# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:15:12 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: (2E)-3-(4-hydroxy-3,5-dimethoxyphenyl)prop-2-enal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(\C=C\C=O)cc(OC)c1O
#
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
 SNY  SNY  (2E)-3-(4-hydroxy-3,5-dimethoxyphenyl)prop-2-enal  ligand  27  15  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SNY
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
 SNY  C1    C  CR6   0   0.175  -0.6697   0.4976   0.0151
 SNY  C2    C  CR16  0  -0.466   0.4288   1.3585   0.0355
 SNY  C3    C  CR6   0   0.331   1.7157   0.8429   0.0522
 SNY  O3    O  O2    0  -0.491   2.8500   1.5729   0.0740
 SNY  C4    C  CR6   0   0.192   1.9203  -0.5392   0.0480
 SNY  O4    O  OH1   0  -0.609   3.1475  -1.0806   0.0640
 SNY  C5    C  CR6   0   0.361   0.8173  -1.4047   0.0268
 SNY  O5    O  O2    0  -0.467   1.1229  -2.7135   0.0239
 SNY  C6    C  CR16  0  -0.492  -0.4665  -0.8859   0.0105
 SNY  C7    C  C1    0  -0.253  -1.9958   1.0835   0.0005
 SNY  C8    C  C1    0  -0.364  -3.1797   0.4447  -0.0126
 SNY  C9    C  C1    0   0.138  -4.4021   1.2268  -0.0243
 SNY  O9    O  O     0  -0.419  -5.5237   0.7608  -0.0341
 SNY  C3M   C  CH3   0  -0.434   2.7472   2.9841   0.0751
 SNY  C5M   C  CH3   0  -0.441   0.0628  -3.6493   0.0112
 SNY  H2    H  HCR6  0   0.289   0.2636   2.4278   0.0385
 SNY  HO4   H  HOH1  0   0.477   3.8152  -0.3833   0.0742
 SNY  H6    H  HCR6  0   0.286  -1.3183  -1.5503  -0.0060
 SNY  H7    H  H     0   0.271  -2.0168   2.1712   0.0012
 SNY  H8    H  H     0   0.271  -3.2656  -0.6363  -0.0135
 SNY  H9    H  H     0   0.188  -4.2462   2.3217  -0.0237
 SNY  H3M   H  HCH3  0   0.266   3.7637   3.3676   0.0903
 SNY  H3MA  H  HCH3  0   0.233   2.2417   3.3520  -0.8211
 SNY  H3MB  H  HCH3  0   0.233   2.2168   3.3493   0.9579
 SNY  H5M   H  HCH3  0   0.264   0.5227  -4.6342   0.0192
 SNY  H5MA  H  HCH3  0   0.231  -0.5782  -3.5532   0.8914
 SNY  H5MB  H  HCH3  0   0.231  -0.5536  -3.5568  -0.8868

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
 SNY  C2   C1    aromatic  1.396  0.020  1.396
 SNY  C6   C1    aromatic  1.398  0.020  1.398
 SNY  C1   C7    single    1.450  0.020  1.450
 SNY  C3   C2    aromatic  1.386  0.020  1.386
 SNY  C2   H2    single    0.930  0.020  1.080
 SNY  O3   C3    single    1.349  0.020  1.349
 SNY  C4   C3    aromatic  1.397  0.020  1.397
 SNY  O3   C3M   single    1.415  0.020  1.415
 SNY  O4   C4    single    1.341  0.020  1.341
 SNY  C4   C5    aromatic  1.402  0.020  1.402
 SNY  O4   HO4   single    0.850  0.020  0.980
 SNY  O5   C5    single    1.344  0.020  1.344
 SNY  C5   C6    aromatic  1.385  0.020  1.385
 SNY  O5   C5M   single    1.414  0.020  1.414
 SNY  C6   H6    single    0.930  0.020  1.080
 SNY  C7   C8    double    1.345  0.020  1.345
 SNY  C7   H7    single    0.930  0.020  1.080
 SNY  C8   C9    single    1.451  0.020  1.451
 SNY  C8   H8    single    0.930  0.020  1.080
 SNY  C9   O9    double    1.215  0.020  1.215
 SNY  C9   H9    single    0.930  0.020  1.080
 SNY  C3M  H3M   single    0.970  0.020  1.090
 SNY  C3M  H3MA  single    0.970  0.020  1.090
 SNY  C3M  H3MB  single    0.970  0.020  1.090
 SNY  C5M  H5M   single    0.970  0.020  1.090
 SNY  C5M  H5MA  single    0.970  0.020  1.090
 SNY  C5M  H5MB  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
 SNY  C7    C1   C6    122.19  3.000
 SNY  C7    C1   C2    118.08  3.000
 SNY  C6    C1   C2    119.73  3.000
 SNY  H2    C2   C3    120.62  3.000
 SNY  H2    C2   C1    119.30  3.000
 SNY  C3    C2   C1    120.08  3.000
 SNY  C4    C3   O3    114.35  3.000
 SNY  C4    C3   C2    120.25  3.000
 SNY  O3    C3   C2    125.40  3.000
 SNY  C3M   O3   C3    118.60  3.000
 SNY  C5    C4   O4    118.08  3.000
 SNY  C5    C4   C3    119.70  3.000
 SNY  O4    C4   C3    122.22  3.000
 SNY  HO4   O4   C4    109.96  3.000
 SNY  C6    C5   O5    125.14  3.000
 SNY  C6    C5   C4    119.88  3.000
 SNY  O5    C5   C4    114.97  3.000
 SNY  C5M   O5   C5    118.29  3.000
 SNY  H6    C6   C5    120.04  3.000
 SNY  H6    C6   C1    119.60  3.000
 SNY  C5    C6   C1    120.36  3.000
 SNY  H7    C7   C8    117.25  3.000
 SNY  H7    C7   C1    114.94  3.000
 SNY  C8    C7   C1    127.81  3.000
 SNY  H8    C8   C9    118.07  3.000
 SNY  H8    C8   C7    122.89  3.000
 SNY  C9    C8   C7    119.04  3.000
 SNY  H9    C9   O9    120.66  3.000
 SNY  H9    C9   C8    114.51  3.000
 SNY  O9    C9   C8    124.83  3.000
 SNY  H3MB  C3M  H3MA  109.00  3.000
 SNY  H3MB  C3M  H3M   108.96  3.000
 SNY  H3MA  C3M  H3M   108.99  3.000
 SNY  H3MB  C3M  O3    111.66  3.000
 SNY  H3MA  C3M  O3    111.64  3.000
 SNY  H3M   C3M  O3    106.50  3.000
 SNY  H5MB  C5M  H5MA  108.86  3.000
 SNY  H5MB  C5M  H5M   108.74  3.000
 SNY  H5MA  C5M  H5M   108.77  3.000
 SNY  H5MB  C5M  O5    111.97  3.000
 SNY  H5MA  C5M  O5    111.98  3.000
 SNY  H5M   C5M  O5    106.40  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
 SNY  CONST_01  C4   C3   C2  C1     0.00   0.0  0
 SNY  CONST_02  C4   C5   C6  C1     0.00   0.0  0
 SNY  CONST_03  C5   C6   C1  C2     0.00   0.0  0
 SNY  CONST_04  C5   C4   C3  C2     0.00   0.0  0
 SNY  CONST_05  C6   C1   C2  C3     0.00   0.0  0
 SNY  CONST_06  C6   C5   C4  C3     0.00   0.0  0
 SNY  CONST_07  O3   C3   C2  C1   180.00   0.0  0
 SNY  CONST_08  O5   C5   C6  C1   180.00   0.0  0
 SNY  CONST_09  O4   C4   C3  C2   180.00   0.0  0
 SNY  CONST_10  C7   C1   C2  C3   180.00   0.0  0
 SNY  CONST_11  O5   C5   C4  C3   180.00   0.0  0
 SNY  CONST_12  C5   C4   C3  O3   180.00   0.0  0
 SNY  CONST_13  C6   C5   C4  O4   180.00   0.0  0
 SNY  CONST_14  C7   C1   C6  C5   180.00   0.0  0
 SNY  CONST_15  H6   C6   C1  C2   180.00   0.0  0
 SNY  CONST_16  H2   C2   C3  C4   180.00   0.0  0
 SNY  Var_01    C8   C7   C1  C2  -179.62  30.0  2
 SNY  Var_02    C9   C8   C7  C1   179.92   0.0  2
 SNY  Var_03    H3M  C3M  O3  C3  -179.79  30.0  3
 SNY  Var_04    H5M  C5M  O5  C5  -179.54  30.0  3
 SNY  Var_05    O9   C9   C8  C7  -179.86  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
 SNY  plan-1  C1  0.020
 SNY  plan-1  C2  0.020
 SNY  plan-1  C3  0.020
 SNY  plan-1  O3  0.020
 SNY  plan-1  C4  0.020
 SNY  plan-1  O4  0.020
 SNY  plan-1  C5  0.020
 SNY  plan-1  O5  0.020
 SNY  plan-1  C6  0.020
 SNY  plan-1  C7  0.020
 SNY  plan-1  H2  0.020
 SNY  plan-1  H6  0.020
 SNY  plan-2  C1  0.020
 SNY  plan-2  C7  0.020
 SNY  plan-2  C8  0.020
 SNY  plan-2  C9  0.020
 SNY  plan-2  H7  0.020
 SNY  plan-2  H8  0.020
 SNY  plan-3  C8  0.020
 SNY  plan-3  C9  0.020
 SNY  plan-3  O9  0.020
 SNY  plan-3  H9  0.020

