# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 07:58:35 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 2-[(6-ethyl-5-phenyl-thieno[2,3-d]pyrimidin-4-yl)amino]-3-oxidanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1sc2ncnc(N[C@H](CO)C(O)=O)c2c1c3ccccc3
#
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
 J1N  J1N  '2-[(6-ethyl-5-phenyl-thieno[2,3-d]pyrimidin-4-yl)amino]-3-oxidanyl-propanoic acid'  ligand  41  24  .  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_J1N
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
 J1N  N01  N  N     0  -0.480   0.5368  -2.7764  -0.0671
 J1N  C02  C  CR16  0   0.043  -0.5260  -3.5712  -0.0910
 J1N  N03  N  N     0  -0.437  -1.7935  -3.2158  -0.0975
 J1N  C04  C  CR6   0   0.505   0.3527  -1.4564  -0.0450
 J1N  S05  S  S2    0   0.218  -3.5383  -1.1623  -0.0722
 J1N  C06  C  CR5   0  -0.237  -2.8471   0.4342  -0.0040
 J1N  C07  C  CR5   0   0.231  -1.4877   0.4087   0.0256
 J1N  C08  C  CR56  0   0.002  -0.9695  -0.9339  -0.0115
 J1N  C09  C  CR56  0  -0.028  -1.9744  -1.8952  -0.0587
 J1N  C10  C  CH2   0  -0.512  -3.7556   1.6196   0.0019
 J1N  C11  C  CH3   0  -0.655  -4.3671   1.9058  -1.3689
 J1N  N12  N  NH1   0  -0.673   1.4347  -0.6674  -0.0758
 J1N  C13  C  CH1   0  -0.244   2.7821  -1.1707  -0.0448
 J1N  C14  C  CH2   0  -0.153   3.2565  -1.4830   1.3714
 J1N  O15  O  OH1   0  -0.662   3.3239  -0.2646   2.0683
 J1N  C16  C  C     0   0.553   3.6894  -0.1392  -0.6914
 J1N  O17  O  O     0  -0.421   3.3239   0.9363  -1.0879
 J1N  O18  O  OH1   0  -0.588   4.9359  -0.5750  -0.7645
 J1N  C19  C  CR6   0  -0.082  -0.6602   1.6310   0.1127
 J1N  C20  C  CR16  0  -0.292   0.0255   1.9329   1.2905
 J1N  C21  C  CR16  0  -0.230   0.8132   3.0720   1.3735
 J1N  C22  C  CR16  0  -0.253   0.9202   3.9254   0.2832
 J1N  C23  C  CR16  0  -0.236   0.2391   3.6342  -0.8906
 J1N  C24  C  CR16  0  -0.266  -0.5451   2.4925  -0.9766
 J1N  H1   H  HCR6  0   0.256  -0.3202  -4.6361  -0.1096
 J1N  H2   H  HCH2  0   0.259  -4.5524   1.4675   0.7342
 J1N  H3   H  HCH2  0   0.257  -3.1896   2.4873   0.3441
 J1N  H4   H  HCH3  0   0.241  -5.0192   2.7775  -1.3211
 J1N  H5   H  HCH3  0   0.230  -3.5922   2.1026  -2.1101
 J1N  H6   H  HCH3  0   0.228  -4.9624   1.0644  -1.7251
 J1N  H7   H  HNH1  0   0.424   1.3139   0.3312  -0.0143
 J1N  H8   H  HCH1  0   0.311   2.8359  -2.0913  -0.6321
 J1N  H9   H  HCH2  0   0.227   2.5454  -2.1841   1.8227
 J1N  H10  H  HCH2  0   0.219   4.2252  -1.9932   1.3250
 J1N  H11  H  HOH1  0   0.462   3.6016  -0.4443   2.9710
 J1N  H12  H  HOH1  0   0.488   5.5047   0.1034  -1.1588
 J1N  H13  H  HCR6  0   0.259  -0.0575   1.2701   2.1433
 J1N  H14  H  HCR6  0   0.260   1.3419   3.2934   2.2913
 J1N  H15  H  HCR6  0   0.259   1.5351   4.8136   0.3476
 J1N  H16  H  HCR6  0   0.260   0.3217   4.2935  -1.7447
 J1N  H17  H  HCR6  0   0.253  -1.0620   2.2593  -1.8991

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
 J1N  O17  C16  double    1.203  0.020  1.203
 J1N  O18  C16  single    1.323  0.020  1.323
 J1N  C16  C13  single    1.518  0.020  1.518
 J1N  C14  O15  single    1.405  0.020  1.405
 J1N  C14  C13  single    1.526  0.020  1.526
 J1N  C23  C24  aromatic  1.388  0.020  1.388
 J1N  C23  C22  aromatic  1.388  0.020  1.388
 J1N  C13  N12  single    1.439  0.020  1.439
 J1N  C24  C19  aromatic  1.394  0.020  1.394
 J1N  C22  C21  aromatic  1.389  0.020  1.389
 J1N  N12  C04  single    1.340  0.020  1.340
 J1N  C04  N01  aromatic  1.333  0.020  1.333
 J1N  C04  C08  aromatic  1.422  0.020  1.422
 J1N  C19  C20  aromatic  1.396  0.020  1.396
 J1N  C19  C07  single    1.479  0.020  1.479
 J1N  C21  C20  aromatic  1.387  0.020  1.387
 J1N  N01  C02  aromatic  1.327  0.020  1.327
 J1N  C08  C07  aromatic  1.440  0.020  1.440
 J1N  C08  C09  aromatic  1.391  0.020  1.391
 J1N  C07  C06  aromatic  1.360  0.020  1.360
 J1N  C02  N03  aromatic  1.316  0.020  1.316
 J1N  C09  N03  aromatic  1.333  0.020  1.333
 J1N  C09  S05  aromatic  1.727  0.020  1.727
 J1N  C06  C10  single    1.493  0.020  1.493
 J1N  C06  S05  aromatic  1.741  0.020  1.741
 J1N  C10  C11  single    1.528  0.020  1.528
 J1N  C02  H1   single    0.930  0.020  1.080
 J1N  C10  H2   single    0.970  0.020  1.090
 J1N  C10  H3   single    0.970  0.020  1.090
 J1N  C11  H4   single    0.970  0.020  1.090
 J1N  C11  H5   single    0.970  0.020  1.090
 J1N  C11  H6   single    0.970  0.020  1.090
 J1N  N12  H7   single    0.860  0.020  1.020
 J1N  C13  H8   single    0.970  0.020  1.090
 J1N  C14  H9   single    0.970  0.020  1.090
 J1N  C14  H10  single    0.970  0.020  1.090
 J1N  O15  H11  single    0.850  0.020  0.980
 J1N  O18  H12  single    0.850  0.020  0.980
 J1N  C20  H13  single    0.930  0.020  1.080
 J1N  C21  H14  single    0.930  0.020  1.080
 J1N  C22  H15  single    0.930  0.020  1.080
 J1N  C23  H16  single    0.930  0.020  1.080
 J1N  C24  H17  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
 J1N  C04  N01  C02  118.86  3.000
 J1N  H1   C02  N03  116.59  3.000
 J1N  H1   C02  N01  115.87  3.000
 J1N  N03  C02  N01  127.54  3.000
 J1N  C09  N03  C02  113.45  3.000
 J1N  N12  C04  C08  122.35  3.000
 J1N  C08  C04  N01  119.52  3.000
 J1N  N12  C04  N01  118.12  3.000
 J1N  C09  S05  C06   91.68  3.000
 J1N  C10  C06  C07  128.53  3.000
 J1N  C10  C06  S05  119.11  3.000
 J1N  C07  C06  S05  112.36  3.000
 J1N  C19  C07  C08  124.82  3.000
 J1N  C08  C07  C06  112.13  3.000
 J1N  C19  C07  C06  123.04  3.000
 J1N  C09  C08  C07  112.66  3.000
 J1N  C09  C08  C04  114.64  3.000
 J1N  C07  C08  C04  132.68  3.000
 J1N  C08  C09  S05  111.17  3.000
 J1N  S05  C09  N03  122.88  3.000
 J1N  C08  C09  N03  125.95  3.000
 J1N  H3   C10  H2   106.18  3.000
 J1N  H3   C10  C11  109.88  3.000
 J1N  H2   C10  C11  109.59  3.000
 J1N  H3   C10  C06  108.48  3.000
 J1N  H2   C10  C06  109.62  3.000
 J1N  C11  C10  C06  112.86  3.000
 J1N  H6   C11  H5   107.77  3.000
 J1N  H6   C11  H4   107.75  3.000
 J1N  H5   C11  H4   108.10  3.000
 J1N  H6   C11  C10  111.53  3.000
 J1N  H5   C11  C10  111.06  3.000
 J1N  H4   C11  C10  110.49  3.000
 J1N  H7   N12  C13  117.23  3.000
 J1N  H7   N12  C04  119.04  3.000
 J1N  C13  N12  C04  123.36  3.000
 J1N  H8   C13  C16  108.30  3.000
 J1N  H8   C13  C14  108.12  3.000
 J1N  C16  C13  C14  110.39  3.000
 J1N  H8   C13  N12  109.22  3.000
 J1N  C14  C13  N12  112.50  3.000
 J1N  C16  C13  N12  108.23  3.000
 J1N  H10  C14  H9   107.05  3.000
 J1N  H10  C14  O15  112.48  3.000
 J1N  H9   C14  O15  112.43  3.000
 J1N  H10  C14  C13  109.32  3.000
 J1N  H9   C14  C13  108.14  3.000
 J1N  O15  C14  C13  107.32  3.000
 J1N  H11  O15  C14  108.50  3.000
 J1N  O18  C16  O17  124.24  3.000
 J1N  O18  C16  C13  111.28  3.000
 J1N  O17  C16  C13  124.48  3.000
 J1N  H12  O18  C16  110.18  3.000
 J1N  C24  C19  C20  119.03  3.000
 J1N  C20  C19  C07  120.23  3.000
 J1N  C24  C19  C07  120.74  3.000
 J1N  H13  C20  C21  119.92  3.000
 J1N  H13  C20  C19  119.62  3.000
 J1N  C21  C20  C19  120.46  3.000
 J1N  H14  C21  C22  120.17  3.000
 J1N  H14  C21  C20  119.74  3.000
 J1N  C22  C21  C20  120.09  3.000
 J1N  H15  C22  C23  120.09  3.000
 J1N  H15  C22  C21  120.10  3.000
 J1N  C23  C22  C21  119.82  3.000
 J1N  H16  C23  C24  119.70  3.000
 J1N  H16  C23  C22  120.15  3.000
 J1N  C24  C23  C22  120.15  3.000
 J1N  H17  C24  C23  119.98  3.000
 J1N  H17  C24  C19  119.56  3.000
 J1N  C23  C24  C19  120.45  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
 J1N  CONST_01  C07  C08  C04  N01   180.00   0.0  0
 J1N  CONST_02  C09  C08  C04  N01     0.00   0.0  0
 J1N  CONST_03  C09  N03  C02  N01     0.00   0.0  0
 J1N  CONST_04  C08  C04  N01  C02     0.00   0.0  0
 J1N  CONST_05  C08  C09  N03  C02     0.00   0.0  0
 J1N  CONST_06  S05  C09  N03  C02   180.00   0.0  0
 J1N  CONST_07  C04  N01  C02  N03     0.00   0.0  0
 J1N  CONST_08  C04  C08  C09  N03     0.00   0.0  0
 J1N  CONST_09  C07  C08  C09  N03   180.00   0.0  0
 J1N  CONST_10  C06  S05  C09  N03   180.00   0.0  0
 J1N  CONST_11  C19  C07  C08  C04     0.00   0.0  0
 J1N  CONST_12  C06  C07  C08  C04   180.00   0.0  0
 J1N  CONST_13  S05  C09  C08  C04   180.00   0.0  0
 J1N  CONST_14  C07  C08  C09  S05     0.00   0.0  0
 J1N  CONST_15  C19  C07  C06  S05   180.00   0.0  0
 J1N  CONST_16  C08  C07  C06  S05     0.00   0.0  0
 J1N  CONST_19  C09  C08  C07  C06     0.00   0.0  0
 J1N  CONST_20  C08  C09  S05  C06     0.00   0.0  0
 J1N  CONST_21  C23  C24  C19  C07   180.00   0.0  0
 J1N  CONST_22  C21  C20  C19  C07   180.00   0.0  0
 J1N  CONST_23  C09  S05  C06  C07     0.00   0.0  0
 J1N  CONST_26  C19  C07  C08  C09   180.00   0.0  0
 J1N  CONST_27  C22  C23  C24  C19     0.00   0.0  0
 J1N  CONST_28  C22  C21  C20  C19     0.00   0.0  0
 J1N  CONST_29  C23  C24  C19  C20     0.00   0.0  0
 J1N  CONST_30  C23  C22  C21  C20     0.00   0.0  0
 J1N  CONST_31  C24  C23  C22  C21     0.00   0.0  0
 J1N  CONST_32  C24  C19  C20  C21     0.00   0.0  0
 J1N  CONST_33  N12  C04  N01  C02   180.00   0.0  0
 J1N  CONST_34  N12  C04  C08  C07     0.00   0.0  0
 J1N  CONST_35  C10  C06  C07  C08   180.00   0.0  0
 J1N  CONST_36  N12  C04  C08  C09   180.00   0.0  0
 J1N  CONST_37  C10  C06  S05  C09   180.00   0.0  0
 J1N  CONST_38  C19  C07  C06  C10     0.00   0.0  0
 J1N  CONST_39  H1   C02  N01  C04   180.00   0.0  0
 J1N  CONST_40  H17  C24  C19  C07     0.00   0.0  0
 J1N  CONST_41  H13  C20  C19  C07     0.00   0.0  0
 J1N  CONST_42  H16  C23  C24  C19   180.00   0.0  0
 J1N  CONST_43  H14  C21  C20  C19   180.00   0.0  0
 J1N  CONST_44  H15  C22  C21  C20   180.00   0.0  0
 J1N  CONST_45  C13  N12  C04  N01     0.00   0.0  0
 J1N  CONST_46  C13  N12  C04  C08   180.00   0.0  0
 J1N  CONST_47  H7   N12  C04  N01   180.00   0.0  0
 J1N  CONST_48  H12  O18  C16  C13   180.00   0.0  0
 J1N  Var_01    C11  C10  C06  S05   -74.79  30.0  2
 J1N  Var_02    H4   C11  C10  C06  -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
 J1N  chir_01  C13  C16  C14  N12  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
 J1N  plan-1  C07  0.020
 J1N  plan-1  C19  0.020
 J1N  plan-1  C20  0.020
 J1N  plan-1  C21  0.020
 J1N  plan-1  C22  0.020
 J1N  plan-1  C23  0.020
 J1N  plan-1  C24  0.020
 J1N  plan-1  H13  0.020
 J1N  plan-1  H14  0.020
 J1N  plan-1  H15  0.020
 J1N  plan-1  H16  0.020
 J1N  plan-1  H17  0.020
 J1N  plan-2  N01  0.020
 J1N  plan-2  C02  0.020
 J1N  plan-2  N03  0.020
 J1N  plan-2  C04  0.020
 J1N  plan-2  S05  0.020
 J1N  plan-2  C06  0.020
 J1N  plan-2  C07  0.020
 J1N  plan-2  C08  0.020
 J1N  plan-2  C09  0.020
 J1N  plan-2  C10  0.020
 J1N  plan-2  N12  0.020
 J1N  plan-2  C19  0.020
 J1N  plan-2  H1   0.020
 J1N  plan-3  C04  0.020
 J1N  plan-3  N12  0.020
 J1N  plan-3  C13  0.020
 J1N  plan-3  H7   0.020
 J1N  plan-4  C13  0.020
 J1N  plan-4  C16  0.020
 J1N  plan-4  O17  0.020
 J1N  plan-4  O18  0.020
 J1N  plan-4  H12  0.020

