# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 04:17:14 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: (2~{R})-2-[[6-ethyl-5-(2-methylphenyl)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)c2c1c4ccccc4C
#
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
 JLK  JLK  '(2~{R})-2-[[6-ethyl-5-(2-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino]-3-phenyl-propanoic acid'  ligand  52  30  .  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_JLK
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
 JLK  N10  N  NH1    0  -0.641  -0.9639  -0.7678   0.3479
 JLK  C11  C  CH1    0  -0.197  -2.2224  -1.2700   0.8437
 JLK  C13  C  C      0   0.415  -2.0775  -1.9918   2.2125
 JLK  C18  C  CR6    0  -0.102   1.3213   1.3193   0.5859
 JLK  C19  C  CR16   0  -0.244   0.1152   3.4650   1.8850
 JLK  C20  C  CR16   0  -0.260   0.5777   2.3872   2.6254
 JLK  C21  C  CR16   0  -0.257   1.1813   1.3217   1.9730
 JLK  C22  C  CR16   0  -0.303   0.2518   3.4658   0.5037
 JLK  C23  C  CR6    0   0.091   0.8442   2.3997  -0.1685
 JLK  C24  C  CH3    0  -0.737   0.9483   2.4032  -1.6650
 JLK  C25  C  CR6    0   0.171  -3.4277   0.5941  -0.3646
 JLK  C27  C  CR16   0  -0.240  -2.9808   2.4512  -1.8509
 JLK  C28  C  CR16   0  -0.276  -3.7621   1.8674  -2.8384
 JLK  C29  C  CR16   0  -0.241  -4.3800   0.6475  -2.5888
 JLK  C30  C  CR16   0  -0.312  -4.2125   0.0190  -1.3628
 JLK  C9   C  CR5    0   0.225   1.9693   0.1601  -0.0709
 JLK  C5   C  CR56   0  -0.017   1.3289  -1.0987  -0.3415
 JLK  C8   C  CR5    0  -0.246   3.2722   0.1674  -0.4562
 JLK  C16  C  CH2    0  -0.513   4.2757   1.2613  -0.2918
 JLK  C17  C  CH3    0  -0.650   5.1587   1.0670   0.9398
 JLK  S7   S  S2     0   0.206   3.7668  -1.3538  -1.1439
 JLK  C6   C  CR56   0  -0.032   2.1894  -2.0253  -0.9189
 JLK  N3   N  N      0  -0.444   1.8742  -3.2738  -1.2676
 JLK  C2   C  CR16   0   0.033   0.6199  -3.5852  -1.0062
 JLK  N1   N  N      0  -0.474  -0.3141  -2.8153  -0.4658
 JLK  C4   C  CR6    0   0.501  -0.0009  -1.5607  -0.1305
 JLK  O15  O  OC    -1  -0.615  -3.1222  -2.5287   2.6318
 JLK  O14  O  O      0  -0.580  -0.9658  -1.9599   2.7620
 JLK  C12  C  CH2    0  -0.559  -3.2194  -0.1101   0.9468
 JLK  C26  C  CR16   0  -0.315  -2.8178   1.8170  -0.6260
 JLK  H1   H  HNH1   0   0.402  -0.6647   0.1165   0.7281
 JLK  H2   H  HCH1   0   0.249  -2.6111  -1.9921   0.1224
 JLK  H3   H  HCR6   0   0.258  -0.3577   4.3041   2.3785
 JLK  H4   H  HCR6   0   0.258   0.4709   2.3736   3.7020
 JLK  H5   H  HCR6   0   0.251   1.5454   0.4746   2.5413
 JLK  H6   H  HCR6   0   0.255  -0.1248   4.3059  -0.0680
 JLK  H7   H  HCH3   0   0.249   1.9879   2.3983  -1.9982
 JLK  H8   H  HCH3   0   0.246   0.4700   1.5221  -2.0962
 JLK  H9   H  HCH3   0   0.247   0.4670   3.2846  -2.0868
 JLK  H10  H  HCR6   0   0.245  -2.4989   3.4036  -2.0334
 JLK  H11  H  HCR6   0   0.251  -3.8912   2.3583  -3.7945
 JLK  H12  H  HCR6   0   0.251  -4.9961   0.1858  -3.3500
 JLK  H13  H  HCR6   0   0.244  -4.6974  -0.9333  -1.1790
 JLK  H14  H  HCH2   0   0.255   4.8998   1.3314  -1.1857
 JLK  H15  H  HCH2   0   0.254   3.7450   2.2122  -0.2137
 JLK  H16  H  HCH3   0   0.238   5.8755   1.8832   1.0296
 JLK  H17  H  HCH3   0   0.230   4.5577   1.0428   1.8490
 JLK  H18  H  HCH3   0   0.227   5.7201   0.1339   0.8843
 JLK  H19  H  HCR6   0   0.249   0.3113  -4.5933  -1.2631
 JLK  H21  H  HCH2   0   0.263  -4.1627  -0.5142   1.3143
 JLK  H22  H  HCH2   0   0.243  -2.8711   0.6067   1.6981
 JLK  H23  H  HCR6   0   0.246  -2.2070   2.2835   0.1380

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
 JLK  C28  C29  aromatic  1.390  0.020  1.390
 JLK  C28  C27  aromatic  1.388  0.020  1.388
 JLK  C29  C30  aromatic  1.388  0.020  1.388
 JLK  C27  C26  aromatic  1.389  0.020  1.389
 JLK  C30  C25  aromatic  1.394  0.020  1.394
 JLK  C26  C25  aromatic  1.391  0.020  1.391
 JLK  C25  C12  single    1.503  0.020  1.503
 JLK  C19  C22  aromatic  1.388  0.020  1.388
 JLK  C19  C20  aromatic  1.387  0.020  1.387
 JLK  C12  C11  single    1.533  0.020  1.533
 JLK  C22  C23  aromatic  1.393  0.020  1.393
 JLK  C20  C21  aromatic  1.387  0.020  1.387
 JLK  C23  C24  single    1.500  0.020  1.500
 JLK  C23  C18  aromatic  1.401  0.020  1.401
 JLK  C11  N10  single    1.443  0.020  1.443
 JLK  C11  C13  single    1.554  0.020  1.554
 JLK  C21  C18  aromatic  1.394  0.020  1.394
 JLK  N10  C4   single    1.336  0.020  1.336
 JLK  O14  C13  deloc     1.241  0.020  1.241
 JLK  C18  C9   single    1.481  0.020  1.481
 JLK  C13  O15  deloc     1.247  0.020  1.247
 JLK  C4   C5   aromatic  1.424  0.020  1.424
 JLK  C4   N1   aromatic  1.336  0.020  1.336
 JLK  C9   C5   aromatic  1.438  0.020  1.438
 JLK  C9   C8   aromatic  1.359  0.020  1.359
 JLK  C5   C6   aromatic  1.390  0.020  1.390
 JLK  N1   C2   aromatic  1.326  0.020  1.326
 JLK  C16  C8   single    1.494  0.020  1.494
 JLK  C16  C17  single    1.528  0.020  1.528
 JLK  C8   S7   aromatic  1.741  0.020  1.741
 JLK  C2   N3   aromatic  1.319  0.020  1.319
 JLK  C6   N3   aromatic  1.334  0.020  1.334
 JLK  C6   S7   aromatic  1.729  0.020  1.729
 JLK  N10  H1   single    0.890  0.020  1.040
 JLK  C11  H2   single    0.970  0.020  1.090
 JLK  C19  H3   single    0.930  0.020  1.080
 JLK  C20  H4   single    0.930  0.020  1.080
 JLK  C21  H5   single    0.930  0.020  1.080
 JLK  C22  H6   single    0.930  0.020  1.080
 JLK  C24  H7   single    0.970  0.020  1.090
 JLK  C24  H8   single    0.970  0.020  1.090
 JLK  C24  H9   single    0.970  0.020  1.090
 JLK  C27  H10  single    0.930  0.020  1.080
 JLK  C28  H11  single    0.930  0.020  1.080
 JLK  C29  H12  single    0.930  0.020  1.080
 JLK  C30  H13  single    0.930  0.020  1.080
 JLK  C16  H14  single    0.970  0.020  1.090
 JLK  C16  H15  single    0.970  0.020  1.090
 JLK  C17  H16  single    0.970  0.020  1.090
 JLK  C17  H17  single    0.970  0.020  1.090
 JLK  C17  H18  single    0.970  0.020  1.090
 JLK  C2   H19  single    0.930  0.020  1.080
 JLK  C12  H21  single    0.970  0.020  1.090
 JLK  C12  H22  single    0.970  0.020  1.090
 JLK  C26  H23  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
 JLK  H1   N10  C4   116.22  3.000
 JLK  H1   N10  C11  115.76  3.000
 JLK  C4   N10  C11  123.03  3.000
 JLK  H2   C11  C12  108.25  3.000
 JLK  H2   C11  C13  107.92  3.000
 JLK  C12  C11  C13  110.66  3.000
 JLK  H2   C11  N10  108.28  3.000
 JLK  C13  C11  N10  112.52  3.000
 JLK  C12  C11  N10  109.09  3.000
 JLK  O14  C13  O15  127.79  3.000
 JLK  O15  C13  C11  114.71  3.000
 JLK  O14  C13  C11  117.50  3.000
 JLK  C9   C18  C23  120.89  3.000
 JLK  C9   C18  C21  119.10  3.000
 JLK  C23  C18  C21  120.00  3.000
 JLK  H3   C19  C22  119.76  3.000
 JLK  H3   C19  C20  120.31  3.000
 JLK  C22  C19  C20  119.92  3.000
 JLK  H4   C20  C21  120.08  3.000
 JLK  H4   C20  C19  120.53  3.000
 JLK  C21  C20  C19  119.40  3.000
 JLK  H5   C21  C20  120.01  3.000
 JLK  H5   C21  C18  119.14  3.000
 JLK  C20  C21  C18  120.85  3.000
 JLK  H6   C22  C23  119.12  3.000
 JLK  H6   C22  C19  119.42  3.000
 JLK  C23  C22  C19  121.45  3.000
 JLK  C24  C23  C22  120.61  3.000
 JLK  C24  C23  C18  121.01  3.000
 JLK  C22  C23  C18  118.37  3.000
 JLK  H9   C24  H8   107.86  3.000
 JLK  H9   C24  H7   107.84  3.000
 JLK  H8   C24  H7   107.04  3.000
 JLK  H9   C24  C23  110.95  3.000
 JLK  H8   C24  C23  111.21  3.000
 JLK  H7   C24  C23  111.75  3.000
 JLK  C26  C25  C12  121.00  3.000
 JLK  C12  C25  C30  120.63  3.000
 JLK  C26  C25  C30  118.35  3.000
 JLK  H10  C27  C26  119.86  3.000
 JLK  H10  C27  C28  120.04  3.000
 JLK  C26  C27  C28  120.10  3.000
 JLK  H11  C28  C29  120.24  3.000
 JLK  H11  C28  C27  120.32  3.000
 JLK  C29  C28  C27  119.45  3.000
 JLK  H12  C29  C30  119.78  3.000
 JLK  H12  C29  C28  120.06  3.000
 JLK  C30  C29  C28  120.16  3.000
 JLK  H13  C30  C29  119.57  3.000
 JLK  H13  C30  C25  119.52  3.000
 JLK  C29  C30  C25  120.91  3.000
 JLK  C8   C9   C5   112.23  3.000
 JLK  C8   C9   C18  122.75  3.000
 JLK  C5   C9   C18  125.00  3.000
 JLK  C4   C5   C6   115.05  3.000
 JLK  C6   C5   C9   112.70  3.000
 JLK  C4   C5   C9   132.24  3.000
 JLK  S7   C8   C16  119.50  3.000
 JLK  S7   C8   C9   112.32  3.000
 JLK  C16  C8   C9   128.10  3.000
 JLK  H15  C16  H14  106.28  3.000
 JLK  H15  C16  C17  109.52  3.000
 JLK  H14  C16  C17  109.73  3.000
 JLK  H15  C16  C8   108.61  3.000
 JLK  H14  C16  C8   109.92  3.000
 JLK  C17  C16  C8   112.58  3.000
 JLK  H18  C17  H17  107.90  3.000
 JLK  H18  C17  H16  107.84  3.000
 JLK  H17  C17  H16  108.09  3.000
 JLK  H18  C17  C16  111.43  3.000
 JLK  H17  C17  C16  110.89  3.000
 JLK  H16  C17  C16  110.56  3.000
 JLK  C6   S7   C8    91.65  3.000
 JLK  N3   C6   S7   123.03  3.000
 JLK  S7   C6   C5   111.09  3.000
 JLK  N3   C6   C5   125.88  3.000
 JLK  C2   N3   C6   113.20  3.000
 JLK  H19  C2   N1   115.83  3.000
 JLK  H19  C2   N3   116.29  3.000
 JLK  N1   C2   N3   127.87  3.000
 JLK  C4   N1   C2   118.86  3.000
 JLK  N1   C4   C5   119.12  3.000
 JLK  N1   C4   N10  118.57  3.000
 JLK  C5   C4   N10  122.26  3.000
 JLK  H22  C12  H21  106.65  3.000
 JLK  H22  C12  C25  109.63  3.000
 JLK  H21  C12  C25  110.36  3.000
 JLK  H22  C12  C11  109.54  3.000
 JLK  H21  C12  C11  107.76  3.000
 JLK  C25  C12  C11  112.70  3.000
 JLK  H23  C26  C27  119.43  3.000
 JLK  H23  C26  C25  119.54  3.000
 JLK  C27  C26  C25  121.03  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
 JLK  CONST_01  C19  C22  C23  C18     0.00   0.0  0
 JLK  CONST_02  C19  C20  C21  C18     0.00   0.0  0
 JLK  CONST_03  C4   C5   C9   C18     0.00   0.0  0
 JLK  CONST_04  C6   C5   C9   C18   180.00   0.0  0
 JLK  CONST_05  S7   C8   C9   C18   180.00   0.0  0
 JLK  CONST_06  C23  C22  C19  C20     0.00   0.0  0
 JLK  CONST_07  C23  C18  C21  C20     0.00   0.0  0
 JLK  CONST_08  C9   C18  C21  C20   180.00   0.0  0
 JLK  CONST_09  C22  C19  C20  C21     0.00   0.0  0
 JLK  CONST_10  C22  C23  C18  C21     0.00   0.0  0
 JLK  CONST_13  C9   C18  C23  C22   180.00   0.0  0
 JLK  CONST_16  C28  C29  C30  C25     0.00   0.0  0
 JLK  CONST_17  C28  C27  C26  C25     0.00   0.0  0
 JLK  CONST_18  C30  C29  C28  C27     0.00   0.0  0
 JLK  CONST_19  C30  C25  C26  C27     0.00   0.0  0
 JLK  CONST_20  C26  C27  C28  C29     0.00   0.0  0
 JLK  CONST_21  C26  C25  C30  C29     0.00   0.0  0
 JLK  CONST_22  N1   C4   C5   C9    180.00   0.0  0
 JLK  CONST_23  N3   C6   C5   C9    180.00   0.0  0
 JLK  CONST_24  S7   C6   C5   C9      0.00   0.0  0
 JLK  CONST_25  C6   S7   C8   C9      0.00   0.0  0
 JLK  CONST_26  C2   N1   C4   C5      0.00   0.0  0
 JLK  CONST_27  S7   C8   C9   C5      0.00   0.0  0
 JLK  CONST_28  C2   N3   C6   C5      0.00   0.0  0
 JLK  CONST_29  C8   S7   C6   C5      0.00   0.0  0
 JLK  CONST_30  C4   C5   C9   C8    180.00   0.0  0
 JLK  CONST_31  C6   C5   C9   C8      0.00   0.0  0
 JLK  CONST_32  N3   C6   S7   C8    180.00   0.0  0
 JLK  CONST_33  C4   C5   C6   S7    180.00   0.0  0
 JLK  CONST_34  C2   N3   C6   S7    180.00   0.0  0
 JLK  CONST_35  N1   C4   C5   C6      0.00   0.0  0
 JLK  CONST_36  N1   C2   N3   C6      0.00   0.0  0
 JLK  CONST_37  C4   N1   C2   N3      0.00   0.0  0
 JLK  CONST_38  C4   C5   C6   N3      0.00   0.0  0
 JLK  CONST_39  C9   C5   C4   N10     0.00   0.0  0
 JLK  CONST_40  C6   C5   C4   N10   180.00   0.0  0
 JLK  CONST_41  C2   N1   C4   N10   180.00   0.0  0
 JLK  CONST_42  C16  C8   C9   C18     0.00   0.0  0
 JLK  CONST_43  C24  C23  C22  C19   180.00   0.0  0
 JLK  CONST_44  C24  C23  C18  C21   180.00   0.0  0
 JLK  CONST_45  C9   C18  C23  C24     0.00   0.0  0
 JLK  CONST_46  C12  C25  C26  C27   180.00   0.0  0
 JLK  CONST_47  C12  C25  C30  C29   180.00   0.0  0
 JLK  CONST_48  C16  C8   C9   C5    180.00   0.0  0
 JLK  CONST_49  C6   S7   C8   C16   180.00   0.0  0
 JLK  CONST_50  H6   C22  C23  C18   180.00   0.0  0
 JLK  CONST_51  H4   C20  C21  C18   180.00   0.0  0
 JLK  CONST_52  H5   C21  C20  C19   180.00   0.0  0
 JLK  CONST_53  H3   C19  C20  C21   180.00   0.0  0
 JLK  CONST_54  H12  C29  C30  C25   180.00   0.0  0
 JLK  CONST_55  H10  C27  C26  C25   180.00   0.0  0
 JLK  CONST_56  H13  C30  C29  C28   180.00   0.0  0
 JLK  CONST_57  H23  C26  C27  C28   180.00   0.0  0
 JLK  CONST_58  H11  C28  C29  C30   180.00   0.0  0
 JLK  CONST_59  H19  C2   N3   C6    180.00   0.0  0
 JLK  CONST_60  C5   C4   N10  C11   180.00   0.0  0
 JLK  CONST_62  H1   N10  C4   C5      0.00   0.0  0
 JLK  Var_01    C30  C25  C12  C11    76.09  30.0  2
 JLK  Var_02    C17  C16  C8   C9     96.96  30.0  2
 JLK  Var_03    H7   C24  C23  C18   -63.57  30.0  2
 JLK  Var_04    H16  C17  C16  C8   -179.84  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
 JLK  chir_01  C11  C12  N10  C13  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
 JLK  plan-1  C18  0.020
 JLK  plan-1  C19  0.020
 JLK  plan-1  C20  0.020
 JLK  plan-1  C21  0.020
 JLK  plan-1  C22  0.020
 JLK  plan-1  C23  0.020
 JLK  plan-1  C24  0.020
 JLK  plan-1  C9   0.020
 JLK  plan-1  H3   0.020
 JLK  plan-1  H4   0.020
 JLK  plan-1  H5   0.020
 JLK  plan-1  H6   0.020
 JLK  plan-2  C25  0.020
 JLK  plan-2  C27  0.020
 JLK  plan-2  C28  0.020
 JLK  plan-2  C29  0.020
 JLK  plan-2  C30  0.020
 JLK  plan-2  C12  0.020
 JLK  plan-2  C26  0.020
 JLK  plan-2  H10  0.020
 JLK  plan-2  H11  0.020
 JLK  plan-2  H12  0.020
 JLK  plan-2  H13  0.020
 JLK  plan-2  H23  0.020
 JLK  plan-3  N10  0.020
 JLK  plan-3  C18  0.020
 JLK  plan-3  C9   0.020
 JLK  plan-3  C5   0.020
 JLK  plan-3  C8   0.020
 JLK  plan-3  C16  0.020
 JLK  plan-3  S7   0.020
 JLK  plan-3  C6   0.020
 JLK  plan-3  N3   0.020
 JLK  plan-3  C2   0.020
 JLK  plan-3  N1   0.020
 JLK  plan-3  C4   0.020
 JLK  plan-3  H19  0.020
 JLK  plan-4  N10  0.020
 JLK  plan-4  C11  0.020
 JLK  plan-4  C4   0.020
 JLK  plan-4  H1   0.020
 JLK  plan-5  C11  0.020
 JLK  plan-5  C13  0.020
 JLK  plan-5  O15  0.020
 JLK  plan-5  O14  0.020

