# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 08:37:13 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  36  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 PERFECT
;

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  -0.019   2.8574   0.7948  -0.8870
 68D  C7   C  CR16   0   0.162   4.8903   1.6794  -1.0060
 68D  C15  C  CR6    0   0.290  -2.7249  -0.9113  -0.3208
 68D  C17  C  CR16   0  -0.278  -4.5489  -2.2058  -1.2197
 68D  C20  C  CR6    0   0.081  -3.5988  -0.2623   0.5628
 68D  C21  C  CH2    0  -0.662  -3.1097   0.7426   1.5735
 68D  C22  C  C      0   0.454  -2.6785   2.0996   0.9746
 68D  C1   C  CH3    0  -0.730   2.3194  -2.3142   1.1752
 68D  C2   C  CR5    0   0.224   2.1610  -1.1331   0.2725
 68D  C3   C  CR5    0  -0.423   0.9952  -0.7159  -0.3098
 68D  S4   S  S2     0   0.263   1.1882   0.7296  -1.2586
 68D  N6   N  N      0  -0.430   3.6566   1.7700  -1.3751
 68D  N8   N  NR16   0  -0.654   5.3738   0.7089  -0.2051
 68D  C9   C  CR6    0   0.554   4.6231  -0.3319   0.3342
 68D  O10  O  O      0  -0.452   5.1450  -1.1724   1.0428
 68D  C11  C  CR56   0  -0.079   3.2368  -0.2520  -0.0628
 68D  C12  C  C      0   0.516  -0.3340  -1.3739  -0.2602
 68D  O13  O  O      0  -0.468  -0.4384  -2.5890  -0.1828
 68D  N14  N  NH1    0  -0.788  -1.3754  -0.5194  -0.3223
 68D  C16  C  CR16   0  -0.279  -3.2018  -1.8784  -1.2016
 68D  C18  C  CR16   0  -0.252  -5.4295  -1.5596  -0.3636
 68D  C19  C  CR16   0  -0.316  -4.9498  -0.5969   0.5128
 68D  O23  O  OC    -1  -0.574  -3.2361   3.1215   1.3892
 68D  O24  O  O      0  -0.596  -1.7617   2.0589   0.1100
 68D  H1   H  HCR6   0   0.310   5.6112   2.4125  -1.3430
 68D  H2   H  HCR6   0   0.253  -4.9087  -2.9585  -1.9093
 68D  H3   H  HCH2   0   0.245  -3.8889   0.9007   2.3184
 68D  H4   H  HCH2   0   0.256  -2.2466   0.3227   2.1032
 68D  H5   H  HCH3   0   0.251   2.9307  -3.0829   0.7011
 68D  H6   H  HCH3   0   0.249   2.8270  -2.0250   2.0936
 68D  H7   H  HCH3   0   0.255   1.3632  -2.7569   1.4311
 68D  H8   H  HNR6   0   0.438   6.3592   0.7312   0.0252
 68D  H9   H  HNH1   0   0.438  -1.2690   0.5089  -0.1639
 68D  H10  H  HCR6   0   0.258  -2.5234  -2.3628  -1.8903
 68D  H11  H  HCR6   0   0.251  -6.4833  -1.8053  -0.3743
 68D  H12  H  HCR6   0   0.249  -5.6363  -0.1034   1.1906

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    1.217  0.020  1.217
 68D  N8   C9   single    1.392  0.020  1.392
 68D  N8   C7   single    1.348  0.020  1.348
 68D  C9   C11  single    1.444  0.020  1.444
 68D  C7   N6   double    1.291  0.020  1.291
 68D  C11  C2   aromatic  1.430  0.020  1.430
 68D  C11  C5   aromatic  1.385  0.020  1.385
 68D  C1   C2   single    1.495  0.020  1.495
 68D  N6   C5   single    1.352  0.020  1.352
 68D  C2   C3   aromatic  1.368  0.020  1.368
 68D  C5   S4   aromatic  1.711  0.020  1.711
 68D  C3   S4   aromatic  1.740  0.020  1.740
 68D  C3   C12  single    1.484  0.020  1.484
 68D  O24  C22  deloc     1.261  0.020  1.261
 68D  C12  N14  single    1.349  0.020  1.349
 68D  C12  O13  double    1.222  0.020  1.222
 68D  N14  C15  single    1.405  0.020  1.405
 68D  C22  O23  deloc     1.236  0.020  1.236
 68D  C22  C21  single    1.545  0.020  1.545
 68D  C15  C16  aromatic  1.392  0.020  1.392
 68D  C15  C20  aromatic  1.402  0.020  1.402
 68D  C16  C17  aromatic  1.386  0.020  1.386
 68D  C20  C21  single    1.507  0.020  1.507
 68D  C20  C19  aromatic  1.393  0.020  1.393
 68D  C17  C18  aromatic  1.388  0.020  1.388
 68D  C19  C18  aromatic  1.387  0.020  1.387
 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

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   126.72  3.000
 68D  N6   C5   S4   121.71  3.000
 68D  C11  C5   S4   111.56  3.000
 68D  H1   C7   N8   115.71  3.000
 68D  H1   C7   N6   120.01  3.000
 68D  N8   C7   N6   124.28  3.000
 68D  C16  C15  N14  121.47  3.000
 68D  C16  C15  C20  120.44  3.000
 68D  N14  C15  C20  118.05  3.000
 68D  H2   C17  C18  120.39  3.000
 68D  H2   C17  C16  119.70  3.000
 68D  C18  C17  C16  119.90  3.000
 68D  C19  C20  C21  119.95  3.000
 68D  C19  C20  C15  118.08  3.000
 68D  C21  C20  C15  121.94  3.000
 68D  H4   C21  H3   106.76  3.000
 68D  H4   C21  C22  107.70  3.000
 68D  H3   C21  C22  109.71  3.000
 68D  H4   C21  C20  108.92  3.000
 68D  H3   C21  C20  108.86  3.000
 68D  C22  C21  C20  114.61  3.000
 68D  O24  C22  O23  125.79  3.000
 68D  O23  C22  C21  118.07  3.000
 68D  O24  C22  C21  116.14  3.000
 68D  H7   C1   H6   108.70  3.000
 68D  H7   C1   H5   108.01  3.000
 68D  H6   C1   H5   107.02  3.000
 68D  H7   C1   C2   111.81  3.000
 68D  H6   C1   C2   110.42  3.000
 68D  H5   C1   C2   110.71  3.000
 68D  C11  C2   C3   110.69  3.000
 68D  C3   C2   C1   126.02  3.000
 68D  C11  C2   C1   123.26  3.000
 68D  C12  C3   S4   119.08  3.000
 68D  C12  C3   C2   127.86  3.000
 68D  S4   C3   C2   113.01  3.000
 68D  C3   S4   C5    91.23  3.000
 68D  C7   N6   C5   114.27  3.000
 68D  H8   N8   C9   116.96  3.000
 68D  H8   N8   C7   117.94  3.000
 68D  C9   N8   C7   125.10  3.000
 68D  C11  C9   O10  127.58  3.000
 68D  C11  C9   N8   111.70  3.000
 68D  O10  C9   N8   120.71  3.000
 68D  C9   C11  C2   128.56  3.000
 68D  C2   C11  C5   113.51  3.000
 68D  C9   C11  C5   117.92  3.000
 68D  N14  C12  O13  124.55  3.000
 68D  O13  C12  C3   121.30  3.000
 68D  N14  C12  C3   114.15  3.000
 68D  H9   N14  C12  122.51  3.000
 68D  H9   N14  C15  111.83  3.000
 68D  C12  N14  C15  124.39  3.000
 68D  H10  C16  C17  119.71  3.000
 68D  H10  C16  C15  119.94  3.000
 68D  C17  C16  C15  120.34  3.000
 68D  H11  C18  C19  120.03  3.000
 68D  H11  C18  C17  120.41  3.000
 68D  C19  C18  C17  119.56  3.000
 68D  H12  C19  C18  119.48  3.000
 68D  H12  C19  C20  118.85  3.000
 68D  C18  C19  C20  121.65  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  Var_01    C22  C21  C20  C15   72.50  30.0  2
 68D  Var_02    N14  C12  C3   C2   149.33  30.0  2
 68D  Var_03    H5   C1   C2   C3   113.32  30.0  2
 68D  Var_04    O24  C22  C21  C20  -58.30  30.0  2

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

