# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 13:47:28 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: (2E)-3-(3-chloro-4-hydroxyphenyl)prop-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)\C=C\c1ccc(O)c(Cl)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
 YAZ  YAZ  '(2E)-3-(3-chloro-4-hydroxyphenyl)prop-2-enoic acid'  ligand  20  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_YAZ
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
 YAZ  C1    C   C     0   0.535   4.0504  -0.3551  -0.0417
 YAZ  C1'   C   CR6   0   0.121   0.2617   0.1666   0.0463
 YAZ  C2    C   C1    0  -0.427   2.7518   0.3314  -0.0184
 YAZ  C2'   C   CR16  0  -0.261  -0.8087  -0.7253   0.1053
 YAZ  C3    C   C1    0  -0.210   1.6125  -0.3710   0.0203
 YAZ  C3'   C   CR6   0  -0.155  -2.1106  -0.2635   0.1353
 YAZ  C4'   C   CR6   0   0.421  -2.3958   1.1026   0.1071
 YAZ  C5'   C   CR16  0  -0.319  -1.3232   1.9954   0.0458
 YAZ  C6'   C   CR16  0  -0.290  -0.0250   1.5368   0.0159
 YAZ  O2    O   O     0  -0.453   4.2124  -1.5546  -0.0321
 YAZ  O4'   O   OH1   0  -0.600  -3.6315   1.6034   0.1345
 YAZ  CL13  CL  CL    0  -0.106  -3.4280  -1.3884   0.2088
 YAZ  O1    O   OH1   0  -0.604   5.0592   0.5121  -0.0754
 YAZ  H1    H   H     0   0.281   2.7615   1.4142  -0.0330
 YAZ  H2    H   HCR6  0   0.287  -0.6248  -1.7918   0.1294
 YAZ  H3    H   H     0   0.272   1.6813  -1.4545   0.0355
 YAZ  H4    H   HCR6  0   0.285  -1.5278   3.0581   0.0224
 YAZ  H5    H   HCR6  0   0.269   0.7747   2.2636  -0.0311
 YAZ  H6    H   HOH1  0   0.474  -4.2969   0.9045   0.1837
 YAZ  H7    H   HOH1  0   0.481   5.9025   0.0359  -0.0892

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
 YAZ  C5'  C6'   aromatic  1.377  0.020  1.377
 YAZ  C5'  C4'   aromatic  1.397  0.020  1.397
 YAZ  O4'  C4'   single    1.334  0.020  1.334
 YAZ  C6'  C1'   aromatic  1.400  0.020  1.400
 YAZ  C4'  C3'   aromatic  1.396  0.020  1.396
 YAZ  C2   C3    double    1.339  0.020  1.339
 YAZ  C2   C1    single    1.469  0.020  1.469
 YAZ  C1'  C3    single    1.454  0.020  1.454
 YAZ  C1'  C2'   aromatic  1.394  0.020  1.394
 YAZ  C3'  C2'   aromatic  1.382  0.020  1.382
 YAZ  C3'  CL13  single    1.734  0.020  1.734
 YAZ  C1   O2    double    1.211  0.020  1.211
 YAZ  C1   O1    single    1.331  0.020  1.331
 YAZ  C2   H1    single    0.930  0.020  1.080
 YAZ  C2'  H2    single    0.930  0.020  1.080
 YAZ  C3   H3    single    0.930  0.020  1.080
 YAZ  C5'  H4    single    0.930  0.020  1.080
 YAZ  C6'  H5    single    0.930  0.020  1.080
 YAZ  O4'  H6    single    0.850  0.020  0.980
 YAZ  O1   H7    single    0.850  0.020  0.980

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
 YAZ  O1    C1   O2   122.99  3.000
 YAZ  O1    C1   C2   111.47  3.000
 YAZ  O2    C1   C2   125.54  3.000
 YAZ  C6'   C1'  C3   123.48  3.000
 YAZ  C3    C1'  C2'  118.51  3.000
 YAZ  C6'   C1'  C2'  118.01  3.000
 YAZ  H1    C2   C3   122.17  3.000
 YAZ  H1    C2   C1   117.33  3.000
 YAZ  C3    C2   C1   120.49  3.000
 YAZ  H2    C2'  C3'  119.26  3.000
 YAZ  H2    C2'  C1'  120.05  3.000
 YAZ  C3'   C2'  C1'  120.69  3.000
 YAZ  H3    C3   C2   118.03  3.000
 YAZ  H3    C3   C1'  115.31  3.000
 YAZ  C2    C3   C1'  126.66  3.000
 YAZ  CL13  C3'  C4'  118.72  3.000
 YAZ  CL13  C3'  C2'  120.00  3.000
 YAZ  C4'   C3'  C2'  121.28  3.000
 YAZ  O4'   C4'  C5'  118.19  3.000
 YAZ  O4'   C4'  C3'  123.81  3.000
 YAZ  C5'   C4'  C3'  118.00  3.000
 YAZ  H4    C5'  C6'  120.30  3.000
 YAZ  H4    C5'  C4'  118.90  3.000
 YAZ  C6'   C5'  C4'  120.80  3.000
 YAZ  H5    C6'  C5'  118.31  3.000
 YAZ  H5    C6'  C1'  120.47  3.000
 YAZ  C5'   C6'  C1'  121.22  3.000
 YAZ  H6    O4'  C4'  111.56  3.000
 YAZ  H7    O1   C1   109.88  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
 YAZ  CONST_01  C4'   C5'  C6'  C1'     0.00   0.0  0
 YAZ  CONST_02  C4'   C3'  C2'  C1'     0.00   0.0  0
 YAZ  CONST_03  C5'   C6'  C1'  C2'     0.00   0.0  0
 YAZ  CONST_04  C5'   C4'  C3'  C2'     0.00   0.0  0
 YAZ  CONST_05  C6'   C5'  C4'  C3'     0.00   0.0  0
 YAZ  CONST_06  C6'   C1'  C2'  C3'     0.00   0.0  0
 YAZ  CONST_07  CL13  C3'  C2'  C1'   180.00   0.0  0
 YAZ  CONST_08  O4'   C4'  C3'  C2'   180.00   0.0  0
 YAZ  CONST_09  C5'   C6'  C1'  C3    180.00   0.0  0
 YAZ  CONST_10  C3'   C2'  C1'  C3    180.00   0.0  0
 YAZ  CONST_11  CL13  C3'  C4'  C5'   180.00   0.0  0
 YAZ  CONST_12  O4'   C4'  C5'  C6'   180.00   0.0  0
 YAZ  CONST_13  H4    C5'  C6'  C1'   180.00   0.0  0
 YAZ  CONST_14  H5    C6'  C1'  C2'   180.00   0.0  0
 YAZ  CONST_15  H2    C2'  C3'  C4'   180.00   0.0  0
 YAZ  CONST_16  H7    O1   C1   C2    180.00   0.0  0
 YAZ  Var_01    C6'   C1'  C3   C2      0.87  30.0  2
 YAZ  Var_02    C1'   C3   C2   C1   -179.96   0.0  2
 YAZ  Var_03    O2    C1   C2   C3      0.18  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
 YAZ  plan-1  C1'   0.020
 YAZ  plan-1  C2'   0.020
 YAZ  plan-1  C3    0.020
 YAZ  plan-1  C3'   0.020
 YAZ  plan-1  C4'   0.020
 YAZ  plan-1  C5'   0.020
 YAZ  plan-1  C6'   0.020
 YAZ  plan-1  O4'   0.020
 YAZ  plan-1  CL13  0.020
 YAZ  plan-1  H2    0.020
 YAZ  plan-1  H4    0.020
 YAZ  plan-1  H5    0.020
 YAZ  plan-2  C1    0.020
 YAZ  plan-2  C2    0.020
 YAZ  plan-2  O2    0.020
 YAZ  plan-2  O1    0.020
 YAZ  plan-2  H7    0.020
 YAZ  plan-3  C1    0.020
 YAZ  plan-3  C1'   0.020
 YAZ  plan-3  C2    0.020
 YAZ  plan-3  C3    0.020
 YAZ  plan-3  H1    0.020
 YAZ  plan-3  H3    0.020

