# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 03:35:31 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: benzyl 6-benzyl-5,7-dioxo-6,7-dihydro-5H-[1,3]thiazolo[3,2-c]pyrimidine-2-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(OCc1ccccc1)C2=CN3C(=O)N(Cc4ccccc4)C(=O)C=C3S2
#
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
 SP6  SP6  'benzyl 6-benzyl-5,7-dioxo-6,7-dihydro-5H-[1,3]thiazolo[3,2-c]pyrimidine-2-carboxylate'  ligand  44  28  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SP6
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
 SP6  N1    N  N     0  -0.635   0.6923  -0.6710   2.0753
 SP6  C4    C  CH2   0  -0.416  -0.2815   1.0863   5.1370
 SP6  C5    C  CR6   0   0.814   0.1078   0.2833   2.9113
 SP6  C6    C  CR15  0   0.224   0.5735  -0.6325   0.7021
 SP6  C7    C  C     0   0.608   1.3286  -1.9590  -1.3195
 SP6  C8    C  CR5   0  -0.463   1.2096  -1.6475   0.1053
 SP6  C10   C  CR16  0  -0.265   1.8345   4.8275   5.1825
 SP6  C13   C  CR16  0  -0.244   0.5378   4.7644   4.6921
 SP6  C15   C  CR16  0  -0.295  -0.1389   3.5516   4.6689
 SP6  C17   C  CR16  0  -0.296   1.7664   2.4655   5.6403
 SP6  C20   C  CR6   0   0.076  -0.1399  -0.2370  -4.1153
 SP6  C21   C  CR6   0   0.129   0.4665   2.3932   5.1435
 SP6  O3    O  O     0  -0.444   1.9637  -2.9071  -1.7119
 SP6  O4    O  O2    0  -0.449   0.6764  -1.1004  -2.0750
 SP6  C11   C  CH2   0  -0.257   0.7203  -1.2974  -3.5041
 SP6  C16   C  CR16  0  -0.285  -1.5204  -0.4071  -4.1826
 SP6  C18   C  CR16  0  -0.242  -2.3252   0.5842  -4.7248
 SP6  C14   C  CR16  0  -0.291   0.4242   0.9388  -4.5992
 SP6  C12   C  CR16  0  -0.242  -0.3788   1.9318  -5.1447
 SP6  C9    C  CR16  0  -0.259  -1.7546   1.7565  -5.2060
 SP6  C3    C  CR56  0   0.289   1.4278  -1.7279   2.5600
 SP6  S1    S  S2    0   0.307   1.9962  -2.7103   1.2525
 SP6  C2    C  CR16  0  -0.547   1.6329  -1.9006   3.8816
 SP6  C1    C  CR6   0   0.624   1.0799  -0.9592   4.8093
 SP6  O1    O  OC    0  -0.472   1.2286  -1.0240   6.0162
 SP6  O2    O  OC    0  -0.448  -0.5384   1.1925   2.4493
 SP6  N6    N  NR6   0  -0.609   0.3254   0.0916   4.2462
 SP6  C19   C  CR16  0  -0.240   2.4479   3.6738   5.6559
 SP6  H41   H  HCH2  0   0.296  -0.3007   0.6516   6.1327
 SP6  H42   H  HCH2  0   0.291  -1.3154   1.2380   4.8322
 SP6  H61   H  HCR5  0   0.343   0.0164   0.1623   0.2332
 SP6  H10   H  HCR6  0   0.257   2.3647   5.7710   5.2017
 SP6  H13   H  HCR6  0   0.256   0.0527   5.6591   4.3237
 SP6  H15   H  HCR6  0   0.251  -1.1481   3.5065   4.2781
 SP6  H17   H  HCR6  0   0.253   2.2488   1.5759   6.0267
 SP6  H111  H  HCH2  0   0.263   0.3510  -2.2958  -3.7440
 SP6  H112  H  HCH2  0   0.264   1.7528  -1.2192  -3.8481
 SP6  H16   H  HCR6  0   0.258  -1.9687  -1.3218  -3.8128
 SP6  H18   H  HCR6  0   0.260  -3.3968   0.4412  -4.7752
 SP6  H14   H  HCR6  0   0.258   1.4978   1.0793  -4.5544
 SP6  H12   H  HCR6  0   0.260   0.0700   2.8409  -5.5227
 SP6  H9    H  HCR6  0   0.260  -2.3807   2.5300  -5.6316
 SP6  H2    H  HCR6  0   0.302   2.2096  -2.7309   4.2590
 SP6  H19   H  HCR6  0   0.256   3.4566   3.7170   6.0463

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
 SP6  N1   C3    aromatic  1.376  0.020  1.376
 SP6  N1   C5    aromatic  1.397  0.020  1.397
 SP6  N1   C6    aromatic  1.379  0.020  1.379
 SP6  C4   N6    single    1.467  0.020  1.467
 SP6  C4   C21   single    1.506  0.020  1.506
 SP6  C4   H41   single    0.970  0.020  1.090
 SP6  C4   H42   single    0.970  0.020  1.090
 SP6  C5   N6    aromatic  1.366  0.020  1.366
 SP6  C5   O2    double    1.207  0.020  1.207
 SP6  C6   C8    aromatic  1.338  0.020  1.338
 SP6  C6   H61   single    0.930  0.020  1.080
 SP6  C7   C8    single    1.463  0.020  1.463
 SP6  C7   O4    single    1.317  0.020  1.317
 SP6  C7   O3    double    1.207  0.020  1.207
 SP6  C8   S1    aromatic  1.750  0.020  1.750
 SP6  C10  C13   aromatic  1.388  0.020  1.388
 SP6  C10  C19   aromatic  1.390  0.020  1.390
 SP6  C10  H10   single    0.930  0.020  1.080
 SP6  C13  C15   aromatic  1.389  0.020  1.389
 SP6  C13  H13   single    0.930  0.020  1.080
 SP6  C15  C21   aromatic  1.391  0.020  1.391
 SP6  C15  H15   single    0.930  0.020  1.080
 SP6  C17  C21   aromatic  1.393  0.020  1.393
 SP6  C17  C19   aromatic  1.387  0.020  1.387
 SP6  C17  H17   single    0.930  0.020  1.080
 SP6  C20  C11   single    1.496  0.020  1.496
 SP6  C20  C14   aromatic  1.391  0.020  1.391
 SP6  C20  C16   aromatic  1.393  0.020  1.393
 SP6  O4   C11   single    1.443  0.020  1.443
 SP6  C11  H111  single    0.970  0.020  1.090
 SP6  C11  H112  single    0.970  0.020  1.090
 SP6  C16  C18   aromatic  1.387  0.020  1.387
 SP6  C16  H16   single    0.930  0.020  1.080
 SP6  C18  C9    aromatic  1.390  0.020  1.390
 SP6  C18  H18   single    0.930  0.020  1.080
 SP6  C14  C12   aromatic  1.389  0.020  1.389
 SP6  C14  H14   single    0.930  0.020  1.080
 SP6  C12  C9    aromatic  1.388  0.020  1.388
 SP6  C12  H12   single    0.930  0.020  1.080
 SP6  C9   H9    single    0.930  0.020  1.080
 SP6  C3   C2    aromatic  1.348  0.020  1.348
 SP6  C3   S1    aromatic  1.731  0.020  1.731
 SP6  C2   C1    aromatic  1.433  0.020  1.433
 SP6  C2   H2    single    0.930  0.020  1.080
 SP6  C1   O1    double    1.218  0.020  1.218
 SP6  C1   N6    aromatic  1.411  0.020  1.411
 SP6  C19  H19   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
 SP6  C3    N1   C6    114.73  3.000
 SP6  C6    N1   C5    122.74  3.000
 SP6  C3    N1   C5    122.52  3.000
 SP6  H42   C4   H41   107.19  3.000
 SP6  H42   C4   N6    108.51  3.000
 SP6  H41   C4   N6    107.01  3.000
 SP6  H42   C4   C21   110.61  3.000
 SP6  H41   C4   C21   110.61  3.000
 SP6  N6    C4   C21   112.68  3.000
 SP6  N6    C5   O2    124.39  3.000
 SP6  O2    C5   N1    120.63  3.000
 SP6  N6    C5   N1    114.98  3.000
 SP6  H61   C6   C8    127.65  3.000
 SP6  H61   C6   N1    119.89  3.000
 SP6  C8    C6   N1    112.46  3.000
 SP6  O4    C7   O3    125.91  3.000
 SP6  O3    C7   C8    121.78  3.000
 SP6  O4    C7   C8    112.32  3.000
 SP6  S1    C8   C7    118.19  3.000
 SP6  S1    C8   C6    112.44  3.000
 SP6  C7    C8   C6    129.37  3.000
 SP6  H10   C10  C19   120.09  3.000
 SP6  H10   C10  C13   120.23  3.000
 SP6  C19   C10  C13   119.68  3.000
 SP6  H13   C13  C15   119.85  3.000
 SP6  H13   C13  C10   120.10  3.000
 SP6  C15   C13  C10   120.05  3.000
 SP6  H15   C15  C21   119.61  3.000
 SP6  H15   C15  C13   119.76  3.000
 SP6  C21   C15  C13   120.64  3.000
 SP6  H17   C17  C19   119.50  3.000
 SP6  H17   C17  C21   120.00  3.000
 SP6  C19   C17  C21   120.49  3.000
 SP6  C14   C20  C16   119.24  3.000
 SP6  C16   C20  C11   120.21  3.000
 SP6  C14   C20  C11   120.54  3.000
 SP6  C17   C21  C15   118.99  3.000
 SP6  C17   C21  C4    120.66  3.000
 SP6  C15   C21  C4    120.35  3.000
 SP6  C11   O4   C7    117.66  3.000
 SP6  H112  C11  H111  108.45  3.000
 SP6  H112  C11  O4    109.34  3.000
 SP6  H111  C11  O4    109.41  3.000
 SP6  H112  C11  C20   111.38  3.000
 SP6  H111  C11  C20   111.35  3.000
 SP6  O4    C11  C20   106.88  3.000
 SP6  H16   C16  C18   119.77  3.000
 SP6  H16   C16  C20   119.78  3.000
 SP6  C18   C16  C20   120.45  3.000
 SP6  H18   C18  C9    120.12  3.000
 SP6  H18   C18  C16   119.88  3.000
 SP6  C9    C18  C16   119.99  3.000
 SP6  H14   C14  C12   119.76  3.000
 SP6  H14   C14  C20   119.80  3.000
 SP6  C12   C14  C20   120.44  3.000
 SP6  H12   C12  C9    120.11  3.000
 SP6  H12   C12  C14   119.88  3.000
 SP6  C9    C12  C14   120.01  3.000
 SP6  H9    C9   C12   120.02  3.000
 SP6  H9    C9   C18   120.10  3.000
 SP6  C12   C9   C18   119.88  3.000
 SP6  C2    C3   S1    128.14  3.000
 SP6  S1    C3   N1    110.20  3.000
 SP6  C2    C3   N1    121.67  3.000
 SP6  C3    S1   C8     90.17  3.000
 SP6  H2    C2   C1    119.04  3.000
 SP6  H2    C2   C3    121.50  3.000
 SP6  C1    C2   C3    119.46  3.000
 SP6  N6    C1   O1    120.03  3.000
 SP6  N6    C1   C2    115.93  3.000
 SP6  O1    C1   C2    124.04  3.000
 SP6  C1    N6   C5    125.43  3.000
 SP6  C1    N6   C4    118.94  3.000
 SP6  C5    N6   C4    115.62  3.000
 SP6  H19   C19  C17   119.77  3.000
 SP6  H19   C19  C10   120.07  3.000
 SP6  C17   C19  C10   120.16  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
 SP6  CONST_01  C1   C2   C3   N1     0.00   0.0  0
 SP6  CONST_02  C8   S1   C3   N1     0.00   0.0  0
 SP6  CONST_03  C1   N6   C5   N1     0.00   0.0  0
 SP6  CONST_04  S1   C8   C6   N1     0.00   0.0  0
 SP6  CONST_05  C2   C3   N1   C5     0.00   0.0  0
 SP6  CONST_06  S1   C3   N1   C5   180.00   0.0  0
 SP6  CONST_07  C8   C6   N1   C5   180.00   0.0  0
 SP6  CONST_08  C2   C1   N6   C5     0.00   0.0  0
 SP6  CONST_09  C2   C3   N1   C6   180.00   0.0  0
 SP6  CONST_10  S1   C3   N1   C6     0.00   0.0  0
 SP6  CONST_11  N6   C5   N1   C6   180.00   0.0  0
 SP6  CONST_12  C3   S1   C8   C6     0.00   0.0  0
 SP6  CONST_13  C3   N1   C6   C8     0.00   0.0  0
 SP6  CONST_14  C2   C3   S1   C8   180.00   0.0  0
 SP6  CONST_15  C21  C15  C13  C10    0.00   0.0  0
 SP6  CONST_16  C21  C17  C19  C10    0.00   0.0  0
 SP6  CONST_17  C17  C19  C10  C13    0.00   0.0  0
 SP6  CONST_18  C17  C21  C15  C13    0.00   0.0  0
 SP6  CONST_19  C19  C10  C13  C15    0.00   0.0  0
 SP6  CONST_20  C19  C17  C21  C15    0.00   0.0  0
 SP6  CONST_21  C9   C12  C14  C20    0.00   0.0  0
 SP6  CONST_22  C9   C18  C16  C20    0.00   0.0  0
 SP6  CONST_23  C12  C14  C20  C16    0.00   0.0  0
 SP6  CONST_24  C12  C9   C18  C16    0.00   0.0  0
 SP6  CONST_25  C14  C20  C16  C18    0.00   0.0  0
 SP6  CONST_26  C14  C12  C9   C18    0.00   0.0  0
 SP6  CONST_27  N6   C5   N1   C3     0.00   0.0  0
 SP6  CONST_28  N6   C1   C2   C3     0.00   0.0  0
 SP6  CONST_29  C1   C2   C3   S1   180.00   0.0  0
 SP6  CONST_30  C4   N6   C5   N1   180.00   0.0  0
 SP6  CONST_31  C7   C8   C6   N1   180.00   0.0  0
 SP6  CONST_32  C2   C1   N6   C4   180.00   0.0  0
 SP6  CONST_33  C13  C15  C21  C4   180.00   0.0  0
 SP6  CONST_34  C19  C17  C21  C4   180.00   0.0  0
 SP6  CONST_35  O1   C1   N6   C5   180.00   0.0  0
 SP6  CONST_36  O2   C5   N1   C6     0.00   0.0  0
 SP6  CONST_37  C3   S1   C8   C7   180.00   0.0  0
 SP6  CONST_38  C12  C14  C20  C11  180.00   0.0  0
 SP6  CONST_39  C18  C16  C20  C11  180.00   0.0  0
 SP6  CONST_40  O2   C5   N1   C3   180.00   0.0  0
 SP6  CONST_41  O1   C1   C2   C3   180.00   0.0  0
 SP6  CONST_42  O2   C5   N6   C1   180.00   0.0  0
 SP6  CONST_43  H2   C2   C3   N1   180.00   0.0  0
 SP6  CONST_44  H61  C6   N1   C5     0.00   0.0  0
 SP6  CONST_45  H15  C15  C13  C10  180.00   0.0  0
 SP6  CONST_46  H17  C17  C19  C10  180.00   0.0  0
 SP6  CONST_47  H19  C19  C10  C13  180.00   0.0  0
 SP6  CONST_48  H10  C10  C13  C15  180.00   0.0  0
 SP6  CONST_49  H12  C12  C14  C20  180.00   0.0  0
 SP6  CONST_50  H18  C18  C16  C20  180.00   0.0  0
 SP6  CONST_51  H13  C13  C15  C21  180.00   0.0  0
 SP6  CONST_52  H14  C14  C20  C16  180.00   0.0  0
 SP6  CONST_53  H9   C9   C18  C16  180.00   0.0  0
 SP6  CONST_54  H16  C16  C20  C14  180.00   0.0  0
 SP6  CONST_55  O2   C5   N6   C4     0.00   0.0  0
 SP6  CONST_56  O1   C1   N6   C4     0.00   0.0  0
 SP6  Var_01    C21  C4   N6   C5   -75.72  30.0  2
 SP6  Var_02    N6   C4   C21  C15  115.52  30.0  1
 SP6  Var_03    O4   C7   C8   C6    -1.43  30.0  2
 SP6  Var_04    C14  C20  C11  O4    96.54  30.0  2
 SP6  Var_05    C20  C11  O4   C7   177.51  30.0  3

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
 SP6  plan-1  C4   0.020
 SP6  plan-1  C10  0.020
 SP6  plan-1  C13  0.020
 SP6  plan-1  C15  0.020
 SP6  plan-1  C17  0.020
 SP6  plan-1  C21  0.020
 SP6  plan-1  C19  0.020
 SP6  plan-1  H10  0.020
 SP6  plan-1  H13  0.020
 SP6  plan-1  H15  0.020
 SP6  plan-1  H17  0.020
 SP6  plan-1  H19  0.020
 SP6  plan-2  C7   0.020
 SP6  plan-2  C8   0.020
 SP6  plan-2  O3   0.020
 SP6  plan-2  O4   0.020
 SP6  plan-3  C20  0.020
 SP6  plan-3  C11  0.020
 SP6  plan-3  C16  0.020
 SP6  plan-3  C18  0.020
 SP6  plan-3  C14  0.020
 SP6  plan-3  C12  0.020
 SP6  plan-3  C9   0.020
 SP6  plan-3  H16  0.020
 SP6  plan-3  H18  0.020
 SP6  plan-3  H14  0.020
 SP6  plan-3  H12  0.020
 SP6  plan-3  H9   0.020
 SP6  plan-4  N1   0.020
 SP6  plan-4  C4   0.020
 SP6  plan-4  C5   0.020
 SP6  plan-4  C6   0.020
 SP6  plan-4  C7   0.020
 SP6  plan-4  C8   0.020
 SP6  plan-4  C3   0.020
 SP6  plan-4  S1   0.020
 SP6  plan-4  C2   0.020
 SP6  plan-4  C1   0.020
 SP6  plan-4  O1   0.020
 SP6  plan-4  O2   0.020
 SP6  plan-4  N6   0.020
 SP6  plan-4  H61  0.020
 SP6  plan-4  H2   0.020

