# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 01:14:42 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: ~{N}-[(2-methylphenyl)methyl]-3-[(2-methylphenyl)methylamino]pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1CNC(=O)c2nccnc2NCc3ccccc3C
#
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
 1AI  1AI  ~{N}-[(2-methylphenyl)methyl]-3-[(2-methylphenyl)methylamino]pyrazine-2-carboxamide  ligand  48  26  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1AI
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
 1AI  C11  C  CH2   0  -0.336  2.1971  35.8556  29.3163
 1AI  C12  C  CR6   0   0.049  1.7719  34.6663  28.4834
 1AI  C13  C  CR6   0   0.076  1.0818  33.6131  29.1012
 1AI  C14  C  CR16  0  -0.298  0.6782  32.5287  28.3283
 1AI  C15  C  CR16  0  -0.255  0.9423  32.4729  26.9660
 1AI  C16  C  CR16  0  -0.260  1.6190  33.5189  26.3591
 1AI  C17  C  CR16  0  -0.290  2.0276  34.6077  27.1190
 1AI  C18  C  CH3   0  -0.746  0.7782  33.6457  30.5718
 1AI  C19  C  CH2   0  -0.366  5.3862  40.7610  25.9027
 1AI  C2   C  CR6   0  -0.006  5.2215  37.4980  27.7834
 1AI  C20  C  CR6   0   0.069  6.3863  41.8143  26.3027
 1AI  C21  C  CR6   0   0.076  6.4094  42.3422  27.6019
 1AI  C22  C  CR16  0  -0.295  7.3602  43.3124  27.9074
 1AI  C23  C  CR16  0  -0.250  8.2755  43.7565  26.9619
 1AI  C24  C  CR16  0  -0.258  8.2490  43.2316  25.6797
 1AI  C25  C  CR16  0  -0.297  7.3052  42.2647  25.3607
 1AI  C26  C  CH3   0  -0.741  5.4443  41.8865  28.6578
 1AI  C3   C  CR6   0   0.519  4.3773  36.5848  28.4788
 1AI  C5   C  CR16  0  -0.083  6.1992  35.2633  28.8553
 1AI  C6   C  CR16  0  -0.160  7.0249  36.1526  28.1824
 1AI  N1   N  N     0  -0.376  6.5117  37.2530  27.6588
 1AI  N10  N  NH1   0  -0.686  3.0622  36.7900  28.6490
 1AI  N4   N  N     0  -0.418  4.9054  35.4711  28.9984
 1AI  N9   N  NH1   0  -0.630  5.6415  39.5056  26.5717
 1AI  O8   O  O     0  -0.499  3.5125  39.0518  27.1981
 1AI  H1   H  HCH2  0   0.254  2.6774  35.5093  30.2338
 1AI  H2   H  HCH2  0   0.273  1.3109  36.4113  29.6322
 1AI  H3   H  HCR6  0   0.244  0.1473  31.7126  28.8045
 1AI  H4   H  HCR6  0   0.248  0.6190  31.6179  26.3862
 1AI  H5   H  HCR6  0   0.248  1.8306  33.4925  25.2978
 1AI  H6   H  HCR6  0   0.242  2.5517  35.4225  26.6355
 1AI  H7   H  HCH3  0   0.246  1.6906  33.6671  31.1725
 1AI  H8   H  HCH3  0   0.244  0.1997  34.5296  30.8482
 1AI  H9   H  HCH3  0   0.254  0.2067  32.7694  30.8736
 1AI  H10  H  HCH2  0   0.265  4.3705  41.0764  26.1421
 1AI  H11  H  HCH2  0   0.268  5.4231  40.6186  24.8193
 1AI  H12  H  HCR6  0   0.246  7.3816  43.7319  28.9065
 1AI  H13  H  HCR6  0   0.252  9.0027  44.5127  27.2286
 1AI  H14  H  HCR6  0   0.251  8.9543  43.5696  24.9316
 1AI  H15  H  HCR6  0   0.249  7.2788  41.8512  24.3590
 1AI  H16  H  HCH3  0   0.248  5.6841  40.8828  29.0133
 1AI  H17  H  HCH3  0   0.253  5.4669  42.5530  29.5189
 1AI  H18  H  HCH3  0   0.241  4.4173  41.8561  28.2910
 1AI  H19  H  HCR6  0   0.274  6.6030  34.3540  29.2864
 1AI  H20  H  HCR6  0   0.269  8.0854  35.9735  28.0653
 1AI  H21  H  HNH1  0   0.415  2.6756  37.6135  28.2115
 1AI  H22  H  HNH1  0   0.405  6.5852  39.1457  26.5742
 1AI  C7   C  C     0   0.573  4.7057  38.7536  27.1595

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
 1AI  C25  C24  aromatic  1.388  0.020  1.388
 1AI  C25  C20  aromatic  1.391  0.020  1.391
 1AI  C19  C20  single    1.507  0.020  1.507
 1AI  C19  N9   single    1.445  0.020  1.445
 1AI  C24  C23  aromatic  1.386  0.020  1.386
 1AI  C16  C15  aromatic  1.386  0.020  1.386
 1AI  C16  C17  aromatic  1.389  0.020  1.389
 1AI  C20  C21  aromatic  1.403  0.020  1.403
 1AI  N9   C7   single    1.337  0.020  1.337
 1AI  C15  C14  aromatic  1.389  0.020  1.389
 1AI  C17  C12  aromatic  1.389  0.020  1.389
 1AI  C23  C22  aromatic  1.389  0.020  1.389
 1AI  C7   O8   double    1.231  0.020  1.231
 1AI  C7   C2   single    1.494  0.020  1.494
 1AI  C21  C22  aromatic  1.392  0.020  1.392
 1AI  C21  C26  single    1.501  0.020  1.501
 1AI  C2   N1   aromatic  1.319  0.020  1.319
 1AI  C2   C3   aromatic  1.425  0.020  1.425
 1AI  N1   C6   aromatic  1.322  0.020  1.322
 1AI  N10  C3   single    1.342  0.020  1.342
 1AI  N10  C11  single    1.438  0.020  1.438
 1AI  C3   N4   aromatic  1.338  0.020  1.338
 1AI  C14  C13  aromatic  1.392  0.020  1.392
 1AI  C12  C13  aromatic  1.403  0.020  1.403
 1AI  C12  C11  single    1.513  0.020  1.513
 1AI  C6   C5   aromatic  1.388  0.020  1.388
 1AI  N4   C5   aromatic  1.318  0.020  1.318
 1AI  C13  C18  single    1.502  0.020  1.502
 1AI  C11  H1   single    0.970  0.020  1.090
 1AI  C11  H2   single    0.970  0.020  1.090
 1AI  C14  H3   single    0.930  0.020  1.080
 1AI  C15  H4   single    0.930  0.020  1.080
 1AI  C16  H5   single    0.930  0.020  1.080
 1AI  C17  H6   single    0.930  0.020  1.080
 1AI  C18  H7   single    0.970  0.020  1.090
 1AI  C18  H8   single    0.970  0.020  1.090
 1AI  C18  H9   single    0.970  0.020  1.090
 1AI  C19  H10  single    0.970  0.020  1.090
 1AI  C19  H11  single    0.970  0.020  1.090
 1AI  C22  H12  single    0.930  0.020  1.080
 1AI  C23  H13  single    0.930  0.020  1.080
 1AI  C24  H14  single    0.930  0.020  1.080
 1AI  C25  H15  single    0.930  0.020  1.080
 1AI  C26  H16  single    0.970  0.020  1.090
 1AI  C26  H17  single    0.970  0.020  1.090
 1AI  C26  H18  single    0.970  0.020  1.090
 1AI  C5   H19  single    0.930  0.020  1.080
 1AI  C6   H20  single    0.930  0.020  1.080
 1AI  N10  H21  single    0.860  0.020  1.020
 1AI  N9   H22  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
 1AI  H2   C11  H1   105.97  3.000
 1AI  H2   C11  N10  106.96  3.000
 1AI  H1   C11  N10  109.36  3.000
 1AI  H2   C11  C12  109.33  3.000
 1AI  H1   C11  C12  109.68  3.000
 1AI  N10  C11  C12  115.12  3.000
 1AI  C17  C12  C13  119.44  3.000
 1AI  C13  C12  C11  119.08  3.000
 1AI  C17  C12  C11  121.47  3.000
 1AI  C18  C13  C14  120.14  3.000
 1AI  C18  C13  C12  120.96  3.000
 1AI  C14  C13  C12  118.90  3.000
 1AI  H3   C14  C15  119.60  3.000
 1AI  H3   C14  C13  119.00  3.000
 1AI  C15  C14  C13  121.40  3.000
 1AI  H4   C15  C16  120.50  3.000
 1AI  H4   C15  C14  120.02  3.000
 1AI  C16  C15  C14  119.49  3.000
 1AI  H5   C16  C17  119.86  3.000
 1AI  H5   C16  C15  120.43  3.000
 1AI  C17  C16  C15  119.71  3.000
 1AI  H6   C17  C16  119.21  3.000
 1AI  H6   C17  C12  119.72  3.000
 1AI  C16  C17  C12  121.07  3.000
 1AI  H9   C18  H8   107.65  3.000
 1AI  H9   C18  H7   107.56  3.000
 1AI  H8   C18  H7   106.70  3.000
 1AI  H9   C18  C13  111.10  3.000
 1AI  H8   C18  C13  111.87  3.000
 1AI  H7   C18  C13  111.71  3.000
 1AI  H11  C19  H10  106.67  3.000
 1AI  H11  C19  N9   109.85  3.000
 1AI  H10  C19  N9   108.31  3.000
 1AI  H11  C19  C20  109.38  3.000
 1AI  H10  C19  C20  110.97  3.000
 1AI  N9   C19  C20  111.54  3.000
 1AI  N1   C2   C7   117.02  3.000
 1AI  N1   C2   C3   120.43  3.000
 1AI  C7   C2   C3   122.54  3.000
 1AI  C25  C20  C21  119.64  3.000
 1AI  C21  C20  C19  121.34  3.000
 1AI  C25  C20  C19  119.02  3.000
 1AI  C26  C21  C22  119.75  3.000
 1AI  C26  C21  C20  121.77  3.000
 1AI  C22  C21  C20  118.47  3.000
 1AI  H12  C22  C23  119.40  3.000
 1AI  H12  C22  C21  119.04  3.000
 1AI  C23  C22  C21  121.57  3.000
 1AI  H13  C23  C24  120.36  3.000
 1AI  H13  C23  C22  119.89  3.000
 1AI  C24  C23  C22  119.75  3.000
 1AI  H14  C24  C25  120.11  3.000
 1AI  H14  C24  C23  120.58  3.000
 1AI  C25  C24  C23  119.30  3.000
 1AI  H15  C25  C24  119.64  3.000
 1AI  H15  C25  C20  119.09  3.000
 1AI  C24  C25  C20  121.27  3.000
 1AI  H18  C26  H17  107.60  3.000
 1AI  H18  C26  H16  106.90  3.000
 1AI  H17  C26  H16  107.50  3.000
 1AI  H18  C26  C21  112.16  3.000
 1AI  H17  C26  C21  110.91  3.000
 1AI  H16  C26  C21  111.53  3.000
 1AI  N4   C3   N10  117.71  3.000
 1AI  N4   C3   C2   119.29  3.000
 1AI  N10  C3   C2   122.99  3.000
 1AI  H19  C5   N4   117.03  3.000
 1AI  H19  C5   C6   120.58  3.000
 1AI  N4   C5   C6   122.39  3.000
 1AI  H20  C6   N1   118.39  3.000
 1AI  H20  C6   C5   121.98  3.000
 1AI  N1   C6   C5   119.63  3.000
 1AI  C6   N1   C2   119.79  3.000
 1AI  H21  N10  C3   116.44  3.000
 1AI  H21  N10  C11  120.06  3.000
 1AI  C3   N10  C11  123.31  3.000
 1AI  C5   N4   C3   118.46  3.000
 1AI  H22  N9   C7   116.90  3.000
 1AI  H22  N9   C19  118.41  3.000
 1AI  C7   N9   C19  124.66  3.000
 1AI  O8   C7   N9   123.80  3.000
 1AI  O8   C7   C2   121.69  3.000
 1AI  N9   C7   C2   114.51  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
 1AI  CONST_01  C15  C16  C17  C12    0.00   0.0  0
 1AI  CONST_02  C15  C14  C13  C12    0.00   0.0  0
 1AI  CONST_03  C16  C15  C14  C13    0.00   0.0  0
 1AI  CONST_04  C16  C17  C12  C13    0.00   0.0  0
 1AI  CONST_05  C17  C16  C15  C14    0.00   0.0  0
 1AI  CONST_06  C17  C12  C13  C14    0.00   0.0  0
 1AI  CONST_07  C5   C6   N1   C2     0.00   0.0  0
 1AI  CONST_08  C5   N4   C3   C2     0.00   0.0  0
 1AI  CONST_09  C23  C24  C25  C20    0.00   0.0  0
 1AI  CONST_10  C23  C22  C21  C20    0.00   0.0  0
 1AI  CONST_11  C24  C25  C20  C21    0.00   0.0  0
 1AI  CONST_12  C24  C23  C22  C21    0.00   0.0  0
 1AI  CONST_13  C25  C24  C23  C22    0.00   0.0  0
 1AI  CONST_14  C25  C20  C21  C22    0.00   0.0  0
 1AI  CONST_15  C6   N1   C2   C3     0.00   0.0  0
 1AI  CONST_16  C6   C5   N4   C3     0.00   0.0  0
 1AI  CONST_17  N4   C3   C2   N1     0.00   0.0  0
 1AI  CONST_18  N4   C5   C6   N1     0.00   0.0  0
 1AI  CONST_19  C16  C17  C12  C11  180.00   0.0  0
 1AI  CONST_20  C14  C13  C12  C11  180.00   0.0  0
 1AI  CONST_21  C18  C13  C14  C15  180.00   0.0  0
 1AI  CONST_22  C18  C13  C12  C17  180.00   0.0  0
 1AI  CONST_23  C24  C25  C20  C19  180.00   0.0  0
 1AI  CONST_24  C22  C21  C20  C19  180.00   0.0  0
 1AI  CONST_25  C26  C21  C22  C23  180.00   0.0  0
 1AI  CONST_26  C26  C21  C20  C25  180.00   0.0  0
 1AI  CONST_27  N10  C3   N4   C5   180.00   0.0  0
 1AI  CONST_28  C7   C2   N1   C6   180.00   0.0  0
 1AI  CONST_29  N4   C3   C2   C7   180.00   0.0  0
 1AI  CONST_30  N10  C3   C2   N1   180.00   0.0  0
 1AI  CONST_31  H5   C16  C17  C12  180.00   0.0  0
 1AI  CONST_32  H3   C14  C13  C12  180.00   0.0  0
 1AI  CONST_33  H4   C15  C14  C13  180.00   0.0  0
 1AI  CONST_34  H6   C17  C12  C13  180.00   0.0  0
 1AI  CONST_35  H20  C6   N1   C2   180.00   0.0  0
 1AI  CONST_36  H14  C24  C25  C20  180.00   0.0  0
 1AI  CONST_37  H12  C22  C21  C20  180.00   0.0  0
 1AI  CONST_38  H15  C25  C20  C21  180.00   0.0  0
 1AI  CONST_39  H13  C23  C22  C21  180.00   0.0  0
 1AI  CONST_40  H19  C5   N4   C3   180.00   0.0  0
 1AI  CONST_41  C2   C3   N10  C11  180.00   0.0  0
 1AI  CONST_42  N4   C3   N10  C11    0.00   0.0  0
 1AI  CONST_43  H21  N10  C3   C2     0.00   0.0  0
 1AI  CONST_44  C2   C7   N9   C19  180.00   0.0  0
 1AI  CONST_45  H22  N9   C7   C2     0.00   0.0  0
 1AI  CONST_46  O8   C7   N9   C19    0.00   0.0  0
 1AI  Var_01    C3   N10  C11  C12  -78.74  30.0  3
 1AI  Var_02    N10  C11  C12  C13  171.35  30.0  2
 1AI  Var_03    N9   C19  C20  C21  -68.15  30.0  3
 1AI  Var_04    N9   C7   C2   C3   178.69  30.0  2
 1AI  Var_05    H7   C18  C13  C12  -62.02  30.0  2
 1AI  Var_06    H16  C26  C21  C20   72.79  30.0  2
 1AI  Var_07    C7   N9   C19  C20  134.11  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
 1AI  plan-1  C11  0.020
 1AI  plan-1  C12  0.020
 1AI  plan-1  C13  0.020
 1AI  plan-1  C14  0.020
 1AI  plan-1  C15  0.020
 1AI  plan-1  C16  0.020
 1AI  plan-1  C17  0.020
 1AI  plan-1  C18  0.020
 1AI  plan-1  H3   0.020
 1AI  plan-1  H4   0.020
 1AI  plan-1  H5   0.020
 1AI  plan-1  H6   0.020
 1AI  plan-2  C2   0.020
 1AI  plan-2  C3   0.020
 1AI  plan-2  C5   0.020
 1AI  plan-2  C6   0.020
 1AI  plan-2  N1   0.020
 1AI  plan-2  N10  0.020
 1AI  plan-2  N4   0.020
 1AI  plan-2  H19  0.020
 1AI  plan-2  H20  0.020
 1AI  plan-2  C7   0.020
 1AI  plan-3  C19  0.020
 1AI  plan-3  C20  0.020
 1AI  plan-3  C21  0.020
 1AI  plan-3  C22  0.020
 1AI  plan-3  C23  0.020
 1AI  plan-3  C24  0.020
 1AI  plan-3  C25  0.020
 1AI  plan-3  C26  0.020
 1AI  plan-3  H12  0.020
 1AI  plan-3  H13  0.020
 1AI  plan-3  H14  0.020
 1AI  plan-3  H15  0.020
 1AI  plan-4  C19  0.020
 1AI  plan-4  C2   0.020
 1AI  plan-4  N9   0.020
 1AI  plan-4  O8   0.020
 1AI  plan-4  H22  0.020
 1AI  plan-4  C7   0.020
 1AI  plan-5  C11  0.020
 1AI  plan-5  C3   0.020
 1AI  plan-5  N10  0.020
 1AI  plan-5  H21  0.020

