# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 17:10:00 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: ~{N}-[(3-chloranyl-4-phenyl-phenyl)methyl]-2-(1~{H}-imidazol-2-yl)ethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(CNCCc2[nH]ccn2)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
 AVK  AVK  ~{N}-[(3-chloranyl-4-phenyl-phenyl)methyl]-2-(1~{H}-imidazol-2-yl)ethanamine  ligand  40  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 PERFECT
;

data_comp_AVK
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
 AVK  CL   CL  CL    0  -0.131  -2.5515  -1.8273   1.2995
 AVK  C    C   CR6   0  -0.107  -1.9279  -0.6612   0.1741
 AVK  C11  C   CR6   0   0.138  -2.7575   0.3444  -0.3256
 AVK  C12  C   CR6   0   0.061  -4.1895   0.4664   0.0251
 AVK  C17  C   CR16  0  -0.283  -5.0968  -0.5479  -0.2792
 AVK  C16  C   CR16  0  -0.243  -6.4430  -0.3998   0.0199
 AVK  C15  C   CR16  0  -0.263  -6.9000   0.7607   0.6326
 AVK  C14  C   CR16  0  -0.242  -6.0039   1.7758   0.9373
 AVK  C13  C   CR16  0  -0.292  -4.6572   1.6300   0.6323
 AVK  C10  C   CR16  0  -0.295  -2.1758   1.2720  -1.1865
 AVK  C9   C   CR16  0  -0.287  -0.8377   1.1949  -1.5435
 AVK  C2   C   CR6   0   0.077  -0.0312   0.1801  -1.0461
 AVK  C1   C   CR16  0  -0.225  -0.5899  -0.7445  -0.1689
 AVK  C3   C   CH2   0  -0.330   1.4256   0.0829  -1.4073
 AVK  N    N   NH1   0  -0.595   2.2557   0.2451  -0.2280
 AVK  C4   C   CH2   0  -0.250   3.6679   0.0843  -0.5111
 AVK  C5   C   CH2   0  -0.551   4.4880   0.2590   0.7615
 AVK  C6   C   CR5   0   0.464   5.9421   0.0333   0.5256
 AVK  N2   N   NR15  0  -0.606   6.9037   0.8717   0.9677
 AVK  C8   C   CR15  0  -0.113   8.1161   0.3656   0.5940
 AVK  C7   C   CR15  0  -0.224   7.8241  -0.7855  -0.0774
 AVK  N1   N   N     0  -0.463   6.4715  -0.9826  -0.1138
 AVK  H1   H   HCR6  0   0.254  -4.7534  -1.4511  -0.7674
 AVK  H2   H   HCR6  0   0.258  -7.1380  -1.1909  -0.2301
 AVK  H3   H   HCR6  0   0.258  -7.9504   0.8735   0.8680
 AVK  H4   H   HCR6  0   0.258  -6.3512   2.6829   1.4142
 AVK  H5   H   HCR6  0   0.255  -3.9610   2.4236   0.8744
 AVK  H6   H   HCR6  0   0.261  -2.7919   2.0648  -1.5917
 AVK  H7   H   HCR6  0   0.257  -0.4211   1.9326  -2.2182
 AVK  H8   H   HCR6  0   0.270   0.0258  -1.5300   0.2502
 AVK  H9   H   HCH2  0   0.243   1.6308  -0.9055  -1.8290
 AVK  H10  H   HCH2  0   0.220   1.6526   0.8103  -2.2005
 AVK  H11  H   HNH1  0   0.344   2.0954   1.1708   0.1534
 AVK  H13  H   HCH2  0   0.229   3.8283  -0.9219  -0.9058
 AVK  H14  H   HCH2  0   0.202   4.0350   0.7815  -1.2799
 AVK  H15  H   HCH2  0   0.253   4.3368   1.2642   1.1635
 AVK  H16  H   HCH2  0   0.258   4.1211  -0.4373   1.5211
 AVK  H17  H   HNR5  0   0.415   6.7551   1.7240   1.4847
 AVK  H18  H   HCR5  0   0.281   9.0451   0.8568   0.8270
 AVK  H19  H   HCR5  0   0.245   8.5140  -1.4781  -0.5347

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
 AVK  C14  C13  aromatic  1.389  0.020  1.389
 AVK  C14  C15  aromatic  1.388  0.020  1.388
 AVK  C13  C12  aromatic  1.393  0.020  1.393
 AVK  C15  C16  aromatic  1.390  0.020  1.390
 AVK  C12  C17  aromatic  1.394  0.020  1.394
 AVK  C12  C11  single    1.479  0.020  1.479
 AVK  C16  C17  aromatic  1.387  0.020  1.387
 AVK  C11  C10  aromatic  1.393  0.020  1.393
 AVK  C11  C    aromatic  1.396  0.020  1.396
 AVK  C10  C9   aromatic  1.387  0.020  1.387
 AVK  C    CL   single    1.736  0.020  1.736
 AVK  C    C1   aromatic  1.384  0.020  1.384
 AVK  C9   C2   aromatic  1.388  0.020  1.388
 AVK  C1   C2   aromatic  1.392  0.020  1.392
 AVK  C2   C3   single    1.504  0.020  1.504
 AVK  C3   N    single    1.451  0.020  1.451
 AVK  N    C4   single    1.449  0.020  1.449
 AVK  C4   C5   single    1.524  0.020  1.524
 AVK  N2   C6   aromatic  1.350  0.020  1.350
 AVK  N2   C8   aromatic  1.366  0.020  1.366
 AVK  C5   C6   single    1.490  0.020  1.490
 AVK  C6   N1   aromatic  1.312  0.020  1.312
 AVK  C8   C7   aromatic  1.364  0.020  1.364
 AVK  N1   C7   aromatic  1.367  0.020  1.367
 AVK  C17  H1   single    0.930  0.020  1.080
 AVK  C16  H2   single    0.930  0.020  1.080
 AVK  C15  H3   single    0.930  0.020  1.080
 AVK  C14  H4   single    0.930  0.020  1.080
 AVK  C13  H5   single    0.930  0.020  1.080
 AVK  C10  H6   single    0.930  0.020  1.080
 AVK  C9   H7   single    0.930  0.020  1.080
 AVK  C1   H8   single    0.930  0.020  1.080
 AVK  C3   H9   single    0.970  0.020  1.090
 AVK  C3   H10  single    0.970  0.020  1.090
 AVK  N    H11  single    0.890  0.020  1.040
 AVK  C4   H13  single    0.970  0.020  1.090
 AVK  C4   H14  single    0.970  0.020  1.090
 AVK  C5   H15  single    0.970  0.020  1.090
 AVK  C5   H16  single    0.970  0.020  1.090
 AVK  N2   H17  single    0.860  0.020  1.020
 AVK  C8   H18  single    0.930  0.020  1.080
 AVK  C7   H19  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
 AVK  C1   C    C11  121.95  3.000
 AVK  C1   C    CL   117.87  3.000
 AVK  C11  C    CL   120.15  3.000
 AVK  C10  C11  C12  119.73  3.000
 AVK  C10  C11  C    116.92  3.000
 AVK  C12  C11  C    123.35  3.000
 AVK  C13  C12  C17  118.96  3.000
 AVK  C17  C12  C11  121.21  3.000
 AVK  C13  C12  C11  119.80  3.000
 AVK  H1   C17  C16  119.62  3.000
 AVK  H1   C17  C12  119.92  3.000
 AVK  C16  C17  C12  120.45  3.000
 AVK  H2   C16  C15  120.07  3.000
 AVK  H2   C16  C17  119.69  3.000
 AVK  C15  C16  C17  120.23  3.000
 AVK  H3   C15  C14  120.18  3.000
 AVK  H3   C15  C16  120.14  3.000
 AVK  C14  C15  C16  119.69  3.000
 AVK  H4   C14  C13  119.74  3.000
 AVK  H4   C14  C15  120.17  3.000
 AVK  C13  C14  C15  120.08  3.000
 AVK  H5   C13  C14  119.83  3.000
 AVK  H5   C13  C12  119.58  3.000
 AVK  C14  C13  C12  120.59  3.000
 AVK  H6   C10  C9   119.56  3.000
 AVK  H6   C10  C11  118.77  3.000
 AVK  C9   C10  C11  121.66  3.000
 AVK  H7   C9   C2   119.84  3.000
 AVK  H7   C9   C10  119.57  3.000
 AVK  C2   C9   C10  120.58  3.000
 AVK  C3   C2   C1   119.82  3.000
 AVK  C3   C2   C9   121.59  3.000
 AVK  C1   C2   C9   118.57  3.000
 AVK  H8   C1   C2   119.86  3.000
 AVK  H8   C1   C    119.84  3.000
 AVK  C2   C1   C    120.30  3.000
 AVK  H10  C3   H9   106.31  3.000
 AVK  H10  C3   N    113.21  3.000
 AVK  H9   C3   N    107.87  3.000
 AVK  H10  C3   C2   109.29  3.000
 AVK  H9   C3   C2   109.43  3.000
 AVK  N    C3   C2   110.59  3.000
 AVK  H11  N    C4   109.20  3.000
 AVK  H11  N    C3   108.50  3.000
 AVK  C4   N    C3   112.72  3.000
 AVK  H14  C4   H13  106.38  3.000
 AVK  H14  C4   C5   109.33  3.000
 AVK  H13  C4   C5   109.16  3.000
 AVK  H14  C4   N    113.02  3.000
 AVK  H13  C4   N    108.41  3.000
 AVK  C5   C4   N    110.40  3.000
 AVK  H16  C5   H15  106.48  3.000
 AVK  H16  C5   C6   109.93  3.000
 AVK  H15  C5   C6   109.42  3.000
 AVK  H16  C5   C4   109.05  3.000
 AVK  H15  C5   C4   109.76  3.000
 AVK  C6   C5   C4   112.06  3.000
 AVK  N1   C6   N2   110.67  3.000
 AVK  N1   C6   C5   126.02  3.000
 AVK  N2   C6   C5   123.30  3.000
 AVK  H17  N2   C8   125.77  3.000
 AVK  H17  N2   C6   126.02  3.000
 AVK  C8   N2   C6   108.21  3.000
 AVK  H18  C8   C7   132.55  3.000
 AVK  H18  C8   N2   122.53  3.000
 AVK  C7   C8   N2   104.91  3.000
 AVK  H19  C7   N1   121.91  3.000
 AVK  H19  C7   C8   127.83  3.000
 AVK  N1   C7   C8   110.27  3.000
 AVK  C7   N1   C6   105.94  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
 AVK  CONST_03  C9   C10  C11  C       0.00   0.0  0
 AVK  CONST_04  C9   C2   C1   C       0.00   0.0  0
 AVK  CONST_05  C14  C13  C12  C11   180.00   0.0  0
 AVK  CONST_06  C16  C17  C12  C11   180.00   0.0  0
 AVK  CONST_07  C2   C9   C10  C11     0.00   0.0  0
 AVK  CONST_08  C2   C1   C    C11     0.00   0.0  0
 AVK  CONST_09  C15  C14  C13  C12     0.00   0.0  0
 AVK  CONST_10  C15  C16  C17  C12     0.00   0.0  0
 AVK  CONST_11  C9   C10  C11  C12   180.00   0.0  0
 AVK  CONST_12  C1   C    C11  C12   180.00   0.0  0
 AVK  CONST_13  C14  C13  C12  C17     0.00   0.0  0
 AVK  CONST_15  C14  C15  C16  C17     0.00   0.0  0
 AVK  CONST_16  C13  C14  C15  C16     0.00   0.0  0
 AVK  CONST_17  C13  C12  C17  C16     0.00   0.0  0
 AVK  CONST_19  C1   C    C11  C10     0.00   0.0  0
 AVK  CONST_20  C1   C2   C9   C10     0.00   0.0  0
 AVK  CONST_21  C7   C8   N2   C6      0.00   0.0  0
 AVK  CONST_22  C8   C7   N1   C6      0.00   0.0  0
 AVK  CONST_23  C7   N1   C6   N2      0.00   0.0  0
 AVK  CONST_24  N1   C7   C8   N2      0.00   0.0  0
 AVK  CONST_25  N1   C6   N2   C8      0.00   0.0  0
 AVK  CONST_26  C12  C11  C    CL      0.00   0.0  0
 AVK  CONST_27  C10  C11  C    CL    180.00   0.0  0
 AVK  CONST_28  C2   C1   C    CL    180.00   0.0  0
 AVK  CONST_29  C3   C2   C1   C     180.00   0.0  0
 AVK  CONST_30  C3   C2   C9   C10   180.00   0.0  0
 AVK  CONST_31  C8   N2   C6   C5    180.00   0.0  0
 AVK  CONST_32  C7   N1   C6   C5    180.00   0.0  0
 AVK  CONST_33  H6   C10  C11  C     180.00   0.0  0
 AVK  CONST_34  H5   C13  C12  C11     0.00   0.0  0
 AVK  CONST_35  H1   C17  C12  C11     0.00   0.0  0
 AVK  CONST_36  H7   C9   C10  C11   180.00   0.0  0
 AVK  CONST_37  H8   C1   C    C11   180.00   0.0  0
 AVK  CONST_38  H4   C14  C13  C12   180.00   0.0  0
 AVK  CONST_39  H2   C16  C17  C12   180.00   0.0  0
 AVK  CONST_40  H3   C15  C16  C17   180.00   0.0  0
 AVK  CONST_41  H18  C8   N2   C6    180.00   0.0  0
 AVK  CONST_42  H19  C7   N1   C6    180.00   0.0  0
 AVK  CONST_43  H17  N2   C8   C7    180.00   0.0  0
 AVK  Var_01    N    C3   C2   C9    116.64  30.0  2
 AVK  Var_02    N2   C6   C5   C4    132.34  30.0  2
 AVK  Var_03    C4   N    C3   C2    176.73  30.0  3
 AVK  Var_04    C6   C5   C4   N     177.14  30.0  3
 AVK  Var_05    C5   C4   N    C3   -179.76  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
 AVK  plan-1  C5   0.020
 AVK  plan-1  C6   0.020
 AVK  plan-1  N2   0.020
 AVK  plan-1  C8   0.020
 AVK  plan-1  C7   0.020
 AVK  plan-1  N1   0.020
 AVK  plan-1  H17  0.020
 AVK  plan-1  H18  0.020
 AVK  plan-1  H19  0.020
 AVK  plan-2  CL   0.020
 AVK  plan-2  C    0.020
 AVK  plan-2  C11  0.020
 AVK  plan-2  C12  0.020
 AVK  plan-2  C10  0.020
 AVK  plan-2  C9   0.020
 AVK  plan-2  C2   0.020
 AVK  plan-2  C1   0.020
 AVK  plan-2  C3   0.020
 AVK  plan-2  H6   0.020
 AVK  plan-2  H7   0.020
 AVK  plan-2  H8   0.020
 AVK  plan-3  C11  0.020
 AVK  plan-3  C12  0.020
 AVK  plan-3  C17  0.020
 AVK  plan-3  C16  0.020
 AVK  plan-3  C15  0.020
 AVK  plan-3  C14  0.020
 AVK  plan-3  C13  0.020
 AVK  plan-3  H1   0.020
 AVK  plan-3  H2   0.020
 AVK  plan-3  H3   0.020
 AVK  plan-3  H4   0.020
 AVK  plan-3  H5   0.020

