# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 14:18:23 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: 2-(2-methyl-1H-benzimidazol-1-yl)ethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc2ccccc2n1CCN
#
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
 02W  02W  2-(2-methyl-1H-benzimidazol-1-yl)ethanamine  ligand  26  13  .  2021-07-27  2021-07-27  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_02W
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
 02W  C1    C  CH2   0  -0.332   1.8571   0.4102  -0.6556
 02W  C2    C  CH2   0  -0.286   2.4807   0.9977   0.6054
 02W  N1    N  NH2   0  -0.799   3.7076   1.6897   0.2569
 02W  C14   C  CR56  0   0.130  -1.4572  -0.7974   0.1251
 02W  C15   C  CR16  0  -0.334  -2.8092  -0.5573   0.3664
 02W  C16   C  CR16  0  -0.275  -3.2632   0.7477   0.2786
 02W  C17   C  CR16  0  -0.278  -2.3964   1.8021  -0.0439
 02W  C18   C  CR16  0  -0.313  -1.0503   1.5831  -0.2888
 02W  C19   C  CR56  0   0.341  -0.6050   0.2699  -0.1984
 02W  N3    N  N     0  -0.486  -0.7455  -1.9722   0.1476
 02W  N4    N  NR5   0  -0.534   0.6296  -0.3018  -0.3789
 02W  C20   C  CR5   0   0.430   0.4831  -1.6390  -0.1480
 02W  C21   C  CH3   0  -0.768   1.6227  -2.5861  -0.2335
 02W  H1    H  HCH2  0   0.267   1.6487   1.2047  -1.3734
 02W  H1A   H  HCH2  0   0.271   2.5532  -0.2745  -1.1420
 02W  H2    H  HCH2  0   0.234   1.7866   1.7185   1.0434
 02W  H2A   H  HCH2  0   0.208   2.6090   0.1971   1.3472
 02W  HN1   H  HNH2  0   0.356   4.0288   2.2310   1.0482
 02W  H16   H  HCR6  0   0.250  -4.3079   0.9618   0.4631
 02W  H17   H  HCR6  0   0.253  -2.7868   2.8100  -0.1003
 02W  H18   H  HCR6  0   0.266  -0.3862   2.4025  -0.5335
 02W  H21   H  HCH3  0   0.263   2.4038  -2.3412   0.4883
 02W  H21A  H  HCH3  0   0.273   1.2712  -3.5938  -0.0277
 02W  H21B  H  HCH3  0   0.266   2.0786  -2.5783  -1.2247
 02W  H3    H  HNH2  0   0.346   4.4379   1.0142   0.0695
 02W  H15   H  HCR6  0   0.251  -3.4808  -1.3693   0.6153

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
 02W  C2   C1    single    1.525  0.020  1.525
 02W  C1   N4    single    1.446  0.020  1.446
 02W  C1   H1    single    0.970  0.020  1.090
 02W  C1   H1A   single    0.970  0.020  1.090
 02W  N1   C2    single    1.451  0.020  1.451
 02W  C2   H2    single    0.970  0.020  1.090
 02W  C2   H2A   single    0.970  0.020  1.090
 02W  N1   HN1   single    0.890  0.020  1.040
 02W  C19  C14   aromatic  1.404  0.020  1.404
 02W  C15  C14   aromatic  1.394  0.020  1.394
 02W  C14  N3    aromatic  1.374  0.020  1.374
 02W  C16  C15   aromatic  1.384  0.020  1.384
 02W  C15  H15   single    0.930  0.020  1.080
 02W  C17  C16   aromatic  1.403  0.020  1.403
 02W  C16  H16   single    0.930  0.020  1.080
 02W  C17  C18   aromatic  1.386  0.020  1.386
 02W  C17  H17   single    0.930  0.020  1.080
 02W  C18  C19   aromatic  1.390  0.020  1.390
 02W  C18  H18   single    0.930  0.020  1.080
 02W  C19  N4    aromatic  1.372  0.020  1.372
 02W  C20  N3    aromatic  1.307  0.020  1.307
 02W  N4   C20   aromatic  1.365  0.020  1.365
 02W  C20  C21   single    1.484  0.020  1.484
 02W  C21  H21   single    0.970  0.020  1.090
 02W  C21  H21A  single    0.970  0.020  1.090
 02W  C21  H21B  single    0.970  0.020  1.090
 02W  N1   H3    single    0.890  0.020  1.040

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
 02W  H1A   C1   H1    106.60  3.000
 02W  H1A   C1   N4    108.54  3.000
 02W  H1    C1   N4    108.81  3.000
 02W  H1A   C1   C2    110.46  3.000
 02W  H1    C1   C2    109.98  3.000
 02W  N4    C1   C2    112.26  3.000
 02W  H2A   C2   H2    106.52  3.000
 02W  H2A   C2   N1    114.26  3.000
 02W  H2    C2   N1    108.59  3.000
 02W  H2A   C2   C1    108.99  3.000
 02W  H2    C2   C1    109.02  3.000
 02W  N1    C2   C1    109.33  3.000
 02W  H3    N1   HN1   105.84  3.000
 02W  H3    N1   C2    109.64  3.000
 02W  HN1   N1   C2    109.62  3.000
 02W  N3    C14  C19   109.84  3.000
 02W  N3    C14  C15   130.31  3.000
 02W  C19   C14  C15   119.85  3.000
 02W  H15   C15  C16   121.20  3.000
 02W  H15   C15  C14   120.81  3.000
 02W  C16   C15  C14   117.99  3.000
 02W  H16   C16  C17   119.14  3.000
 02W  H16   C16  C15   119.49  3.000
 02W  C17   C16  C15   121.37  3.000
 02W  H17   C17  C18   119.24  3.000
 02W  H17   C17  C16   119.29  3.000
 02W  C18   C17  C16   121.48  3.000
 02W  H18   C18  C19   122.23  3.000
 02W  H18   C18  C17   121.08  3.000
 02W  C19   C18  C17   116.70  3.000
 02W  N4    C19  C18   132.33  3.000
 02W  N4    C19  C14   105.06  3.000
 02W  C18   C19  C14   122.61  3.000
 02W  C20   N3   C14   105.39  3.000
 02W  C20   N4   C19   106.82  3.000
 02W  C20   N4   C1    127.30  3.000
 02W  C19   N4   C1    125.72  3.000
 02W  C21   C20  N4    122.21  3.000
 02W  C21   C20  N3    124.90  3.000
 02W  N4    C20  N3    112.89  3.000
 02W  H21B  C21  H21A  108.29  3.000
 02W  H21B  C21  H21   107.47  3.000
 02W  H21A  C21  H21   108.31  3.000
 02W  H21B  C21  C20   111.63  3.000
 02W  H21A  C21  C20   109.42  3.000
 02W  H21   C21  C20   111.61  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
 02W  CONST_01  C17  C18  C19  C14     0.00   0.0  0
 02W  CONST_02  C20  N4   C19  C14     0.00   0.0  0
 02W  CONST_03  C17  C16  C15  C14     0.00   0.0  0
 02W  CONST_04  N4   C20  N3   C14     0.00   0.0  0
 02W  CONST_05  C18  C19  C14  C15     0.00   0.0  0
 02W  CONST_06  N4   C19  C14  C15   180.00   0.0  0
 02W  CONST_07  C20  N3   C14  C15   180.00   0.0  0
 02W  CONST_08  C18  C17  C16  C15     0.00   0.0  0
 02W  CONST_09  C19  C14  C15  C16     0.00   0.0  0
 02W  CONST_10  N3   C14  C15  C16   180.00   0.0  0
 02W  CONST_11  C19  C18  C17  C16     0.00   0.0  0
 02W  CONST_12  N4   C19  C18  C17   180.00   0.0  0
 02W  CONST_13  N3   C14  C19  C18   180.00   0.0  0
 02W  CONST_14  C20  N4   C19  C18   180.00   0.0  0
 02W  CONST_15  C20  N3   C14  C19     0.00   0.0  0
 02W  CONST_16  N3   C20  N4   C19     0.00   0.0  0
 02W  CONST_17  N4   C19  C14  N3      0.00   0.0  0
 02W  CONST_18  C14  C19  N4   C1    180.00   0.0  0
 02W  CONST_19  C18  C19  N4   C1      0.00   0.0  0
 02W  CONST_20  N3   C20  N4   C1    180.00   0.0  0
 02W  CONST_21  C21  C20  N3   C14   180.00   0.0  0
 02W  CONST_22  C21  C20  N4   C19   180.00   0.0  0
 02W  CONST_23  H18  C18  C19  C14   180.00   0.0  0
 02W  CONST_24  H16  C16  C15  C14   180.00   0.0  0
 02W  CONST_25  H17  C17  C16  C15   180.00   0.0  0
 02W  CONST_26  H15  C15  C16  C17   180.00   0.0  0
 02W  Var_01    C19  N4   C1   C2     80.62  30.0  2
 02W  Var_02    H21  C21  C20  N3   -119.01  30.0  2
 02W  Var_03    N4   C1   C2   N1    179.72  30.0  3
 02W  Var_04    HN1  N1   C2   C1    168.98  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
 02W  plan-1  C1   0.020
 02W  plan-1  C14  0.020
 02W  plan-1  C15  0.020
 02W  plan-1  C16  0.020
 02W  plan-1  C17  0.020
 02W  plan-1  C18  0.020
 02W  plan-1  C19  0.020
 02W  plan-1  N3   0.020
 02W  plan-1  N4   0.020
 02W  plan-1  C20  0.020
 02W  plan-1  C21  0.020
 02W  plan-1  H16  0.020
 02W  plan-1  H17  0.020
 02W  plan-1  H18  0.020
 02W  plan-1  H15  0.020

