# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 05:09:12 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 5-[(4-chlorophenyl)methyl]-1,2,3-triaza-4-azanidacyclopenta-2,5-diene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(Cc2[n-]nnn2)cc1
#
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
 YIE  YIE  5-[(4-chlorophenyl)methyl]-1,2,3-triaza-4-azanidacyclopenta-2,5-diene  ligand  19  13  .  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_YIE
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
 YIE  CL1   CL  CL     0  -0.137  -4.0988   0.0037   0.7224
 YIE  C2    C   CR6    0  -0.057  -2.4888   0.0042   0.0725
 YIE  C5    C   CR16   0  -0.198  -1.8590   1.2103  -0.1899
 YIE  C6    C   CR16   0  -0.310  -0.5744   1.1998  -0.7139
 YIE  C7    C   CR6    0   0.148   0.0869   0.0050  -0.9816
 YIE  C4    C   CR16   0  -0.308  -0.5700  -1.1904  -0.7051
 YIE  C3    C   CR16   0  -0.198  -1.8546  -1.2017  -0.1810
 YIE  C8    C   CH2    0  -0.591   1.4968   0.0054  -1.5159
 YIE  C9    C   CR5    0   0.290   2.5005  -0.0099  -0.4111
 YIE  N10   N   N     -1  -0.390   2.9587   1.0753   0.1997
 YIE  N11   N   N      0  -0.227   3.7782   0.6142   1.1314
 YIE  N12   N   N      0  -0.228   3.8110  -0.6812   1.0833
 YIE  N13   N   N      0  -0.391   3.0142  -1.1128   0.1186
 YIE  H4    H   HCR6   0   0.258  -0.0768  -2.1341  -0.9035
 YIE  H3    H   HCR6   0   0.277  -2.3521  -2.1399   0.0249
 YIE  H6    H   HCR6   0   0.258  -0.0844   2.1435  -0.9192
 YIE  H5    H   HCR6   0   0.277  -2.3600   2.1482   0.0090
 YIE  H81C  H   HCH2   0   0.264   1.6469  -0.8667  -2.1545
 YIE  H82C  H   HCH2   0   0.264   1.6513   0.8885  -2.1383

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
 YIE  C4   C3    aromatic  1.387  0.020  1.387
 YIE  C4   C7    aromatic  1.392  0.020  1.392
 YIE  C6   C5    aromatic  1.387  0.020  1.387
 YIE  C6   C7    aromatic  1.392  0.020  1.392
 YIE  C3   C2    aromatic  1.386  0.020  1.386
 YIE  C5   C2    aromatic  1.386  0.020  1.386
 YIE  C7   C8    single    1.508  0.020  1.508
 YIE  C2   CL1   single    1.736  0.020  1.736
 YIE  C9   C8    single    1.493  0.020  1.493
 YIE  C9   N13   aromatic  1.327  0.020  1.327
 YIE  C9   N10   aromatic  1.327  0.020  1.327
 YIE  N13  N12   aromatic  1.324  0.020  1.324
 YIE  N10  N11   aromatic  1.324  0.020  1.324
 YIE  N12  N11   aromatic  1.297  0.020  1.297
 YIE  C4   H4    single    0.930  0.020  1.080
 YIE  C3   H3    single    0.930  0.020  1.080
 YIE  C6   H6    single    0.930  0.020  1.080
 YIE  C5   H5    single    0.930  0.020  1.080
 YIE  C8   H81C  single    0.970  0.020  1.090
 YIE  C8   H82C  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
 YIE  C3    C2   C5    120.98  3.000
 YIE  C5    C2   CL1   119.51  3.000
 YIE  C3    C2   CL1   119.51  3.000
 YIE  H5    C5   C6    120.32  3.000
 YIE  H5    C5   C2    120.62  3.000
 YIE  C6    C5   C2    119.06  3.000
 YIE  H6    C6   C7    119.79  3.000
 YIE  H6    C6   C5    118.94  3.000
 YIE  C7    C6   C5    121.28  3.000
 YIE  C8    C7   C4    120.80  3.000
 YIE  C8    C7   C6    120.82  3.000
 YIE  C4    C7   C6    118.36  3.000
 YIE  H4    C4   C3    118.93  3.000
 YIE  H4    C4   C7    119.80  3.000
 YIE  C3    C4   C7    121.27  3.000
 YIE  H3    C3   C4    120.32  3.000
 YIE  H3    C3   C2    120.62  3.000
 YIE  C4    C3   C2    119.06  3.000
 YIE  H82C  C8   H81C  107.06  3.000
 YIE  H82C  C8   C9    109.58  3.000
 YIE  H81C  C8   C9    109.42  3.000
 YIE  H82C  C8   C7    109.55  3.000
 YIE  H81C  C8   C7    109.62  3.000
 YIE  C9    C8   C7    111.50  3.000
 YIE  N13   C9   N10   111.24  3.000
 YIE  N10   C9   C8    124.37  3.000
 YIE  N13   C9   C8    124.35  3.000
 YIE  N11   N10  C9    104.65  3.000
 YIE  N12   N11  N10   109.73  3.000
 YIE  N13   N12  N11   109.73  3.000
 YIE  N12   N13  C9    104.65  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
 YIE  CONST_01  C7   C4   C3   C2     0.00   0.0  0
 YIE  CONST_02  C7   C6   C5   C2     0.00   0.0  0
 YIE  CONST_03  C4   C7   C6   C5     0.00   0.0  0
 YIE  CONST_04  C4   C3   C2   C5     0.00   0.0  0
 YIE  CONST_05  C3   C2   C5   C6     0.00   0.0  0
 YIE  CONST_06  C3   C4   C7   C6     0.00   0.0  0
 YIE  CONST_07  N11  N12  N13  C9     0.00   0.0  0
 YIE  CONST_08  N12  N11  N10  C9     0.00   0.0  0
 YIE  CONST_09  N12  N13  C9   N10    0.00   0.0  0
 YIE  CONST_10  N13  N12  N11  N10    0.00   0.0  0
 YIE  CONST_11  N13  C9   N10  N11    0.00   0.0  0
 YIE  CONST_12  C4   C3   C2   CL1  180.00   0.0  0
 YIE  CONST_13  C6   C5   C2   CL1  180.00   0.0  0
 YIE  CONST_14  C8   C7   C6   C5   180.00   0.0  0
 YIE  CONST_15  C8   C7   C4   C3   180.00   0.0  0
 YIE  CONST_16  N12  N13  C9   C8   180.00   0.0  0
 YIE  CONST_17  N11  N10  C9   C8   180.00   0.0  0
 YIE  CONST_18  H4   C4   C3   C2   180.00   0.0  0
 YIE  CONST_19  H6   C6   C5   C2   180.00   0.0  0
 YIE  CONST_20  H3   C3   C2   C5   180.00   0.0  0
 YIE  CONST_21  H5   C5   C6   C7   180.00   0.0  0
 YIE  Var_01    C9   C8   C7   C6    89.87  30.0  2
 YIE  Var_02    N13  C9   C8   C7    91.01  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
 YIE  plan-1  C8   0.020
 YIE  plan-1  C9   0.020
 YIE  plan-1  N10  0.020
 YIE  plan-1  N11  0.020
 YIE  plan-1  N12  0.020
 YIE  plan-1  N13  0.020
 YIE  plan-2  CL1  0.020
 YIE  plan-2  C2   0.020
 YIE  plan-2  C5   0.020
 YIE  plan-2  C6   0.020
 YIE  plan-2  C7   0.020
 YIE  plan-2  C4   0.020
 YIE  plan-2  C3   0.020
 YIE  plan-2  C8   0.020
 YIE  plan-2  H4   0.020
 YIE  plan-2  H3   0.020
 YIE  plan-2  H6   0.020
 YIE  plan-2  H5   0.020

