# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 14:13:22 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 1-(2,4-dihydroxy-5-propylphenyl)-1,3-dihydro-2H-benzimidazol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCc1cc(N2C(=O)Nc3ccccc23)c(O)cc1O
#
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
 4EP  4EP  1-(2,4-dihydroxy-5-propylphenyl)-1,3-dihydro-2H-benzimidazol-2-one  ligand  37  21  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4EP
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
 4EP  O1   O  O     0  -0.492   0.7913  -1.0412   2.5394
 4EP  C7   C  CR5   0   0.635   1.5224  -0.8254   1.5927
 4EP  N2   N  NR15  0  -0.747   2.8619  -1.0914   1.4882
 4EP  C8   C  CR56  0   0.325   3.3518  -0.6871   0.2645
 4EP  C13  C  CR56  0   0.324   2.2702  -0.1484  -0.4373
 4EP  C12  C  CR16  0  -0.310   2.4154   0.3592  -1.7122
 4EP  C11  C  CR16  0  -0.276   3.6888   0.3137  -2.2762
 4EP  C10  C  CR16  0  -0.276   4.7676  -0.2223  -1.5788
 4EP  C9   C  CR16  0  -0.310   4.6154  -0.7343  -0.2918
 4EP  N1   N  NR5   0  -0.674   1.1627  -0.2559   0.3858
 4EP  C6   C  CR6   0   0.196  -0.1264   0.2380   0.1016
 4EP  C5   C  CR16  0  -0.322  -1.1424  -0.6117  -0.3128
 4EP  C14  C  CR6   0   0.346  -0.3813   1.6025   0.2290
 4EP  O2   O  OH1   0  -0.614   0.6253   2.3915   0.6340
 4EP  C15  C  CR16  0  -0.518  -1.6497   2.0864  -0.0688
 4EP  C16  C  CR6   0   0.345  -2.6556   1.2162  -0.4770
 4EP  O3   O  OH1   0  -0.624  -3.8914   1.6607  -0.7662
 4EP  C4   C  CR6   0   0.013  -2.4188  -0.1590  -0.6071
 4EP  C3   C  CH2   0  -0.484  -3.5076  -1.1099  -1.0186
 4EP  C2   C  CH2   0  -0.417  -4.4380  -1.4967   0.1333
 4EP  C1   C  CH3   0  -0.665  -5.5376  -2.4514  -0.3090
 4EP  H9   H  HNR5  0   0.419   3.3942  -1.5207   2.2275
 4EP  H13  H  HCR6  0   0.267   1.5755   0.7776  -2.2515
 4EP  H12  H  HCR6  0   0.256   3.8406   0.7054  -3.2731
 4EP  H11  H  HCR6  0   0.256   5.7456  -0.2409  -2.0409
 4EP  H10  H  HCR6  0   0.269   5.4552  -1.1490   0.2496
 4EP  H8   H  HCR6  0   0.259  -0.9218  -1.6684  -0.4115
 4EP  H14  H  HOH1  0   0.481   0.3445   3.3134   0.6591
 4EP  H15  H  HCR6  0   0.285  -1.8560   3.1483   0.0235
 4EP  H16  H  HOH1  0   0.478  -3.9466   2.6164  -0.6533
 4EP  H6   H  HCH2  0   0.233  -4.0991  -0.6825  -1.8324
 4EP  H7   H  HCH2  0   0.236  -3.0499  -2.0177  -1.4210
 4EP  H5   H  HCH2  0   0.219  -3.8453  -1.9581   0.9281
 4EP  H4   H  HCH2  0   0.223  -4.8829  -0.5971   0.5652
 4EP  H1   H  HCH3  0   0.218  -5.1202  -3.3696  -0.7264
 4EP  H2   H  HCH3  0   0.229  -6.1805  -2.7307   0.5266
 4EP  H3   H  HCH3  0   0.218  -6.1699  -1.9989  -1.0754

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
 4EP  O3   C16  single    1.345  0.020  1.345
 4EP  C16  C15  aromatic  1.391  0.020  1.391
 4EP  C16  C4   aromatic  1.402  0.020  1.402
 4EP  C3   C4   single    1.503  0.020  1.503
 4EP  C3   C2   single    1.530  0.020  1.530
 4EP  C15  C14  aromatic  1.390  0.020  1.390
 4EP  C4   C5   aromatic  1.386  0.020  1.386
 4EP  C2   C1   single    1.522  0.020  1.522
 4EP  C14  O2   single    1.342  0.020  1.342
 4EP  C14  C6   aromatic  1.394  0.020  1.394
 4EP  C5   C6   aromatic  1.388  0.020  1.388
 4EP  C6   N1   single    1.409  0.020  1.409
 4EP  C12  C11  aromatic  1.393  0.020  1.393
 4EP  C12  C13  aromatic  1.380  0.020  1.380
 4EP  C11  C10  aromatic  1.392  0.020  1.392
 4EP  C13  N1   single    1.384  0.020  1.384
 4EP  C13  C8   aromatic  1.397  0.020  1.397
 4EP  N1   C7   single    1.382  0.020  1.382
 4EP  C10  C9   aromatic  1.393  0.020  1.393
 4EP  C8   C9   aromatic  1.381  0.020  1.381
 4EP  C8   N2   single    1.379  0.020  1.379
 4EP  C7   O1   double    1.215  0.020  1.215
 4EP  C7   N2   single    1.370  0.020  1.370
 4EP  N2   H9   single    0.860  0.020  1.020
 4EP  C12  H13  single    0.930  0.020  1.080
 4EP  C11  H12  single    0.930  0.020  1.080
 4EP  C10  H11  single    0.930  0.020  1.080
 4EP  C9   H10  single    0.930  0.020  1.080
 4EP  C5   H8   single    0.930  0.020  1.080
 4EP  O2   H14  single    0.850  0.020  0.980
 4EP  C15  H15  single    0.930  0.020  1.080
 4EP  O3   H16  single    0.850  0.020  0.980
 4EP  C3   H6   single    0.970  0.020  1.090
 4EP  C3   H7   single    0.970  0.020  1.090
 4EP  C2   H5   single    0.970  0.020  1.090
 4EP  C2   H4   single    0.970  0.020  1.090
 4EP  C1   H1   single    0.970  0.020  1.090
 4EP  C1   H2   single    0.970  0.020  1.090
 4EP  C1   H3   single    0.970  0.020  1.090

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
 4EP  N1   C7   N2   105.54  3.000
 4EP  N2   C7   O1   127.82  3.000
 4EP  N1   C7   O1   126.64  3.000
 4EP  H9   N2   C8   126.07  3.000
 4EP  H9   N2   C7   122.93  3.000
 4EP  C8   N2   C7   111.00  3.000
 4EP  C9   C8   C13  121.26  3.000
 4EP  C9   C8   N2   132.26  3.000
 4EP  C13  C8   N2   106.48  3.000
 4EP  N1   C13  C12  131.47  3.000
 4EP  N1   C13  C8   106.90  3.000
 4EP  C12  C13  C8   121.63  3.000
 4EP  H13  C12  C11  121.34  3.000
 4EP  H13  C12  C13  121.39  3.000
 4EP  C11  C12  C13  117.27  3.000
 4EP  H12  C11  C10  119.50  3.000
 4EP  H12  C11  C12  119.30  3.000
 4EP  C10  C11  C12  121.20  3.000
 4EP  H11  C10  C9   119.14  3.000
 4EP  H11  C10  C11  119.56  3.000
 4EP  C9   C10  C11  121.30  3.000
 4EP  H10  C9   C10  121.21  3.000
 4EP  H10  C9   C8   121.44  3.000
 4EP  C10  C9   C8   117.34  3.000
 4EP  C6   N1   C13  125.79  3.000
 4EP  C13  N1   C7   110.06  3.000
 4EP  C6   N1   C7   123.95  3.000
 4EP  C14  C6   C5   119.52  3.000
 4EP  C5   C6   N1   121.02  3.000
 4EP  C14  C6   N1   119.46  3.000
 4EP  H8   C5   C4   119.11  3.000
 4EP  H8   C5   C6   118.36  3.000
 4EP  C4   C5   C6   122.53  3.000
 4EP  C15  C14  O2   123.00  3.000
 4EP  O2   C14  C6   117.78  3.000
 4EP  C15  C14  C6   119.21  3.000
 4EP  H14  O2   C14  110.59  3.000
 4EP  H15  C15  C16  119.96  3.000
 4EP  H15  C15  C14  119.71  3.000
 4EP  C16  C15  C14  120.33  3.000
 4EP  C4   C16  O3   117.36  3.000
 4EP  C4   C16  C15  121.25  3.000
 4EP  O3   C16  C15  121.39  3.000
 4EP  H16  O3   C16  110.80  3.000
 4EP  C3   C4   C16  121.59  3.000
 4EP  C3   C4   C5   121.24  3.000
 4EP  C16  C4   C5   117.15  3.000
 4EP  H7   C3   H6   106.09  3.000
 4EP  H7   C3   C2   108.76  3.000
 4EP  H6   C3   C2   109.28  3.000
 4EP  H7   C3   C4   108.83  3.000
 4EP  H6   C3   C4   110.39  3.000
 4EP  C2   C3   C4   113.22  3.000
 4EP  H4   C2   H5   106.31  3.000
 4EP  H4   C2   C1   109.71  3.000
 4EP  H5   C2   C1   109.77  3.000
 4EP  H4   C2   C3   109.69  3.000
 4EP  H5   C2   C3   108.92  3.000
 4EP  C1   C2   C3   112.27  3.000
 4EP  H3   C1   H2   107.61  3.000
 4EP  H3   C1   H1   107.55  3.000
 4EP  H2   C1   H1   107.63  3.000
 4EP  H3   C1   C2   111.26  3.000
 4EP  H2   C1   C2   111.34  3.000
 4EP  H1   C1   C2   111.26  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
 4EP  CONST_01  C11  C12  C13  C8     0.00   0.0  0
 4EP  CONST_02  C11  C10  C9   C8     0.00   0.0  0
 4EP  CONST_03  C10  C11  C12  C13    0.00   0.0  0
 4EP  CONST_04  C10  C9   C8   C13    0.00   0.0  0
 4EP  CONST_05  C9   C10  C11  C12    0.00   0.0  0
 4EP  CONST_06  C9   C8   C13  C12    0.00   0.0  0
 4EP  CONST_07  C16  C15  C14  C6     0.00   0.0  0
 4EP  CONST_08  C16  C4   C5   C6     0.00   0.0  0
 4EP  CONST_09  C15  C16  C4   C5     0.00   0.0  0
 4EP  CONST_10  C15  C14  C6   C5     0.00   0.0  0
 4EP  CONST_11  C4   C16  C15  C14    0.00   0.0  0
 4EP  CONST_12  C4   C5   C6   C14    0.00   0.0  0
 4EP  CONST_13  C15  C14  C6   N1   180.00   0.0  0
 4EP  CONST_14  C4   C5   C6   N1   180.00   0.0  0
 4EP  CONST_15  C8   C13  N1   C7     0.00   0.0  0
 4EP  CONST_16  C13  C8   N2   C7     0.00   0.0  0
 4EP  CONST_17  N1   C13  C8   N2     0.00   0.0  0
 4EP  CONST_18  C6   N1   C7   N2   180.00   0.0  0
 4EP  CONST_19  C13  N1   C7   N2     0.00   0.0  0
 4EP  CONST_20  C6   N1   C13  C8   180.00   0.0  0
 4EP  CONST_21  N1   C7   N2   C8     0.00   0.0  0
 4EP  CONST_22  O2   C14  C6   N1     0.00   0.0  0
 4EP  CONST_23  C3   C4   C5   C6   180.00   0.0  0
 4EP  CONST_24  O3   C16  C4   C5   180.00   0.0  0
 4EP  CONST_25  O2   C14  C6   C5   180.00   0.0  0
 4EP  CONST_26  O3   C16  C15  C14  180.00   0.0  0
 4EP  CONST_27  C16  C15  C14  O2   180.00   0.0  0
 4EP  CONST_28  C3   C4   C16  C15  180.00   0.0  0
 4EP  CONST_29  C6   N1   C7   O1     0.00   0.0  0
 4EP  CONST_30  C13  N1   C7   O1   180.00   0.0  0
 4EP  CONST_31  C8   N2   C7   O1   180.00   0.0  0
 4EP  CONST_32  H10  C9   C8   N2     0.00   0.0  0
 4EP  CONST_33  H13  C12  C13  C8   180.00   0.0  0
 4EP  CONST_34  H11  C10  C9   C8   180.00   0.0  0
 4EP  CONST_35  H12  C11  C12  C13  180.00   0.0  0
 4EP  CONST_36  H8   C5   C6   N1     0.00   0.0  0
 4EP  CONST_37  H15  C15  C14  C6   180.00   0.0  0
 4EP  CONST_38  H9   N2   C8   C13  180.00   0.0  0
 4EP  Var_01    C14  C6   N1   C7    97.67  30.0  2
 4EP  Var_02    C2   C3   C4   C5    98.27  30.0  2
 4EP  Var_03    C1   C2   C3   C4   179.58  30.0  3
 4EP  Var_04    H1   C1   C2   C3    58.93  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
 4EP  plan-1  N1   0.020
 4EP  plan-1  C6   0.020
 4EP  plan-1  C5   0.020
 4EP  plan-1  C14  0.020
 4EP  plan-1  O2   0.020
 4EP  plan-1  C15  0.020
 4EP  plan-1  C16  0.020
 4EP  plan-1  O3   0.020
 4EP  plan-1  C4   0.020
 4EP  plan-1  C3   0.020
 4EP  plan-1  H8   0.020
 4EP  plan-1  H15  0.020
 4EP  plan-2  O1   0.020
 4EP  plan-2  C7   0.020
 4EP  plan-2  N2   0.020
 4EP  plan-2  C8   0.020
 4EP  plan-2  C13  0.020
 4EP  plan-2  C12  0.020
 4EP  plan-2  C11  0.020
 4EP  plan-2  C10  0.020
 4EP  plan-2  C9   0.020
 4EP  plan-2  N1   0.020
 4EP  plan-2  C6   0.020
 4EP  plan-2  H9   0.020
 4EP  plan-2  H13  0.020
 4EP  plan-2  H12  0.020
 4EP  plan-2  H11  0.020
 4EP  plan-2  H10  0.020

