# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 20:21:54 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: (2~{R})-2-[[6-ethyl-5-(1~{H}-indol-4-yl)thieno[2,3-d]pyrimidin-4-yl]amino]-3-phenyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1sc2ncnc(N[C@H](Cc3ccccc3)C(O)=O)c2c1c4cccc5[nH]ccc45
#
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
 JLE  JLE  '(2~{R})-2-[[6-ethyl-5-(1~{H}-indol-4-yl)thieno[2,3-d]pyrimidin-4-yl]amino]-3-phenyl-propanoic acid'  ligand  54  32  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JLE
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
 JLE  C5   C  CR56  0  -0.004  -1.3596  -1.4062   0.2868
 JLE  C6   C  CR56  0  -0.027  -2.2375  -2.3139   0.8727
 JLE  C4   C  CR6   0   0.491  -0.0584  -1.9186   0.0448
 JLE  C2   C  CR16  0   0.042  -0.7311  -3.9408   0.8773
 JLE  C8   C  CR5   0  -0.252  -3.2418  -0.0668   0.5078
 JLE  N3   N  N     0  -0.434  -1.9597  -3.5802   1.1835
 JLE  C25  C  CR16  0  -0.271   3.7461   1.9873   2.2979
 JLE  C24  C  CR16  0  -0.240   4.3063   0.7150   2.2785
 JLE  C23  C  CR16  0  -0.301   4.1368  -0.1035   1.1717
 JLE  C22  C  CR6   0   0.152   3.4068   0.3341   0.0677
 JLE  C21  C  CH2   0  -0.570   3.2009  -0.5769  -1.1110
 JLE  C9   C  CR5   0   0.234  -1.9552  -0.1142   0.0689
 JLE  N1   N  N     0  -0.476   0.2179  -3.1888   0.3315
 JLE  C11  C  CR16  0  -0.306   0.0137   3.1917  -1.9051
 JLE  C12  C  CR16  0  -0.269  -0.3296   2.0421  -2.5897
 JLE  C13  C  CR16  0  -0.337  -0.9744   0.9752  -1.9452
 JLE  C14  C  CR56  0   0.355  -0.2978   3.2452  -0.5486
 JLE  C10  C  CR6   0  -0.103  -1.2851   1.0238  -0.5933
 JLE  C15  C  CR56  0   0.071  -0.9371   2.1789   0.1248
 JLE  C20  C  CH1   0  -0.176   2.2189  -1.7129  -0.7797
 JLE  C17  C  CR15  0  -0.020  -0.5351   3.8234   1.5893
 JLE  C16  C  CR15  0  -0.445  -1.0763   2.5742   1.4892
 JLE  C26  C  CR16  0  -0.230   3.0224   2.4339   1.2019
 JLE  C27  C  CR16  0  -0.319   2.8573   1.6115   0.0941
 JLE  C28  C  C     0   0.544   2.1071  -2.6607  -1.9656
 JLE  O30  O  O     0  -0.428   1.2192  -2.6340  -2.7760
 JLE  O29  O  OH1   0  -0.590   3.1379  -3.4917  -2.0133
 JLE  N19  N  NH1   0  -0.667   0.9391  -1.1616  -0.4416
 JLE  S7   S  S2    0   0.220  -3.7726  -1.5838   1.1772
 JLE  C31  C  CH2   0  -0.514  -4.2238   1.0520   0.3825
 JLE  C32  C  CH3   0  -0.651  -5.1317   0.8924  -0.8364
 JLE  N18  N  NR15  0  -0.684  -0.0704   4.2259   0.3706
 JLE  H1   H  HCR6  0   0.258  -0.4570  -4.9673   1.0945
 JLE  H3   H  HCR6  0   0.255   4.8783   0.3609   3.1266
 JLE  H4   H  HCR6  0   0.250   4.5811  -1.0926   1.1652
 JLE  H5   H  HCH2  0   0.269   2.8279  -0.0143  -1.9713
 JLE  H6   H  HCH2  0   0.290   4.1519  -1.0183  -1.4139
 JLE  H7   H  HCR6  0   0.266   0.5124   4.0140  -2.4018
 JLE  H8   H  HCR6  0   0.257  -0.1035   1.9605  -3.6446
 JLE  H9   H  HCR6  0   0.254  -1.2397   0.0950  -2.5185
 JLE  H10  H  HCH1  0   0.295   2.6114  -2.2760   0.0701
 JLE  H11  H  HCR5  0   0.284  -0.4433   4.4678   2.4485
 JLE  H12  H  HCR5  0   0.245  -1.5191   2.0066   2.2916
 JLE  H13  H  HCR6  0   0.248   2.5842   3.4229   1.2056
 JLE  H14  H  HCR6  0   0.251   2.2994   1.9760  -0.7606
 JLE  H15  H  HOH1  0   0.485   3.0848  -4.0508  -2.8034
 JLE  H16  H  HNH1  0   0.419   0.7082  -0.2446  -0.7916
 JLE  H17  H  HCH2  0   0.255  -4.8301   1.1176   1.2888
 JLE  H18  H  HCH2  0   0.261  -3.6774   1.9927   0.3118
 JLE  H19  H  HCH3  0   0.239  -5.8287   1.7277  -0.9040
 JLE  H20  H  HCH3  0   0.230  -4.5459   0.8651  -1.7552
 JLE  H21  H  HCH3  0   0.227  -5.7156  -0.0268  -0.7826
 JLE  H22  H  HNR5  0   0.411   0.3745   5.1094   0.1853
 JLE  H2   H  HCR6  0   0.255   3.8768   2.6274   3.1609

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
 JLE  C21  C22  single    1.504  0.020  1.504
 JLE  C21  C20  single    1.538  0.020  1.538
 JLE  C22  C23  aromatic  1.394  0.020  1.394
 JLE  C22  C27  aromatic  1.391  0.020  1.391
 JLE  C23  C24  aromatic  1.387  0.020  1.387
 JLE  C12  C11  aromatic  1.381  0.020  1.381
 JLE  C12  C13  aromatic  1.403  0.020  1.403
 JLE  C27  C26  aromatic  1.389  0.020  1.389
 JLE  O30  C28  double    1.202  0.020  1.202
 JLE  C11  C14  aromatic  1.393  0.020  1.393
 JLE  C24  C25  aromatic  1.390  0.020  1.390
 JLE  C26  C25  aromatic  1.387  0.020  1.387
 JLE  C28  O29  single    1.325  0.020  1.325
 JLE  C28  C20  single    1.522  0.020  1.522
 JLE  C20  N19  single    1.434  0.020  1.434
 JLE  C13  C10  aromatic  1.388  0.020  1.388
 JLE  C14  N18  aromatic  1.363  0.020  1.363
 JLE  C14  C15  aromatic  1.414  0.020  1.414
 JLE  N19  C4   single    1.343  0.020  1.343
 JLE  N18  C17  aromatic  1.365  0.020  1.365
 JLE  C10  C15  aromatic  1.404  0.020  1.404
 JLE  C10  C9   single    1.477  0.020  1.477
 JLE  C15  C16  aromatic  1.427  0.020  1.427
 JLE  C4   N1   aromatic  1.331  0.020  1.331
 JLE  C4   C5   aromatic  1.419  0.020  1.419
 JLE  C17  C16  aromatic  1.365  0.020  1.365
 JLE  N1   C2   aromatic  1.328  0.020  1.328
 JLE  C9   C5   aromatic  1.439  0.020  1.439
 JLE  C9   C8   aromatic  1.360  0.020  1.360
 JLE  C5   C6   aromatic  1.392  0.020  1.392
 JLE  C2   N3   aromatic  1.316  0.020  1.316
 JLE  C8   C31  single    1.494  0.020  1.494
 JLE  C8   S7   aromatic  1.741  0.020  1.741
 JLE  C31  C32  single    1.528  0.020  1.528
 JLE  C6   N3   aromatic  1.333  0.020  1.333
 JLE  C6   S7   aromatic  1.727  0.020  1.727
 JLE  C2   H1   single    0.930  0.020  1.080
 JLE  C25  H2   single    0.930  0.020  1.080
 JLE  C24  H3   single    0.930  0.020  1.080
 JLE  C23  H4   single    0.930  0.020  1.080
 JLE  C21  H5   single    0.970  0.020  1.090
 JLE  C21  H6   single    0.970  0.020  1.090
 JLE  C11  H7   single    0.930  0.020  1.080
 JLE  C12  H8   single    0.930  0.020  1.080
 JLE  C13  H9   single    0.930  0.020  1.080
 JLE  C20  H10  single    0.970  0.020  1.090
 JLE  C17  H11  single    0.930  0.020  1.080
 JLE  C16  H12  single    0.930  0.020  1.080
 JLE  C26  H13  single    0.930  0.020  1.080
 JLE  C27  H14  single    0.930  0.020  1.080
 JLE  O29  H15  single    0.850  0.020  0.980
 JLE  N19  H16  single    0.860  0.020  1.020
 JLE  C31  H17  single    0.970  0.020  1.090
 JLE  C31  H18  single    0.970  0.020  1.090
 JLE  C32  H19  single    0.970  0.020  1.090
 JLE  C32  H20  single    0.970  0.020  1.090
 JLE  C32  H21  single    0.970  0.020  1.090
 JLE  N18  H22  single    0.860  0.020  1.020

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
 JLE  C9   C5   C4   132.66  3.000
 JLE  C9   C5   C6   112.83  3.000
 JLE  C4   C5   C6   114.49  3.000
 JLE  S7   C6   N3   123.07  3.000
 JLE  S7   C6   C5   111.05  3.000
 JLE  N3   C6   C5   125.88  3.000
 JLE  N19  C4   N1   117.49  3.000
 JLE  N1   C4   C5   119.87  3.000
 JLE  N19  C4   C5   122.62  3.000
 JLE  H1   C2   N1   115.95  3.000
 JLE  H1   C2   N3   116.65  3.000
 JLE  N1   C2   N3   127.40  3.000
 JLE  C31  C8   S7   118.97  3.000
 JLE  S7   C8   C9   112.46  3.000
 JLE  C31  C8   C9   128.38  3.000
 JLE  C2   N3   C6   113.60  3.000
 JLE  H2   C25  C26  120.17  3.000
 JLE  H2   C25  C24  120.24  3.000
 JLE  C26  C25  C24  119.59  3.000
 JLE  H3   C24  C23  119.79  3.000
 JLE  H3   C24  C25  120.09  3.000
 JLE  C23  C24  C25  120.13  3.000
 JLE  H4   C23  C22  119.74  3.000
 JLE  H4   C23  C24  119.54  3.000
 JLE  C22  C23  C24  120.72  3.000
 JLE  C27  C22  C21  121.14  3.000
 JLE  C27  C22  C23  118.69  3.000
 JLE  C21  C22  C23  120.15  3.000
 JLE  H6   C21  H5   106.68  3.000
 JLE  H6   C21  C20  108.52  3.000
 JLE  H5   C21  C20  109.38  3.000
 JLE  H6   C21  C22  110.07  3.000
 JLE  H5   C21  C22  110.59  3.000
 JLE  C20  C21  C22  111.47  3.000
 JLE  C10  C9   C8   123.14  3.000
 JLE  C8   C9   C5   111.96  3.000
 JLE  C10  C9   C5   124.87  3.000
 JLE  C2   N1   C4   118.72  3.000
 JLE  H7   C11  C14  121.38  3.000
 JLE  H7   C11  C12  121.29  3.000
 JLE  C14  C11  C12  117.32  3.000
 JLE  H8   C12  C13  119.11  3.000
 JLE  H8   C12  C11  119.60  3.000
 JLE  C13  C12  C11  121.29  3.000
 JLE  H9   C13  C10  119.28  3.000
 JLE  H9   C13  C12  119.16  3.000
 JLE  C10  C13  C12  121.57  3.000
 JLE  N18  C14  C15  107.27  3.000
 JLE  C15  C14  C11  122.41  3.000
 JLE  N18  C14  C11  130.31  3.000
 JLE  C15  C10  C13  118.13  3.000
 JLE  C15  C10  C9   121.13  3.000
 JLE  C13  C10  C9   120.74  3.000
 JLE  C16  C15  C10  133.84  3.000
 JLE  C16  C15  C14  106.89  3.000
 JLE  C10  C15  C14  119.27  3.000
 JLE  H10  C20  N19  109.60  3.000
 JLE  H10  C20  C28  108.15  3.000
 JLE  N19  C20  C28  110.94  3.000
 JLE  H10  C20  C21  108.60  3.000
 JLE  N19  C20  C21  109.68  3.000
 JLE  C28  C20  C21  109.82  3.000
 JLE  H11  C17  N18  120.42  3.000
 JLE  H11  C17  C16  129.75  3.000
 JLE  N18  C17  C16  109.83  3.000
 JLE  H12  C16  C17  126.16  3.000
 JLE  H12  C16  C15  127.28  3.000
 JLE  C17  C16  C15  106.56  3.000
 JLE  H13  C26  C27  119.72  3.000
 JLE  H13  C26  C25  120.20  3.000
 JLE  C27  C26  C25  120.09  3.000
 JLE  H14  C27  C26  119.39  3.000
 JLE  H14  C27  C22  119.82  3.000
 JLE  C26  C27  C22  120.78  3.000
 JLE  O29  C28  O30  124.34  3.000
 JLE  O29  C28  C20  111.19  3.000
 JLE  O30  C28  C20  124.44  3.000
 JLE  H15  O29  C28  110.40  3.000
 JLE  H16  N19  C20  118.17  3.000
 JLE  H16  N19  C4   117.91  3.000
 JLE  C20  N19  C4   122.11  3.000
 JLE  C8   S7   C6    91.70  3.000
 JLE  H18  C31  H17  106.27  3.000
 JLE  H18  C31  C32  109.64  3.000
 JLE  H17  C31  C32  109.77  3.000
 JLE  H18  C31  C8   108.79  3.000
 JLE  H17  C31  C8   109.89  3.000
 JLE  C32  C31  C8   112.29  3.000
 JLE  H21  C32  H20  107.96  3.000
 JLE  H21  C32  H19  107.86  3.000
 JLE  H20  C32  H19  108.09  3.000
 JLE  H21  C32  C31  111.52  3.000
 JLE  H20  C32  C31  110.83  3.000
 JLE  H19  C32  C31  110.45  3.000
 JLE  H22  N18  C17  125.01  3.000
 JLE  H22  N18  C14  125.53  3.000
 JLE  C17  N18  C14  109.45  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
 JLE  CONST_01  C2   N1   C4   C5      0.00   0.0  0
 JLE  CONST_04  S7   C8   C9   C5      0.00   0.0  0
 JLE  CONST_05  C2   N3   C6   C5      0.00   0.0  0
 JLE  CONST_06  C8   S7   C6   C5      0.00   0.0  0
 JLE  CONST_07  N1   C4   C5   C6      0.00   0.0  0
 JLE  CONST_08  C10  C9   C5   C6    180.00   0.0  0
 JLE  CONST_09  C8   C9   C5   C6      0.00   0.0  0
 JLE  CONST_10  N1   C2   N3   C6      0.00   0.0  0
 JLE  CONST_11  C9   C8   S7   C6      0.00   0.0  0
 JLE  CONST_12  N3   C2   N1   C4      0.00   0.0  0
 JLE  CONST_13  C10  C9   C5   C4      0.00   0.0  0
 JLE  CONST_14  C8   C9   C5   C4    180.00   0.0  0
 JLE  CONST_15  N3   C6   C5   C4      0.00   0.0  0
 JLE  CONST_16  S7   C6   C5   C4    180.00   0.0  0
 JLE  CONST_17  S7   C6   N3   C2    180.00   0.0  0
 JLE  CONST_20  N3   C6   S7   C8    180.00   0.0  0
 JLE  CONST_21  C9   C5   C6   N3    180.00   0.0  0
 JLE  CONST_22  C22  C23  C24  C25     0.00   0.0  0
 JLE  CONST_23  C22  C27  C26  C25     0.00   0.0  0
 JLE  CONST_24  C27  C22  C23  C24     0.00   0.0  0
 JLE  CONST_25  C27  C26  C25  C24     0.00   0.0  0
 JLE  CONST_26  C26  C27  C22  C23     0.00   0.0  0
 JLE  CONST_27  C26  C25  C24  C23     0.00   0.0  0
 JLE  CONST_28  C12  C13  C10  C9    180.00   0.0  0
 JLE  CONST_29  C14  C15  C10  C9    180.00   0.0  0
 JLE  CONST_30  C16  C15  C10  C9      0.00   0.0  0
 JLE  CONST_31  N1   C4   C5   C9    180.00   0.0  0
 JLE  CONST_32  S7   C6   C5   C9      0.00   0.0  0
 JLE  CONST_33  C10  C13  C12  C11     0.00   0.0  0
 JLE  CONST_34  C17  N18  C14  C11   180.00   0.0  0
 JLE  CONST_35  C10  C15  C14  C11     0.00   0.0  0
 JLE  CONST_36  C16  C15  C14  C11   180.00   0.0  0
 JLE  CONST_37  N18  C14  C11  C12   180.00   0.0  0
 JLE  CONST_38  C15  C14  C11  C12     0.00   0.0  0
 JLE  CONST_39  C15  C10  C13  C12     0.00   0.0  0
 JLE  CONST_40  C14  C11  C12  C13     0.00   0.0  0
 JLE  CONST_41  C14  C15  C10  C13     0.00   0.0  0
 JLE  CONST_42  C16  C15  C10  C13   180.00   0.0  0
 JLE  CONST_43  C16  C17  N18  C14     0.00   0.0  0
 JLE  CONST_44  C17  C16  C15  C14     0.00   0.0  0
 JLE  CONST_45  N18  C14  C15  C10   180.00   0.0  0
 JLE  CONST_46  C17  C16  C15  C10   180.00   0.0  0
 JLE  CONST_47  S7   C8   C9   C10   180.00   0.0  0
 JLE  CONST_48  C17  N18  C14  C15     0.00   0.0  0
 JLE  CONST_49  N18  C17  C16  C15     0.00   0.0  0
 JLE  CONST_50  N18  C14  C15  C16     0.00   0.0  0
 JLE  CONST_51  C31  C8   C9   C5    180.00   0.0  0
 JLE  CONST_52  N19  C4   C5   C6    180.00   0.0  0
 JLE  CONST_53  C31  C8   S7   C6    180.00   0.0  0
 JLE  CONST_54  N19  C4   N1   C2    180.00   0.0  0
 JLE  CONST_55  C21  C22  C23  C24   180.00   0.0  0
 JLE  CONST_56  C26  C27  C22  C21   180.00   0.0  0
 JLE  CONST_57  N19  C4   C5   C9      0.00   0.0  0
 JLE  CONST_58  C31  C8   C9   C10     0.00   0.0  0
 JLE  CONST_59  H1   C2   N3   C6    180.00   0.0  0
 JLE  CONST_60  H4   C23  C24  C25   180.00   0.0  0
 JLE  CONST_61  H14  C27  C26  C25   180.00   0.0  0
 JLE  CONST_62  H13  C26  C25  C24   180.00   0.0  0
 JLE  CONST_63  H2   C25  C24  C23   180.00   0.0  0
 JLE  CONST_64  H3   C24  C23  C22   180.00   0.0  0
 JLE  CONST_65  H9   C13  C10  C9      0.00   0.0  0
 JLE  CONST_66  H22  N18  C14  C11     0.00   0.0  0
 JLE  CONST_67  H7   C11  C12  C13   180.00   0.0  0
 JLE  CONST_68  H8   C12  C11  C14   180.00   0.0  0
 JLE  CONST_69  H11  C17  N18  C14   180.00   0.0  0
 JLE  CONST_70  H12  C16  C15  C14   180.00   0.0  0
 JLE  CONST_71  C20  N19  C4   C5    180.00   0.0  0
 JLE  CONST_72  C20  N19  C4   N1      0.00   0.0  0
 JLE  CONST_73  H16  N19  C4   C5      0.00   0.0  0
 JLE  CONST_74  H15  O29  C28  C20   180.00   0.0  0
 JLE  Var_01    C20  C21  C22  C23    71.75  30.0  3
 JLE  Var_02    C32  C31  C8   C9     95.18  30.0  2
 JLE  Var_03    H19  C32  C31  C8   -179.48  30.0  3

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
 JLE  chir_01  C20  C21  C28  N19  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
 JLE  plan-1  C25  0.020
 JLE  plan-1  C24  0.020
 JLE  plan-1  C23  0.020
 JLE  plan-1  C22  0.020
 JLE  plan-1  C21  0.020
 JLE  plan-1  C26  0.020
 JLE  plan-1  C27  0.020
 JLE  plan-1  H3   0.020
 JLE  plan-1  H4   0.020
 JLE  plan-1  H13  0.020
 JLE  plan-1  H14  0.020
 JLE  plan-1  H2   0.020
 JLE  plan-2  C5   0.020
 JLE  plan-2  C6   0.020
 JLE  plan-2  C4   0.020
 JLE  plan-2  C2   0.020
 JLE  plan-2  C8   0.020
 JLE  plan-2  N3   0.020
 JLE  plan-2  C9   0.020
 JLE  plan-2  N1   0.020
 JLE  plan-2  C10  0.020
 JLE  plan-2  N19  0.020
 JLE  plan-2  S7   0.020
 JLE  plan-2  C31  0.020
 JLE  plan-2  H1   0.020
 JLE  plan-3  C9   0.020
 JLE  plan-3  C11  0.020
 JLE  plan-3  C12  0.020
 JLE  plan-3  C13  0.020
 JLE  plan-3  C14  0.020
 JLE  plan-3  C10  0.020
 JLE  plan-3  C15  0.020
 JLE  plan-3  C17  0.020
 JLE  plan-3  C16  0.020
 JLE  plan-3  N18  0.020
 JLE  plan-3  H7   0.020
 JLE  plan-3  H8   0.020
 JLE  plan-3  H9   0.020
 JLE  plan-3  H11  0.020
 JLE  plan-3  H12  0.020
 JLE  plan-3  H22  0.020
 JLE  plan-4  C4   0.020
 JLE  plan-4  C20  0.020
 JLE  plan-4  N19  0.020
 JLE  plan-4  H16  0.020
 JLE  plan-5  C20  0.020
 JLE  plan-5  C28  0.020
 JLE  plan-5  O30  0.020
 JLE  plan-5  O29  0.020
 JLE  plan-5  H15  0.020

