# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 23:38:00 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 5-chloro-N-{[(4R)-2,5-dioxo-4-(1,3-thiazol-2-yl)imidazolidin-4-yl]methyl}-1-benzofuran-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc2oc(cc2c1)C(=O)NC[C@]3(NC(=O)NC3=O)c4sccn4
#
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
 3PU  3PU  5-chloro-N-{[(4R)-2,5-dioxo-4-(1,3-thiazol-2-yl)imidazolidin-4-yl]methyl}-1-benzofuran-2-carboxamide  ligand  37  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3PU
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
 3PU  C7   C   CH2   0  -0.282  -1.9564   1.1032  -0.6759
 3PU  C6   C   CR15  0  -0.352   2.7357   1.0953   0.9945
 3PU  C1   C   CR16  0  -0.223   5.4848  -1.1413  -1.1903
 3PU  C5   C   CR16  0  -0.292   5.2108   0.3072   0.7532
 3PU  C4   C   CR15  0  -0.503  -6.6724   0.2099  -0.4845
 3PU  C3   C   CR15  0  -0.017  -6.1500   1.4636  -0.4749
 3PU  C2   C   CR16  0  -0.338   4.1463  -1.0409  -1.5215
 3PU  C8   C   CR6   0  -0.043   5.9960  -0.4731  -0.0694
 3PU  C9   C   CR56  0   0.388   3.3617  -0.2571  -0.6937
 3PU  C10  C   CR56  0   0.054   3.8580   0.4134   0.4262
 3PU  C11  C   CR5   0   0.257   1.6840   0.7948   0.2002
 3PU  C12  C   CR5   0   0.097  -4.2895   0.3517  -0.1785
 3PU  C13  C   CR5   0   0.578  -2.5650   0.1346   1.5907
 3PU  C14  C   CR5   0   0.668  -1.8335  -1.8892   0.8019
 3PU  C15  C   C     0   0.497   0.2779   1.2215   0.3227
 3PU  C16  C   CR5   0  -0.083  -2.8397   0.0797   0.0768
 3PU  N17  N   N     0  -0.374  -4.7980   1.5318  -0.2994
 3PU  N18  N   NR15  0  -0.691  -1.9114  -1.0194   1.8853
 3PU  N19  N   NR15  0  -0.667  -2.4863  -1.2806  -0.2235
 3PU  N20  N   NH1   0  -0.657  -0.5617   0.7622  -0.6246
 3PU  O21  O   O     0  -0.396  -2.8876   1.0171   2.3388
 3PU  O22  O   O     0  -0.452  -1.3040  -2.9728   0.8066
 3PU  O23  O   O     0  -0.460  -0.0614   1.9431   1.2455
 3PU  O24  O   O     0  -0.463   2.0414  -0.0224  -0.8269
 3PU  S25  S   S2    0   0.270  -5.4240  -0.9418  -0.2720
 3PU  H1   H   HCH2  0   0.300  -2.2632   1.1130  -1.7211
 3PU  H2   H   HCH2  0   0.289  -2.1280   2.0996  -0.2728
 3PU  H3   H   HCR5  0   0.283   2.7195   1.7215   1.8713
 3PU  H4   H   HCR6  0   0.289   6.1426  -1.7424  -1.8024
 3PU  H5   H   HCR6  0   0.288   5.6236   0.8141   1.6145
 3PU  H6   H   HCR5  0   0.314  -7.7011  -0.0851  -0.6162
 3PU  H7   H   HCR5  0   0.278  -6.7220   2.3716  -0.5987
 3PU  H8   H   HCR6  0   0.288   3.7427  -1.5518  -2.3848
 3PU  H9   H   HNR5  0   0.436  -1.6029  -1.2774   2.8128
 3PU  H10  H   HNR5  0   0.423  -2.3810  -1.6178  -1.1696
 3PU  H11  H   HNH1  0   0.420  -0.1971   0.2015  -1.3781
 3PU  CL2  CL  CL    0  -0.124   7.6854  -0.6410   0.2874

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
 3PU  CL2  C8   single    1.735  0.020  1.735
 3PU  C1   C2   aromatic  1.382  0.020  1.382
 3PU  C1   C8   aromatic  1.402  0.020  1.402
 3PU  C2   C9   aromatic  1.384  0.020  1.384
 3PU  C8   C5   aromatic  1.379  0.020  1.379
 3PU  C9   C10  aromatic  1.396  0.020  1.396
 3PU  C9   O24  aromatic  1.348  0.020  1.348
 3PU  C5   C10  aromatic  1.396  0.020  1.396
 3PU  C10  C6   aromatic  1.431  0.020  1.431
 3PU  O24  C11  aromatic  1.360  0.020  1.360
 3PU  C11  C6   aromatic  1.352  0.020  1.352
 3PU  C11  C15  single    1.475  0.020  1.475
 3PU  N20  C15  single    1.347  0.020  1.347
 3PU  N20  C7   single    1.437  0.020  1.437
 3PU  O21  C13  double    1.201  0.020  1.201
 3PU  C15  O23  double    1.220  0.020  1.220
 3PU  C7   C16  single    1.547  0.020  1.547
 3PU  C13  N18  single    1.358  0.020  1.358
 3PU  C13  C16  single    1.540  0.020  1.540
 3PU  N18  C14  single    1.392  0.020  1.392
 3PU  C16  N19  single    1.437  0.020  1.437
 3PU  C16  C12  single    1.497  0.020  1.497
 3PU  C14  N19  single    1.359  0.020  1.359
 3PU  C14  O22  double    1.206  0.020  1.206
 3PU  N17  C12  aromatic  1.291  0.020  1.291
 3PU  N17  C3   aromatic  1.365  0.020  1.365
 3PU  C12  S25  aromatic  1.723  0.020  1.723
 3PU  C3   C4   aromatic  1.358  0.020  1.358
 3PU  S25  C4   aromatic  1.712  0.020  1.712
 3PU  C7   H1   single    0.970  0.020  1.090
 3PU  C7   H2   single    0.970  0.020  1.090
 3PU  C6   H3   single    0.930  0.020  1.080
 3PU  C1   H4   single    0.930  0.020  1.080
 3PU  C5   H5   single    0.930  0.020  1.080
 3PU  C4   H6   single    0.930  0.020  1.080
 3PU  C3   H7   single    0.930  0.020  1.080
 3PU  C2   H8   single    0.930  0.020  1.080
 3PU  N18  H9   single    0.860  0.020  1.020
 3PU  N19  H10  single    0.890  0.020  1.040
 3PU  N20  H11  single    0.860  0.020  1.020

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
 3PU  H2   C7   H1   107.62  3.000
 3PU  H2   C7   N20  110.93  3.000
 3PU  H1   C7   N20  108.05  3.000
 3PU  H2   C7   C16  109.59  3.000
 3PU  H1   C7   C16  108.17  3.000
 3PU  N20  C7   C16  112.32  3.000
 3PU  H3   C6   C11  126.56  3.000
 3PU  H3   C6   C10  127.72  3.000
 3PU  C11  C6   C10  105.72  3.000
 3PU  H4   C1   C8   119.74  3.000
 3PU  H4   C1   C2   119.59  3.000
 3PU  C8   C1   C2   120.67  3.000
 3PU  H5   C5   C10  121.40  3.000
 3PU  H5   C5   C8   121.53  3.000
 3PU  C10  C5   C8   117.07  3.000
 3PU  H6   C4   S25  121.80  3.000
 3PU  H6   C4   C3   128.35  3.000
 3PU  S25  C4   C3   109.85  3.000
 3PU  H7   C3   N17  119.81  3.000
 3PU  H7   C3   C4   124.85  3.000
 3PU  N17  C3   C4   115.34  3.000
 3PU  H8   C2   C9   122.24  3.000
 3PU  H8   C2   C1   121.22  3.000
 3PU  C9   C2   C1   116.54  3.000
 3PU  CL2  C8   C5   119.11  3.000
 3PU  C5   C8   C1   122.63  3.000
 3PU  CL2  C8   C1   118.26  3.000
 3PU  O24  C9   C10  110.11  3.000
 3PU  O24  C9   C2   126.51  3.000
 3PU  C10  C9   C2   123.38  3.000
 3PU  C9   C10  C5   119.72  3.000
 3PU  C5   C10  C6   134.70  3.000
 3PU  C9   C10  C6   105.58  3.000
 3PU  O24  C11  C15  119.15  3.000
 3PU  C15  C11  C6   128.96  3.000
 3PU  O24  C11  C6   111.89  3.000
 3PU  S25  C12  N17  114.95  3.000
 3PU  S25  C12  C16  120.70  3.000
 3PU  N17  C12  C16  124.31  3.000
 3PU  O21  C13  N18  128.20  3.000
 3PU  N18  C13  C16  105.59  3.000
 3PU  O21  C13  C16  126.21  3.000
 3PU  O22  C14  N19  128.03  3.000
 3PU  O22  C14  N18  125.67  3.000
 3PU  N19  C14  N18  106.29  3.000
 3PU  O23  C15  N20  124.10  3.000
 3PU  O23  C15  C11  119.96  3.000
 3PU  N20  C15  C11  115.94  3.000
 3PU  N19  C16  C13  101.27  3.000
 3PU  N19  C16  C12  111.99  3.000
 3PU  C13  C16  C12  109.51  3.000
 3PU  C12  C16  C7   110.47  3.000
 3PU  N19  C16  C7   112.59  3.000
 3PU  C13  C16  C7   110.66  3.000
 3PU  C12  N17  C3   110.89  3.000
 3PU  H9   N18  C14  122.53  3.000
 3PU  H9   N18  C13  124.23  3.000
 3PU  C14  N18  C13  112.90  3.000
 3PU  H10  N19  C16  122.51  3.000
 3PU  H10  N19  C14  120.47  3.000
 3PU  C16  N19  C14  112.59  3.000
 3PU  H11  N20  C15  119.36  3.000
 3PU  H11  N20  C7   117.18  3.000
 3PU  C15  N20  C7   123.33  3.000
 3PU  C11  O24  C9   106.70  3.000
 3PU  C12  S25  C4    88.96  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
 3PU  CONST_01  C2   C9   C10  C6    180.00   0.0  0
 3PU  CONST_02  O24  C9   C10  C6      0.00   0.0  0
 3PU  CONST_03  C8   C5   C10  C6    180.00   0.0  0
 3PU  CONST_04  C9   O24  C11  C6      0.00   0.0  0
 3PU  CONST_05  C10  C9   C2   C1      0.00   0.0  0
 3PU  CONST_06  O24  C9   C2   C1    180.00   0.0  0
 3PU  CONST_07  C10  C5   C8   C1      0.00   0.0  0
 3PU  CONST_08  C2   C1   C8   C5      0.00   0.0  0
 3PU  CONST_09  C2   C9   C10  C5      0.00   0.0  0
 3PU  CONST_10  O24  C9   C10  C5    180.00   0.0  0
 3PU  CONST_11  C11  C6   C10  C5    180.00   0.0  0
 3PU  CONST_12  C12  N17  C3   C4      0.00   0.0  0
 3PU  CONST_13  N17  C12  S25  C4      0.00   0.0  0
 3PU  CONST_14  S25  C12  N17  C3      0.00   0.0  0
 3PU  CONST_15  C12  S25  C4   C3      0.00   0.0  0
 3PU  CONST_16  C11  O24  C9   C2    180.00   0.0  0
 3PU  CONST_17  C9   C2   C1   C8      0.00   0.0  0
 3PU  CONST_18  C9   C10  C5   C8      0.00   0.0  0
 3PU  CONST_19  C11  C6   C10  C9      0.00   0.0  0
 3PU  CONST_20  C11  O24  C9   C10     0.00   0.0  0
 3PU  CONST_21  O24  C11  C6   C10     0.00   0.0  0
 3PU  CONST_22  S25  C4   C3   N17     0.00   0.0  0
 3PU  CONST_23  C16  C12  S25  C4    180.00   0.0  0
 3PU  CONST_24  C16  C12  N17  C3    180.00   0.0  0
 3PU  CONST_25  N19  C14  N18  C13     0.00   0.0  0
 3PU  CONST_26  C16  C13  N18  C14     0.00   0.0  0
 3PU  CONST_27  N18  C14  N19  C16     0.00   0.0  0
 3PU  CONST_28  CL2  C8   C1   C2    180.00   0.0  0
 3PU  CONST_29  C15  C11  O24  C9    180.00   0.0  0
 3PU  CONST_30  CL2  C8   C5   C10   180.00   0.0  0
 3PU  CONST_31  C15  C11  C6   C10   180.00   0.0  0
 3PU  CONST_32  O22  C14  N18  C13   180.00   0.0  0
 3PU  CONST_33  O21  C13  N18  C14   180.00   0.0  0
 3PU  CONST_34  O22  C14  N19  C16   180.00   0.0  0
 3PU  CONST_35  H5   C5   C10  C6      0.00   0.0  0
 3PU  CONST_36  H4   C1   C8   C5    180.00   0.0  0
 3PU  CONST_37  H3   C6   C10  C5      0.00   0.0  0
 3PU  CONST_38  H8   C2   C1   C8    180.00   0.0  0
 3PU  CONST_39  H7   C3   N17  C12   180.00   0.0  0
 3PU  CONST_40  H6   C4   S25  C12   180.00   0.0  0
 3PU  CONST_41  H9   N18  C13  C16   180.00   0.0  0
 3PU  CONST_42  H10  N19  C14  N18   180.00   0.0  0
 3PU  CONST_43  C11  C15  N20  C7    180.00   0.0  0
 3PU  CONST_44  H11  N20  C15  C11     0.00   0.0  0
 3PU  CONST_45  O23  C15  N20  C7      0.00   0.0  0
 3PU  Var_01    N20  C15  C11  C6   -179.99  30.0  2
 3PU  Var_02    C16  C7   N20  C15   -92.28  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
 3PU  chir_01  C16  C13  N19  C12  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
 3PU  plan-1  C4   0.020
 3PU  plan-1  C3   0.020
 3PU  plan-1  C12  0.020
 3PU  plan-1  C16  0.020
 3PU  plan-1  N17  0.020
 3PU  plan-1  S25  0.020
 3PU  plan-1  H6   0.020
 3PU  plan-1  H7   0.020
 3PU  plan-2  C6   0.020
 3PU  plan-2  C1   0.020
 3PU  plan-2  C5   0.020
 3PU  plan-2  C2   0.020
 3PU  plan-2  C8   0.020
 3PU  plan-2  C9   0.020
 3PU  plan-2  C10  0.020
 3PU  plan-2  C11  0.020
 3PU  plan-2  C15  0.020
 3PU  plan-2  O24  0.020
 3PU  plan-2  H3   0.020
 3PU  plan-2  H4   0.020
 3PU  plan-2  H5   0.020
 3PU  plan-2  H8   0.020
 3PU  plan-2  CL2  0.020
 3PU  plan-3  C7   0.020
 3PU  plan-3  C11  0.020
 3PU  plan-3  C15  0.020
 3PU  plan-3  N20  0.020
 3PU  plan-3  O23  0.020
 3PU  plan-3  H11  0.020
 3PU  plan-4  C13  0.020
 3PU  plan-4  C14  0.020
 3PU  plan-4  C16  0.020
 3PU  plan-4  N18  0.020
 3PU  plan-4  N19  0.020
 3PU  plan-4  O21  0.020
 3PU  plan-4  O22  0.020
 3PU  plan-4  H9   0.020
 3PU  plan-4  H10  0.020

