# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 00:52:33 2021
#   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  20  12  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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   0.551  13.1690  37.0812  36.5741
 OMD  C2   C  CH2   0  -0.633  13.3692  36.2292  35.3445
 OMD  C1'  C  CR6   0   0.046  12.1790  36.1453  34.4347
 OMD  C2'  C  CR16  0  -0.387  12.2463  36.5768  33.1192
 OMD  C3'  C  CR6   0   0.343  11.1476  36.4752  32.2687
 OMD  O3'  O  OH1   0  -0.643  11.2912  36.9200  30.9978
 OMD  C4'  C  CR16  0  -0.381   9.9670  35.9299  32.7531
 OMD  C5'  C  CR16  0  -0.360   9.8895  35.4942  34.0707
 OMD  C6'  C  CR6   0   0.315  10.9857  35.5980  34.9127
 OMD  O6'  O  OH1   0  -0.637  10.9722  35.1966  36.2058
 OMD  O1   O  O     0  -0.452  13.7106  36.8780  37.6322
 OMD  O2   O  OH1   0  -0.585  12.3737  38.1189  36.3518
 OMD  H21  H  HCH2  0   0.302  14.2174  36.6579  34.8021
 OMD  H22  H  HCH2  0   0.289  13.6876  35.2397  35.6771
 OMD  H2'  H  HCR6  0   0.262  13.1706  37.0009  32.7441
 OMD  HO3  H  HOH1  0   0.471  10.4736  36.7903  30.5055
 OMD  H4'  H  HCR6  0   0.273   9.0967  35.8403  32.1129
 OMD  H5'  H  HCR6  0   0.272   8.9598  35.0720  34.4348
 OMD  HO6  H  HOH1  0   0.475  10.0960  34.8821  36.4539
 OMD  HO2  H  HOH1  0   0.480  12.3009  38.6523  37.1577

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    1.509  0.020  1.509
 OMD  C1   O1   double    1.206  0.020  1.206
 OMD  C1   O2   single    1.326  0.020  1.326
 OMD  C2   C1'  single    1.500  0.020  1.500
 OMD  C2   H21  single    0.970  0.020  1.090
 OMD  C2   H22  single    0.970  0.020  1.090
 OMD  C1'  C2'  aromatic  1.386  0.020  1.386
 OMD  C1'  C6'  aromatic  1.397  0.020  1.397
 OMD  C2'  C3'  aromatic  1.393  0.020  1.393
 OMD  C2'  H2'  single    0.930  0.020  1.080
 OMD  C3'  O3'  single    1.354  0.020  1.354
 OMD  C3'  C4'  aromatic  1.388  0.020  1.388
 OMD  O3'  HO3  single    0.850  0.020  0.980
 OMD  C4'  C5'  aromatic  1.390  0.020  1.390
 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    1.354  0.020  1.354
 OMD  O6'  HO6  single    0.850  0.020  0.980
 OMD  O2   HO2  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   123.25  3.000
 OMD  O2   C1   C2   112.63  3.000
 OMD  O1   C1   C2   124.07  3.000
 OMD  H22  C2   H21  106.27  3.000
 OMD  H22  C2   C1'  111.44  3.000
 OMD  H21  C2   C1'  109.65  3.000
 OMD  H22  C2   C1   107.59  3.000
 OMD  H21  C2   C1   106.59  3.000
 OMD  C1'  C2   C1   114.85  3.000
 OMD  C6'  C1'  C2'  119.22  3.000
 OMD  C6'  C1'  C2   119.47  3.000
 OMD  C2'  C1'  C2   121.30  3.000
 OMD  H2'  C2'  C3'  119.32  3.000
 OMD  H2'  C2'  C1'  119.45  3.000
 OMD  C3'  C2'  C1'  121.23  3.000
 OMD  C4'  C3'  O3'  123.15  3.000
 OMD  C4'  C3'  C2'  119.11  3.000
 OMD  O3'  C3'  C2'  117.74  3.000
 OMD  HO3  O3'  C3'  110.21  3.000
 OMD  H4'  C4'  C5'  119.28  3.000
 OMD  H4'  C4'  C3'  120.62  3.000
 OMD  C5'  C4'  C3'  120.10  3.000
 OMD  H5'  C5'  C6'  120.23  3.000
 OMD  H5'  C5'  C4'  119.22  3.000
 OMD  C6'  C5'  C4'  120.55  3.000
 OMD  O6'  C6'  C5'  123.37  3.000
 OMD  O6'  C6'  C1'  116.83  3.000
 OMD  C5'  C6'  C1'  119.80  3.000
 OMD  HO6  O6'  C6'  110.59  3.000
 OMD  HO2  O2   C1   109.65  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  CONST_16  HO2  O2   C1   C2   180.00   0.0  0
 OMD  Var_01    C2'  C1'  C2   C1   119.82  30.0  2
 OMD  Var_02    O1   C1   C2   C1'  148.88  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
 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
 OMD  plan-2  HO2  0.020

