3   102.79  3.000
 U0N  C11  N4   C10  118.92  3.000
 U0N  H12  C5   H11  107.89  3.000
 U0N  H12  C5   C4   112.67  3.000
 U0N  H11  C5   C4   110.31  3.000
 U0N  H12  C5   N1   111.14  3.000
 U0N  H11  C5   N1   111.30  3.000
 U0N  C4   C5   N1   103.54  3.000
 U0N  H13  N5   C12  117.08  3.000
 U0N  H13  N5   C11  115.14  3.000
 U0N  C12  N5   C11  127.76  3.000
 U0N  N9   C6   C7   108.19  3.000
 U0N  C7   C6   N1   131.02  3.000
 U0N  N9   C6   N1   120.78  3.000
 U0N  C14  N6   C13  126.82  3.000
 U0N  C14  N6   N7   120.47  3.000
 U0N  C13  N6   N7   112.71  3.000
 U0N  C9   C7   C8   125.45  3.000
 U0N  C9   C7   C6   106.69  3.000
 U0N  C8   C7   C6   127.65  3.000
 U0N  C15  N7   N6   106.12  3.000
 U0N  C7   C8   N2   180.00  3.000
 U0N  C17  N8   C11  112.82  3.000
 U0N  C17  C9   C10  115.14  3.000
 U0N  C10  C9   C7   138.09  3.000
 U0N  C17  C9   C7   106.77  3.000
 U0N  C18  N9   C17  123.56  3.000
 U0N  C17  N9   C6   109.49  3.000
 U0N  C18  N9   C6   126.29  3.000
 U0N  C9   C10  N4   119.47  3.000
 U0N  N4   C10  N3   117.77  3.000
 U0N  C9   C10  N3   122.75  3.000
 U0N  N8   C11  N5   118.37  3.000
 U0N  N5   C11  N4   114.63  3.000
 U0N  N8   C11  N4   127.00  3.000
 U0N  C15  C12  C13  104.80  3.000
 U0N  C15  C12  N5   123.78  3.000
 U0N  C13  C12  N5   131.42  3.000
 U0N  H14  C13  C12  131.81  3.000
 U0N  H14  C13  N6   122.16  3.000
 U0N  C12  C13  N6   106.03  3.000
 U0N  C16  C15  C12  127.36  3.000
 U0N  C16  C15  N7   122.30  3.000
 U0N  C12  C15  N7   110.34  3.000
 U0N  H20  C16  H19  107.13  3.000
 U0N  H20  C16  H18  107.76  3.000
 U0N  H19  C16  H18  107.76  3.000
 U0N  H20  C16  C15  111.61  3.000
 U0N  H19  C16  C15  111.81  3.000
 U0N  H18  C16  C15  110.58  3.000
 U0N  N9   C17  C9   108.84  3.000
 U0N  C9   C17  N8   126.65  3.000
 U0N  N9   C17  N8   124.50  3.000
 U0N  H23  C18  H22  109.30  3.000
 U0N  H23  C18  H21  108.52  3.000
 U0N  H22  C18  H21  108.69  3.000
 U0N  H23  C18  N9   111.98  3.000
 U0N  H22  C18  N9   110.00  3.000
 U0N  H21  C18  N9   108.28  3.000
 U0N  H17  C14  H16  108.73  3.000
 U0N  H17  C14  H15  109.07  3.000
 U0N  H16  C14  H15  108.76  3.000
 U0N  H17  C14  N6   110.68  3.000
 U0N  H16  C14  N6   108.84  3.000
 U0N  H15  C14  N6   110.70  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
 U0N  CONST_01  C7   C9   C10  N4    180.00   0.0  0
 U0N  CONST_02  C17  C9   C10  N4      0.00   0.0  0
 U0N  CONST_03  C17  N8   C11  N4      0.00   0.0  0
 U0N  CONST_04  C9   C17  N9   C6      0.00   0.0  0
 U0N  CONST_05  N8   C17  N9   C6    180.00   0.0  0
 U0N  CONST_06  C17  C9   C7   C6      0.00   0.0  0
 U0N  CONST_07  C10  C9   C7   C6    180.00   0.0  0
 U0N  CONST_08  C15  C12  C13  N6      0.00   0.0  0
 U0N  CONST_09  C12  C15  N7   N6      0.00   0.0  0
 U0N  CONST_10  C17  N9   C6   C7      0.00   0.0  0
 U0N  CONST_11  N9   C17  C9   C7      0.00   0.0  0
 U0N  CONST_12  N8   C17  C9   C7    180.00   0.0  0
 U0N  CONST_13  C12  C13  N6   N7      0.00   0.0  0
 U0N  CONST_14  C13  C12  C15  N7      0.00   0.0  0
 U0N  CONST_15  C10  C9   C17  N8      0.00   0.0  0
 U0N  CONST_16  C10  N4   C11  N8      0.00   0.0  0
 U0N  CONST_17  N9   C6   C7   C9      0.00   0.0  0
 U0N  CONST_18  C11  N8   C17  C9      0.00   0.0  0
 U0N  CONST_19  C11  N4   C10  C9      0.00   0.0  0
 U0N  CONST_20  C10  C9   C17  N9    180.00   0.0  0
 U0N  CONST_21  C11  N8   C17  N9    180.00   0.0  0
 U0N  CONST_22  C15  N7   N6   C13     0.00   0.0  0
 U0N  CONST_23  C17  N9   C6   N1    180.00   0.0  0
 U0N  CONST_24  C9   C7   C6   N1    180.00   0.0  0
 U0N  CONST_25  C18  N9   C6   N1      0.00   0.0  0
 U0N  CONST_26  C8   C7   C6   N1      0.00   0.0  0
 U0N  CONST_27  C7   C9   C10  N3      0.00   0.0  0
 U0N  CONST_28  C17  C9   C10  N3    180.00   0.0  0
 U0N  CONST_29  C11  N4   C10  N3    180.00   0.0  0
 U0N  CONST_30  C17  N8   C11  N5    180.00   0.0  0
 U0N  CONST_31  C10  N4   C11  N5    180.00   0.0  0
 U0N  CONST_32  N6   C13  C12  N5    180.00   0.0  0
 U0N  CONST_33  N7   C15  C12  N5    180.00   0.0  0
 U0N  CONST_34  C16  C15  N7   N6    180.00   0.0  0
 U0N  CONST_35  C18  N9   C6   C7    180.00   0.0  0
 U0N  CONST_36  N9   C6   C7   C8    180.00   0.0  0
 U0N  CONST_37  C17  C9   C7   C8    180.00   0.0  0
 U0N  CONST_38  C10  C9   C7   C8      0.00   0.0  0
 U0N  CONST_39  C18  N9   C17  N8      0.00   0.0  0
 U0N  CONST_40  C18  N9   C17  C9    180.00   0.0  0
 U0N  CONST_41  C14  N6   C13  C12   180.00   0.0  0
 U0N  CONST_42  C16  C15  C12  C13   180.00   0.0  0
 U0N  CONST_43  C15  N7   N6   C14   180.00   0.0  0
 U0N  CONST_44  H14  C13  N6   N7    180.00   0.0  0
 U0N  CONST_45  H7   N3   C10  N4      0.00   0.0  0
 U0N  CONST_46  H8   N3   C10  N4    180.00   0.0  0
 U0N  Var_01    C3   C4   C5   N1    -29.66  30.0  1
 U0N  Var_02    C5   C4   C3   C2     40.74  30.0  1
 U0N  Var_03    C4   C5   N1   C2      7.71  30.0  1
 U0N  Var_04    N9   C6   N1   C2    157.69  30.0  2
 U0N  Var_05    C12  N5   C11  N4   -178.92  30.0  2
 U0N  Var_06    C13  C12  N5   C11     2.06  30.0  2
 U0N  Var_07    H21  C18  N9   C6   -157.14  30.0  2
 U0N  Var_08    H15  C14  N6   N7     59.86  30.0  2
 U0N  Var_09    H18  C16  C15  N7     -1.47  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
 U0N  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
 U0N  plan-1  N5   0.020
 U0N  plan-1  N6   0.020
 U0N  plan-1  N7   0.020
 U0N  plan-1  C12  0.020
 U0N  plan-1  C13  0.020
 U0N  plan-1  C15  0.020
 U0N  plan-1  C16  0.020
 U0N  plan-1  H14  0.020
 U0N  plan-1  C14  0.020
 U0N  plan-2  N1   0.020
 U0N  plan-2  N2   0.020
 U0N  plan-2  N3   0.020
 U0N  plan-2  N4   0.020
 U0N  plan-2  N5   0.020
 U0N  plan-2  C6   0.020
 U0N  plan-2  C7   0.020
 U0N  plan-2  C8   0.020
 U0N  plan-2  N8   0.020
 U0N  plan-2  C9   0.020
 U0N  plan-2  N9   0.020
 U0N  plan-2  C10  0.020
 U0N  plan-2  C11  0.020
 U0N  plan-2  C17  0.020
 U0N  plan-2  C18  0.020
 U0N  plan-3  N3   0.020
 U0N  plan-3  C10  0.020
 U0N  plan-3  H7   0.020
 U0N  plan-3  H8   0.020

