# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 03:11:56 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: N~1~-(1-propyl-1,3-dihydro-2H-benzimidazol-2-ylidene)benzene-1,3-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCN1C(Nc2ccccc12)=NC(=O)c3cccc(c3)C(N)=O
#
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
 EDH  EDH  N~1~-(1-propyl-1,3-dihydro-2H-benzimidazol-2-ylidene)benzene-1,3-dicarboxamide  ligand  42  24  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EDH
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
 EDH  C01  C  C     0   0.490   5.7868   0.7802   0.1093
 EDH  C02  C  CR6   0  -0.019   4.5534  -0.0678   0.1350
 EDH  C03  C  CR16  0  -0.282   4.5985  -1.4545   0.2659
 EDH  C04  C  CR16  0  -0.228   3.4222  -2.1877   0.3157
 EDH  C05  C  CR16  0  -0.277   2.1960  -1.5474   0.2346
 EDH  C06  C  CR6   0  -0.051   2.1357  -0.1607   0.1047
 EDH  C07  C  C     0   0.475   0.8283   0.5621   0.0123
 EDH  C08  C  CR5   0   0.746  -1.4543   0.2740   0.1134
 EDH  C09  C  CR56  0   0.324  -3.2463   1.6004  -0.0826
 EDH  C10  C  CR56  0   0.321  -3.6882   0.2996   0.1689
 EDH  C11  C  CR16  0  -0.316  -5.0374  -0.0004   0.2567
 EDH  C12  C  CR16  0  -0.268  -5.9307   1.0498   0.0847
 EDH  C13  C  CR16  0  -0.273  -5.4875   2.3496  -0.1650
 EDH  C14  C  CR16  0  -0.311  -4.1335   2.6483  -0.2528
 EDH  C16  C  CH2   0  -0.438  -2.7699  -2.7168  -0.7575
 EDH  C17  C  CH3   0  -0.668  -2.7689  -4.2127  -0.4800
 EDH  C18  C  CR16  0  -0.300   3.3190   0.5684   0.0652
 EDH  N01  N  NH2   0  -0.813   6.9167   0.1718  -0.2810
 EDH  N02  N  N     0  -0.585  -0.2461  -0.2354   0.1661
 EDH  N03  N  NR15  0  -0.726  -1.8711   1.5420  -0.1074
 EDH  N04  N  NR5   0  -0.583  -2.5624  -0.4885   0.2953
 EDH  O01  O  O     0  -0.501   0.8180   1.7794  -0.1852
 EDH  O02  O  O     0  -0.480   5.7474   1.9584   0.4369
 EDH  H03  H  HCR6  0   0.264   5.5424  -1.9769   0.3555
 EDH  H04  H  HCR6  0   0.266   3.4645  -3.2631   0.4242
 EDH  H05  H  HCR6  0   0.267   1.2808  -2.1213   0.2744
 EDH  H06  H  HCR6  0   0.275  -5.3883  -1.0056   0.4487
 EDH  H07  H  HCR6  0   0.262  -6.9926   0.8534   0.1448
 EDH  H08  H  HCR6  0   0.262  -6.2127   3.1415  -0.2941
 EDH  H09  H  HCR6  0   0.275  -3.7888   3.6550  -0.4463
 EDH  H10  H  HCH2  0   0.260  -3.3267  -2.1470   1.2569
 EDH  H11  H  HCH2  0   0.275  -1.5940  -2.1732   0.9707
 EDH  H12  H  HCH2  0   0.232  -3.7172  -2.4252  -1.2179
 EDH  H13  H  HCH2  0   0.236  -1.9811  -2.4680  -1.4716
 EDH  H18  H  HCH3  0   0.225  -1.8115  -4.5387  -0.0708
 EDH  H16  H  HCH3  0   0.225  -3.5454  -4.4843   0.2370
 EDH  H17  H  HCH3  0   0.239  -2.9492  -4.7793  -1.3929
 EDH  H14  H  HCR6  0   0.257   3.2778   1.6454  -0.0249
 EDH  H01  H  HNH2  0   0.413   6.9244  -0.7435  -0.6963
 EDH  H02  H  HNH2  0   0.406   7.7727   0.7002  -0.3325
 EDH  H15  H  HNR5  0   0.432  -1.2202   2.2976  -0.2625
 EDH  C15  C  CH2   0  -0.309  -2.5528  -1.9195   0.5212

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
 EDH  C17  C16  single    1.521  0.020  1.521
 EDH  C16  C15  single    1.522  0.020  1.522
 EDH  C12  C11  aromatic  1.389  0.020  1.389
 EDH  C12  C13  aromatic  1.396  0.020  1.396
 EDH  C11  C10  aromatic  1.385  0.020  1.385
 EDH  C13  C14  aromatic  1.389  0.020  1.389
 EDH  C15  N04  single    1.449  0.020  1.449
 EDH  C10  N04  single    1.380  0.020  1.380
 EDH  C10  C09  aromatic  1.397  0.020  1.397
 EDH  N04  C08  single    1.357  0.020  1.357
 EDH  C14  C09  aromatic  1.384  0.020  1.384
 EDH  C09  N03  single    1.377  0.020  1.377
 EDH  C08  N03  single    1.353  0.020  1.353
 EDH  C08  N02  double    1.312  0.020  1.312
 EDH  N01  C01  single    1.341  0.020  1.341
 EDH  N02  C07  single    1.347  0.020  1.347
 EDH  C01  C02  single    1.497  0.020  1.497
 EDH  C01  O02  double    1.224  0.020  1.224
 EDH  C07  C06  single    1.497  0.020  1.497
 EDH  C07  O01  double    1.233  0.020  1.233
 EDH  C18  C02  aromatic  1.390  0.020  1.390
 EDH  C18  C06  aromatic  1.391  0.020  1.391
 EDH  C02  C03  aromatic  1.394  0.020  1.394
 EDH  C06  C05  aromatic  1.394  0.020  1.394
 EDH  C03  C04  aromatic  1.387  0.020  1.387
 EDH  C05  C04  aromatic  1.386  0.020  1.386
 EDH  C03  H03  single    0.930  0.020  1.080
 EDH  C04  H04  single    0.930  0.020  1.080
 EDH  C05  H05  single    0.930  0.020  1.080
 EDH  C11  H06  single    0.930  0.020  1.080
 EDH  C12  H07  single    0.930  0.020  1.080
 EDH  C13  H08  single    0.930  0.020  1.080
 EDH  C14  H09  single    0.930  0.020  1.080
 EDH  C15  H10  single    0.970  0.020  1.090
 EDH  C15  H11  single    0.970  0.020  1.090
 EDH  C16  H12  single    0.970  0.020  1.090
 EDH  C16  H13  single    0.970  0.020  1.090
 EDH  C17  H18  single    0.970  0.020  1.090
 EDH  C17  H16  single    0.970  0.020  1.090
 EDH  C17  H17  single    0.970  0.020  1.090
 EDH  C18  H14  single    0.930  0.020  1.080
 EDH  N01  H01  single    0.860  0.020  1.020
 EDH  N01  H02  single    0.860  0.020  1.020
 EDH  N03  H15  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
 EDH  O02  C01  N01  122.81  3.000
 EDH  O02  C01  C02  120.95  3.000
 EDH  N01  C01  C02  116.24  3.000
 EDH  C18  C02  C03  119.26  3.000
 EDH  C03  C02  C01  122.59  3.000
 EDH  C18  C02  C01  118.13  3.000
 EDH  H03  C03  C04  118.78  3.000
 EDH  H03  C03  C02  121.08  3.000
 EDH  C04  C03  C02  120.13  3.000
 EDH  H04  C04  C05  119.99  3.000
 EDH  H04  C04  C03  119.74  3.000
 EDH  C05  C04  C03  120.27  3.000
 EDH  H05  C05  C06  119.66  3.000
 EDH  H05  C05  C04  120.11  3.000
 EDH  C06  C05  C04  120.23  3.000
 EDH  C18  C06  C07  119.23  3.000
 EDH  C18  C06  C05  119.17  3.000
 EDH  C07  C06  C05  121.60  3.000
 EDH  O01  C07  N02  126.59  3.000
 EDH  O01  C07  C06  119.59  3.000
 EDH  N02  C07  C06  113.81  3.000
 EDH  N04  C08  N03  107.27  3.000
 EDH  N03  C08  N02  130.84  3.000
 EDH  N04  C08  N02  121.89  3.000
 EDH  N03  C09  C14  132.10  3.000
 EDH  N03  C09  C10  106.25  3.000
 EDH  C14  C09  C10  121.65  3.000
 EDH  N04  C10  C11  131.70  3.000
 EDH  N04  C10  C09  106.87  3.000
 EDH  C11  C10  C09  121.43  3.000
 EDH  H06  C11  C12  121.05  3.000
 EDH  H06  C11  C10  121.90  3.000
 EDH  C12  C11  C10  117.05  3.000
 EDH  H07  C12  C13  119.39  3.000
 EDH  H07  C12  C11  119.15  3.000
 EDH  C13  C12  C11  121.46  3.000
 EDH  H08  C13  C14  119.24  3.000
 EDH  H08  C13  C12  119.36  3.000
 EDH  C14  C13  C12  121.40  3.000
 EDH  H09  C14  C13  121.47  3.000
 EDH  H09  C14  C09  121.51  3.000
 EDH  C13  C14  C09  117.02  3.000
 EDH  H13  C16  H12  106.84  3.000
 EDH  H13  C16  C17  110.04  3.000
 EDH  H12  C16  C17  109.86  3.000
 EDH  H13  C16  C15  109.07  3.000
 EDH  H12  C16  C15  109.74  3.000
 EDH  C17  C16  C15  111.20  3.000
 EDH  H17  C17  H16  107.66  3.000
 EDH  H17  C17  H18  107.70  3.000
 EDH  H16  C17  H18  107.68  3.000
 EDH  H17  C17  C16  111.00  3.000
 EDH  H16  C17  C16  111.35  3.000
 EDH  H18  C17  C16  111.27  3.000
 EDH  H14  C18  C06  119.48  3.000
 EDH  H14  C18  C02  119.58  3.000
 EDH  C06  C18  C02  120.94  3.000
 EDH  H02  N01  H01  116.75  3.000
 EDH  H02  N01  C01  119.52  3.000
 EDH  H01  N01  C01  122.67  3.000
 EDH  C08  N02  C07  120.00  3.000
 EDH  H15  N03  C09  127.98  3.000
 EDH  H15  N03  C08  121.87  3.000
 EDH  C09  N03  C08  110.16  3.000
 EDH  C15  N04  C10  125.71  3.000
 EDH  C10  N04  C08  109.45  3.000
 EDH  C15  N04  C08  124.78  3.000
 EDH  H11  C15  H10  107.31  3.000
 EDH  H11  C15  N04  107.48  3.000
 EDH  H10  C15  N04  107.83  3.000
 EDH  H11  C15  C16  110.50  3.000
 EDH  H10  C15  C16  110.84  3.000
 EDH  N04  C15  C16  112.66  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
 EDH  CONST_01  C05  C06  C18  C02     0.00   0.0  0
 EDH  CONST_02  C05  C04  C03  C02     0.00   0.0  0
 EDH  CONST_03  C06  C18  C02  C03     0.00   0.0  0
 EDH  CONST_04  C06  C05  C04  C03     0.00   0.0  0
 EDH  CONST_05  C18  C02  C03  C04     0.00   0.0  0
 EDH  CONST_06  C18  C06  C05  C04     0.00   0.0  0
 EDH  CONST_07  C12  C11  C10  C09     0.00   0.0  0
 EDH  CONST_08  C12  C13  C14  C09     0.00   0.0  0
 EDH  CONST_09  C13  C12  C11  C10     0.00   0.0  0
 EDH  CONST_10  C13  C14  C09  C10     0.00   0.0  0
 EDH  CONST_11  C14  C13  C12  C11     0.00   0.0  0
 EDH  CONST_12  C14  C09  C10  C11     0.00   0.0  0
 EDH  CONST_13  C09  C10  N04  C08     0.00   0.0  0
 EDH  CONST_14  C10  C09  N03  C08     0.00   0.0  0
 EDH  CONST_15  N04  C08  N03  C09     0.00   0.0  0
 EDH  CONST_16  N03  C08  N04  C10     0.00   0.0  0
 EDH  CONST_17  N04  C10  C09  N03     0.00   0.0  0
 EDH  CONST_18  C06  C18  C02  C01   180.00   0.0  0
 EDH  CONST_19  C04  C03  C02  C01   180.00   0.0  0
 EDH  CONST_20  C07  C06  C18  C02   180.00   0.0  0
 EDH  CONST_21  C07  C06  C05  C04   180.00   0.0  0
 EDH  CONST_22  C15  N04  C10  C09   180.00   0.0  0
 EDH  CONST_23  N02  C08  N03  C09   180.00   0.0  0
 EDH  CONST_24  N02  C08  N04  C10   180.00   0.0  0
 EDH  CONST_25  N03  C08  N04  C15   180.00   0.0  0
 EDH  CONST_26  H04  C04  C03  C02   180.00   0.0  0
 EDH  CONST_27  H14  C18  C02  C03   180.00   0.0  0
 EDH  CONST_28  H05  C05  C04  C03   180.00   0.0  0
 EDH  CONST_29  H03  C03  C04  C05   180.00   0.0  0
 EDH  CONST_30  H06  C11  C10  C09   180.00   0.0  0
 EDH  CONST_31  H08  C13  C14  C09   180.00   0.0  0
 EDH  CONST_32  H07  C12  C11  C10   180.00   0.0  0
 EDH  CONST_33  H09  C14  C09  C10   180.00   0.0  0
 EDH  CONST_34  H15  N03  C09  C10   180.00   0.0  0
 EDH  CONST_35  C08  N02  C07  C06   180.00   0.0  0
 EDH  CONST_36  N04  C08  N02  C07   180.00   0.0  0
 EDH  CONST_37  N03  C08  N02  C07     0.00   0.0  0
 EDH  CONST_38  N02  C08  N04  C15     0.00   0.0  0
 EDH  CONST_39  O01  C07  N02  C08     0.00   0.0  0
 EDH  CONST_40  H01  N01  C01  C02     0.00   0.0  0
 EDH  CONST_41  H02  N01  C01  C02   180.00   0.0  0
 EDH  Var_01    N01  C01  C02  C03    24.19  30.0  2
 EDH  Var_02    N02  C07  C06  C05     4.66  30.0  2
 EDH  Var_03    C16  C15  N04  C08   -95.92  30.0  2
 EDH  Var_04    N04  C15  C16  C17  -179.38  30.0  3
 EDH  Var_05    H18  C17  C16  C15   -61.48  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
 EDH  plan-1  C01  0.020
 EDH  plan-1  C02  0.020
 EDH  plan-1  C03  0.020
 EDH  plan-1  C04  0.020
 EDH  plan-1  C05  0.020
 EDH  plan-1  C06  0.020
 EDH  plan-1  C07  0.020
 EDH  plan-1  C18  0.020
 EDH  plan-1  H03  0.020
 EDH  plan-1  H04  0.020
 EDH  plan-1  H05  0.020
 EDH  plan-1  H14  0.020
 EDH  plan-2  C01  0.020
 EDH  plan-2  C02  0.020
 EDH  plan-2  N01  0.020
 EDH  plan-2  O02  0.020
 EDH  plan-2  H01  0.020
 EDH  plan-2  H02  0.020
 EDH  plan-3  C06  0.020
 EDH  plan-3  C07  0.020
 EDH  plan-3  C08  0.020
 EDH  plan-3  C09  0.020
 EDH  plan-3  C10  0.020
 EDH  plan-3  C11  0.020
 EDH  plan-3  C12  0.020
 EDH  plan-3  C13  0.020
 EDH  plan-3  C14  0.020
 EDH  plan-3  N02  0.020
 EDH  plan-3  N03  0.020
 EDH  plan-3  N04  0.020
 EDH  plan-3  O01  0.020
 EDH  plan-3  H06  0.020
 EDH  plan-3  H07  0.020
 EDH  plan-3  H08  0.020
 EDH  plan-3  H09  0.020
 EDH  plan-3  H15  0.020
 EDH  plan-3  C15  0.020

