# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 06:36:34 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: 5-[(3-chloranylphenoxy)methyl]-1,2,4-triaza-3-azanidacyclopenta-1,4-diene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(OCc2n[n-]nn2)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
 YIP  YIP  5-[(3-chloranylphenoxy)methyl]-1,2,4-triaza-3-azanidacyclopenta-1,4-diene  ligand  20  14  .  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_YIP
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
 YIP  C3    C   CR16   0  -0.311   1.6202  -0.6026  -0.0001
 YIP  C2    C   CR6    0  -0.020   2.9502  -0.2315  -0.0107
 YIP  C14   C   CR16   0  -0.244   3.3455   1.0997  -0.0164
 YIP  C13   C   CR16   0  -0.243   2.3558   2.0681  -0.0053
 YIP  C12   C   CR16   0  -0.378   1.0074   1.7327   0.0127
 YIP  C4    C   CR6    0   0.393   0.6351   0.3902   0.0136
 YIP  O5    O   O2     0  -0.472  -0.6345  -0.0496   0.0277
 YIP  C6    C   CH2    0  -0.252  -1.6939   0.9057  -0.0168
 YIP  C7    C   CR5    0   0.263  -2.9746   0.1585  -0.0430
 YIP  N11   N   N      0  -0.381  -3.5820  -0.2495  -1.1505
 YIP  N10   N   N      0  -0.222  -4.6565  -0.8852  -0.7260
 YIP  N9    N   N     -1  -0.223  -4.6956  -0.8620   0.5742
 YIP  N8    N   N      0  -0.381  -3.6502  -0.2068   1.0397
 YIP  CL1   CL  CL     0  -0.129   4.1631  -1.4725  -0.0265
 YIP  H13   H   HCR6   0   0.271   2.6358   3.1133  -0.0110
 YIP  H12   H   HCR6   0   0.287   0.2732   2.5252   0.0195
 YIP  H14   H   HCR6   0   0.276   4.3923   1.3685  -0.0280
 YIP  H3    H   HCR6   0   0.284   1.3314  -1.6457   0.0011
 YIP  H61C  H   HCH2   0   0.242  -1.6551   1.5574   0.8607
 YIP  H62C  H   HCH2   0   0.242  -1.6027   1.5292  -0.9112

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
 YIP  C13  C12   aromatic  1.390  0.020  1.390
 YIP  C13  C14   aromatic  1.385  0.020  1.385
 YIP  C12  C4    aromatic  1.393  0.020  1.393
 YIP  C14  C2    aromatic  1.389  0.020  1.389
 YIP  C3   C4    aromatic  1.399  0.020  1.399
 YIP  C3   C2    aromatic  1.381  0.020  1.381
 YIP  C4   O5    single    1.344  0.020  1.344
 YIP  C2   CL1   single    1.735  0.020  1.735
 YIP  C7   C6    single    1.483  0.020  1.483
 YIP  C7   N8    aromatic  1.327  0.020  1.327
 YIP  C7   N11   aromatic  1.327  0.020  1.327
 YIP  C6   O5    single    1.427  0.020  1.427
 YIP  N9   N8    aromatic  1.319  0.020  1.319
 YIP  N9   N10   aromatic  1.301  0.020  1.301
 YIP  N11  N10   aromatic  1.319  0.020  1.319
 YIP  C13  H13   single    0.930  0.020  1.080
 YIP  C12  H12   single    0.930  0.020  1.080
 YIP  C14  H14   single    0.930  0.020  1.080
 YIP  C3   H3    single    0.930  0.020  1.080
 YIP  C6   H61C  single    0.970  0.020  1.090
 YIP  C6   H62C  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
 YIP  H3    C3   C4    119.75  3.000
 YIP  H3    C3   C2    121.06  3.000
 YIP  C4    C3   C2    119.19  3.000
 YIP  CL1   C2   C14   119.11  3.000
 YIP  CL1   C2   C3    118.76  3.000
 YIP  C14   C2   C3    122.13  3.000
 YIP  H14   C14  C13   121.22  3.000
 YIP  H14   C14  C2    120.94  3.000
 YIP  C13   C14  C2    117.83  3.000
 YIP  H13   C13  C12   118.97  3.000
 YIP  H13   C13  C14   119.37  3.000
 YIP  C12   C13  C14   121.66  3.000
 YIP  H12   C12  C4    121.69  3.000
 YIP  H12   C12  C13   118.85  3.000
 YIP  C4    C12  C13   119.46  3.000
 YIP  O5    C4   C12   124.60  3.000
 YIP  O5    C4   C3    115.68  3.000
 YIP  C12   C4   C3    119.72  3.000
 YIP  C6    O5   C4    118.82  3.000
 YIP  H62C  C6   H61C  108.26  3.000
 YIP  H62C  C6   C7    110.17  3.000
 YIP  H61C  C6   C7    110.18  3.000
 YIP  H62C  C6   O5    110.19  3.000
 YIP  H61C  C6   O5    110.33  3.000
 YIP  C7    C6   O5    107.72  3.000
 YIP  N8    C7   N11   111.29  3.000
 YIP  N11   C7   C6    124.39  3.000
 YIP  N8    C7   C6    124.32  3.000
 YIP  N10   N11  C7    104.62  3.000
 YIP  N9    N10  N11   109.73  3.000
 YIP  N8    N9   N10   109.74  3.000
 YIP  N9    N8   C7    104.62  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
 YIP  CONST_01  C13  C12  C4   C3     0.00   0.0  0
 YIP  CONST_02  C13  C14  C2   C3     0.00   0.0  0
 YIP  CONST_03  C12  C13  C14  C2     0.00   0.0  0
 YIP  CONST_04  C12  C4   C3   C2     0.00   0.0  0
 YIP  CONST_05  C4   C12  C13  C14    0.00   0.0  0
 YIP  CONST_06  C4   C3   C2   C14    0.00   0.0  0
 YIP  CONST_07  N10  N9   N8   C7     0.00   0.0  0
 YIP  CONST_08  N9   N10  N11  C7     0.00   0.0  0
 YIP  CONST_09  N9   N8   C7   N11    0.00   0.0  0
 YIP  CONST_10  N8   N9   N10  N11    0.00   0.0  0
 YIP  CONST_11  N8   C7   N11  N10    0.00   0.0  0
 YIP  CONST_12  O5   C4   C3   C2   180.00   0.0  0
 YIP  CONST_13  O5   C4   C12  C13  180.00   0.0  0
 YIP  CONST_14  CL1  C2   C14  C13  180.00   0.0  0
 YIP  CONST_15  CL1  C2   C3   C4   180.00   0.0  0
 YIP  CONST_16  N9   N8   C7   C6   180.00   0.0  0
 YIP  CONST_17  N10  N11  C7   C6   180.00   0.0  0
 YIP  CONST_18  H12  C12  C4   C3   180.00   0.0  0
 YIP  CONST_19  H14  C14  C2   C3   180.00   0.0  0
 YIP  CONST_20  H13  C13  C14  C2   180.00   0.0  0
 YIP  CONST_21  H3   C3   C2   C14  180.00   0.0  0
 YIP  Var_01    C7   C6   O5   C4   177.84  30.0  1
 YIP  Var_02    N8   C7   C6   O5    89.75  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
 YIP  plan-1  C6   0.020
 YIP  plan-1  C7   0.020
 YIP  plan-1  N11  0.020
 YIP  plan-1  N10  0.020
 YIP  plan-1  N9   0.020
 YIP  plan-1  N8   0.020
 YIP  plan-2  C3   0.020
 YIP  plan-2  C2   0.020
 YIP  plan-2  C14  0.020
 YIP  plan-2  C13  0.020
 YIP  plan-2  C12  0.020
 YIP  plan-2  C4   0.020
 YIP  plan-2  O5   0.020
 YIP  plan-2  CL1  0.020
 YIP  plan-2  H13  0.020
 YIP  plan-2  H12  0.020
 YIP  plan-2  H14  0.020
 YIP  plan-2  H3   0.020

