# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 08:27:02 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: (2,5-dihydroxyphenyl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)Cc1cc(O)ccc1O
#
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
 OMD  OMD  '(2,5-dihydroxyphenyl)acetic acid'  ligand  19  12  .  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_OMD
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
 OMD  C1   C  C      0   0.420   0.2908   0.1292   2.5003
 OMD  C2   C  CH2    0  -0.671   0.3039  -1.0211   1.4647
 OMD  C1'  C  CR6    0   0.097   0.0319  -0.5938   0.0580
 OMD  C2'  C  CR16   0  -0.397   1.0269  -0.6190  -0.9081
 OMD  C3'  C  CR6    0   0.337   0.7839  -0.2276  -2.2233
 OMD  O3'  O  OH1    0  -0.648   1.8162  -0.2851  -3.1021
 OMD  C4'  C  CR16   0  -0.391  -0.4878   0.1953  -2.5781
 OMD  C5'  C  CR16   0  -0.371  -1.4971   0.2254  -1.6205
 OMD  C6'  C  CR6    0   0.295  -1.2467  -0.1619  -0.3133
 OMD  O6'  O  OH1    0  -0.638  -2.2048  -0.1521   0.6471
 OMD  O1   O  O      0  -0.599   0.4359   1.2866   2.0712
 OMD  O2   O  OC    -1  -0.627   0.1721  -0.2193   3.6925
 OMD  H21  H  HCH2   0   0.248   1.2940  -1.4870   1.5083
 OMD  H22  H  HCH2   0   0.232  -0.3999  -1.7962   1.7795
 OMD  H2'  H  HCR6   0   0.248   2.0209  -0.9526  -0.6307
 OMD  HO3  H  HOH1   0   0.468   1.5236   0.0058  -3.9722
 OMD  H4'  H  HCR6   0   0.265  -0.7089   0.4981  -3.5955
 OMD  H5'  H  HCR6   0   0.263  -2.4883   0.5556  -1.9113
 OMD  HO6  H  HOH1   0   0.467  -3.0438   0.1375   0.2733

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
 OMD  C1   C2   single    1.548  0.020  1.548
 OMD  C1   O1   deloc     1.243  0.020  1.243
 OMD  C1   O2   deloc     1.248  0.020  1.248
 OMD  C2   C1'  single    1.495  0.020  1.495
 OMD  C2   H21  single    0.970  0.020  1.090
 OMD  C2   H22  single    0.970  0.020  1.090
 OMD  C1'  C2'  aromatic  1.387  0.020  1.387
 OMD  C1'  C6'  aromatic  1.400  0.020  1.400
 OMD  C2'  C3'  aromatic  1.394  0.020  1.394
 OMD  C2'  H2'  single    0.930  0.020  1.080
 OMD  C3'  O3'  single    1.357  0.020  1.357
 OMD  C3'  C4'  aromatic  1.386  0.020  1.386
 OMD  O3'  HO3  single    0.850  0.020  0.980
 OMD  C4'  C5'  aromatic  1.392  0.020  1.392
 OMD  C4'  H4'  single    0.930  0.020  1.080
 OMD  C5'  C6'  aromatic  1.386  0.020  1.386
 OMD  C5'  H5'  single    0.930  0.020  1.080
 OMD  C6'  O6'  single    1.357  0.020  1.357
 OMD  O6'  HO6  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
 OMD  O2   C1   O1   126.95  3.000
 OMD  O2   C1   C2   115.63  3.000
 OMD  O1   C1   C2   117.39  3.000
 OMD  H22  C2   H21  105.60  3.000
 OMD  H22  C2   C1'  110.88  3.000
 OMD  H21  C2   C1'  108.88  3.000
 OMD  H22  C2   C1   109.19  3.000
 OMD  H21  C2   C1   107.29  3.000
 OMD  C1'  C2   C1   114.55  3.000
 OMD  C6'  C1'  C2'  118.43  3.000
 OMD  C6'  C1'  C2   120.26  3.000
 OMD  C2'  C1'  C2   121.31  3.000
 OMD  H2'  C2'  C3'  119.18  3.000
 OMD  H2'  C2'  C1'  119.00  3.000
 OMD  C3'  C2'  C1'  121.82  3.000
 OMD  C4'  C3'  O3'  123.02  3.000
 OMD  C4'  C3'  C2'  119.16  3.000
 OMD  O3'  C3'  C2'  117.82  3.000
 OMD  HO3  O3'  C3'  109.95  3.000
 OMD  H4'  C4'  C5'  119.45  3.000
 OMD  H4'  C4'  C3'  120.83  3.000
 OMD  C5'  C4'  C3'  119.72  3.000
 OMD  H5'  C5'  C6'  120.20  3.000
 OMD  H5'  C5'  C4'  119.01  3.000
 OMD  C6'  C5'  C4'  120.79  3.000
 OMD  O6'  C6'  C5'  122.55  3.000
 OMD  O6'  C6'  C1'  117.36  3.000
 OMD  C5'  C6'  C1'  120.09  3.000
 OMD  HO6  O6'  C6'  110.04  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
 OMD  CONST_01  C4'  C3'  C2'  C1'    0.00   0.0  0
 OMD  CONST_02  C4'  C5'  C6'  C1'    0.00   0.0  0
 OMD  CONST_03  C5'  C6'  C1'  C2'    0.00   0.0  0
 OMD  CONST_04  C5'  C4'  C3'  C2'    0.00   0.0  0
 OMD  CONST_05  C6'  C1'  C2'  C3'    0.00   0.0  0
 OMD  CONST_06  C6'  C5'  C4'  C3'    0.00   0.0  0
 OMD  CONST_07  C3'  C2'  C1'  C2   180.00   0.0  0
 OMD  CONST_08  C5'  C6'  C1'  C2   180.00   0.0  0
 OMD  CONST_09  O3'  C3'  C2'  C1'  180.00   0.0  0
 OMD  CONST_10  O6'  C6'  C1'  C2'  180.00   0.0  0
 OMD  CONST_11  C5'  C4'  C3'  O3'  180.00   0.0  0
 OMD  CONST_12  O6'  C6'  C5'  C4'  180.00   0.0  0
 OMD  CONST_13  H5'  C5'  C6'  C1'  180.00   0.0  0
 OMD  CONST_14  H4'  C4'  C3'  C2'  180.00   0.0  0
 OMD  CONST_15  H2'  C2'  C3'  C4'  180.00   0.0  0
 OMD  Var_01    C2'  C1'  C2   C1   110.30  30.0  2
 OMD  Var_02    O1   C1   C2   C1'  -19.58  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
 OMD  plan-1  C2   0.020
 OMD  plan-1  C1'  0.020
 OMD  plan-1  C2'  0.020
 OMD  plan-1  C3'  0.020
 OMD  plan-1  O3'  0.020
 OMD  plan-1  C4'  0.020
 OMD  plan-1  C5'  0.020
 OMD  plan-1  C6'  0.020
 OMD  plan-1  O6'  0.020
 OMD  plan-1  H2'  0.020
 OMD  plan-1  H4'  0.020
 OMD  plan-1  H5'  0.020
 OMD  plan-2  C1   0.020
 OMD  plan-2  C2   0.020
 OMD  plan-2  O1   0.020
 OMD  plan-2  O2   0.020

