# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 14:46:17 2021
#   Inital geometry file: a 83 line input string
#   Ligand name: 1-ethyl-~{N}-(furan-2-ylmethyl)benzimidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCn1c(NCc2occc2)nc3ccccc13
#
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
 SZK  SZK  1-ethyl-~{N}-(furan-2-ylmethyl)benzimidazol-2-amine  ligand  33  18  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SZK
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
 SZK  C10  C  CR15  0  -0.090  -54.6003  16.4660  -24.8683
 SZK  N12  N  N     0  -0.480  -50.1230  15.0941  -26.7476
 SZK  C13  C  CR56  0   0.058  -49.4991  14.7095  -27.9102
 SZK  C15  C  CR16  0  -0.191  -48.8331  13.3950  -29.7878
 SZK  C17  C  CR16  0  -0.440  -47.9551  15.6477  -29.5645
 SZK  C01  C  CH3   0  -0.642  -49.1312  19.0569  -28.3700
 SZK  N03  N  NR5   0  -0.524  -48.8275  16.7723  -27.4789
 SZK  C04  C  CR5   0   0.578  -49.7062  16.3186  -26.5346
 SZK  N05  N  NH1   0  -0.689  -50.0773  17.0782  -25.4858
 SZK  C06  C  CH2   0  -0.360  -51.0407  16.6145  -24.5273
 SZK  C07  C  CR5   0   0.195  -52.4411  16.7365  -25.0341
 SZK  C08  C  CR15  0  -0.319  -52.9778  17.2911  -26.1466
 SZK  C09  C  CR15  0  -0.372  -54.3935  17.1122  -26.0368
 SZK  O11  O  O     0  -0.237  -53.4182  16.2339  -24.2516
 SZK  C14  C  CR16  0  -0.348  -49.5703  13.5129  -28.6151
 SZK  C16  C  CR16  0  -0.296  -48.0400  14.4440  -30.2572
 SZK  C18  C  CR56  0   0.489  -48.6892  15.7510  -28.3959
 SZK  H1   H  HCR5  0   0.290  -55.4863  16.1187  -24.3624
 SZK  H2   H  HCR6  0   0.261  -48.8749  12.4716  -30.3512
 SZK  H3   H  HCR6  0   0.262  -47.3412  16.4596  -29.9341
 SZK  H4   H  HCH3  0   0.270  -48.6364  20.0230  -28.4640
 SZK  H5   H  HCH3  0   0.209  -49.3330  18.6812  -29.3730
 SZK  H6   H  HCH3  0   0.240  -50.0856  19.2177  -27.8680
 SZK  H7   H  HCH2  0   0.262  -48.0313  18.4780  -26.5968
 SZK  H8   H  HCH2  0   0.266  -47.2801  17.9843  -28.0831
 SZK  H9   H  HNH1  0   0.385  -49.7491  18.0239  -25.4031
 SZK  H10  H  HCH2  0   0.258  -50.8258  15.5791  -24.2511
 SZK  H11  H  HCH2  0   0.287  -50.9193  17.2114  -23.6213
 SZK  H12  H  HCR5  0   0.254  -52.4426  17.7673  -26.9517
 SZK  H13  H  HCR5  0   0.240  -55.1494  17.4239  -26.7393
 SZK  H14  H  HCR6  0   0.251  -50.1865  12.6967  -28.2596
 SZK  H15  H  HCR6  0   0.256  -47.4827  14.3226  -31.1767
 SZK  C02  C  CH2   0  -0.324  -48.2483  18.0939  -27.5943

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
 SZK  C15  C14  aromatic  1.390  0.020  1.390
 SZK  C15  C16  aromatic  1.396  0.020  1.396
 SZK  C14  C13  aromatic  1.391  0.020  1.391
 SZK  C16  C17  aromatic  1.391  0.020  1.391
 SZK  C13  N12  aromatic  1.374  0.020  1.374
 SZK  C13  C18  aromatic  1.406  0.020  1.406
 SZK  C17  C18  aromatic  1.384  0.020  1.384
 SZK  N12  C04  aromatic  1.311  0.020  1.311
 SZK  C18  N03  aromatic  1.380  0.020  1.380
 SZK  C04  N03  aromatic  1.367  0.020  1.367
 SZK  C04  N05  single    1.347  0.020  1.347
 SZK  N03  C02  single    1.448  0.020  1.448
 SZK  C01  C02  single    1.519  0.020  1.519
 SZK  N05  C06  single    1.436  0.020  1.436
 SZK  C06  C07  single    1.494  0.020  1.494
 SZK  C08  C07  aromatic  1.354  0.020  1.354
 SZK  C08  C09  aromatic  1.431  0.020  1.431
 SZK  C07  O11  aromatic  1.349  0.020  1.349
 SZK  C09  C10  aromatic  1.351  0.020  1.351
 SZK  O11  C10  aromatic  1.353  0.020  1.353
 SZK  C10  H1   single    0.930  0.020  1.080
 SZK  C15  H2   single    0.930  0.020  1.080
 SZK  C17  H3   single    0.930  0.020  1.080
 SZK  C01  H4   single    0.970  0.020  1.090
 SZK  C01  H5   single    0.970  0.020  1.090
 SZK  C01  H6   single    0.970  0.020  1.090
 SZK  C02  H7   single    0.970  0.020  1.090
 SZK  C02  H8   single    0.970  0.020  1.090
 SZK  N05  H9   single    0.860  0.020  1.020
 SZK  C06  H10  single    0.970  0.020  1.090
 SZK  C06  H11  single    0.970  0.020  1.090
 SZK  C08  H12  single    0.930  0.020  1.080
 SZK  C09  H13  single    0.930  0.020  1.080
 SZK  C14  H14  single    0.930  0.020  1.080
 SZK  C16  H15  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
 SZK  H1   C10  O11  116.67  3.000
 SZK  H1   C10  C09  133.30  3.000
 SZK  O11  C10  C09  110.02  3.000
 SZK  C04  N12  C13  104.75  3.000
 SZK  C18  C13  C14  119.46  3.000
 SZK  C18  C13  N12  110.27  3.000
 SZK  C14  C13  N12  130.27  3.000
 SZK  H2   C15  C16  119.19  3.000
 SZK  H2   C15  C14  119.41  3.000
 SZK  C16  C15  C14  121.40  3.000
 SZK  H3   C17  C18  122.21  3.000
 SZK  H3   C17  C16  120.89  3.000
 SZK  C18  C17  C16  116.91  3.000
 SZK  H6   C01  H5   108.21  3.000
 SZK  H6   C01  H4   107.85  3.000
 SZK  H5   C01  H4   108.08  3.000
 SZK  H6   C01  C02  111.54  3.000
 SZK  H5   C01  C02  111.03  3.000
 SZK  H4   C01  C02  110.01  3.000
 SZK  C18  N03  C04  106.13  3.000
 SZK  C04  N03  C02  127.96  3.000
 SZK  C18  N03  C02  125.65  3.000
 SZK  N05  C04  N03  121.84  3.000
 SZK  N05  C04  N12  124.45  3.000
 SZK  N03  C04  N12  113.70  3.000
 SZK  H9   N05  C06  117.93  3.000
 SZK  H9   N05  C04  120.33  3.000
 SZK  C06  N05  C04  121.49  3.000
 SZK  H11  C06  H10  106.64  3.000
 SZK  H11  C06  C07  109.94  3.000
 SZK  H10  C06  C07  110.33  3.000
 SZK  H11  C06  N05  107.63  3.000
 SZK  H10  C06  N05  110.04  3.000
 SZK  C07  C06  N05  112.09  3.000
 SZK  O11  C07  C08  110.01  3.000
 SZK  O11  C07  C06  116.85  3.000
 SZK  C08  C07  C06  133.12  3.000
 SZK  H12  C08  C09  127.15  3.000
 SZK  H12  C08  C07  126.72  3.000
 SZK  C09  C08  C07  106.13  3.000
 SZK  H13  C09  C08  127.41  3.000
 SZK  H13  C09  C10  126.48  3.000
 SZK  C08  C09  C10  106.11  3.000
 SZK  C07  O11  C10  107.72  3.000
 SZK  H14  C14  C15  120.98  3.000
 SZK  H14  C14  C13  120.76  3.000
 SZK  C15  C14  C13  118.26  3.000
 SZK  H15  C16  C17  119.26  3.000
 SZK  H15  C16  C15  119.59  3.000
 SZK  C17  C16  C15  121.15  3.000
 SZK  N03  C18  C17  132.05  3.000
 SZK  N03  C18  C13  105.13  3.000
 SZK  C17  C18  C13  122.82  3.000
 SZK  H8   C02  H7   105.59  3.000
 SZK  H8   C02  N03  107.42  3.000
 SZK  H7   C02  N03  109.16  3.000
 SZK  H8   C02  C01  110.55  3.000
 SZK  H7   C02  C01  111.06  3.000
 SZK  N03  C02  C01  112.76  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
 SZK  CONST_01  C07  C08  C09  C10     0.00   0.0  0
 SZK  CONST_02  C08  C07  O11  C10     0.00   0.0  0
 SZK  CONST_03  C15  C14  C13  N12   180.00   0.0  0
 SZK  CONST_04  C17  C18  C13  N12   180.00   0.0  0
 SZK  CONST_05  N03  C18  C13  N12     0.00   0.0  0
 SZK  CONST_06  C18  N03  C04  N12     0.00   0.0  0
 SZK  CONST_07  C16  C15  C14  C13     0.00   0.0  0
 SZK  CONST_08  N03  C04  N12  C13     0.00   0.0  0
 SZK  CONST_09  C16  C17  C18  C13     0.00   0.0  0
 SZK  CONST_10  C04  N03  C18  C13     0.00   0.0  0
 SZK  CONST_11  C18  C13  C14  C15     0.00   0.0  0
 SZK  CONST_12  C18  C17  C16  C15     0.00   0.0  0
 SZK  CONST_13  C14  C15  C16  C17     0.00   0.0  0
 SZK  CONST_14  C14  C13  C18  C17     0.00   0.0  0
 SZK  CONST_15  C04  N03  C18  C17   180.00   0.0  0
 SZK  CONST_16  C14  C13  C18  N03   180.00   0.0  0
 SZK  CONST_17  C16  C17  C18  N03   180.00   0.0  0
 SZK  CONST_18  C14  C13  N12  C04   180.00   0.0  0
 SZK  CONST_19  C18  C13  N12  C04     0.00   0.0  0
 SZK  CONST_20  C09  C10  O11  C07     0.00   0.0  0
 SZK  CONST_21  O11  C10  C09  C08     0.00   0.0  0
 SZK  CONST_22  O11  C07  C08  C09     0.00   0.0  0
 SZK  CONST_23  C06  C07  O11  C10   180.00   0.0  0
 SZK  CONST_24  C02  N03  C04  N12   180.00   0.0  0
 SZK  CONST_25  N05  C04  N12  C13   180.00   0.0  0
 SZK  CONST_26  C02  N03  C18  C13   180.00   0.0  0
 SZK  CONST_27  C02  N03  C18  C17     0.00   0.0  0
 SZK  CONST_28  C18  N03  C04  N05   180.00   0.0  0
 SZK  CONST_29  C09  C08  C07  C06   180.00   0.0  0
 SZK  CONST_30  H12  C08  C09  C10   180.00   0.0  0
 SZK  CONST_31  H14  C14  C13  N12     0.00   0.0  0
 SZK  CONST_32  H2   C15  C14  C13   180.00   0.0  0
 SZK  CONST_33  H3   C17  C18  C13   180.00   0.0  0
 SZK  CONST_34  H13  C09  C08  C07   180.00   0.0  0
 SZK  CONST_35  H1   C10  O11  C07   180.00   0.0  0
 SZK  CONST_36  H15  C16  C15  C14   180.00   0.0  0
 SZK  CONST_37  C06  N05  C04  N12     0.00   0.0  0
 SZK  CONST_38  C06  N05  C04  N03   180.00   0.0  0
 SZK  CONST_39  H9   N05  C04  N12   180.00   0.0  0
 SZK  Var_01    C18  N03  C02  C01    87.15  30.0  2
 SZK  Var_02    C07  C06  N05  C04   -78.59  30.0  3
 SZK  Var_03    C08  C07  C06  N05    -6.59  30.0  2
 SZK  Var_04    H4   C01  C02  N03  -177.74  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
 SZK  plan-1  C10  0.020
 SZK  plan-1  C06  0.020
 SZK  plan-1  C07  0.020
 SZK  plan-1  C08  0.020
 SZK  plan-1  C09  0.020
 SZK  plan-1  O11  0.020
 SZK  plan-1  H1   0.020
 SZK  plan-1  H12  0.020
 SZK  plan-1  H13  0.020
 SZK  plan-2  N12  0.020
 SZK  plan-2  C13  0.020
 SZK  plan-2  C15  0.020
 SZK  plan-2  C17  0.020
 SZK  plan-2  N03  0.020
 SZK  plan-2  C04  0.020
 SZK  plan-2  N05  0.020
 SZK  plan-2  C14  0.020
 SZK  plan-2  C16  0.020
 SZK  plan-2  C18  0.020
 SZK  plan-2  H2   0.020
 SZK  plan-2  H3   0.020
 SZK  plan-2  H14  0.020
 SZK  plan-2  H15  0.020
 SZK  plan-2  C02  0.020
 SZK  plan-3  C04  0.020
 SZK  plan-3  N05  0.020
 SZK  plan-3  C06  0.020
 SZK  plan-3  H9   0.020

