# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 05:27:26 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: 5-[[3,4-bis(chloranyl)phenoxy]methyl]-1,2,4-triaza-3-azanidacyclopenta-1,4-diene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(OCc2n[n-]nn2)cc1Cl
#
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
 YIH  YIH  5-[[3,4-bis(chloranyl)phenoxy]methyl]-1,2,4-triaza-3-azanidacyclopenta-1,4-diene  ligand  20  15  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YIH
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
 YIH  C6    C   CR16   0  -0.330  -0.6702  -1.8413   0.0128
 YIH  C5    C   CR16   0  -0.186  -2.0482  -1.8770   0.0140
 YIH  C15   C   CR16   0  -0.333  -0.7350   0.5633   0.0095
 YIH  C7    C   CR6    0   0.406   0.0016  -0.6166   0.0111
 YIH  C3    C   CR6    0  -0.042  -2.7922  -0.7023   0.0135
 YIH  C2    C   CR6    0   0.025  -2.1243   0.5127   0.0107
 YIH  C10   C   CR5    0   0.267   3.5169   0.2364  -0.0002
 YIH  C9    C   CH2    0  -0.242   2.0711   0.5565  -0.0012
 YIH  N12   N   N     -1  -0.221   5.4506  -0.2309  -0.6482
 YIH  N11   N   N      0  -0.379   4.2406   0.0408  -1.0952
 YIH  N14   N   N      0  -0.378   4.2504   0.0945   1.0966
 YIH  N13   N   N      0  -0.221   5.4566  -0.1987   0.6525
 YIH  O8    O   O2     0  -0.466   1.3418  -0.6684   0.0130
 YIH  CL4   CL  CL     0  -0.089  -4.5111  -0.7773   0.0167
 YIH  CL1   CL  CL     0  -0.078  -3.0006   1.9923   0.0095
 YIH  H6    H   HCR6   0   0.258  -0.1045  -2.7633   0.0124
 YIH  H5    H   HCR6   0   0.266  -2.5585  -2.8302   0.0157
 YIH  H15   H   HCR6   0   0.282  -0.2571   1.5324   0.0072
 YIH  H91C  H   HCH2   0   0.230   1.8194   1.1549   0.8798
 YIH  H92C  H   HCH2   0   0.230   1.8142   1.1360  -0.8931

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
 YIH  C6   C5    aromatic  1.378  0.020  1.378
 YIH  C6   C7    aromatic  1.397  0.020  1.397
 YIH  C5   C3    aromatic  1.391  0.020  1.391
 YIH  C15  C7    aromatic  1.391  0.020  1.391
 YIH  C15  C2    aromatic  1.390  0.020  1.390
 YIH  C7   O8    single    1.341  0.020  1.341
 YIH  C3   C2    aromatic  1.386  0.020  1.386
 YIH  C3   CL4   single    1.721  0.020  1.721
 YIH  C2   CL1   single    1.720  0.020  1.720
 YIH  C10  C9    single    1.481  0.020  1.481
 YIH  C10  N11   aromatic  1.327  0.020  1.327
 YIH  C10  N14   aromatic  1.327  0.020  1.327
 YIH  C9   O8    single    1.426  0.020  1.426
 YIH  N12  N11   aromatic  1.318  0.020  1.318
 YIH  N12  N13   aromatic  1.301  0.020  1.301
 YIH  N14  N13   aromatic  1.318  0.020  1.318
 YIH  C6   H6    single    0.930  0.020  1.080
 YIH  C5   H5    single    0.930  0.020  1.080
 YIH  C15  H15   single    0.930  0.020  1.080
 YIH  C9   H91C  single    0.970  0.020  1.090
 YIH  C9   H92C  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
 YIH  H6    C6   C7    119.72  3.000
 YIH  H6    C6   C5    120.05  3.000
 YIH  C7    C6   C5    120.23  3.000
 YIH  H5    C5   C3    119.49  3.000
 YIH  H5    C5   C6    119.65  3.000
 YIH  C3    C5   C6    120.86  3.000
 YIH  H15   C15  C2    118.34  3.000
 YIH  H15   C15  C7    121.77  3.000
 YIH  C2    C15  C7    119.89  3.000
 YIH  O8    C7   C15   124.19  3.000
 YIH  O8    C7   C6    116.53  3.000
 YIH  C15   C7   C6    119.28  3.000
 YIH  CL4   C3   C2    121.30  3.000
 YIH  CL4   C3   C5    119.85  3.000
 YIH  C2    C3   C5    118.86  3.000
 YIH  CL1   C2   C3    120.57  3.000
 YIH  CL1   C2   C15   118.55  3.000
 YIH  C3    C2   C15   120.89  3.000
 YIH  N14   C10  N11   111.39  3.000
 YIH  N14   C10  C9    124.29  3.000
 YIH  N11   C10  C9    124.31  3.000
 YIH  H92C  C9   H91C  108.22  3.000
 YIH  H92C  C9   O8    110.06  3.000
 YIH  H91C  C9   O8    110.13  3.000
 YIH  H92C  C9   C10   110.14  3.000
 YIH  H91C  C9   C10   110.01  3.000
 YIH  O8    C9   C10   108.29  3.000
 YIH  N13   N12  N11   109.76  3.000
 YIH  N12   N11  C10   104.54  3.000
 YIH  N13   N14  C10   104.54  3.000
 YIH  N14   N13  N12   109.76  3.000
 YIH  C9    O8   C7    118.56  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
 YIH  CONST_01  C2   C3   C5   C6      0.00   0.0  0
 YIH  CONST_02  C2   C15  C7   C6      0.00   0.0  0
 YIH  CONST_03  C15  C7   C6   C5      0.00   0.0  0
 YIH  CONST_04  C15  C2   C3   C5      0.00   0.0  0
 YIH  CONST_05  C3   C5   C6   C7      0.00   0.0  0
 YIH  CONST_06  C3   C2   C15  C7      0.00   0.0  0
 YIH  CONST_07  N13  N12  N11  C10     0.00   0.0  0
 YIH  CONST_08  N12  N13  N14  C10     0.00   0.0  0
 YIH  CONST_09  N14  C10  N11  N12     0.00   0.0  0
 YIH  CONST_10  N13  N14  C10  N11     0.00   0.0  0
 YIH  CONST_11  N14  N13  N12  N11     0.00   0.0  0
 YIH  CONST_12  CL4  C3   C5   C6    180.00   0.0  0
 YIH  CONST_13  O8   C7   C6   C5    180.00   0.0  0
 YIH  CONST_14  CL1  C2   C3   C5    180.00   0.0  0
 YIH  CONST_15  CL4  C3   C2   C15   180.00   0.0  0
 YIH  CONST_16  CL1  C2   C15  C7    180.00   0.0  0
 YIH  CONST_17  O8   C7   C15  C2    180.00   0.0  0
 YIH  CONST_18  N12  N11  C10  C9    180.00   0.0  0
 YIH  CONST_19  N13  N14  C10  C9    180.00   0.0  0
 YIH  CONST_20  H15  C15  C7   C6    180.00   0.0  0
 YIH  CONST_21  H6   C6   C7   C15   180.00   0.0  0
 YIH  CONST_22  H5   C5   C6   C7    180.00   0.0  0
 YIH  Var_01    C10  C9   O8   C7   -179.83  30.0  1
 YIH  Var_02    O8   C9   C10  N11    88.81  30.0  2

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
 YIH  plan-1  C10  0.020
 YIH  plan-1  C9   0.020
 YIH  plan-1  N12  0.020
 YIH  plan-1  N11  0.020
 YIH  plan-1  N14  0.020
 YIH  plan-1  N13  0.020
 YIH  plan-2  C6   0.020
 YIH  plan-2  C5   0.020
 YIH  plan-2  C15  0.020
 YIH  plan-2  C7   0.020
 YIH  plan-2  C3   0.020
 YIH  plan-2  C2   0.020
 YIH  plan-2  O8   0.020
 YIH  plan-2  CL4  0.020
 YIH  plan-2  CL1  0.020
 YIH  plan-2  H6   0.020
 YIH  plan-2  H5   0.020
 YIH  plan-2  H15  0.020

