# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 11:30:32 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: methyl 4-hydroxy-3,5-dimethoxybenzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1cc(OC)c(O)c(OC)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
 SYR  SYR  'methyl 4-hydroxy-3,5-dimethoxybenzoate'  ligand  27  15  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SYR
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
 SYR  O3    O  O     0  -0.455  -1.8474  -0.0245   2.7944
 SYR  C8    C  C     0   0.599  -0.7112  -0.0053   2.3807
 SYR  O4    O  O2    0  -0.460   0.3493  -0.0076   3.1749
 SYR  C10   C  CH3   0  -0.420   0.1225  -0.0328   4.5828
 SYR  C6    C  CR6   0  -0.073  -0.3531   0.0215   0.9447
 SYR  C5    C  CR16  0  -0.429  -1.3940   0.0265   0.0193
 SYR  C4    C  CR6   0   0.344  -1.1164   0.0509  -1.3394
 SYR  O2    O  O2    0  -0.467  -2.0411   0.0581  -2.3165
 SYR  C7    C  CH3   0  -0.440  -3.4042   0.0406  -1.9423
 SYR  C1    C  CR16  0  -0.436   0.9733   0.0409   0.5198
 SYR  C2    C  CR6   0   0.339   1.2501   0.0655  -0.8381
 SYR  O5    O  O2    0  -0.492   2.4843   0.0846  -1.3825
 SYR  C9    C  CH3   0  -0.434   3.6071   0.0989  -0.5220
 SYR  C3    C  CR6   0   0.202   0.2121   0.0708  -1.7759
 SYR  O1    O  OH1   0  -0.611   0.4471   0.0950  -3.0969
 SYR  H101  H  HCH3  0   0.252   1.1068  -0.0286   5.0418
 SYR  H102  H  HCH3  0   0.239  -0.4335   0.8444   4.9130
 SYR  H103  H  HCH3  0   0.239  -0.4127  -0.9329   4.8842
 SYR  H5    H  HCR6  0   0.284  -2.4149   0.0105   0.3744
 SYR  H7C1  H  HCH3  0   0.262  -3.9772   0.0509  -2.8661
 SYR  H7C2  H  HCH3  0   0.230  -3.6616  -0.8601  -1.3785
 SYR  H7C3  H  HCH3  0   0.230  -3.6763   0.9178  -1.3493
 SYR  H1    H  HCR6  0   0.289   1.7773   0.0357   1.2404
 SYR  H9C1  H  HCH3  0   0.265   4.4851   0.1223  -1.1621
 SYR  H9C2  H  HCH3  0   0.233   3.6137   0.9832   0.1195
 SYR  H9C3  H  HCH3  0   0.233   3.6499  -0.7967   0.1021
 SYR  HA    H  HOH1  0   0.477   1.3988   0.1050  -3.2598

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
 SYR  O3   C8    double    1.209  0.020  1.209
 SYR  C8   O4    single    1.325  0.020  1.325
 SYR  C8   C6    single    1.480  0.020  1.480
 SYR  O4   C10   single    1.426  0.020  1.426
 SYR  C10  H101  single    0.970  0.020  1.090
 SYR  C10  H102  single    0.970  0.020  1.090
 SYR  C10  H103  single    0.970  0.020  1.090
 SYR  C6   C5    aromatic  1.393  0.020  1.393
 SYR  C6   C1    aromatic  1.393  0.020  1.393
 SYR  C5   C4    aromatic  1.387  0.020  1.387
 SYR  C5   H5    single    0.930  0.020  1.080
 SYR  C4   O2    single    1.345  0.020  1.345
 SYR  C4   C3    aromatic  1.399  0.020  1.399
 SYR  O2   C7    single    1.414  0.020  1.414
 SYR  C7   H7C1  single    0.970  0.020  1.090
 SYR  C7   H7C2  single    0.970  0.020  1.090
 SYR  C7   H7C3  single    0.970  0.020  1.090
 SYR  C1   C2    aromatic  1.386  0.020  1.386
 SYR  C1   H1    single    0.930  0.020  1.080
 SYR  C2   O5    single    1.349  0.020  1.349
 SYR  C2   C3    aromatic  1.399  0.020  1.399
 SYR  O5   C9    single    1.415  0.020  1.415
 SYR  C9   H9C1  single    0.970  0.020  1.090
 SYR  C9   H9C2  single    0.970  0.020  1.090
 SYR  C9   H9C3  single    0.970  0.020  1.090
 SYR  C3   O1    single    1.342  0.020  1.342
 SYR  O1   HA    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
 SYR  C6    C8   O4    112.82  3.000
 SYR  C6    C8   O3    124.01  3.000
 SYR  O4    C8   O3    123.16  3.000
 SYR  C10   O4   C8    117.67  3.000
 SYR  H103  C10  H102  109.30  3.000
 SYR  H103  C10  H101  109.35  3.000
 SYR  H102  C10  H101  109.35  3.000
 SYR  H103  C10  O4    111.45  3.000
 SYR  H102  C10  O4    111.47  3.000
 SYR  H101  C10  O4    105.84  3.000
 SYR  C1    C6   C5    120.59  3.000
 SYR  C1    C6   C8    121.77  3.000
 SYR  C5    C6   C8    117.63  3.000
 SYR  H5    C5   C4    120.74  3.000
 SYR  H5    C5   C6    119.18  3.000
 SYR  C4    C5   C6    120.09  3.000
 SYR  C3    C4   O2    115.23  3.000
 SYR  C3    C4   C5    119.74  3.000
 SYR  O2    C4   C5    125.03  3.000
 SYR  C7    O2   C4    118.06  3.000
 SYR  H7C3  C7   H7C2  108.83  3.000
 SYR  H7C3  C7   H7C1  108.79  3.000
 SYR  H7C2  C7   H7C1  108.78  3.000
 SYR  H7C3  C7   O2    111.94  3.000
 SYR  H7C2  C7   O2    111.95  3.000
 SYR  H7C1  C7   O2    106.45  3.000
 SYR  H1    C1   C2    120.35  3.000
 SYR  H1    C1   C6    120.36  3.000
 SYR  C2    C1   C6    119.29  3.000
 SYR  C3    C2   O5    114.09  3.000
 SYR  C3    C2   C1    120.58  3.000
 SYR  O5    C2   C1    125.33  3.000
 SYR  C9    O5   C2    118.74  3.000
 SYR  H9C3  C9   H9C2  109.14  3.000
 SYR  H9C3  C9   H9C1  108.81  3.000
 SYR  H9C2  C9   H9C1  108.88  3.000
 SYR  H9C3  C9   O5    111.73  3.000
 SYR  H9C2  C9   O5    111.72  3.000
 SYR  H9C1  C9   O5    106.45  3.000
 SYR  O1    C3   C2    122.01  3.000
 SYR  O1    C3   C4    118.28  3.000
 SYR  C2    C3   C4    119.71  3.000
 SYR  HA    O1   C3    109.80  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
 SYR  CONST_01  C3    C4   C5  C6      0.00   0.0  0
 SYR  CONST_02  C3    C2   C1  C6      0.00   0.0  0
 SYR  CONST_03  C2    C1   C6  C5      0.00   0.0  0
 SYR  CONST_04  C2    C3   C4  C5      0.00   0.0  0
 SYR  CONST_05  C1    C6   C5  C4      0.00   0.0  0
 SYR  CONST_06  C1    C2   C3  C4      0.00   0.0  0
 SYR  CONST_07  C4    C5   C6  C8    180.00   0.0  0
 SYR  CONST_08  C2    C1   C6  C8    180.00   0.0  0
 SYR  CONST_09  O2    C4   C5  C6    180.00   0.0  0
 SYR  CONST_10  O5    C2   C1  C6    180.00   0.0  0
 SYR  CONST_11  O1    C3   C4  C5    180.00   0.0  0
 SYR  CONST_12  O5    C2   C3  C4    180.00   0.0  0
 SYR  CONST_13  C2    C3   C4  O2    180.00   0.0  0
 SYR  CONST_14  O1    C3   C2  C1    180.00   0.0  0
 SYR  CONST_15  H1    C1   C6  C5    180.00   0.0  0
 SYR  CONST_16  H5    C5   C6  C1    180.00   0.0  0
 SYR  Var_01    C5    C6   C8  O3      0.09  30.0  2
 SYR  Var_02    C3    C4   O2  C7   -179.92  30.0  2
 SYR  Var_03    C3    C2   O5  C9    179.18  30.0  2
 SYR  Var_04    C6    C8   O4  C10  -180.00  30.0  1
 SYR  Var_05    H7C1  C7   O2  C4    179.95  30.0  3
 SYR  Var_06    H9C1  C9   O5  C2   -179.49  30.0  3
 SYR  Var_07    H101  C10  O4  C8   -179.90  30.0  3

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
 SYR  plan-1  C8  0.020
 SYR  plan-1  C6  0.020
 SYR  plan-1  C5  0.020
 SYR  plan-1  C4  0.020
 SYR  plan-1  O2  0.020
 SYR  plan-1  C1  0.020
 SYR  plan-1  C2  0.020
 SYR  plan-1  O5  0.020
 SYR  plan-1  C3  0.020
 SYR  plan-1  O1  0.020
 SYR  plan-1  H5  0.020
 SYR  plan-1  H1  0.020
 SYR  plan-2  O3  0.020
 SYR  plan-2  C8  0.020
 SYR  plan-2  O4  0.020
 SYR  plan-2  C6  0.020

