# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 16:12:42 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: ~{N}-(1-ethylbenzimidazol-2-yl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCn1c(NC(C)=O)nc2ccccc12
#
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
 TEK  TEK  "~{N}-(1-ethylbenzimidazol-2-yl)ethanamide"
  ligand  28  15  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_TEK
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
 TEK  N12  N  NH1   0  -0.753  -0.1244  -6.3589  5.7483
 TEK  C13  C  C     0   0.493  -0.8316  -6.4138  4.5718
 TEK  C15  C  CH3   0  -0.791  -2.2051  -7.0095  4.7319
 TEK  C01  C  CH3   0  -0.657   2.4906  -8.8118  6.1537
 TEK  C02  C  CH2   0  -0.337   2.0732  -7.7580  7.1646
 TEK  C04  C  CR56  0   0.350   3.2035  -5.6019  6.5450
 TEK  C05  C  CR16  0  -0.309   4.4825  -5.7206  7.0740
 TEK  C06  C  CR16  0  -0.275   5.3647  -4.6861  6.8070
 TEK  C07  C  CR16  0  -0.271   4.9811  -3.5742  6.0439
 TEK  C08  C  CR16  0  -0.332   3.7041  -3.4658  5.5201
 TEK  C09  C  CR56  0   0.148   2.8039  -4.4986  5.7743
 TEK  C11  C  CR5   0   0.675   1.1270  -5.7880  5.8867
 TEK  N03  N  NR5   0  -0.550   2.1002  -6.4181  6.6067
 TEK  N10  N  N     0  -0.469   1.4931  -4.6420  5.3906
 TEK  O14  O  O     0  -0.434  -0.3870  -6.0185  3.5178
 TEK  H1   H  HNH1  0   0.428  -0.5477  -6.7695  6.5682
 TEK  H2   H  HCH3  0   0.268  -2.6741  -7.1382  3.7605
 TEK  H3   H  HCH3  0   0.268  -2.1621  -7.9751  5.2367
 TEK  H4   H  HCH3  0   0.274  -2.8304  -6.3529  5.3391
 TEK  H5   H  HCH3  0   0.242   2.4777  -9.7969  6.6191
 TEK  H6   H  HCH3  0   0.237   1.8107  -8.8318  5.3021
 TEK  H7   H  HCH3  0   0.237   3.4992  -8.6256  5.7851
 TEK  H8   H  HCH2  0   0.271   2.7388  -7.7645  8.0274
 TEK  H9   H  HCH2  0   0.268   1.0767  -7.9643  7.5524
 TEK  H10  H  HCR6  0   0.267   4.7864  -6.5782  7.6605
 TEK  H11  H  HCR6  0   0.252   6.3733  -4.7393  7.1955
 TEK  H12  H  HCR6  0   0.250   5.7010  -2.7872  5.8609
 TEK  H13  H  HCR6  0   0.251   3.4103  -2.6072  4.9301

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
 TEK  O14  C13  double    1.210  0.020  1.210
 TEK  C15  C13  single    1.506  0.020  1.506
 TEK  C13  N12  single    1.374  0.020  1.374
 TEK  N10  C09  aromatic  1.373  0.020  1.373
 TEK  N10  C11  aromatic  1.301  0.020  1.301
 TEK  C08  C09  aromatic  1.394  0.020  1.394
 TEK  C08  C07  aromatic  1.384  0.020  1.384
 TEK  C09  C04  aromatic  1.404  0.020  1.404
 TEK  N12  C11  single    1.382  0.020  1.382
 TEK  C07  C06  aromatic  1.402  0.020  1.402
 TEK  C11  N03  aromatic  1.365  0.020  1.365
 TEK  C04  N03  aromatic  1.374  0.020  1.374
 TEK  C04  C05  aromatic  1.389  0.020  1.389
 TEK  N03  C02  single    1.452  0.020  1.452
 TEK  C06  C05  aromatic  1.385  0.020  1.385
 TEK  C01  C02  single    1.519  0.020  1.519
 TEK  N12  H1   single    0.860  0.020  1.020
 TEK  C15  H2   single    0.970  0.020  1.090
 TEK  C15  H3   single    0.970  0.020  1.090
 TEK  C15  H4   single    0.970  0.020  1.090
 TEK  C01  H5   single    0.970  0.020  1.090
 TEK  C01  H6   single    0.970  0.020  1.090
 TEK  C01  H7   single    0.970  0.020  1.090
 TEK  C02  H8   single    0.970  0.020  1.090
 TEK  C02  H9   single    0.970  0.020  1.090
 TEK  C05  H10  single    0.930  0.020  1.080
 TEK  C06  H11  single    0.930  0.020  1.080
 TEK  C07  H12  single    0.930  0.020  1.080
 TEK  C08  H13  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
 TEK  H1   N12  C11  117.78  3.000
 TEK  H1   N12  C13  117.59  3.000
 TEK  C11  N12  C13  124.63  3.000
 TEK  O14  C13  C15  123.85  3.000
 TEK  C15  C13  N12  113.23  3.000
 TEK  O14  C13  N12  122.92  3.000
 TEK  H4   C15  H3   107.33  3.000
 TEK  H4   C15  H2   108.75  3.000
 TEK  H3   C15  H2   109.03  3.000
 TEK  H4   C15  C13  110.11  3.000
 TEK  H3   C15  C13  111.32  3.000
 TEK  H2   C15  C13  110.22  3.000
 TEK  H7   C01  H6   108.44  3.000
 TEK  H7   C01  H5   108.05  3.000
 TEK  H6   C01  H5   108.04  3.000
 TEK  H7   C01  C02  111.15  3.000
 TEK  H6   C01  C02  111.18  3.000
 TEK  H5   C01  C02  109.86  3.000
 TEK  H9   C02  H8   106.01  3.000
 TEK  H9   C02  N03  109.19  3.000
 TEK  H8   C02  N03  107.37  3.000
 TEK  H9   C02  C01  110.91  3.000
 TEK  H8   C02  C01  110.80  3.000
 TEK  N03  C02  C01  112.30  3.000
 TEK  N03  C04  C09  105.25  3.000
 TEK  N03  C04  C05  132.19  3.000
 TEK  C09  C04  C05  122.57  3.000
 TEK  H10  C05  C06  121.14  3.000
 TEK  H10  C05  C04  122.18  3.000
 TEK  C06  C05  C04  116.69  3.000
 TEK  H11  C06  C07  119.30  3.000
 TEK  H11  C06  C05  119.18  3.000
 TEK  C07  C06  C05  121.52  3.000
 TEK  H12  C07  C08  119.52  3.000
 TEK  H12  C07  C06  119.12  3.000
 TEK  C08  C07  C06  121.36  3.000
 TEK  H13  C08  C09  120.79  3.000
 TEK  H13  C08  C07  121.25  3.000
 TEK  C09  C08  C07  117.95  3.000
 TEK  N10  C09  C08  130.02  3.000
 TEK  C08  C09  C04  119.92  3.000
 TEK  N10  C09  C04  110.06  3.000
 TEK  N10  C11  N03  114.02  3.000
 TEK  N03  C11  N12  120.51  3.000
 TEK  N10  C11  N12  125.46  3.000
 TEK  C11  N03  C04  105.94  3.000
 TEK  C04  N03  C02  125.49  3.000
 TEK  C11  N03  C02  128.00  3.000
 TEK  C11  N10  C09  104.71  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
 TEK  CONST_01  C11  N10  C09  C04     0.00   0.0  0
 TEK  CONST_02  C07  C08  C09  C04     0.00   0.0  0
 TEK  CONST_03  N10  C11  N03  C04     0.00   0.0  0
 TEK  CONST_04  C07  C06  C05  C04     0.00   0.0  0
 TEK  CONST_05  N10  C09  C04  C05   180.00   0.0  0
 TEK  CONST_06  C08  C09  C04  C05     0.00   0.0  0
 TEK  CONST_07  C11  N03  C04  C05   180.00   0.0  0
 TEK  CONST_08  C08  C07  C06  C05     0.00   0.0  0
 TEK  CONST_09  C09  C08  C07  C06     0.00   0.0  0
 TEK  CONST_10  C09  C04  C05  C06     0.00   0.0  0
 TEK  CONST_11  N03  C04  C05  C06   180.00   0.0  0
 TEK  CONST_12  N10  C09  C08  C07   180.00   0.0  0
 TEK  CONST_13  C11  N10  C09  C08   180.00   0.0  0
 TEK  CONST_14  N03  C04  C09  C08   180.00   0.0  0
 TEK  CONST_15  N03  C11  N10  C09     0.00   0.0  0
 TEK  CONST_16  C11  N03  C04  C09     0.00   0.0  0
 TEK  CONST_17  N10  C09  C04  N03     0.00   0.0  0
 TEK  CONST_18  C09  N10  C11  N12   180.00   0.0  0
 TEK  CONST_19  C04  N03  C11  N12   180.00   0.0  0
 TEK  CONST_20  N10  C11  N03  C02   180.00   0.0  0
 TEK  CONST_21  C09  C04  N03  C02   180.00   0.0  0
 TEK  CONST_22  C05  C04  N03  C02     0.00   0.0  0
 TEK  CONST_23  H13  C08  C09  C04   180.00   0.0  0
 TEK  CONST_24  H11  C06  C05  C04   180.00   0.0  0
 TEK  CONST_25  H12  C07  C06  C05   180.00   0.0  0
 TEK  CONST_26  H13  C08  C07  C06   180.00   0.0  0
 TEK  CONST_27  H10  C05  C06  C07   180.00   0.0  0
 TEK  CONST_28  H11  C06  C07  C08   180.00   0.0  0
 TEK  CONST_29  H12  C07  C08  C09   180.00   0.0  0
 TEK  CONST_30  H10  C05  C04  C09   180.00   0.0  0
 TEK  CONST_31  H10  C05  C04  N03     0.00   0.0  0
 TEK  CONST_32  H13  C08  C09  N10     0.00   0.0  0
 TEK  CONST_37  C11  N12  C13  C15   180.00   0.0  0
 TEK  CONST_38  O14  C13  N12  C11     0.00   0.0  0
 TEK  CONST_39  H1   N12  C13  C15     0.00   0.0  0
 TEK  CONST_40  H1   N12  C13  O14   180.00   0.0  0
 TEK  Var_01    C11  N03  C02  C01    84.61  30.0  2
 TEK  Var_02    C04  N03  C02  C01   -85.53  30.0  2
 TEK  Var_03    H8   C02  N03  C04    36.50  30.0  2
 TEK  Var_04    H9   C02  N03  C04   151.01  30.0  2
 TEK  Var_05    H8   C02  N03  C11  -153.36  30.0  2
 TEK  Var_06    H9   C02  N03  C11   -38.85  30.0  2
 TEK  Var_07    H5   C01  C02  N03   178.74  30.0  3
 TEK  Var_08    H6   C01  C02  N03   -61.71  30.0  3
 TEK  Var_09    H7   C01  C02  N03    59.20  30.0  3
 TEK  Var_10    H2   C15  C13  N12  -173.31  30.0  3
 TEK  Var_11    H3   C15  C13  N12   -52.20  30.0  3
 TEK  Var_12    H4   C15  C13  N12    66.71  30.0  3
 TEK  Var_13    H2   C15  C13  O14     6.80  30.0  3
 TEK  Var_14    H3   C15  C13  O14   127.91  30.0  3
 TEK  Var_15    H4   C15  C13  O14  -113.18  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
 TEK  plan-1  N12  0.020
 TEK  plan-1  C02  0.020
 TEK  plan-1  C04  0.020
 TEK  plan-1  C05  0.020
 TEK  plan-1  C06  0.020
 TEK  plan-1  C07  0.020
 TEK  plan-1  C08  0.020
 TEK  plan-1  C09  0.020
 TEK  plan-1  C11  0.020
 TEK  plan-1  N03  0.020
 TEK  plan-1  N10  0.020
 TEK  plan-1  H10  0.020
 TEK  plan-1  H11  0.020
 TEK  plan-1  H12  0.020
 TEK  plan-1  H13  0.020
 TEK  plan-2  N12  0.020
 TEK  plan-2  C13  0.020
 TEK  plan-2  C15  0.020
 TEK  plan-2  C11  0.020
 TEK  plan-2  O14  0.020
 TEK  plan-2  H1   0.020

