# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 11:59:15 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 3-[3-[2-[(3,4,5-trimethoxyphenyl)amino]pyrrolo[2,3-d]pyrimidin-7-yl]phenyl]propanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(Nc2ncc3ccn(c4cccc(CCC#N)c4)c3n2)cc(OC)c1OC
#
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
 JL2  JL2  3-[3-[2-[(3,4,5-trimethoxyphenyl)amino]pyrrolo[2,3-d]pyrimidin-7-yl]phenyl]propanenitrile  ligand  55  32  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JL2
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
 JL2  C4   C  CR6   0   0.424    2.9500  -0.2075  -0.1485
 JL2  C14  C  CR16  0  -0.299   -3.1910  -0.8804  -1.3882
 JL2  C5   C  CR16  0  -0.521    3.7512   0.9281  -0.0483
 JL2  C6   C  CR6   0   0.377    5.1360   0.7800   0.0201
 JL2  C11  C  CR15  0  -0.009   -3.3876   2.5880  -0.3179
 JL2  C7   C  CR6   0   0.599    0.6589   0.8404  -0.2109
 JL2  C8   C  CR56  0   0.531   -1.4854   1.4270  -0.3110
 JL2  C9   C  CR56  0  -0.054   -1.1722   2.7952  -0.1794
 JL2  C10  C  CR16  0  -0.036    0.1806   3.0683  -0.0718
 JL2  C12  C  CR15  0  -0.440   -2.4081   3.5158  -0.1885
 JL2  C13  C  CR6   0   0.358   -3.5824   0.1167  -0.5014
 JL2  N1   N  NH1   0  -0.783    1.5636  -0.1829  -0.2260
 JL2  N2   N  N     0  -0.492   -0.6084   0.4443  -0.3225
 JL2  C3   C  CR16  0  -0.549    3.5356  -1.4777  -0.1818
 JL2  N3   N  N     0  -0.480    1.0858   2.1017  -0.0902
 JL2  C1   C  CR6   0   0.147    5.7322  -0.4798  -0.0229
 JL2  C2   C  CR6   0   0.350    4.9165  -1.6109  -0.1140
 JL2  N4   N  NR5   0  -0.637   -2.8410   1.3118  -0.3979
 JL2  C15  C  CR16  0  -0.237   -3.9420  -2.0421  -1.4713
 JL2  C16  C  CR16  0  -0.309   -5.0804  -2.2063  -0.6945
 JL2  C17  C  CR6   0   0.130   -5.4789  -1.2083   0.1884
 JL2  C18  C  CR16  0  -0.355   -4.7155  -0.0498   0.2857
 JL2  C19  C  CH2   0  -0.520   -6.7270  -1.3593   1.0116
 JL2  C20  C  CH2   0  -0.532   -7.9087  -0.6565   0.3265
 JL2  C21  C  CSP   0   0.119   -9.1342  -0.7750   1.1010
 JL2  N5   N  NS    0  -0.273  -10.0971  -0.8782   1.7225
 JL2  O1   O  O2    0  -0.468    5.9860   1.8171   0.1222
 JL2  C22  C  CH3   0  -0.438    5.4551   3.1261   0.1657
 JL2  O2   O  O2    0  -0.483    7.0873  -0.6084   0.0072
 JL2  C23  C  CH3   0  -0.406    7.6324  -0.7371   1.3120
 JL2  O3   O  O2    0  -0.465    5.5602  -2.7905  -0.1374
 JL2  C24  C  CH3   0  -0.438    4.7985  -3.9745  -0.2639
 JL2  H2   H  HCR6  0   0.308    3.2906   1.9010  -0.0225
 JL2  H3   H  HCR5  0   0.302   -4.4551   2.7199  -0.3874
 JL2  H4   H  HCR6  0   0.272    0.5524   4.0821   0.0332
 JL2  H5   H  HCR5  0   0.263   -2.5489   4.5821  -0.1219
 JL2  H6   H  HNH1  0   0.408    1.1252  -1.0864  -0.3186
 JL2  H7   H  HCR6  0   0.287    2.8981  -2.3487  -0.2584
 JL2  H8   H  HCR6  0   0.264   -3.6401  -2.8225  -2.1573
 JL2  H9   H  HCR6  0   0.257   -5.6607  -3.1177  -0.7719
 JL2  H10  H  HCR6  0   0.272   -4.9989   0.7224   0.9920
 JL2  H11  H  HCH2  0   0.276   -6.9645  -2.4154   1.1447
 JL2  H12  H  HCH2  0   0.276   -6.5806  -0.9327   2.0052
 JL2  H13  H  HCH2  0   0.314   -7.6983   0.4057   0.1868
 JL2  H14  H  HCH2  0   0.315   -8.0897  -1.0820  -0.6623
 JL2  H15  H  HCH3  0   0.261    6.3034   3.7984   0.2682
 JL2  H16  H  HCH3  0   0.228    4.9139   3.3791  -0.7498
 JL2  H17  H  HCH3  0   0.227    4.7884   3.2697   1.0198
 JL2  H18  H  HCH3  0   0.218    7.4389   0.1480   1.9233
 JL2  H19  H  HCH3  0   0.218    7.2394  -1.6141   1.8328
 JL2  H20  H  HCH3  0   0.234    8.7096  -0.8536   1.2019
 JL2  H21  H  HCH3  0   0.228    4.1089  -4.1093   0.5732
 JL2  H22  H  HCH3  0   0.229    4.2295  -3.9952  -1.1968
 JL2  H23  H  HCH3  0   0.262    5.5075  -4.7985  -0.2679
 JL2  H1   H  HCR6  0   0.273   -2.3168  -0.7528  -2.0103

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
 JL2  C19  C20  single    1.536  0.020  1.536
 JL2  C19  C17  single    1.503  0.020  1.503
 JL2  C20  C21  single    1.455  0.020  1.455
 JL2  C17  C18  aromatic  1.391  0.020  1.391
 JL2  C17  C16  aromatic  1.391  0.020  1.391
 JL2  C18  C13  aromatic  1.390  0.020  1.390
 JL2  C21  N5   triple    1.151  0.020  1.151
 JL2  C11  C12  aromatic  1.355  0.020  1.355
 JL2  C11  N4   aromatic  1.391  0.020  1.391
 JL2  C12  C9   aromatic  1.431  0.020  1.431
 JL2  C22  O1   single    1.413  0.020  1.413
 JL2  C16  C15  aromatic  1.388  0.020  1.388
 JL2  C13  N4   single    1.410  0.020  1.410
 JL2  C13  C14  aromatic  1.391  0.020  1.391
 JL2  N4   C8   aromatic  1.363  0.020  1.363
 JL2  C9   C8   aromatic  1.410  0.020  1.410
 JL2  C9   C10  aromatic  1.384  0.020  1.384
 JL2  C8   N2   aromatic  1.317  0.020  1.317
 JL2  C10  N3   aromatic  1.324  0.020  1.324
 JL2  O1   C6   single    1.345  0.020  1.345
 JL2  C15  C14  aromatic  1.386  0.020  1.386
 JL2  N2   C7   aromatic  1.332  0.020  1.332
 JL2  N3   C7   aromatic  1.337  0.020  1.337
 JL2  C5   C6   aromatic  1.394  0.020  1.394
 JL2  C5   C4   aromatic  1.393  0.020  1.393
 JL2  C23  O2   single    1.420  0.020  1.420
 JL2  C7   N1   single    1.366  0.020  1.366
 JL2  C6   C1   aromatic  1.394  0.020  1.394
 JL2  N1   C4   single    1.389  0.020  1.389
 JL2  C4   C3   aromatic  1.399  0.020  1.399
 JL2  C1   O2   single    1.362  0.020  1.362
 JL2  C1   C2   aromatic  1.398  0.020  1.398
 JL2  C3   C2   aromatic  1.389  0.020  1.389
 JL2  C2   O3   single    1.344  0.020  1.344
 JL2  O3   C24  single    1.414  0.020  1.414
 JL2  C14  H1   single    0.930  0.020  1.080
 JL2  C5   H2   single    0.930  0.020  1.080
 JL2  C11  H3   single    0.930  0.020  1.080
 JL2  C10  H4   single    0.930  0.020  1.080
 JL2  C12  H5   single    0.930  0.020  1.080
 JL2  N1   H6   single    0.860  0.020  1.020
 JL2  C3   H7   single    0.930  0.020  1.080
 JL2  C15  H8   single    0.930  0.020  1.080
 JL2  C16  H9   single    0.930  0.020  1.080
 JL2  C18  H10  single    0.930  0.020  1.080
 JL2  C19  H11  single    0.970  0.020  1.090
 JL2  C19  H12  single    0.970  0.020  1.090
 JL2  C20  H13  single    0.970  0.020  1.090
 JL2  C20  H14  single    0.970  0.020  1.090
 JL2  C22  H15  single    0.970  0.020  1.090
 JL2  C22  H16  single    0.970  0.020  1.090
 JL2  C22  H17  single    0.970  0.020  1.090
 JL2  C23  H18  single    0.970  0.020  1.090
 JL2  C23  H19  single    0.970  0.020  1.090
 JL2  C23  H20  single    0.970  0.020  1.090
 JL2  C24  H21  single    0.970  0.020  1.090
 JL2  C24  H22  single    0.970  0.020  1.090
 JL2  C24  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
 JL2  C3   C4   N1   115.63  3.000
 JL2  C3   C4   C5   120.06  3.000
 JL2  N1   C4   C5   124.31  3.000
 JL2  H1   C14  C15  120.19  3.000
 JL2  H1   C14  C13  120.68  3.000
 JL2  C15  C14  C13  119.13  3.000
 JL2  H2   C5   C6   121.31  3.000
 JL2  H2   C5   C4   119.48  3.000
 JL2  C6   C5   C4   119.21  3.000
 JL2  O1   C6   C1   115.40  3.000
 JL2  C1   C6   C5   121.27  3.000
 JL2  O1   C6   C5   123.33  3.000
 JL2  H3   C11  N4   119.85  3.000
 JL2  H3   C11  C12  129.66  3.000
 JL2  N4   C11  C12  110.46  3.000
 JL2  N3   C7   N2   126.28  3.000
 JL2  N3   C7   N1   119.75  3.000
 JL2  N2   C7   N1   113.97  3.000
 JL2  N4   C8   N2   126.76  3.000
 JL2  N2   C8   C9   125.24  3.000
 JL2  N4   C8   C9   107.99  3.000
 JL2  C12  C9   C10  138.19  3.000
 JL2  C10  C9   C8   114.57  3.000
 JL2  C12  C9   C8   107.23  3.000
 JL2  H4   C10  N3   116.68  3.000
 JL2  H4   C10  C9   121.79  3.000
 JL2  N3   C10  C9   121.52  3.000
 JL2  H5   C12  C9   127.65  3.000
 JL2  H5   C12  C11  126.07  3.000
 JL2  C9   C12  C11  106.27  3.000
 JL2  C18  C13  N4   119.25  3.000
 JL2  N4   C13  C14  120.42  3.000
 JL2  C18  C13  C14  120.32  3.000
 JL2  H6   N1   C7   112.60  3.000
 JL2  H6   N1   C4   115.04  3.000
 JL2  C7   N1   C4   132.36  3.000
 JL2  C8   N2   C7   114.25  3.000
 JL2  H7   C3   C2   120.80  3.000
 JL2  H7   C3   C4   119.07  3.000
 JL2  C2   C3   C4   120.13  3.000
 JL2  C10  N3   C7   118.13  3.000
 JL2  O2   C1   C2   120.40  3.000
 JL2  C2   C1   C6   118.92  3.000
 JL2  O2   C1   C6   120.68  3.000
 JL2  O3   C2   C1   115.59  3.000
 JL2  O3   C2   C3   124.02  3.000
 JL2  C1   C2   C3   120.39  3.000
 JL2  C13  N4   C8   126.81  3.000
 JL2  C8   N4   C11  108.04  3.000
 JL2  C13  N4   C11  125.12  3.000
 JL2  H8   C15  C16  119.89  3.000
 JL2  H8   C15  C14  119.44  3.000
 JL2  C16  C15  C14  120.67  3.000
 JL2  H9   C16  C17  119.71  3.000
 JL2  H9   C16  C15  119.93  3.000
 JL2  C17  C16  C15  120.36  3.000
 JL2  C19  C17  C18  120.08  3.000
 JL2  C18  C17  C16  119.01  3.000
 JL2  C19  C17  C16  120.90  3.000
 JL2  H10  C18  C17  119.69  3.000
 JL2  H10  C18  C13  119.79  3.000
 JL2  C17  C18  C13  120.51  3.000
 JL2  H12  C19  H11  107.26  3.000
 JL2  H12  C19  C20  109.30  3.000
 JL2  H11  C19  C20  109.27  3.000
 JL2  H12  C19  C17  110.37  3.000
 JL2  H11  C19  C17  110.18  3.000
 JL2  C20  C19  C17  110.40  3.000
 JL2  H14  C20  H13  107.18  3.000
 JL2  H14  C20  C21  108.11  3.000
 JL2  H13  C20  C21  108.05  3.000
 JL2  H14  C20  C19  110.69  3.000
 JL2  H13  C20  C19  110.73  3.000
 JL2  C21  C20  C19  111.92  3.000
 JL2  N5   C21  C20  180.00  3.000
 JL2  C22  O1   C6   118.64  3.000
 JL2  H17  C22  H16  108.79  3.000
 JL2  H17  C22  H15  108.73  3.000
 JL2  H16  C22  H15  108.79  3.000
 JL2  H17  C22  O1   112.02  3.000
 JL2  H16  C22  O1   111.99  3.000
 JL2  H15  C22  O1   106.41  3.000
 JL2  C23  O2   C1   114.26  3.000
 JL2  H20  C23  H19  108.54  3.000
 JL2  H20  C23  H18  108.56  3.000
 JL2  H19  C23  H18  108.64  3.000
 JL2  H20  C23  O2   107.24  3.000
 JL2  H19  C23  O2   111.87  3.000
 JL2  H18  C23  O2   111.88  3.000
 JL2  C24  O3   C2   118.60  3.000
 JL2  H23  C24  H22  108.79  3.000
 JL2  H23  C24  H21  108.71  3.000
 JL2  H22  C24  H21  108.84  3.000
 JL2  H23  C24  O3   106.49  3.000
 JL2  H22  C24  O3   111.89  3.000
 JL2  H21  C24  O3   112.01  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
 JL2  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 JL2  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 JL2  CONST_03  C17  C18  C13  C14     0.00   0.0  0
 JL2  CONST_06  C17  C16  C15  C14     0.00   0.0  0
 JL2  CONST_07  C2   C1   C6   C5      0.00   0.0  0
 JL2  CONST_08  C2   C3   C4   C5      0.00   0.0  0
 JL2  CONST_09  C3   C4   C5   C6      0.00   0.0  0
 JL2  CONST_10  C3   C2   C1   C6      0.00   0.0  0
 JL2  CONST_11  C8   C9   C12  C11     0.00   0.0  0
 JL2  CONST_12  C10  C9   C12  C11   180.00   0.0  0
 JL2  CONST_14  C9   C8   N4   C11     0.00   0.0  0
 JL2  CONST_15  N2   C8   N4   C11   180.00   0.0  0
 JL2  CONST_16  N4   C8   N2   C7    180.00   0.0  0
 JL2  CONST_17  C9   C8   N2   C7      0.00   0.0  0
 JL2  CONST_18  C9   C10  N3   C7      0.00   0.0  0
 JL2  CONST_19  C12  C11  N4   C8      0.00   0.0  0
 JL2  CONST_21  N3   C10  C9   C8      0.00   0.0  0
 JL2  CONST_22  N3   C7   N2   C8      0.00   0.0  0
 JL2  CONST_23  N4   C11  C12  C9      0.00   0.0  0
 JL2  CONST_24  C13  N4   C8   C9    180.00   0.0  0
 JL2  CONST_25  N4   C8   C9   C10   180.00   0.0  0
 JL2  CONST_26  N2   C8   C9   C10     0.00   0.0  0
 JL2  CONST_27  N2   C7   N3   C10     0.00   0.0  0
 JL2  CONST_28  C13  N4   C11  C12   180.00   0.0  0
 JL2  CONST_29  N4   C8   C9   C12     0.00   0.0  0
 JL2  CONST_30  N2   C8   C9   C12   180.00   0.0  0
 JL2  CONST_31  N3   C10  C9   C12   180.00   0.0  0
 JL2  CONST_32  C16  C17  C18  C13     0.00   0.0  0
 JL2  CONST_33  N2   C8   N4   C13     0.00   0.0  0
 JL2  CONST_34  C16  C15  C14  C13     0.00   0.0  0
 JL2  CONST_35  C17  C18  C13  N4    180.00   0.0  0
 JL2  CONST_36  C15  C14  C13  N4    180.00   0.0  0
 JL2  CONST_37  C18  C17  C16  C15     0.00   0.0  0
 JL2  CONST_38  C18  C13  C14  C15     0.00   0.0  0
 JL2  CONST_39  O1   C6   C5   C4    180.00   0.0  0
 JL2  CONST_40  O3   C2   C3   C4    180.00   0.0  0
 JL2  CONST_41  O2   C1   C6   C5    180.00   0.0  0
 JL2  CONST_42  N1   C4   C5   C6    180.00   0.0  0
 JL2  CONST_43  O3   C2   C1   C6    180.00   0.0  0
 JL2  CONST_44  N1   C7   N2   C8    180.00   0.0  0
 JL2  CONST_45  N1   C7   N3   C10   180.00   0.0  0
 JL2  CONST_46  C19  C17  C18  C13   180.00   0.0  0
 JL2  CONST_47  C2   C3   C4   N1    180.00   0.0  0
 JL2  CONST_48  O2   C1   C2   C3    180.00   0.0  0
 JL2  CONST_49  O1   C6   C1   C2    180.00   0.0  0
 JL2  CONST_50  C19  C17  C16  C15   180.00   0.0  0
 JL2  CONST_51  H10  C18  C13  C14   180.00   0.0  0
 JL2  CONST_52  H9   C16  C15  C14   180.00   0.0  0
 JL2  CONST_53  H7   C3   C4   C5    180.00   0.0  0
 JL2  CONST_54  H4   C10  N3   C7    180.00   0.0  0
 JL2  CONST_55  H3   C11  N4   C8    180.00   0.0  0
 JL2  CONST_56  H5   C12  C9   C8    180.00   0.0  0
 JL2  CONST_57  H8   C15  C14  C13   180.00   0.0  0
 JL2  CONST_58  H2   C5   C4   C3    180.00   0.0  0
 JL2  CONST_59  H1   C14  C13  N4      0.00   0.0  0
 JL2  Var_01    N2   C7   N1   C4    179.37  30.0  1
 JL2  Var_02    C7   N1   C4   C5     -0.98  30.0  3
 JL2  Var_03    C20  C19  C17  C16   -96.18  30.0  2
 JL2  Var_04    C21  C20  C19  C17  -179.63  30.0  3
 JL2  Var_05    H15  C22  O1   C6    178.88  30.0  3
 JL2  Var_06    H18  C23  O2   C1    -62.29  30.0  3
 JL2  Var_07    H21  C24  O3   C2    -61.64  30.0  3

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
 JL2  plan-1  C4   0.020
 JL2  plan-1  C5   0.020
 JL2  plan-1  C6   0.020
 JL2  plan-1  N1   0.020
 JL2  plan-1  C3   0.020
 JL2  plan-1  C1   0.020
 JL2  plan-1  C2   0.020
 JL2  plan-1  O1   0.020
 JL2  plan-1  O2   0.020
 JL2  plan-1  O3   0.020
 JL2  plan-1  H2   0.020
 JL2  plan-1  H7   0.020
 JL2  plan-2  C14  0.020
 JL2  plan-2  C13  0.020
 JL2  plan-2  N4   0.020
 JL2  plan-2  C15  0.020
 JL2  plan-2  C16  0.020
 JL2  plan-2  C17  0.020
 JL2  plan-2  C18  0.020
 JL2  plan-2  C19  0.020
 JL2  plan-2  H8   0.020
 JL2  plan-2  H9   0.020
 JL2  plan-2  H10  0.020
 JL2  plan-2  H1   0.020
 JL2  plan-3  C11  0.020
 JL2  plan-3  C7   0.020
 JL2  plan-3  C8   0.020
 JL2  plan-3  C9   0.020
 JL2  plan-3  C10  0.020
 JL2  plan-3  C12  0.020
 JL2  plan-3  C13  0.020
 JL2  plan-3  N1   0.020
 JL2  plan-3  N2   0.020
 JL2  plan-3  N3   0.020
 JL2  plan-3  N4   0.020
 JL2  plan-3  H3   0.020
 JL2  plan-3  H4   0.020
 JL2  plan-3  H5   0.020

