# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 11:22:26 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: (5S)-5-benzyl-4,5-dihydro-1H-imidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC[C@H](Cc2ccccc2)N1
#
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
 KJ7  KJ7  (5S)-5-benzyl-4,5-dihydro-1H-imidazol-2-amine  ligand  26  13  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KJ7
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
 KJ7  C02  C  CR5   0   0.585  -2.5482  -0.5604   0.1238
 KJ7  C04  C  CH2   0  -0.317  -2.4014   1.6105  -0.0888
 KJ7  C05  C  CR15  0  -0.115  -1.0173   1.0959   0.3576
 KJ7  C06  C  CH2   0  -0.528  -0.0038   1.0999  -0.7954
 KJ7  C07  C  CR6   0   0.124   1.2809   0.4114  -0.4353
 KJ7  C08  C  CR16  0  -0.301   2.2604   1.0755   0.3034
 KJ7  C09  C  CR16  0  -0.240   3.4234   0.4262   0.6905
 KJ7  C10  C  CR16  0  -0.271   3.6273  -0.9056   0.3481
 KJ7  C11  C  CR16  0  -0.241   2.6618  -1.5778  -0.3877
 KJ7  C12  C  CR16  0  -0.326   1.4990  -0.9225  -0.7754
 KJ7  N01  N  NH2   0  -0.841  -2.9286  -1.8656   0.0473
 KJ7  N03  N  N     0  -0.503  -3.1856   0.4237  -0.3950
 KJ7  N13  N  NR15  0  -0.645  -1.3802  -0.2469   0.7910
 KJ7  H1   H  HCH2  0   0.222  -2.8750   2.1868   0.7147
 KJ7  H2   H  HCH2  0   0.220  -2.3231   2.2806  -0.9492
 KJ7  H3   H  HCR5  0   0.249  -0.6148   1.6740   1.1923
 KJ7  H4   H  HCH2  0   0.250  -0.4569   0.6234  -1.6697
 KJ7  H5   H  HCH2  0   0.256   0.1883   2.1411  -1.0667
 KJ7  H6   H  HCR6  0   0.248   2.1117   2.1143   0.5760
 KJ7  H7   H  HCR6  0   0.255   4.1733   0.9599   1.2603
 KJ7  H8   H  HCR6  0   0.255   4.5343  -1.4129   0.6508
 KJ7  H9   H  HCR6  0   0.255   2.8136  -2.6130  -0.6649
 KJ7  H10  H  HCR6  0   0.254   0.7564  -1.4535  -1.3604
 KJ7  H11  H  HNH2  0   0.390  -2.6038  -2.4760   0.7798
 KJ7  H12  H  HNH2  0   0.386  -3.8972  -2.0132  -0.1861
 KJ7  H13  H  HNR5  0   0.380  -0.6491  -0.9446   0.8196

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
 KJ7  N03  C04  single    1.455  0.020  1.455
 KJ7  N03  C02  double    1.282  0.020  1.282
 KJ7  C04  C05  single    1.543  0.020  1.543
 KJ7  C06  C05  single    1.535  0.020  1.535
 KJ7  C06  C07  single    1.501  0.020  1.501
 KJ7  C02  N01  single    1.362  0.020  1.362
 KJ7  C02  N13  single    1.381  0.020  1.381
 KJ7  C05  N13  single    1.457  0.020  1.457
 KJ7  C08  C07  aromatic  1.395  0.020  1.395
 KJ7  C08  C09  aromatic  1.387  0.020  1.387
 KJ7  C07  C12  aromatic  1.394  0.020  1.394
 KJ7  C09  C10  aromatic  1.390  0.020  1.390
 KJ7  C12  C11  aromatic  1.390  0.020  1.390
 KJ7  C10  C11  aromatic  1.388  0.020  1.388
 KJ7  C04  H1   single    0.970  0.020  1.090
 KJ7  C04  H2   single    0.970  0.020  1.090
 KJ7  C05  H3   single    0.970  0.020  1.090
 KJ7  C06  H4   single    0.970  0.020  1.090
 KJ7  C06  H5   single    0.970  0.020  1.090
 KJ7  C08  H6   single    0.930  0.020  1.080
 KJ7  C09  H7   single    0.930  0.020  1.080
 KJ7  C10  H8   single    0.930  0.020  1.080
 KJ7  C11  H9   single    0.930  0.020  1.080
 KJ7  C12  H10  single    0.930  0.020  1.080
 KJ7  N01  H11  single    0.890  0.020  1.040
 KJ7  N01  H12  single    0.890  0.020  1.040
 KJ7  N13  H13  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
 KJ7  N13  C02  N03  116.21  3.000
 KJ7  N13  C02  N01  118.75  3.000
 KJ7  N03  C02  N01  125.04  3.000
 KJ7  H2   C04  H1   106.59  3.000
 KJ7  H2   C04  N03  111.90  3.000
 KJ7  H1   C04  N03  110.50  3.000
 KJ7  H2   C04  C05  111.58  3.000
 KJ7  H1   C04  C05  110.54  3.000
 KJ7  N03  C04  C05  105.80  3.000
 KJ7  H3   C05  N13  110.62  3.000
 KJ7  H3   C05  C06  109.23  3.000
 KJ7  N13  C05  C06  112.97  3.000
 KJ7  H3   C05  C04  112.04  3.000
 KJ7  N13  C05  C04   99.79  3.000
 KJ7  C06  C05  C04  111.97  3.000
 KJ7  H5   C06  H4   106.82  3.000
 KJ7  H5   C06  C07  110.25  3.000
 KJ7  H4   C06  C07  110.27  3.000
 KJ7  H5   C06  C05  107.75  3.000
 KJ7  H4   C06  C05  109.01  3.000
 KJ7  C07  C06  C05  112.56  3.000
 KJ7  C12  C07  C08  118.36  3.000
 KJ7  C12  C07  C06  120.94  3.000
 KJ7  C08  C07  C06  120.63  3.000
 KJ7  H6   C08  C09  119.56  3.000
 KJ7  H6   C08  C07  119.53  3.000
 KJ7  C09  C08  C07  120.91  3.000
 KJ7  H7   C09  C10  120.02  3.000
 KJ7  H7   C09  C08  119.80  3.000
 KJ7  C10  C09  C08  120.18  3.000
 KJ7  H8   C10  C11  120.29  3.000
 KJ7  H8   C10  C09  120.20  3.000
 KJ7  C11  C10  C09  119.51  3.000
 KJ7  H9   C11  C12  119.79  3.000
 KJ7  H9   C11  C10  120.11  3.000
 KJ7  C12  C11  C10  120.11  3.000
 KJ7  H10  C12  C11  119.51  3.000
 KJ7  H10  C12  C07  119.55  3.000
 KJ7  C11  C12  C07  120.93  3.000
 KJ7  H12  N01  H11  112.94  3.000
 KJ7  H12  N01  C02  114.97  3.000
 KJ7  H11  N01  C02  116.74  3.000
 KJ7  C04  N03  C02  105.84  3.000
 KJ7  H13  N13  C05  117.66  3.000
 KJ7  H13  N13  C02  117.94  3.000
 KJ7  C05  N13  C02  106.03  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
 KJ7  CONST_01  C10  C09  C08  C07     0.00   0.0  0
 KJ7  CONST_02  C10  C11  C12  C07     0.00   0.0  0
 KJ7  CONST_03  C11  C12  C07  C08     0.00   0.0  0
 KJ7  CONST_04  C11  C10  C09  C08     0.00   0.0  0
 KJ7  CONST_05  C12  C07  C08  C09     0.00   0.0  0
 KJ7  CONST_06  C12  C11  C10  C09     0.00   0.0  0
 KJ7  CONST_08  N13  C02  N03  C04     0.00   0.0  0
 KJ7  CONST_10  C09  C08  C07  C06   180.00   0.0  0
 KJ7  CONST_11  C11  C12  C07  C06   180.00   0.0  0
 KJ7  CONST_12  N01  C02  N03  C04   180.00   0.0  0
 KJ7  CONST_14  H7   C09  C08  C07   180.00   0.0  0
 KJ7  CONST_15  H9   C11  C12  C07   180.00   0.0  0
 KJ7  CONST_16  H10  C12  C07  C08   180.00   0.0  0
 KJ7  CONST_17  H8   C10  C09  C08   180.00   0.0  0
 KJ7  CONST_18  H6   C08  C09  C10   180.00   0.0  0
 KJ7  Var_01    C08  C07  C06  C05   -80.71  30.0  2
 KJ7  Var_02    H1   C04  N03  C02  -104.53  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 KJ7  chir_01  C05  C04  C06  N13  positiv

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
 KJ7  plan-1  C06  0.020
 KJ7  plan-1  C07  0.020
 KJ7  plan-1  C08  0.020
 KJ7  plan-1  C09  0.020
 KJ7  plan-1  C10  0.020
 KJ7  plan-1  C11  0.020
 KJ7  plan-1  C12  0.020
 KJ7  plan-1  H6   0.020
 KJ7  plan-1  H7   0.020
 KJ7  plan-1  H8   0.020
 KJ7  plan-1  H9   0.020
 KJ7  plan-1  H10  0.020
 KJ7  plan-2  C02  0.020
 KJ7  plan-2  C04  0.020
 KJ7  plan-2  C05  0.020
 KJ7  plan-2  N01  0.020
 KJ7  plan-2  N03  0.020
 KJ7  plan-2  N13  0.020
 KJ7  plan-2  H11  0.020
 KJ7  plan-2  H12  0.020
 KJ7  plan-2  H13  0.020

