# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 05:26:01 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (2~{R})-2-[[6-ethyl-5-(1~{H}-indol-5-yl)thieno[2,3-d]pyrimidin-4-yl]amino]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1sc2ncnc(N[C@H](C)C(O)=O)c2c1c3ccc4[nH]ccc4c3
#
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
 JKQ  JKQ  '(2~{R})-2-[[6-ethyl-5-(1~{H}-indol-5-yl)thieno[2,3-d]pyrimidin-4-yl]amino]propanoic acid'  ligand  44  26  .  2021-08-12  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JKQ
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
 JKQ  N1   N  N     0  -0.438  -3.9598   1.2180  -0.2056
 JKQ  N3   N  NH1   0  -0.684   0.1091   1.8201  -0.1048
 JKQ  C4   C  CR5   0   0.226  -1.1141  -1.0287   0.1082
 JKQ  C5   C  CR56  0   0.002  -1.7370   0.2594  -0.0380
 JKQ  C6   C  CR56  0  -0.029  -3.1254   0.1859  -0.0738
 JKQ  C7   C  CR16  0   0.040  -3.3453   2.3784  -0.3063
 JKQ  C8   C  CR6   0   0.500  -1.2070   1.5738  -0.1480
 JKQ  C10  C  CH3   0  -0.659   0.7112   3.5475  -1.7671
 JKQ  C13  C  CR16  0  -0.359   1.1105  -1.2952  -0.9677
 JKQ  C15  C  CR56  0   0.360   3.0741  -1.6367   0.4106
 JKQ  C17  C  CR15  0  -0.426   3.5538  -1.5806  -1.8195
 JKQ  C1   C  CH3   0  -0.657  -2.1464  -3.9906   1.7554
 JKQ  O1   O  OH1   0  -0.587   2.5638   4.3453   0.3917
 JKQ  S1   S  S2    0   0.210  -3.6657  -1.4489   0.0738
 JKQ  C2   C  CH2   0  -0.507  -1.7764  -3.4937   0.3588
 JKQ  N2   N  N     0  -0.477  -2.0375   2.6075  -0.2879
 JKQ  O2   O  O     0  -0.422   2.6889   2.1210   0.5622
 JKQ  C3   C  CR5   0  -0.241  -2.0270  -2.0331   0.1784
 JKQ  N4   N  NR15  0  -0.681   4.4149  -1.8007   0.2306
 JKQ  C9   C  CH1   0  -0.197   0.6758   3.1320  -0.2920
 JKQ  C11  C  C     0   0.546   2.0791   3.1200   0.2782
 JKQ  C12  C  CR6   0  -0.110   0.3468  -1.2543   0.1878
 JKQ  C14  C  CR56  0   0.080   2.4915  -1.4880  -0.8687
 JKQ  C16  C  CR15  0  -0.024   4.7007  -1.7716  -1.1046
 JKQ  C18  C  CR16  0  -0.291   2.3159  -1.5985   1.5780
 JKQ  C19  C  CR16  0  -0.282   0.9557  -1.4059   1.4500
 JKQ  H1   H  HNH1  0   0.426   0.7512   1.0447  -0.0300
 JKQ  H2   H  HCR6  0   0.255  -3.9774   3.2527  -0.4200
 JKQ  H3   H  HCH3  0   0.256  -0.3011   3.5355  -2.1668
 JKQ  H4   H  HCH3  0   0.247   1.1071   4.5549  -1.8866
 JKQ  H5   H  HCH3  0   0.236   1.3236   2.8602  -2.3512
 JKQ  H6   H  HCR6  0   0.248   0.6391  -1.1711  -1.9356
 JKQ  H7   H  HCR5  0   0.248   3.4767  -1.5137  -2.8928
 JKQ  H8   H  HCH3  0   0.230  -1.5689  -3.4701   2.5198
 JKQ  H9   H  HCH3  0   0.227  -3.2042  -3.8333   1.9692
 JKQ  H10  H  HCH3  0   0.239  -1.9460  -5.0579   1.8473
 JKQ  H11  H  HOH1  0   0.488   3.4766   4.3162   0.7163
 JKQ  H12  H  HCH2  0   0.256  -0.7184  -3.6803   0.1680
 JKQ  H13  H  HCH2  0   0.256  -2.3313  -4.0601  -0.3931
 JKQ  H14  H  HNR5  0   0.411   5.0887  -1.9613   0.9605
 JKQ  H15  H  HCH1  0   0.293   0.0836   3.8626   0.2638
 JKQ  H16  H  HCR5  0   0.282   5.7163  -1.8883  -1.4471
 JKQ  H17  H  HCR6  0   0.261   2.7716  -1.7157   2.5529
 JKQ  H18  H  HCR6  0   0.247   0.3358  -1.3624   2.3369

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
 JKQ  C16  C17  aromatic  1.365  0.020  1.365
 JKQ  C16  N4   aromatic  1.366  0.020  1.366
 JKQ  C17  C14  aromatic  1.429  0.020  1.429
 JKQ  O2   C11  double    1.204  0.020  1.204
 JKQ  O1   C11  single    1.323  0.020  1.323
 JKQ  C11  C9   single    1.515  0.020  1.515
 JKQ  C10  C9   single    1.533  0.020  1.533
 JKQ  N4   C15  aromatic  1.363  0.020  1.363
 JKQ  C14  C15  aromatic  1.414  0.020  1.414
 JKQ  C14  C13  aromatic  1.398  0.020  1.398
 JKQ  C9   N3   single    1.441  0.020  1.441
 JKQ  C15  C18  aromatic  1.393  0.020  1.393
 JKQ  C13  C12  aromatic  1.386  0.020  1.386
 JKQ  N3   C8   single    1.340  0.020  1.340
 JKQ  C18  C19  aromatic  1.380  0.020  1.380
 JKQ  C8   N2   aromatic  1.333  0.020  1.333
 JKQ  C8   C5   aromatic  1.421  0.020  1.421
 JKQ  C12  C19  aromatic  1.410  0.020  1.410
 JKQ  C12  C4   single    1.480  0.020  1.480
 JKQ  N2   C7   aromatic  1.328  0.020  1.328
 JKQ  C5   C4   aromatic  1.438  0.020  1.438
 JKQ  C5   C6   aromatic  1.391  0.020  1.391
 JKQ  C4   C3   aromatic  1.359  0.020  1.359
 JKQ  C7   N1   aromatic  1.317  0.020  1.317
 JKQ  C6   N1   aromatic  1.334  0.020  1.334
 JKQ  C6   S1   aromatic  1.728  0.020  1.728
 JKQ  C3   C2   single    1.493  0.020  1.493
 JKQ  C3   S1   aromatic  1.743  0.020  1.743
 JKQ  C1   C2   single    1.528  0.020  1.528
 JKQ  N3   H1   single    0.860  0.020  1.020
 JKQ  C7   H2   single    0.930  0.020  1.080
 JKQ  C10  H3   single    0.970  0.020  1.090
 JKQ  C10  H4   single    0.970  0.020  1.090
 JKQ  C10  H5   single    0.970  0.020  1.090
 JKQ  C13  H6   single    0.930  0.020  1.080
 JKQ  C17  H7   single    0.930  0.020  1.080
 JKQ  C1   H8   single    0.970  0.020  1.090
 JKQ  C1   H9   single    0.970  0.020  1.090
 JKQ  C1   H10  single    0.970  0.020  1.090
 JKQ  O1   H11  single    0.850  0.020  0.980
 JKQ  C2   H12  single    0.970  0.020  1.090
 JKQ  C2   H13  single    0.970  0.020  1.090
 JKQ  N4   H14  single    0.860  0.020  1.020
 JKQ  C9   H15  single    0.970  0.020  1.090
 JKQ  C16  H16  single    0.930  0.020  1.080
 JKQ  C18  H17  single    0.930  0.020  1.080
 JKQ  C19  H18  single    0.930  0.020  1.080

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
 JKQ  C7   N1   C6   113.42  3.000
 JKQ  H1   N3   C9   117.30  3.000
 JKQ  H1   N3   C8   119.08  3.000
 JKQ  C9   N3   C8   123.33  3.000
 JKQ  C12  C4   C3   123.20  3.000
 JKQ  C3   C4   C5   112.10  3.000
 JKQ  C12  C4   C5   124.70  3.000
 JKQ  C8   C5   C6   114.77  3.000
 JKQ  C6   C5   C4   112.81  3.000
 JKQ  C8   C5   C4   132.42  3.000
 JKQ  S1   C6   C5   111.09  3.000
 JKQ  S1   C6   N1   123.02  3.000
 JKQ  C5   C6   N1   125.89  3.000
 JKQ  H2   C7   N2   115.87  3.000
 JKQ  H2   C7   N1   116.50  3.000
 JKQ  N2   C7   N1   127.63  3.000
 JKQ  N2   C8   C5   119.53  3.000
 JKQ  C5   C8   N3   122.26  3.000
 JKQ  N2   C8   N3   118.21  3.000
 JKQ  H5   C10  H4   108.67  3.000
 JKQ  H5   C10  H3   108.59  3.000
 JKQ  H4   C10  H3   107.94  3.000
 JKQ  H5   C10  C9   110.96  3.000
 JKQ  H4   C10  C9   111.39  3.000
 JKQ  H3   C10  C9   109.20  3.000
 JKQ  H6   C13  C14  120.58  3.000
 JKQ  H6   C13  C12  120.11  3.000
 JKQ  C14  C13  C12  119.31  3.000
 JKQ  C18  C15  C14  122.10  3.000
 JKQ  C18  C15  N4   130.52  3.000
 JKQ  C14  C15  N4   107.38  3.000
 JKQ  H7   C17  C16  126.17  3.000
 JKQ  H7   C17  C14  127.25  3.000
 JKQ  C16  C17  C14  106.58  3.000
 JKQ  H10  C1   H9   107.65  3.000
 JKQ  H10  C1   H8   108.11  3.000
 JKQ  H9   C1   H8   107.90  3.000
 JKQ  H10  C1   C2   110.56  3.000
 JKQ  H9   C1   C2   111.54  3.000
 JKQ  H8   C1   C2   110.94  3.000
 JKQ  H11  O1   C11  110.25  3.000
 JKQ  C3   S1   C6    91.62  3.000
 JKQ  H13  C2   H12  106.47  3.000
 JKQ  H13  C2   C3   109.80  3.000
 JKQ  H12  C2   C3   108.00  3.000
 JKQ  H13  C2   C1   109.72  3.000
 JKQ  H12  C2   C1   109.82  3.000
 JKQ  C3   C2   C1   112.83  3.000
 JKQ  C8   N2   C7   118.76  3.000
 JKQ  C2   C3   S1   119.54  3.000
 JKQ  S1   C3   C4   112.38  3.000
 JKQ  C2   C3   C4   128.06  3.000
 JKQ  H14  N4   C16  124.91  3.000
 JKQ  H14  N4   C15  125.61  3.000
 JKQ  C16  N4   C15  109.42  3.000
 JKQ  H15  C9   C11  108.42  3.000
 JKQ  H15  C9   C10  108.72  3.000
 JKQ  C11  C9   C10  110.06  3.000
 JKQ  H15  C9   N3   109.24  3.000
 JKQ  C10  C9   N3   112.38  3.000
 JKQ  C11  C9   N3   107.95  3.000
 JKQ  C9   C11  O2   124.36  3.000
 JKQ  C9   C11  O1   111.38  3.000
 JKQ  O2   C11  O1   124.24  3.000
 JKQ  C19  C12  C13  120.36  3.000
 JKQ  C19  C12  C4   119.40  3.000
 JKQ  C13  C12  C4   120.24  3.000
 JKQ  C17  C14  C15  106.80  3.000
 JKQ  C15  C14  C13  119.06  3.000
 JKQ  C17  C14  C13  134.14  3.000
 JKQ  H16  C16  N4   120.36  3.000
 JKQ  H16  C16  C17  129.81  3.000
 JKQ  N4   C16  C17  109.83  3.000
 JKQ  H17  C18  C19  120.91  3.000
 JKQ  H17  C18  C15  121.52  3.000
 JKQ  C19  C18  C15  117.57  3.000
 JKQ  H18  C19  C18  119.60  3.000
 JKQ  H18  C19  C12  118.80  3.000
 JKQ  C18  C19  C12  121.59  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
 JKQ  CONST_01  C8   N2   C7   N1     0.00   0.0  0
 JKQ  CONST_02  C8   C5   C6   N1     0.00   0.0  0
 JKQ  CONST_03  C4   C5   C6   N1   180.00   0.0  0
 JKQ  CONST_04  C3   S1   C6   N1   180.00   0.0  0
 JKQ  CONST_05  C14  C13  C12  C4   180.00   0.0  0
 JKQ  CONST_06  C18  C19  C12  C4   180.00   0.0  0
 JKQ  CONST_07  N2   C8   C5   C4   180.00   0.0  0
 JKQ  CONST_08  S1   C6   C5   C4     0.00   0.0  0
 JKQ  CONST_09  C6   S1   C3   C4     0.00   0.0  0
 JKQ  CONST_10  C7   N2   C8   C5     0.00   0.0  0
 JKQ  CONST_13  S1   C3   C4   C5     0.00   0.0  0
 JKQ  CONST_14  C7   N1   C6   C5     0.00   0.0  0
 JKQ  CONST_15  C3   S1   C6   C5     0.00   0.0  0
 JKQ  CONST_16  N2   C8   C5   C6     0.00   0.0  0
 JKQ  CONST_17  C12  C4   C5   C6   180.00   0.0  0
 JKQ  CONST_18  C3   C4   C5   C6     0.00   0.0  0
 JKQ  CONST_19  N2   C7   N1   C6     0.00   0.0  0
 JKQ  CONST_20  S1   C6   N1   C7   180.00   0.0  0
 JKQ  CONST_21  C12  C4   C5   C8     0.00   0.0  0
 JKQ  CONST_22  C3   C4   C5   C8   180.00   0.0  0
 JKQ  CONST_23  S1   C6   C5   C8   180.00   0.0  0
 JKQ  CONST_24  C16  C17  C14  C13  180.00   0.0  0
 JKQ  CONST_25  N4   C15  C14  C13  180.00   0.0  0
 JKQ  CONST_26  C18  C15  C14  C13    0.00   0.0  0
 JKQ  CONST_27  C18  C19  C12  C13    0.00   0.0  0
 JKQ  CONST_29  C17  C16  N4   C15    0.00   0.0  0
 JKQ  CONST_30  C16  C17  C14  C15    0.00   0.0  0
 JKQ  CONST_31  C12  C13  C14  C15    0.00   0.0  0
 JKQ  CONST_32  C12  C19  C18  C15    0.00   0.0  0
 JKQ  CONST_33  N4   C15  C14  C17    0.00   0.0  0
 JKQ  CONST_34  C18  C15  C14  C17  180.00   0.0  0
 JKQ  CONST_35  C12  C13  C14  C17  180.00   0.0  0
 JKQ  CONST_36  C12  C4   C3   S1   180.00   0.0  0
 JKQ  CONST_38  C14  C17  C16  N4     0.00   0.0  0
 JKQ  CONST_39  C19  C18  C15  N4   180.00   0.0  0
 JKQ  CONST_40  C16  N4   C15  C14    0.00   0.0  0
 JKQ  CONST_41  C19  C18  C15  C14    0.00   0.0  0
 JKQ  CONST_42  C19  C12  C13  C14    0.00   0.0  0
 JKQ  CONST_43  C18  C15  N4   C16  180.00   0.0  0
 JKQ  CONST_44  C7   N2   C8   N3   180.00   0.0  0
 JKQ  CONST_45  C4   C5   C8   N3     0.00   0.0  0
 JKQ  CONST_46  C6   C5   C8   N3   180.00   0.0  0
 JKQ  CONST_47  C2   C3   C4   C5   180.00   0.0  0
 JKQ  CONST_48  C2   C3   S1   C6   180.00   0.0  0
 JKQ  CONST_49  C12  C4   C3   C2     0.00   0.0  0
 JKQ  CONST_50  H6   C13  C12  C4     0.00   0.0  0
 JKQ  CONST_51  H18  C19  C12  C4     0.00   0.0  0
 JKQ  CONST_52  H2   C7   N1   C6   180.00   0.0  0
 JKQ  CONST_53  H7   C17  C14  C13    0.00   0.0  0
 JKQ  CONST_54  H16  C16  N4   C15  180.00   0.0  0
 JKQ  CONST_55  H14  N4   C16  C17  180.00   0.0  0
 JKQ  CONST_56  H17  C18  C15  N4     0.00   0.0  0
 JKQ  CONST_57  C9   N3   C8   C5   180.00   0.0  0
 JKQ  CONST_58  C9   N3   C8   N2     0.00   0.0  0
 JKQ  CONST_59  H1   N3   C8   C5     0.00   0.0  0
 JKQ  CONST_60  H11  O1   C11  O2     0.00   0.0  0
 JKQ  Var_01    C1   C2   C3   C4   106.91  30.0  2
 JKQ  Var_02    H8   C1   C2   C3   -59.87  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
 JKQ  chir_01  C9  C11  C10  N3  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
 JKQ  plan-1  N1   0.020
 JKQ  plan-1  N3   0.020
 JKQ  plan-1  C4   0.020
 JKQ  plan-1  C5   0.020
 JKQ  plan-1  C6   0.020
 JKQ  plan-1  C7   0.020
 JKQ  plan-1  C8   0.020
 JKQ  plan-1  S1   0.020
 JKQ  plan-1  C2   0.020
 JKQ  plan-1  N2   0.020
 JKQ  plan-1  C3   0.020
 JKQ  plan-1  C12  0.020
 JKQ  plan-1  H2   0.020
 JKQ  plan-2  C4   0.020
 JKQ  plan-2  C13  0.020
 JKQ  plan-2  C15  0.020
 JKQ  plan-2  C17  0.020
 JKQ  plan-2  N4   0.020
 JKQ  plan-2  C12  0.020
 JKQ  plan-2  C14  0.020
 JKQ  plan-2  C16  0.020
 JKQ  plan-2  C18  0.020
 JKQ  plan-2  C19  0.020
 JKQ  plan-2  H6   0.020
 JKQ  plan-2  H7   0.020
 JKQ  plan-2  H14  0.020
 JKQ  plan-2  H16  0.020
 JKQ  plan-2  H17  0.020
 JKQ  plan-2  H18  0.020
 JKQ  plan-3  N3   0.020
 JKQ  plan-3  C8   0.020
 JKQ  plan-3  C9   0.020
 JKQ  plan-3  H1   0.020
 JKQ  plan-4  O1   0.020
 JKQ  plan-4  O2   0.020
 JKQ  plan-4  C9   0.020
 JKQ  plan-4  C11  0.020
 JKQ  plan-4  H11  0.020

