# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 18:53:15 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 1-(4-methoxy-3-methylbenzyl)-5,6,7,8-tetrahydro-1H-naphtho[2,3-d]imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(Cn2cnc3cc4CCCCc4cc23)cc1C
#
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
 1JT  1JT  1-(4-methoxy-3-methylbenzyl)-5,6,7,8-tetrahydro-1H-naphtho[2,3-d]imidazole  ligand  45  23  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1JT
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
 1JT  C1   C  CR6   0   0.054  -3.3987   0.1826  -0.6643
 1JT  C2   C  CR6   0   0.056  -2.5745  -0.6115   0.1661
 1JT  C3   C  CR16  0  -0.376  -3.0969   1.5210  -0.8788
 1JT  C4   C  CR16  0  -0.351  -1.4560  -0.0635   0.7824
 1JT  C5   C  CR56  0   0.357  -1.1744   1.2749   0.5558
 1JT  C6   C  CR56  0   0.121  -1.9783   2.0767  -0.2669
 1JT  N7   N  N     0  -0.475  -1.4753   3.3587  -0.3127
 1JT  C8   C  CR15  0   0.096  -0.4197   3.3230   0.4488
 1JT  N9   N  NR5   0  -0.501  -0.1820   2.1087   1.0082
 1JT  C10  C  CH2   0  -0.412   0.9484   1.7389   1.8325
 1JT  C11  C  CR6   0   0.114   1.9114   0.8343   1.1086
 1JT  C12  C  CR16  0  -0.344   2.1883  -0.4419   1.5899
 1JT  C13  C  CR6   0   0.020   3.0616  -1.3059   0.9451
 1JT  C14  C  CR6   0   0.342   3.6780  -0.8641  -0.2349
 1JT  C15  C  CR16  0  -0.370   3.4150   0.4105  -0.7302
 1JT  C16  C  CR16  0  -0.289   2.5372   1.2488  -0.0569
 1JT  C17  C  CH2   0  -0.496  -2.8631  -2.0797   0.3755
 1JT  C18  C  CH2   0  -0.443  -4.2940  -2.4680   0.0346
 1JT  C19  C  CH2   0  -0.443  -4.6706  -1.9125  -1.3303
 1JT  C20  C  CH2   0  -0.494  -4.6444  -0.3909  -1.3009
 1JT  O21  O  O2    0  -0.464   4.5121  -1.7424  -0.8244
 1JT  C22  C  CH3   0  -0.437   5.1441  -1.3747  -2.0335
 1JT  C23  C  CH3   0  -0.713   3.3389  -2.6795   1.4793
 1JT  H1   H  HCR6  0   0.241  -3.7290   2.1286  -1.5169
 1JT  H2   H  HCR6  0   0.255  -0.8294  -0.6787   1.4174
 1JT  H3   H  HCR5  0   0.288   0.2340   4.1608   0.6483
 1JT  H4   H  HCH2  0   0.287   1.4369   2.6641   2.1415
 1JT  H5   H  HCH2  0   0.282   0.5844   1.2552   2.7406
 1JT  H6   H  HCR6  0   0.248   1.7044  -0.7780   2.5011
 1JT  H7   H  HCR6  0   0.279   3.8846   0.7657  -1.6374
 1JT  H8   H  HCR6  0   0.253   2.3467   2.2374  -0.4586
 1JT  H9   H  HCH2  0   0.239  -2.1809  -2.6630  -0.2527
 1JT  H10  H  HCH2  0   0.244  -2.6270  -2.3553   1.4063
 1JT  H11  H  HCH2  0   0.235  -4.3947  -3.5550   0.0556
 1JT  H12  H  HCH2  0   0.219  -4.9797  -2.0738   0.7915
 1JT  H13  H  HCH2  0   0.219  -3.9671  -2.2861  -2.0814
 1JT  H14  H  HCH2  0   0.234  -5.6622  -2.2551  -1.6321
 1JT  H15  H  HCH2  0   0.237  -5.5177  -0.0349  -0.7433
 1JT  H16  H  HCH2  0   0.243  -4.7566   0.0092  -2.3115
 1JT  H17  H  HCH3  0   0.259   5.7483  -2.2259  -2.3377
 1JT  H18  H  HCH3  0   0.228   4.4195  -1.1565  -2.8226
 1JT  H19  H  HCH3  0   0.228   5.7980  -0.5076  -1.9076
 1JT  H20  H  HCH3  0   0.243   4.3974  -2.8200   1.7048
 1JT  H21  H  HCH3  0   0.242   2.7782  -2.8600   2.3953
 1JT  H22  H  HCH3  0   0.243   3.0624  -3.4543   0.7621

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
 1JT  C23  C13  single    1.500  0.020  1.500
 1JT  O21  C22  single    1.413  0.020  1.413
 1JT  O21  C14  single    1.347  0.020  1.347
 1JT  C13  C14  aromatic  1.403  0.020  1.403
 1JT  C13  C12  aromatic  1.387  0.020  1.387
 1JT  C14  C15  aromatic  1.393  0.020  1.393
 1JT  C12  C11  aromatic  1.392  0.020  1.392
 1JT  C15  C16  aromatic  1.388  0.020  1.388
 1JT  C11  C16  aromatic  1.386  0.020  1.386
 1JT  C11  C10  single    1.507  0.020  1.507
 1JT  C10  N9   single    1.447  0.020  1.447
 1JT  C17  C18  single    1.521  0.020  1.521
 1JT  C17  C2   single    1.511  0.020  1.511
 1JT  C4   C2   aromatic  1.390  0.020  1.390
 1JT  C4   C5   aromatic  1.386  0.020  1.386
 1JT  C18  C19  single    1.521  0.020  1.521
 1JT  C2   C1   aromatic  1.414  0.020  1.414
 1JT  N9   C5   aromatic  1.373  0.020  1.373
 1JT  N9   C8   aromatic  1.358  0.020  1.358
 1JT  C5   C6   aromatic  1.402  0.020  1.402
 1JT  C19  C20  single    1.522  0.020  1.522
 1JT  C8   N7   aromatic  1.302  0.020  1.302
 1JT  C1   C20  single    1.512  0.020  1.512
 1JT  C1   C3   aromatic  1.389  0.020  1.389
 1JT  C6   C3   aromatic  1.391  0.020  1.391
 1JT  C6   N7   aromatic  1.378  0.020  1.378
 1JT  C3   H1   single    0.930  0.020  1.080
 1JT  C4   H2   single    0.930  0.020  1.080
 1JT  C8   H3   single    0.930  0.020  1.080
 1JT  C10  H4   single    0.970  0.020  1.090
 1JT  C10  H5   single    0.970  0.020  1.090
 1JT  C12  H6   single    0.930  0.020  1.080
 1JT  C15  H7   single    0.930  0.020  1.080
 1JT  C16  H8   single    0.930  0.020  1.080
 1JT  C17  H9   single    0.970  0.020  1.090
 1JT  C17  H10  single    0.970  0.020  1.090
 1JT  C18  H11  single    0.970  0.020  1.090
 1JT  C18  H12  single    0.970  0.020  1.090
 1JT  C19  H13  single    0.970  0.020  1.090
 1JT  C19  H14  single    0.970  0.020  1.090
 1JT  C20  H15  single    0.970  0.020  1.090
 1JT  C20  H16  single    0.970  0.020  1.090
 1JT  C22  H17  single    0.970  0.020  1.090
 1JT  C22  H18  single    0.970  0.020  1.090
 1JT  C22  H19  single    0.970  0.020  1.090
 1JT  C23  H20  single    0.970  0.020  1.090
 1JT  C23  H21  single    0.970  0.020  1.090
 1JT  C23  H22  single    0.970  0.020  1.090

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
 1JT  C20  C1   C3   118.66  3.000
 1JT  C3   C1   C2   120.35  3.000
 1JT  C20  C1   C2   120.96  3.000
 1JT  C17  C2   C4   118.39  3.000
 1JT  C4   C2   C1   120.54  3.000
 1JT  C17  C2   C1   121.05  3.000
 1JT  H1   C3   C6   120.26  3.000
 1JT  H1   C3   C1   120.28  3.000
 1JT  C6   C3   C1   119.46  3.000
 1JT  H2   C4   C5   121.76  3.000
 1JT  H2   C4   C2   120.09  3.000
 1JT  C5   C4   C2   118.15  3.000
 1JT  N9   C5   C6   105.10  3.000
 1JT  C6   C5   C4   122.11  3.000
 1JT  N9   C5   C4   132.79  3.000
 1JT  N7   C6   C5   110.01  3.000
 1JT  N7   C6   C3   130.59  3.000
 1JT  C5   C6   C3   119.39  3.000
 1JT  C8   N7   C6   104.54  3.000
 1JT  H3   C8   N9   120.74  3.000
 1JT  H3   C8   N7   125.23  3.000
 1JT  N9   C8   N7   114.04  3.000
 1JT  C10  N9   C8   126.86  3.000
 1JT  C8   N9   C5   106.31  3.000
 1JT  C10  N9   C5   126.67  3.000
 1JT  H5   C10  H4   106.83  3.000
 1JT  H5   C10  C11  110.30  3.000
 1JT  H4   C10  C11  111.04  3.000
 1JT  H5   C10  N9   109.07  3.000
 1JT  H4   C10  N9   107.12  3.000
 1JT  C11  C10  N9   112.28  3.000
 1JT  C16  C11  C12  118.37  3.000
 1JT  C16  C11  C10  120.86  3.000
 1JT  C12  C11  C10  120.77  3.000
 1JT  H6   C12  C13  118.56  3.000
 1JT  H6   C12  C11  119.06  3.000
 1JT  C13  C12  C11  122.38  3.000
 1JT  C23  C13  C14  120.46  3.000
 1JT  C14  C13  C12  118.13  3.000
 1JT  C23  C13  C12  121.41  3.000
 1JT  O21  C14  C15  123.93  3.000
 1JT  C15  C14  C13  120.30  3.000
 1JT  O21  C14  C13  115.78  3.000
 1JT  H7   C15  C16  118.89  3.000
 1JT  H7   C15  C14  121.12  3.000
 1JT  C16  C15  C14  119.99  3.000
 1JT  H8   C16  C15  118.83  3.000
 1JT  H8   C16  C11  120.33  3.000
 1JT  C15  C16  C11  120.84  3.000
 1JT  H10  C17  H9   105.79  3.000
 1JT  H10  C17  C18  110.50  3.000
 1JT  H9   C17  C18  108.74  3.000
 1JT  H10  C17  C2   109.55  3.000
 1JT  H9   C17  C2   108.60  3.000
 1JT  C18  C17  C2   113.37  3.000
 1JT  H12  C18  H11  106.70  3.000
 1JT  H12  C18  C19  109.50  3.000
 1JT  H11  C18  C19  110.98  3.000
 1JT  H12  C18  C17  110.01  3.000
 1JT  H11  C18  C17  109.67  3.000
 1JT  C19  C18  C17  109.92  3.000
 1JT  H14  C19  H13  106.67  3.000
 1JT  H14  C19  C20  109.55  3.000
 1JT  H13  C19  C20  110.09  3.000
 1JT  H14  C19  C18  111.00  3.000
 1JT  H13  C19  C18  109.38  3.000
 1JT  C20  C19  C18  110.09  3.000
 1JT  H16  C20  H15  105.66  3.000
 1JT  H16  C20  C19  110.26  3.000
 1JT  H15  C20  C19  108.72  3.000
 1JT  H16  C20  C1   109.58  3.000
 1JT  H15  C20  C1   108.62  3.000
 1JT  C19  C20  C1   113.67  3.000
 1JT  C22  O21  C14  118.80  3.000
 1JT  H19  C22  H18  108.74  3.000
 1JT  H19  C22  H17  108.71  3.000
 1JT  H18  C22  H17  108.82  3.000
 1JT  H19  C22  O21  112.05  3.000
 1JT  H18  C22  O21  111.90  3.000
 1JT  H17  C22  O21  106.51  3.000
 1JT  H22  C23  H21  107.73  3.000
 1JT  H22  C23  H20  106.87  3.000
 1JT  H21  C23  H20  107.71  3.000
 1JT  H22  C23  C13  111.68  3.000
 1JT  H21  C23  C13  110.87  3.000
 1JT  H20  C23  C13  111.77  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
 1JT  CONST_01  C5   C4   C2   C1      0.00   0.0  0
 1JT  CONST_02  C5   C6   C3   C1      0.00   0.0  0
 1JT  CONST_03  N7   C6   C3   C1    180.00   0.0  0
 1JT  CONST_04  N9   C5   C4   C2    180.00   0.0  0
 1JT  CONST_05  C6   C5   C4   C2      0.00   0.0  0
 1JT  CONST_06  C6   C3   C1   C2      0.00   0.0  0
 1JT  CONST_07  C4   C2   C1   C3      0.00   0.0  0
 1JT  CONST_08  C4   C5   C6   C3      0.00   0.0  0
 1JT  CONST_09  N9   C5   C6   C3    180.00   0.0  0
 1JT  CONST_10  C8   N7   C6   C3    180.00   0.0  0
 1JT  CONST_11  C8   N9   C5   C4    180.00   0.0  0
 1JT  CONST_12  N7   C6   C5   C4    180.00   0.0  0
 1JT  CONST_13  N7   C8   N9   C5      0.00   0.0  0
 1JT  CONST_14  C8   N7   C6   C5      0.00   0.0  0
 1JT  CONST_15  C8   N9   C5   C6      0.00   0.0  0
 1JT  CONST_16  N9   C8   N7   C6      0.00   0.0  0
 1JT  CONST_17  N9   C5   C6   N7      0.00   0.0  0
 1JT  CONST_18  C14  C13  C12  C11     0.00   0.0  0
 1JT  CONST_19  C14  C15  C16  C11     0.00   0.0  0
 1JT  CONST_20  C15  C14  C13  C12     0.00   0.0  0
 1JT  CONST_21  C15  C16  C11  C12     0.00   0.0  0
 1JT  CONST_22  C16  C15  C14  C13     0.00   0.0  0
 1JT  CONST_23  C16  C11  C12  C13     0.00   0.0  0
 1JT  CONST_24  C10  N9   C5   C4      0.00   0.0  0
 1JT  CONST_25  C10  N9   C5   C6    180.00   0.0  0
 1JT  CONST_26  C10  N9   C8   N7    180.00   0.0  0
 1JT  CONST_27  C13  C12  C11  C10   180.00   0.0  0
 1JT  CONST_28  C15  C16  C11  C10   180.00   0.0  0
 1JT  CONST_29  C23  C13  C12  C11   180.00   0.0  0
 1JT  CONST_30  O21  C14  C13  C12   180.00   0.0  0
 1JT  CONST_31  C23  C13  C14  C15   180.00   0.0  0
 1JT  CONST_32  O21  C14  C15  C16   180.00   0.0  0
 1JT  CONST_33  H2   C4   C2   C1    180.00   0.0  0
 1JT  CONST_34  H1   C3   C1   C2    180.00   0.0  0
 1JT  CONST_35  H3   C8   N9   C5    180.00   0.0  0
 1JT  CONST_36  H7   C15  C16  C11   180.00   0.0  0
 1JT  CONST_37  H8   C16  C11  C12   180.00   0.0  0
 1JT  CONST_38  H6   C12  C13  C14   180.00   0.0  0
 1JT  Var_01    C18  C17  C2   C1    -19.56  30.0  1
 1JT  Var_02    C18  C19  C20  C1     47.49  30.0  1
 1JT  Var_03    C19  C18  C17  C2     48.91  30.0  1
 1JT  Var_04    C19  C20  C1   C2    -18.08  30.0  1
 1JT  Var_05    C20  C19  C18  C17   -63.59  30.0  1
 1JT  Var_06    C11  C10  N9   C5     67.22  30.0  3
 1JT  Var_07    C12  C11  C10  N9   -119.61  30.0  2
 1JT  Var_08    H20  C23  C13  C12  -120.42  30.0  2
 1JT  Var_09    H17  C22  O21  C14  -178.98  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
 1JT  plan-1  C10  0.020
 1JT  plan-1  C11  0.020
 1JT  plan-1  C12  0.020
 1JT  plan-1  C13  0.020
 1JT  plan-1  C14  0.020
 1JT  plan-1  C15  0.020
 1JT  plan-1  C16  0.020
 1JT  plan-1  O21  0.020
 1JT  plan-1  C23  0.020
 1JT  plan-1  H6   0.020
 1JT  plan-1  H7   0.020
 1JT  plan-1  H8   0.020
 1JT  plan-2  C1   0.020
 1JT  plan-2  C2   0.020
 1JT  plan-2  C3   0.020
 1JT  plan-2  C4   0.020
 1JT  plan-2  C5   0.020
 1JT  plan-2  C6   0.020
 1JT  plan-2  N7   0.020
 1JT  plan-2  C8   0.020
 1JT  plan-2  N9   0.020
 1JT  plan-2  C10  0.020
 1JT  plan-2  C17  0.020
 1JT  plan-2  C20  0.020
 1JT  plan-2  H1   0.020
 1JT  plan-2  H2   0.020
 1JT  plan-2  H3   0.020

