# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 17:42:07 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: N-[3-(2,4-dichlorophenoxy)propyl]-1H-imidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(OCCCNc2[nH]ccn2)c(Cl)c1
#
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
 HH7  HH7  N-[3-(2,4-dichlorophenoxy)propyl]-1H-imidazol-2-amine  ligand  31  18  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HH7
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
 HH7  N11  N   NH1   0  -0.676   4.1409   0.6598   0.0576
 HH7  C02  C   CR6   0  -0.073  -4.5080  -0.8379  -0.0618
 HH7  C03  C   CR16  0  -0.163  -4.2682   0.5225   0.0635
 HH7  C04  C   CR6   0  -0.162  -2.9623   0.9715   0.1016
 HH7  CL2  CL  CL    0  -0.099  -2.6492   2.6616   0.2595
 HH7  C06  C   CR6   0   0.474  -1.8791   0.0890   0.0162
 HH7  O07  O   O2    0  -0.456  -0.6569   0.6273   0.0625
 HH7  C08  C   CH2   0  -0.178   0.4759  -0.2260  -0.0218
 HH7  C09  C   CH2   0  -0.490   1.7105   0.6466   0.0568
 HH7  C10  C   CH2   0  -0.286   2.9740  -0.1941  -0.0364
 HH7  C12  C   CR5   0   0.656   5.3961   0.1127  -0.0116
 HH7  N13  N   NR15  0  -0.638   5.6648  -1.1787   0.2812
 HH7  C14  C   CR15  0  -0.121   7.0284  -1.3534   0.1612
 HH7  C15  C   CR15  0  -0.208   7.5073  -0.1376  -0.2063
 HH7  N16  N   N     0  -0.510   6.4864   0.7754  -0.3155
 HH7  C17  C   CR16  0  -0.395  -2.1516  -1.2702  -0.1097
 HH7  C18  C   CR16  0  -0.193  -3.4592  -1.7340  -0.1484
 HH7  H1   H   HNH1  0   0.382   4.0763   1.5077  -0.4871
 HH7  H2   H   HCR6  0   0.301  -5.0846   1.2281   0.1309
 HH7  H3   H   HCH2  0   0.234   0.4667  -0.9512   0.7993
 HH7  H4   H   HCH2  0   0.234   0.4601  -0.7852  -0.9636
 HH7  H5   H   HCH2  0   0.248   1.6927   1.3747  -0.7592
 HH7  H6   H   HCH2  0   0.251   1.7139   1.2031   0.9970
 HH7  H7   H   HCH2  0   0.229   2.9647  -0.7831  -0.9633
 HH7  H8   H   HCH2  0   0.236   2.9842  -0.9059   0.7940
 HH7  H9   H   HNR5  0   0.417   5.0067  -1.8951   0.5408
 HH7  H10  H   HCR5  0   0.276   7.5017  -2.3028   0.3421
 HH7  H11  H   HCR5  0   0.243   8.5326   0.1373  -0.4005
 HH7  H13  H   HCR6  0   0.301  -1.3505  -1.9926  -0.1778
 HH7  H14  H   HCR6  0   0.289  -3.6451  -2.7946  -0.2448
 HH7  CL1  CL  CL    0  -0.125  -6.1426  -1.4095  -0.1082

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
 HH7  C15  N16  aromatic  1.374  0.020  1.374
 HH7  C15  C14  aromatic  1.357  0.020  1.357
 HH7  N16  C12  aromatic  1.312  0.020  1.312
 HH7  C14  N13  aromatic  1.380  0.020  1.380
 HH7  C12  N13  aromatic  1.351  0.020  1.351
 HH7  C12  N11  single    1.371  0.020  1.371
 HH7  N11  C10  single    1.449  0.020  1.449
 HH7  C10  C09  single    1.520  0.020  1.520
 HH7  C09  C08  single    1.514  0.020  1.514
 HH7  C08  O07  single    1.421  0.020  1.421
 HH7  O07  C06  single    1.336  0.020  1.336
 HH7  CL2  C04  single    1.726  0.020  1.726
 HH7  C06  C04  aromatic  1.400  0.020  1.400
 HH7  C06  C17  aromatic  1.392  0.020  1.392
 HH7  C04  C03  aromatic  1.381  0.020  1.381
 HH7  C17  C18  aromatic  1.388  0.020  1.388
 HH7  C03  C02  aromatic  1.387  0.020  1.387
 HH7  C18  C02  aromatic  1.382  0.020  1.382
 HH7  C02  CL1  single    1.732  0.020  1.732
 HH7  N11  H1   single    0.890  0.020  1.040
 HH7  C03  H2   single    0.930  0.020  1.080
 HH7  C08  H3   single    0.970  0.020  1.090
 HH7  C08  H4   single    0.970  0.020  1.090
 HH7  C09  H5   single    0.970  0.020  1.090
 HH7  C09  H6   single    0.970  0.020  1.090
 HH7  C10  H7   single    0.970  0.020  1.090
 HH7  C10  H8   single    0.970  0.020  1.090
 HH7  N13  H9   single    0.860  0.020  1.020
 HH7  C14  H10  single    0.930  0.020  1.080
 HH7  C15  H11  single    0.930  0.020  1.080
 HH7  C17  H13  single    0.930  0.020  1.080
 HH7  C18  H14  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
 HH7  H1   N11  C12  111.49  3.000
 HH7  H1   N11  C10  114.10  3.000
 HH7  C12  N11  C10  119.92  3.000
 HH7  C18  C02  C03  120.68  3.000
 HH7  C18  C02  CL1  120.03  3.000
 HH7  C03  C02  CL1  119.29  3.000
 HH7  H2   C03  C04  120.00  3.000
 HH7  H2   C03  C02  121.01  3.000
 HH7  C04  C03  C02  118.99  3.000
 HH7  C06  C04  CL2  118.85  3.000
 HH7  C06  C04  C03  121.67  3.000
 HH7  CL2  C04  C03  119.48  3.000
 HH7  C17  C06  O07  125.14  3.000
 HH7  C17  C06  C04  118.01  3.000
 HH7  O07  C06  C04  116.85  3.000
 HH7  C08  O07  C06  119.03  3.000
 HH7  H4   C08  H3   107.84  3.000
 HH7  H4   C08  C09  110.52  3.000
 HH7  H3   C08  C09  110.46  3.000
 HH7  H4   C08  O07  110.25  3.000
 HH7  H3   C08  O07  110.27  3.000
 HH7  C09  C08  O07  107.52  3.000
 HH7  H6   C09  H5   107.63  3.000
 HH7  H6   C09  C10  109.38  3.000
 HH7  H5   C09  C10  109.63  3.000
 HH7  H6   C09  C08  109.92  3.000
 HH7  H5   C09  C08  109.37  3.000
 HH7  C10  C09  C08  110.84  3.000
 HH7  H8   C10  H7   106.97  3.000
 HH7  H8   C10  C09  108.73  3.000
 HH7  H7   C10  C09  109.95  3.000
 HH7  H8   C10  N11  109.07  3.000
 HH7  H7   C10  N11  112.18  3.000
 HH7  C09  C10  N11  109.84  3.000
 HH7  N16  C12  N13  111.58  3.000
 HH7  N13  C12  N11  123.54  3.000
 HH7  N16  C12  N11  124.82  3.000
 HH7  H9   N13  C14  125.33  3.000
 HH7  H9   N13  C12  127.29  3.000
 HH7  C14  N13  C12  107.38  3.000
 HH7  H10  C14  C15  132.89  3.000
 HH7  H10  C14  N13  122.12  3.000
 HH7  C15  C14  N13  104.99  3.000
 HH7  H11  C15  N16  121.49  3.000
 HH7  H11  C15  C14  127.74  3.000
 HH7  N16  C15  C14  110.77  3.000
 HH7  C15  N16  C12  105.27  3.000
 HH7  H13  C17  C18  118.24  3.000
 HH7  H13  C17  C06  120.88  3.000
 HH7  C18  C17  C06  120.88  3.000
 HH7  H14  C18  C17  119.49  3.000
 HH7  H14  C18  C02  120.74  3.000
 HH7  C17  C18  C02  119.77  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
 HH7  CONST_01  C06  C04  C03  C02     0.00   0.0  0
 HH7  CONST_02  C06  C17  C18  C02     0.00   0.0  0
 HH7  CONST_03  C17  C06  C04  C03     0.00   0.0  0
 HH7  CONST_04  C17  C18  C02  C03     0.00   0.0  0
 HH7  CONST_05  C18  C17  C06  C04     0.00   0.0  0
 HH7  CONST_06  C18  C02  C03  C04     0.00   0.0  0
 HH7  CONST_07  C14  C15  N16  C12     0.00   0.0  0
 HH7  CONST_08  C15  C14  N13  C12     0.00   0.0  0
 HH7  CONST_09  N16  C15  C14  N13     0.00   0.0  0
 HH7  CONST_10  C15  N16  C12  N13     0.00   0.0  0
 HH7  CONST_11  N16  C12  N13  C14     0.00   0.0  0
 HH7  CONST_12  C15  N16  C12  N11   180.00   0.0  0
 HH7  CONST_13  C14  N13  C12  N11   180.00   0.0  0
 HH7  CONST_14  C04  C03  C02  CL1   180.00   0.0  0
 HH7  CONST_15  C17  C18  C02  CL1   180.00   0.0  0
 HH7  CONST_16  CL2  C04  C03  C02   180.00   0.0  0
 HH7  CONST_17  O07  C06  C04  C03   180.00   0.0  0
 HH7  CONST_18  C17  C06  C04  CL2   180.00   0.0  0
 HH7  CONST_19  C18  C17  C06  O07   180.00   0.0  0
 HH7  CONST_20  H13  C17  C18  C02   180.00   0.0  0
 HH7  CONST_21  H14  C18  C02  C03   180.00   0.0  0
 HH7  CONST_22  H2   C03  C04  C06   180.00   0.0  0
 HH7  CONST_23  H11  C15  N16  C12   180.00   0.0  0
 HH7  CONST_24  H10  C14  N13  C12   180.00   0.0  0
 HH7  CONST_25  H9   N13  C14  C15   180.00   0.0  0
 HH7  Var_01    C17  C06  O07  C08     0.05  30.0  2
 HH7  Var_02    C09  C08  O07  C06  -179.97  30.0  1
 HH7  Var_03    C12  N11  C10  C09  -179.59  30.0  2
 HH7  Var_04    C08  C09  C10  N11  -179.30  30.0  3
 HH7  Var_05    C10  C09  C08  O07  -179.61  30.0  1

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
 HH7  plan-1  N11  0.020
 HH7  plan-1  C12  0.020
 HH7  plan-1  N13  0.020
 HH7  plan-1  C14  0.020
 HH7  plan-1  C15  0.020
 HH7  plan-1  N16  0.020
 HH7  plan-1  H9   0.020
 HH7  plan-1  H10  0.020
 HH7  plan-1  H11  0.020
 HH7  plan-2  C02  0.020
 HH7  plan-2  C03  0.020
 HH7  plan-2  C04  0.020
 HH7  plan-2  CL2  0.020
 HH7  plan-2  C06  0.020
 HH7  plan-2  O07  0.020
 HH7  plan-2  C17  0.020
 HH7  plan-2  C18  0.020
 HH7  plan-2  H2   0.020
 HH7  plan-2  H13  0.020
 HH7  plan-2  H14  0.020
 HH7  plan-2  CL1  0.020
 HH7  plan-3  N11  0.020
 HH7  plan-3  C10  0.020
 HH7  plan-3  C12  0.020
 HH7  plan-3  H1   0.020

