# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 08:49:42 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: {2-[(5-methyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-6-carbonyl)amino]phenyl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(sc2N=CNC(=O)c12)C(=O)Nc3ccccc3CC(O)=O
#
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
 68D  68D  '{2-[(5-methyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-6-carbonyl)amino]phenyl}acetic acid'  ligand  37  24  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_68D
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
 68D  C5   C  CR56  0  -0.012   2.9024   0.6982  -1.0477
 68D  C7   C  CR16  0   0.166   4.9428   1.5501  -1.2307
 68D  C15  C  CR6   0   0.294  -2.7130  -0.8923  -0.4018
 68D  C17  C  CR16  0  -0.271  -4.4765  -2.2698  -1.2911
 68D  C20  C  CR6   0   0.105  -3.6173  -0.2693   0.4621
 68D  C21  C  CH2   0  -0.682  -3.1827   0.7746   1.4545
 68D  C22  C  C     0   0.574  -2.9265   2.1243   0.8298
 68D  C1   C  CH3   0  -0.730   2.2964  -2.1221   1.3776
 68D  C2   C  CR5   0   0.232   2.1646  -1.0635   0.3315
 68D  C3   C  CR5   0  -0.426   1.0146  -0.7157  -0.3236
 68D  S4   S  S2    0   0.257   1.2414   0.5912  -1.4514
 68D  N6   N  N     0  -0.429   3.7177   1.5996  -1.6365
 68D  N8   N  NR16  0  -0.653   5.4019   0.6849  -0.3058
 68D  C9   C  CR6   0   0.558   4.6325  -0.2775   0.3419
 68D  O10  O  O     0  -0.448   5.1311  -1.0264   1.1602
 68D  C11  C  CR56  0  -0.078   3.2544  -0.2396  -0.0918
 68D  C12  C  C     0   0.532  -0.3213  -1.3399  -0.1986
 68D  O13  O  O     0  -0.450  -0.4638  -2.5225   0.0545
 68D  N14  N  NH1   0  -0.775  -1.3614  -0.4914  -0.4019
 68D  C16  C  CR16  0  -0.268  -3.1451  -1.8877  -1.2725
 68D  C18  C  CR16  0  -0.244  -5.3872  -1.6487  -0.4479
 68D  C19  C  CR16  0  -0.305  -4.9541  -0.6542   0.4153
 68D  O23  O  OH1   0  -0.577  -3.3003   3.1221   1.6099
 68D  O24  O  O     0  -0.446  -2.4078   2.2825  -0.2508
 68D  H1   H  HCR6  0   0.313   5.6753   2.2334  -1.6397
 68D  H2   H  HCR6  0   0.262  -4.8017  -3.0465  -1.9708
 68D  H3   H  HCH2  0   0.302  -3.9232   0.8667   2.2479
 68D  H4   H  HCH2  0   0.314  -2.2471   0.4727   1.9394
 68D  H5   H  HCH3  0   0.255   2.8957  -2.9542   1.0056
 68D  H6   H  HCH3  0   0.252   2.8072  -1.7296   2.2546
 68D  H7   H  HCH3  0   0.257   1.3328  -2.5142   1.6828
 68D  H8   H  HNR6  0   0.440   6.3828   0.7307  -0.0596
 68D  H9   H  HNH1  0   0.410  -1.2002   0.5063  -0.4285
 68D  H10  H  HCR6  0   0.268  -2.4417  -2.3525  -1.9501
 68D  H11  H  HCR6  0   0.260  -6.4297  -1.9373  -0.4603
 68D  H12  H  HCR6  0   0.260  -5.6628  -0.1760   1.0805
 68D  H13  H  HOH1  0   0.485  -3.0800   3.9719   1.1976

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
 68D  O10  C9   double    1.216  0.020  1.216
 68D  N8   C9   single    1.392  0.020  1.392
 68D  N8   C7   single    1.347  0.020  1.347
 68D  C9   C11  single    1.445  0.020  1.445
 68D  C7   N6   double    1.292  0.020  1.292
 68D  C11  C2   aromatic  1.430  0.020  1.430
 68D  C11  C5   aromatic  1.385  0.020  1.385
 68D  C1   C2   single    1.494  0.020  1.494
 68D  N6   C5   single    1.351  0.020  1.351
 68D  C2   C3   aromatic  1.368  0.020  1.368
 68D  C5   S4   aromatic  1.713  0.020  1.713
 68D  C3   S4   aromatic  1.741  0.020  1.741
 68D  C3   C12  single    1.480  0.020  1.480
 68D  O24  C22  double    1.209  0.020  1.209
 68D  C12  N14  single    1.358  0.020  1.358
 68D  C12  O13  double    1.218  0.020  1.218
 68D  N14  C15  single    1.410  0.020  1.410
 68D  C22  O23  single    1.321  0.020  1.321
 68D  C22  C21  single    1.509  0.020  1.509
 68D  C15  C16  aromatic  1.391  0.020  1.391
 68D  C15  C20  aromatic  1.397  0.020  1.397
 68D  C16  C17  aromatic  1.385  0.020  1.385
 68D  C20  C21  single    1.505  0.020  1.505
 68D  C20  C19  aromatic  1.392  0.020  1.392
 68D  C17  C18  aromatic  1.388  0.020  1.388
 68D  C19  C18  aromatic  1.386  0.020  1.386
 68D  C7   H1   single    0.930  0.020  1.080
 68D  C17  H2   single    0.930  0.020  1.080
 68D  C21  H3   single    0.970  0.020  1.090
 68D  C21  H4   single    0.970  0.020  1.090
 68D  C1   H5   single    0.970  0.020  1.090
 68D  C1   H6   single    0.970  0.020  1.090
 68D  C1   H7   single    0.970  0.020  1.090
 68D  N8   H8   single    0.860  0.020  1.020
 68D  N14  H9   single    0.860  0.020  1.020
 68D  C16  H10  single    0.930  0.020  1.080
 68D  C18  H11  single    0.930  0.020  1.080
 68D  C19  H12  single    0.930  0.020  1.080
 68D  O23  H13  single    0.850  0.020  0.980

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
 68D  C11  C5   N6   126.84  3.000
 68D  N6   C5   S4   121.63  3.000
 68D  C11  C5   S4   111.53  3.000
 68D  H1   C7   N8   115.75  3.000
 68D  H1   C7   N6   119.94  3.000
 68D  N8   C7   N6   124.30  3.000
 68D  C16  C15  N14  120.07  3.000
 68D  C16  C15  C20  120.33  3.000
 68D  N14  C15  C20  119.59  3.000
 68D  H2   C17  C18  120.37  3.000
 68D  H2   C17  C16  119.69  3.000
 68D  C18  C17  C16  119.94  3.000
 68D  C19  C20  C21  119.44  3.000
 68D  C19  C20  C15  118.53  3.000
 68D  C21  C20  C15  122.02  3.000
 68D  H4   C21  H3   106.34  3.000
 68D  H4   C21  C22  106.53  3.000
 68D  H3   C21  C22  109.95  3.000
 68D  H4   C21  C20  110.32  3.000
 68D  H3   C21  C20  110.05  3.000
 68D  C22  C21  C20  113.36  3.000
 68D  O24  C22  O23  123.40  3.000
 68D  O23  C22  C21  112.53  3.000
 68D  O24  C22  C21  124.05  3.000
 68D  H7   C1   H6   108.71  3.000
 68D  H7   C1   H5   107.96  3.000
 68D  H6   C1   H5   106.98  3.000
 68D  H7   C1   C2   112.02  3.000
 68D  H6   C1   C2   110.50  3.000
 68D  H5   C1   C2   110.50  3.000
 68D  C11  C2   C3   110.63  3.000
 68D  C3   C2   C1   126.12  3.000
 68D  C11  C2   C1   123.24  3.000
 68D  C12  C3   S4   119.27  3.000
 68D  C12  C3   C2   127.66  3.000
 68D  S4   C3   C2   113.04  3.000
 68D  C3   S4   C5    91.18  3.000
 68D  C7   N6   C5   114.21  3.000
 68D  H8   N8   C9   116.97  3.000
 68D  H8   N8   C7   117.91  3.000
 68D  C9   N8   C7   125.11  3.000
 68D  C11  C9   O10  127.52  3.000
 68D  C11  C9   N8   111.67  3.000
 68D  O10  C9   N8   120.81  3.000
 68D  C9   C11  C2   128.51  3.000
 68D  C2   C11  C5   113.62  3.000
 68D  C9   C11  C5   117.86  3.000
 68D  N14  C12  O13  123.26  3.000
 68D  O13  C12  C3   122.20  3.000
 68D  N14  C12  C3   114.54  3.000
 68D  H9   N14  C12  119.91  3.000
 68D  H9   N14  C15  115.69  3.000
 68D  C12  N14  C15  123.83  3.000
 68D  H10  C16  C17  119.87  3.000
 68D  H10  C16  C15  119.84  3.000
 68D  C17  C16  C15  120.28  3.000
 68D  H11  C18  C19  119.97  3.000
 68D  H11  C18  C17  120.40  3.000
 68D  C19  C18  C17  119.63  3.000
 68D  H12  C19  C18  119.65  3.000
 68D  H12  C19  C20  119.05  3.000
 68D  C18  C19  C20  121.29  3.000
 68D  H13  O23  C22  110.28  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
 68D  CONST_01  C3   C2   C11  C5     0.00   0.0  0
 68D  CONST_02  C2   C3   S4   C5     0.00   0.0  0
 68D  CONST_03  C18  C17  C16  C15    0.00   0.0  0
 68D  CONST_04  C18  C19  C20  C15    0.00   0.0  0
 68D  CONST_05  C20  C15  C16  C17    0.00   0.0  0
 68D  CONST_06  C20  C19  C18  C17    0.00   0.0  0
 68D  CONST_07  S4   C5   C11  C2     0.00   0.0  0
 68D  CONST_08  C11  C5   S4   C3     0.00   0.0  0
 68D  CONST_09  C11  C2   C3   S4     0.00   0.0  0
 68D  CONST_10  C19  C20  C15  C16    0.00   0.0  0
 68D  CONST_11  C19  C18  C17  C16    0.00   0.0  0
 68D  CONST_12  N8   C7   N6   C5     0.00   0.0  0
 68D  CONST_13  C11  C9   N8   C7     0.00   0.0  0
 68D  CONST_14  C9   N8   C7   N6     0.00   0.0  0
 68D  CONST_15  C1   C2   C11  C5   180.00   0.0  0
 68D  CONST_16  C12  C3   S4   C5   180.00   0.0  0
 68D  CONST_17  N14  C15  C16  C17  180.00   0.0  0
 68D  CONST_18  C16  C15  C20  C21  180.00   0.0  0
 68D  CONST_19  C18  C19  C20  C21  180.00   0.0  0
 68D  CONST_20  C9   C11  C2   C1     0.00   0.0  0
 68D  CONST_21  S4   C3   C2   C1   180.00   0.0  0
 68D  CONST_22  C12  C3   C2   C11  180.00   0.0  0
 68D  CONST_23  C19  C20  C15  N14  180.00   0.0  0
 68D  CONST_24  O10  C9   N8   C7   180.00   0.0  0
 68D  CONST_25  H2   C17  C16  C15  180.00   0.0  0
 68D  CONST_26  H12  C19  C20  C15  180.00   0.0  0
 68D  CONST_27  H10  C16  C15  C20  180.00   0.0  0
 68D  CONST_28  H11  C18  C19  C20  180.00   0.0  0
 68D  CONST_29  H1   C7   N6   C5   180.00   0.0  0
 68D  CONST_30  H8   N8   C7   N6   180.00   0.0  0
 68D  CONST_31  C3   C12  N14  C15  180.00   0.0  0
 68D  CONST_35  O13  C12  N14  C15    0.00   0.0  0
 68D  CONST_36  H13  O23  C22  C21  180.00   0.0  0
 68D  Var_01    C22  C21  C20  C15   76.84  30.0  2
 68D  Var_02    N14  C12  C3   C2   149.52  30.0  2
 68D  Var_03    H5   C1   C2   C3   112.20  30.0  2
 68D  Var_04    O24  C22  C21  C20  -38.32  30.0  1

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
 68D  plan-1  C15  0.020
 68D  plan-1  C17  0.020
 68D  plan-1  C20  0.020
 68D  plan-1  C21  0.020
 68D  plan-1  N14  0.020
 68D  plan-1  C16  0.020
 68D  plan-1  C18  0.020
 68D  plan-1  C19  0.020
 68D  plan-1  H2   0.020
 68D  plan-1  H10  0.020
 68D  plan-1  H11  0.020
 68D  plan-1  H12  0.020
 68D  plan-2  C5   0.020
 68D  plan-2  C7   0.020
 68D  plan-2  C1   0.020
 68D  plan-2  C2   0.020
 68D  plan-2  C3   0.020
 68D  plan-2  S4   0.020
 68D  plan-2  N6   0.020
 68D  plan-2  N8   0.020
 68D  plan-2  C9   0.020
 68D  plan-2  O10  0.020
 68D  plan-2  C11  0.020
 68D  plan-2  C12  0.020
 68D  plan-2  H1   0.020
 68D  plan-2  H8   0.020
 68D  plan-3  C15  0.020
 68D  plan-3  C3   0.020
 68D  plan-3  C12  0.020
 68D  plan-3  O13  0.020
 68D  plan-3  N14  0.020
 68D  plan-3  H9   0.020
 68D  plan-4  C21  0.020
 68D  plan-4  C22  0.020
 68D  plan-4  O23  0.020
 68D  plan-4  O24  0.020
 68D  plan-4  H13  0.020

