# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 17:55:50 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: (3-chloranyl-4-phenyl-phenyl)methyl-[2-(1~{H}-imidazol-4-yl)ethyl]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(C[NH2+]CCc2c[nH]cn2)ccc1c3ccccc3
#
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
 AVZ  AVZ  (3-chloranyl-4-phenyl-phenyl)methyl-[2-(1~{H}-imidazol-4-yl)ethyl]azanium  ligand  41  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AVZ
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
 AVZ  N1   N   N     0  -0.458  -6.4447  -0.9876  -0.3379
 AVZ  C2   C   CR6   0   0.057   0.0894   0.0197   1.0096
 AVZ  C4   C   CH2   0  -0.283  -3.6715   0.1113   0.4172
 AVZ  C5   C   CH2   0  -0.557  -4.4726   0.4671  -0.8252
 AVZ  C6   C   CR5   0   0.142  -5.9283   0.2553  -0.5838
 AVZ  C    C   CR6   0  -0.108   2.1031  -0.9120   0.0863
 AVZ  C11  C   CR6   0   0.154   2.8120   0.2628   0.3409
 AVZ  C12  C   CR6   0   0.060   4.2428   0.4373   0.0108
 AVZ  C17  C   CR16  0  -0.282   5.2156  -0.4122   0.5362
 AVZ  C16  C   CR16  0  -0.243   6.5562  -0.2092   0.2454
 AVZ  C15  C   CR16  0  -0.260   6.9427   0.8425  -0.5762
 AVZ  C14  C   CR16  0  -0.242   5.9806   1.6948  -1.1000
 AVZ  C13  C   CR16  0  -0.290   4.6388   1.4952  -0.8053
 AVZ  C10  C   CR16  0  -0.296   2.1111   1.3153   0.9300
 AVZ  C9   C   CR16  0  -0.257   0.7715   1.2040   1.2605
 AVZ  C1   C   CR16  0  -0.219   0.7636  -1.0398   0.4164
 AVZ  C3   C   CH2   0  -0.381  -1.3645  -0.1153   1.3427
 AVZ  N    N   NT2   1  -0.664  -2.2101   0.2346   0.1622
 AVZ  C8   C   CR15  0  -0.121  -6.9256   1.1894  -0.5465
 AVZ  N2   N   NR15  0  -0.561  -8.0652   0.4903  -0.2769
 AVZ  C7   C   CR15  0   0.089  -7.7285  -0.8073  -0.1585
 AVZ  H2   H   HCH2  0   0.300  -3.9067   0.7757   1.2465
 AVZ  H3   H   HCH2  0   0.298  -3.8535  -0.9166   0.7254
 AVZ  H4   H   HCH2  0   0.272  -4.2930   1.5086  -1.0994
 AVZ  H5   H   HCH2  0   0.268  -4.1372  -0.1499  -1.6642
 AVZ  H6   H   HCR6  0   0.257   4.9287  -1.2287   1.1862
 AVZ  H7   H   HCR6  0   0.260   7.3009  -0.8736   0.6639
 AVZ  H8   H   HCR6  0   0.260   7.9890   0.9976  -0.8050
 AVZ  H9   H   HCR6  0   0.260   6.2720   2.5174  -1.7400
 AVZ  H10  H   HCR6  0   0.258   3.8929   2.1605  -1.2225
 AVZ  H11  H   HCR6  0   0.272   2.6378   2.2357   1.1470
 AVZ  H12  H   HCR6  0   0.272   0.2622   2.0384   1.7258
 AVZ  H13  H   HCR6  0   0.288   0.2448  -1.9672   0.2081
 AVZ  H14  H   HCH2  0   0.321  -1.6236  -1.1350   1.6207
 AVZ  H15  H   HCH2  0   0.321  -1.6590   0.5526   2.1499
 AVZ  H16  H   HNT2  0   0.469  -1.9527  -0.3629  -0.6263
 AVZ  H17  H   HNT2  0   0.471  -1.9952   1.1882  -0.1357
 AVZ  H18  H   HCR5  0   0.287  -6.9174   2.2572  -0.6857
 AVZ  H19  H   HNR5  0   0.422  -8.9923   0.8743  -0.1852
 AVZ  H20  H   HCR5  0   0.279  -8.4543  -1.5763   0.0565
 AVZ  CL   CL  CL    0  -0.116   2.8704  -2.2528  -0.6971

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
 AVZ  CL   C    single    1.732  0.020  1.732
 AVZ  C16  C17  aromatic  1.387  0.020  1.387
 AVZ  C16  C15  aromatic  1.389  0.020  1.389
 AVZ  C17  C12  aromatic  1.394  0.020  1.394
 AVZ  C15  C14  aromatic  1.388  0.020  1.388
 AVZ  C    C1   aromatic  1.385  0.020  1.385
 AVZ  C    C11  aromatic  1.396  0.020  1.396
 AVZ  C12  C11  single    1.479  0.020  1.479
 AVZ  C12  C13  aromatic  1.394  0.020  1.394
 AVZ  C1   C2   aromatic  1.389  0.020  1.389
 AVZ  C11  C10  aromatic  1.395  0.020  1.395
 AVZ  C14  C13  aromatic  1.388  0.020  1.388
 AVZ  C2   C3   single    1.498  0.020  1.498
 AVZ  C2   C9   aromatic  1.389  0.020  1.389
 AVZ  C3   N    single    1.494  0.020  1.494
 AVZ  C10  C9   aromatic  1.384  0.020  1.384
 AVZ  N    C4   single    1.489  0.020  1.489
 AVZ  C4   C5   single    1.521  0.020  1.521
 AVZ  C5   C6   single    1.491  0.020  1.491
 AVZ  C8   C6   aromatic  1.367  0.020  1.367
 AVZ  C8   N2   aromatic  1.364  0.020  1.364
 AVZ  C6   N1   aromatic  1.368  0.020  1.368
 AVZ  N2   C7   aromatic  1.346  0.020  1.346
 AVZ  N1   C7   aromatic  1.309  0.020  1.309
 AVZ  C4   H2   single    0.970  0.020  1.090
 AVZ  C4   H3   single    0.970  0.020  1.090
 AVZ  C5   H4   single    0.970  0.020  1.090
 AVZ  C5   H5   single    0.970  0.020  1.090
 AVZ  C17  H6   single    0.930  0.020  1.080
 AVZ  C16  H7   single    0.930  0.020  1.080
 AVZ  C15  H8   single    0.930  0.020  1.080
 AVZ  C14  H9   single    0.930  0.020  1.080
 AVZ  C13  H10  single    0.930  0.020  1.080
 AVZ  C10  H11  single    0.930  0.020  1.080
 AVZ  C9   H12  single    0.930  0.020  1.080
 AVZ  C1   H13  single    0.930  0.020  1.080
 AVZ  C3   H14  single    0.970  0.020  1.090
 AVZ  C3   H15  single    0.970  0.020  1.090
 AVZ  N    H16  single    0.890  0.020  1.040
 AVZ  N    H17  single    0.890  0.020  1.040
 AVZ  C8   H18  single    0.930  0.020  1.080
 AVZ  N2   H19  single    0.860  0.020  1.020
 AVZ  C7   H20  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
 AVZ  C7   N1   C6   105.64  3.000
 AVZ  C3   C2   C1   119.83  3.000
 AVZ  C3   C2   C9   120.88  3.000
 AVZ  C1   C2   C9   119.28  3.000
 AVZ  H3   C4   H2   108.94  3.000
 AVZ  H3   C4   N    106.91  3.000
 AVZ  H2   C4   N    106.99  3.000
 AVZ  H3   C4   C5   111.37  3.000
 AVZ  H2   C4   C5   111.46  3.000
 AVZ  N    C4   C5   110.97  3.000
 AVZ  H5   C5   H4   107.16  3.000
 AVZ  H5   C5   C6   110.08  3.000
 AVZ  H4   C5   C6   109.68  3.000
 AVZ  H5   C5   C4   109.45  3.000
 AVZ  H4   C5   C4   109.99  3.000
 AVZ  C6   C5   C4   110.42  3.000
 AVZ  C8   C6   C5   128.30  3.000
 AVZ  C8   C6   N1   109.91  3.000
 AVZ  C5   C6   N1   121.78  3.000
 AVZ  C1   C    C11  121.69  3.000
 AVZ  C11  C    CL   120.60  3.000
 AVZ  C1   C    CL   117.69  3.000
 AVZ  C10  C11  C12  119.43  3.000
 AVZ  C10  C11  C    117.19  3.000
 AVZ  C12  C11  C    123.38  3.000
 AVZ  C13  C12  C17  119.01  3.000
 AVZ  C13  C12  C11  119.69  3.000
 AVZ  C17  C12  C11  121.27  3.000
 AVZ  H6   C17  C16  119.52  3.000
 AVZ  H6   C17  C12  120.06  3.000
 AVZ  C16  C17  C12  120.41  3.000
 AVZ  H7   C16  C15  120.13  3.000
 AVZ  H7   C16  C17  119.62  3.000
 AVZ  C15  C16  C17  120.25  3.000
 AVZ  H8   C15  C14  120.16  3.000
 AVZ  H8   C15  C16  120.16  3.000
 AVZ  C14  C15  C16  119.68  3.000
 AVZ  H9   C14  C13  119.67  3.000
 AVZ  H9   C14  C15  120.22  3.000
 AVZ  C13  C14  C15  120.10  3.000
 AVZ  H10  C13  C14  119.70  3.000
 AVZ  H10  C13  C12  119.75  3.000
 AVZ  C14  C13  C12  120.54  3.000
 AVZ  H11  C10  C9   119.44  3.000
 AVZ  H11  C10  C11  118.80  3.000
 AVZ  C9   C10  C11  121.76  3.000
 AVZ  H12  C9   C10  119.72  3.000
 AVZ  H12  C9   C2   120.24  3.000
 AVZ  C10  C9   C2   120.03  3.000
 AVZ  H13  C1   C    119.77  3.000
 AVZ  H13  C1   C2   120.19  3.000
 AVZ  C    C1   C2   120.04  3.000
 AVZ  H15  C3   H14  108.74  3.000
 AVZ  H15  C3   N    106.81  3.000
 AVZ  H14  C3   N    106.65  3.000
 AVZ  H15  C3   C2   111.86  3.000
 AVZ  H14  C3   C2   111.87  3.000
 AVZ  N    C3   C2   110.65  3.000
 AVZ  H17  N    H16  105.52  3.000
 AVZ  H17  N    C3   109.26  3.000
 AVZ  H16  N    C3   109.28  3.000
 AVZ  H17  N    C4   109.49  3.000
 AVZ  H16  N    C4   109.33  3.000
 AVZ  C3   N    C4   113.64  3.000
 AVZ  H18  C8   N2   122.69  3.000
 AVZ  H18  C8   C6   131.96  3.000
 AVZ  N2   C8   C6   105.35  3.000
 AVZ  H19  N2   C7   126.13  3.000
 AVZ  H19  N2   C8   126.26  3.000
 AVZ  C7   N2   C8   107.61  3.000
 AVZ  H20  C7   N2   122.44  3.000
 AVZ  H20  C7   N1   126.08  3.000
 AVZ  N2   C7   N1   111.48  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
 AVZ  CONST_01  N2   C8   C6   N1      0.00   0.0  0
 AVZ  CONST_02  C8   N2   C7   N1      0.00   0.0  0
 AVZ  CONST_03  C11  C    C1   C2      0.00   0.0  0
 AVZ  CONST_04  C11  C10  C9   C2      0.00   0.0  0
 AVZ  CONST_05  C7   N2   C8   C6      0.00   0.0  0
 AVZ  CONST_06  N2   C7   N1   C6      0.00   0.0  0
 AVZ  CONST_07  C9   C2   C1   C       0.00   0.0  0
 AVZ  CONST_10  C9   C10  C11  C       0.00   0.0  0
 AVZ  CONST_11  C16  C17  C12  C11   180.00   0.0  0
 AVZ  CONST_12  C14  C13  C12  C11   180.00   0.0  0
 AVZ  CONST_13  C15  C16  C17  C12     0.00   0.0  0
 AVZ  CONST_14  C1   C    C11  C12   180.00   0.0  0
 AVZ  CONST_15  C9   C10  C11  C12   180.00   0.0  0
 AVZ  CONST_16  C15  C14  C13  C12     0.00   0.0  0
 AVZ  CONST_17  C14  C15  C16  C17     0.00   0.0  0
 AVZ  CONST_19  C14  C13  C12  C17     0.00   0.0  0
 AVZ  CONST_20  C13  C12  C17  C16     0.00   0.0  0
 AVZ  CONST_21  C13  C14  C15  C16     0.00   0.0  0
 AVZ  CONST_23  C1   C    C11  C10     0.00   0.0  0
 AVZ  CONST_24  C1   C2   C9   C10     0.00   0.0  0
 AVZ  CONST_25  C7   N1   C6   C8      0.00   0.0  0
 AVZ  CONST_26  CL   C    C1   C2    180.00   0.0  0
 AVZ  CONST_27  N2   C8   C6   C5    180.00   0.0  0
 AVZ  CONST_28  C7   N1   C6   C5    180.00   0.0  0
 AVZ  CONST_29  C12  C11  C    CL      0.00   0.0  0
 AVZ  CONST_30  C10  C11  C    CL    180.00   0.0  0
 AVZ  CONST_31  C3   C2   C1   C     180.00   0.0  0
 AVZ  CONST_32  C3   C2   C9   C10   180.00   0.0  0
 AVZ  CONST_33  H18  C8   C6   N1    180.00   0.0  0
 AVZ  CONST_34  H19  N2   C7   N1    180.00   0.0  0
 AVZ  CONST_35  H11  C10  C9   C2    180.00   0.0  0
 AVZ  CONST_36  H20  C7   N1   C6    180.00   0.0  0
 AVZ  CONST_37  H13  C1   C    C11   180.00   0.0  0
 AVZ  CONST_38  H6   C17  C12  C11     0.00   0.0  0
 AVZ  CONST_39  H10  C13  C12  C11     0.00   0.0  0
 AVZ  CONST_40  H12  C9   C10  C11   180.00   0.0  0
 AVZ  CONST_41  H7   C16  C17  C12   180.00   0.0  0
 AVZ  CONST_42  H9   C14  C13  C12   180.00   0.0  0
 AVZ  CONST_43  H8   C15  C16  C17   180.00   0.0  0
 AVZ  Var_01    C4   C5   C6   N1    -64.38  30.0  1
 AVZ  Var_02    N    C3   C2   C9     92.85  30.0  2
 AVZ  Var_03    C4   N    C3   C2    179.50  30.0  3
 AVZ  Var_04    N    C4   C5   C6    176.36  30.0  1
 AVZ  Var_05    C3   N    C4   C5   -179.43  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
 AVZ  plan-1  N1   0.020
 AVZ  plan-1  C5   0.020
 AVZ  plan-1  C6   0.020
 AVZ  plan-1  C8   0.020
 AVZ  plan-1  N2   0.020
 AVZ  plan-1  C7   0.020
 AVZ  plan-1  H18  0.020
 AVZ  plan-1  H19  0.020
 AVZ  plan-1  H20  0.020
 AVZ  plan-2  C2   0.020
 AVZ  plan-2  C    0.020
 AVZ  plan-2  C11  0.020
 AVZ  plan-2  C12  0.020
 AVZ  plan-2  C10  0.020
 AVZ  plan-2  C9   0.020
 AVZ  plan-2  C1   0.020
 AVZ  plan-2  C3   0.020
 AVZ  plan-2  H11  0.020
 AVZ  plan-2  H12  0.020
 AVZ  plan-2  H13  0.020
 AVZ  plan-2  CL   0.020
 AVZ  plan-3  C11  0.020
 AVZ  plan-3  C12  0.020
 AVZ  plan-3  C17  0.020
 AVZ  plan-3  C16  0.020
 AVZ  plan-3  C15  0.020
 AVZ  plan-3  C14  0.020
 AVZ  plan-3  C13  0.020
 AVZ  plan-3  H6   0.020
 AVZ  plan-3  H7   0.020
 AVZ  plan-3  H8   0.020
 AVZ  plan-3  H9   0.020
 AVZ  plan-3  H10  0.020

