# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 07:32:41 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 1-(4-acetyl-6-pyridin-3-yl-1H-benzimidazol-2-yl)-3-ethylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)Nc1[nH]c2cc(cc(C(C)=O)c2n1)c3cccnc3
#
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
 1EU  1EU  1-(4-acetyl-6-pyridin-3-yl-1H-benzimidazol-2-yl)-3-ethylurea  ligand  41  24  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1EU
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
 1EU  C1    C  CH3   0  -0.703   7.9730  -0.9715   0.0596
 1EU  C2    C  CH2   0  -0.258   6.5843  -1.5811   0.0392
 1EU  N3    N  NH1   0  -0.677   5.5820  -0.5324   0.0037
 1EU  C4    C  C     0   0.764   4.2708  -0.8005   0.0513
 1EU  O5    O  O     0  -0.525   3.8084  -1.9295   0.1467
 1EU  N6    N  NH1   0  -0.777   3.4602   0.3213  -0.0128
 1EU  C7    C  CR5   0   0.687   2.0979   0.3200   0.0058
 1EU  N8    N  NR15  0  -0.720   1.3382  -0.7939   0.0816
 1EU  C9    C  CR56  0   0.386   0.0307  -0.3766   0.0629
 1EU  C10   C  CR16  0  -0.366  -1.1496  -1.0850   0.1138
 1EU  C11   C  CR6   0   0.087  -2.3405  -0.3583   0.0740
 1EU  C12   C  CR16  0  -0.391  -2.2936   1.0364  -0.0165
 1EU  C13   C  CR6   0  -0.091  -1.1020   1.7607  -0.0564
 1EU  C14   C  C     0   0.356  -1.1120   3.2412  -0.1356
 1EU  O15   O  O     0  -0.392  -0.0845   3.8798  -0.0334
 1EU  C16   C  CH3   0  -0.807  -2.4338   3.9355  -0.3434
 1EU  C17   C  CR56  0   0.149   0.0973   1.0298  -0.0160
 1EU  N18   N  N     0  -0.498   1.4030   1.4310  -0.0528
 1EU  C20   C  CR6   0  -0.003  -3.6350  -1.0602   0.1246
 1EU  C21   C  CR16  0  -0.199  -3.8376  -2.2806  -0.5171
 1EU  C22   C  CR16  0  -0.315  -5.0736  -2.8983  -0.4311
 1EU  C23   C  CR16  0  -0.073  -6.0795  -2.2739   0.2908
 1EU  N24   N  N     0  -0.398  -5.9064  -1.1129   0.9117
 1EU  C25   C  CR16  0  -0.104  -4.7178  -0.5327   0.8308
 1EU  H1    H  HCH3  0   0.237   8.1146  -0.3374   0.9355
 1EU  H1A   H  HCH3  0   0.249   8.7230  -1.7597   0.0908
 1EU  H1B   H  HCH3  0   0.236   8.1564  -0.3702  -0.8319
 1EU  H2    H  HCH2  0   0.238   6.4771  -2.2350  -0.8298
 1EU  H2A   H  HCH2  0   0.240   6.4380  -2.2006   0.9262
 1EU  HN3   H  HNH1  0   0.407   5.8971   0.4168  -0.1178
 1EU  HN6   H  HNH1  0   0.425   3.8741   1.2398  -0.0850
 1EU  H10   H  HCR6  0   0.276  -1.1509  -2.1641   0.2001
 1EU  H12   H  HCR6  0   0.263  -3.2316   1.5725  -0.0755
 1EU  H16   H  HCH3  0   0.266  -3.1091   3.7560   0.4948
 1EU  H16A  H  HCH3  0   0.269  -2.2772   5.0079  -0.4345
 1EU  H16B  H  HCH3  0   0.266  -2.9344   3.5749  -1.2429
 1EU  H21   H  HCR6  0   0.271  -3.0432  -2.7378  -1.0940
 1EU  H22   H  HCR6  0   0.273  -5.2598  -3.8433  -0.9224
 1EU  H23   H  HCR6  0   0.266  -7.0610  -2.7276   0.3705
 1EU  H25   H  HCR6  0   0.258  -4.6053   0.4012   1.3728
 1EU  HN8   H  HNR5  0   0.429   1.6931  -1.7372   0.1311

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
 1EU  C1   C2    single    1.517  0.020  1.517
 1EU  C1   H1    single    0.970  0.020  1.090
 1EU  C1   H1A   single    0.970  0.020  1.090
 1EU  C1   H1B   single    0.970  0.020  1.090
 1EU  N3   C2    single    1.451  0.020  1.451
 1EU  C2   H2    single    0.970  0.020  1.090
 1EU  C2   H2A   single    0.970  0.020  1.090
 1EU  N3   C4    single    1.339  0.020  1.339
 1EU  N3   HN3   single    0.860  0.020  1.020
 1EU  N6   C4    single    1.385  0.020  1.385
 1EU  C4   O5    double    1.224  0.020  1.224
 1EU  N6   C7    single    1.362  0.020  1.362
 1EU  N6   HN6   single    0.860  0.020  1.020
 1EU  N8   C7    aromatic  1.350  0.020  1.350
 1EU  C7   N18   aromatic  1.312  0.020  1.312
 1EU  N8   C9    aromatic  1.373  0.020  1.373
 1EU  C10  C9    aromatic  1.378  0.020  1.378
 1EU  C9   C17   aromatic  1.410  0.020  1.410
 1EU  C10  C11   aromatic  1.396  0.020  1.396
 1EU  C10  H10   single    0.930  0.020  1.080
 1EU  C20  C11   single    1.473  0.020  1.473
 1EU  C11  C12   aromatic  1.398  0.020  1.398
 1EU  C12  C13   aromatic  1.395  0.020  1.395
 1EU  C12  H12   single    0.930  0.020  1.080
 1EU  C17  C13   aromatic  1.405  0.020  1.405
 1EU  C13  C14   single    1.483  0.020  1.483
 1EU  C14  O15   double    1.214  0.020  1.214
 1EU  C14  C16   single    1.507  0.020  1.507
 1EU  C16  H16   single    0.970  0.020  1.090
 1EU  C16  H16A  single    0.970  0.020  1.090
 1EU  C16  H16B  single    0.970  0.020  1.090
 1EU  C17  N18   aromatic  1.366  0.020  1.366
 1EU  C25  C20   aromatic  1.396  0.020  1.396
 1EU  C20  C21   aromatic  1.394  0.020  1.394
 1EU  C22  C21   aromatic  1.384  0.020  1.384
 1EU  C21  H21   single    0.930  0.020  1.080
 1EU  C23  C22   aromatic  1.387  0.020  1.387
 1EU  C22  H22   single    0.930  0.020  1.080
 1EU  N24  C23   aromatic  1.328  0.020  1.328
 1EU  C23  H23   single    0.930  0.020  1.080
 1EU  N24  C25   aromatic  1.325  0.020  1.325
 1EU  C25  H25   single    0.930  0.020  1.080
 1EU  N8   HN8   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
 1EU  H1B   C1   H1A   107.86  3.000
 1EU  H1B   C1   H1    108.30  3.000
 1EU  H1A   C1   H1    107.97  3.000
 1EU  H1B   C1   C2    111.38  3.000
 1EU  H1A   C1   C2    109.89  3.000
 1EU  H1    C1   C2    111.31  3.000
 1EU  H2A   C2   H2    107.06  3.000
 1EU  H2A   C2   N3    109.71  3.000
 1EU  H2    C2   N3    110.19  3.000
 1EU  H2A   C2   C1    109.87  3.000
 1EU  H2    C2   C1    109.94  3.000
 1EU  N3    C2   C1    110.01  3.000
 1EU  HN3   N3   C4    119.94  3.000
 1EU  HN3   N3   C2    117.89  3.000
 1EU  C4    N3   C2    122.06  3.000
 1EU  N6    C4   O5    121.97  3.000
 1EU  O5    C4   N3    123.87  3.000
 1EU  N6    C4   N3    114.15  3.000
 1EU  HN6   N6   C7    114.30  3.000
 1EU  HN6   N6   C4    119.99  3.000
 1EU  C7    N6   C4    125.71  3.000
 1EU  N18   C7   N8    113.77  3.000
 1EU  N18   C7   N6    121.89  3.000
 1EU  N8    C7   N6    124.33  3.000
 1EU  HN8   N8   C9    128.31  3.000
 1EU  HN8   N8   C7    125.17  3.000
 1EU  C9    N8   C7    106.52  3.000
 1EU  C17   C9   C10   123.74  3.000
 1EU  C17   C9   N8    105.01  3.000
 1EU  C10   C9   N8    131.25  3.000
 1EU  H10   C10  C11   121.35  3.000
 1EU  H10   C10  C9    121.11  3.000
 1EU  C11   C10  C9    117.53  3.000
 1EU  C20   C11  C12   120.45  3.000
 1EU  C12   C11  C10   119.51  3.000
 1EU  C20   C11  C10   120.04  3.000
 1EU  H12   C12  C13   118.79  3.000
 1EU  H12   C12  C11   117.94  3.000
 1EU  C13   C12  C11   123.26  3.000
 1EU  C17   C13  C14   121.78  3.000
 1EU  C14   C13  C12   120.95  3.000
 1EU  C17   C13  C12   117.27  3.000
 1EU  C16   C14  O15   120.76  3.000
 1EU  C16   C14  C13   118.24  3.000
 1EU  O15   C14  C13   121.00  3.000
 1EU  H16B  C16  H16A  108.85  3.000
 1EU  H16B  C16  H16   107.15  3.000
 1EU  H16A  C16  H16   108.40  3.000
 1EU  H16B  C16  C14   111.34  3.000
 1EU  H16A  C16  C14   109.85  3.000
 1EU  H16   C16  C14   111.16  3.000
 1EU  N18   C17  C13   131.46  3.000
 1EU  N18   C17  C9    109.84  3.000
 1EU  C13   C17  C9    118.69  3.000
 1EU  C17   N18  C7    104.85  3.000
 1EU  C25   C20  C21   116.81  3.000
 1EU  C21   C20  C11   121.94  3.000
 1EU  C25   C20  C11   121.25  3.000
 1EU  H21   C21  C22   119.97  3.000
 1EU  H21   C21  C20   120.55  3.000
 1EU  C22   C21  C20   119.47  3.000
 1EU  H22   C22  C23   120.34  3.000
 1EU  H22   C22  C21   121.03  3.000
 1EU  C23   C22  C21   118.63  3.000
 1EU  H23   C23  N24   116.71  3.000
 1EU  H23   C23  C22   120.44  3.000
 1EU  N24   C23  C22   122.85  3.000
 1EU  C25   N24  C23   118.11  3.000
 1EU  H25   C25  N24   116.05  3.000
 1EU  H25   C25  C20   119.81  3.000
 1EU  N24   C25  C20   124.13  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
 1EU  CONST_01  C10  C9   N8   C7    180.00   0.0  0
 1EU  CONST_02  C17  C9   N8   C7      0.00   0.0  0
 1EU  CONST_03  C9   C17  N18  C7      0.00   0.0  0
 1EU  CONST_04  C13  C17  N18  C7    180.00   0.0  0
 1EU  CONST_05  C17  N18  C7   N8      0.00   0.0  0
 1EU  CONST_06  C11  C10  C9   N8    180.00   0.0  0
 1EU  CONST_07  C13  C17  C9   N8    180.00   0.0  0
 1EU  CONST_08  N18  C17  C9   N8      0.00   0.0  0
 1EU  CONST_09  N18  C7   N8   C9      0.00   0.0  0
 1EU  CONST_10  C20  C11  C10  C9    180.00   0.0  0
 1EU  CONST_11  C12  C11  C10  C9      0.00   0.0  0
 1EU  CONST_12  C12  C13  C17  C9      0.00   0.0  0
 1EU  CONST_13  C13  C17  C9   C10     0.00   0.0  0
 1EU  CONST_14  N18  C17  C9   C10   180.00   0.0  0
 1EU  CONST_17  C13  C12  C11  C10     0.00   0.0  0
 1EU  CONST_18  C17  C9   C10  C11     0.00   0.0  0
 1EU  CONST_19  N24  C25  C20  C11   180.00   0.0  0
 1EU  CONST_20  C22  C21  C20  C11   180.00   0.0  0
 1EU  CONST_21  C17  C13  C12  C11     0.00   0.0  0
 1EU  CONST_24  N18  C17  C13  C12   180.00   0.0  0
 1EU  CONST_25  C20  C11  C12  C13   180.00   0.0  0
 1EU  CONST_26  C23  N24  C25  C20     0.00   0.0  0
 1EU  CONST_27  C23  C22  C21  C20     0.00   0.0  0
 1EU  CONST_28  N24  C25  C20  C21     0.00   0.0  0
 1EU  CONST_29  N24  C23  C22  C21     0.00   0.0  0
 1EU  CONST_30  C25  C20  C21  C22     0.00   0.0  0
 1EU  CONST_31  C25  N24  C23  C22     0.00   0.0  0
 1EU  CONST_32  C9   N8   C7   N6    180.00   0.0  0
 1EU  CONST_33  C17  N18  C7   N6    180.00   0.0  0
 1EU  CONST_34  C14  C13  C17  C9    180.00   0.0  0
 1EU  CONST_35  C14  C13  C12  C11   180.00   0.0  0
 1EU  CONST_36  N18  C17  C13  C14     0.00   0.0  0
 1EU  CONST_37  H10  C10  C9   N8      0.00   0.0  0
 1EU  CONST_38  HN8  N8   C9   C10     0.00   0.0  0
 1EU  CONST_39  H12  C12  C11  C10   180.00   0.0  0
 1EU  CONST_40  H25  C25  C20  C11     0.00   0.0  0
 1EU  CONST_41  H21  C21  C20  C11     0.00   0.0  0
 1EU  CONST_42  H22  C22  C21  C20   180.00   0.0  0
 1EU  CONST_43  H23  C23  C22  C21   180.00   0.0  0
 1EU  CONST_44  N8   C7   N6   C4      0.00   0.0  0
 1EU  CONST_45  N18  C7   N6   C4    180.00   0.0  0
 1EU  CONST_46  HN6  N6   C7   N8    180.00   0.0  0
 1EU  CONST_47  C7   N6   C4   O5      0.00   0.0  0
 1EU  CONST_48  C7   N6   C4   N3    180.00   0.0  0
 1EU  CONST_49  O5   C4   N3   C2      0.00   0.0  0
 1EU  CONST_50  N6   C4   N3   C2    180.00   0.0  0
 1EU  CONST_51  HN3  N3   C4   O5    180.00   0.0  0
 1EU  Var_01    O15  C14  C13  C12   172.43  30.0  2
 1EU  Var_02    H16  C16  C14  C13    63.08  30.0  3
 1EU  Var_03    C4   N3   C2   C1   -176.40  30.0  2
 1EU  Var_04    H1   C1   C2   N3     60.19  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
 1EU  plan-1  C11  0.020
 1EU  plan-1  C20  0.020
 1EU  plan-1  C21  0.020
 1EU  plan-1  C22  0.020
 1EU  plan-1  C23  0.020
 1EU  plan-1  N24  0.020
 1EU  plan-1  C25  0.020
 1EU  plan-1  H21  0.020
 1EU  plan-1  H22  0.020
 1EU  plan-1  H23  0.020
 1EU  plan-1  H25  0.020
 1EU  plan-2  N6   0.020
 1EU  plan-2  C7   0.020
 1EU  plan-2  N8   0.020
 1EU  plan-2  C9   0.020
 1EU  plan-2  C10  0.020
 1EU  plan-2  C11  0.020
 1EU  plan-2  C12  0.020
 1EU  plan-2  C13  0.020
 1EU  plan-2  C14  0.020
 1EU  plan-2  C17  0.020
 1EU  plan-2  N18  0.020
 1EU  plan-2  C20  0.020
 1EU  plan-2  H10  0.020
 1EU  plan-2  H12  0.020
 1EU  plan-2  HN8  0.020
 1EU  plan-3  C2   0.020
 1EU  plan-3  N3   0.020
 1EU  plan-3  C4   0.020
 1EU  plan-3  O5   0.020
 1EU  plan-3  N6   0.020
 1EU  plan-3  C7   0.020
 1EU  plan-3  HN3  0.020
 1EU  plan-3  HN6  0.020
 1EU  plan-4  C13  0.020
 1EU  plan-4  C14  0.020
 1EU  plan-4  O15  0.020
 1EU  plan-4  C16  0.020

