# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 28 22:45:53 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: 2-(hydroxymethyl)butane-1,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCC(CO)CO
#
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
 1MI  1MI  "2-(hydroxymethyl)butane-1,4-diol"  ligand  20  8  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1MI
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
 1MI  C1   C  CH2   0  -0.468  26.7438  40.5515  27.4649
 1MI  C2   C  CH2   0  -0.138  26.7050  38.0728  27.9413
 1MI  C3   C  CH2   0  -0.149  24.5586  39.3255  27.6946
 1MI  C4   C  CH2   0  -0.153  26.6883  41.8949  28.1668
 1MI  O2   O  OH1   0  -0.664  25.3631  42.3780  28.2201
 1MI  C    C  CH1   0  -0.287  26.0033  39.4057  28.1713
 1MI  O1   O  OH1   0  -0.671  23.8496  38.3846  28.4744
 1MI  O    O  OH1   0  -0.669  27.9915  38.1173  28.5219
 1MI  H1   H  HCH2  0   0.221  26.3809  40.6547  26.4358
 1MI  H2   H  HCH2  0   0.241  27.8036  40.3015  27.3808
 1MI  H3   H  HCH2  0   0.181  26.7598  37.8867  26.8584
 1MI  H4   H  HCH2  0   0.203  26.1089  37.2617  28.3746
 1MI  H5   H  HCH2  0   0.182  24.5566  39.0466  26.6301
 1MI  H6   H  HCH2  0   0.213  24.1031  40.3177  27.7616
 1MI  H7   H  HCH2  0   0.197  27.3416  42.5959  27.6302
 1MI  H8   H  HCH2  0   0.189  27.1094  41.7812  29.1749
 1MI  H9   H  HOH1  0   0.450  25.3598  43.1950  28.7268
 1MI  H10  H  HCH1  0   0.223  25.9971  39.6008  29.2517
 1MI  H11  H  HOH1  0   0.449  22.9543  38.3253  28.1299
 1MI  H12  H  HOH1  0   0.449  28.4410  37.2932  28.3165

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
 1MI  O2  C4   single  1.412  0.020  1.412
 1MI  O   C2   single  1.412  0.020  1.412
 1MI  C2  C    single  1.524  0.020  1.524
 1MI  C1  C4   single  1.517  0.020  1.517
 1MI  C1  C    single  1.536  0.020  1.536
 1MI  O1  C3   single  1.413  0.020  1.413
 1MI  C3  C    single  1.523  0.020  1.523
 1MI  C1  H1   single  0.970  0.020  1.090
 1MI  C1  H2   single  0.970  0.020  1.090
 1MI  C2  H3   single  0.970  0.020  1.090
 1MI  C2  H4   single  0.970  0.020  1.090
 1MI  C3  H5   single  0.970  0.020  1.090
 1MI  C3  H6   single  0.970  0.020  1.090
 1MI  C4  H7   single  0.970  0.020  1.090
 1MI  C4  H8   single  0.970  0.020  1.090
 1MI  O2  H9   single  0.850  0.020  0.980
 1MI  C   H10  single  0.970  0.020  1.090
 1MI  O1  H11  single  0.850  0.020  0.980
 1MI  O   H12  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
 1MI  H2   C1  H1  105.70  3.000
 1MI  H2   C1  C   109.42  3.000
 1MI  H1   C1  C   110.02  3.000
 1MI  H2   C1  C4  105.89  3.000
 1MI  H1   C1  C4  109.81  3.000
 1MI  C    C1  C4  115.48  3.000
 1MI  H4   C2  H3  106.92  3.000
 1MI  H4   C2  O   110.88  3.000
 1MI  H3   C2  O   111.39  3.000
 1MI  H4   C2  C   109.71  3.000
 1MI  H3   C2  C   108.63  3.000
 1MI  O    C2  C   109.26  3.000
 1MI  H6   C3  H5  106.76  3.000
 1MI  H6   C3  O1  111.18  3.000
 1MI  H5   C3  O1  111.36  3.000
 1MI  H6   C3  C   109.15  3.000
 1MI  H5   C3  C   108.53  3.000
 1MI  O1   C3  C   109.77  3.000
 1MI  H8   C4  H7  106.65  3.000
 1MI  H8   C4  O2  111.14  3.000
 1MI  H7   C4  O2  111.01  3.000
 1MI  H8   C4  C1  108.60  3.000
 1MI  H7   C4  C1  108.51  3.000
 1MI  O2   C4  C1  110.79  3.000
 1MI  H9   O2  C4  108.29  3.000
 1MI  H10  C   C3  108.18  3.000
 1MI  H10  C   C2  107.85  3.000
 1MI  C3   C   C2  110.09  3.000
 1MI  H10  C   C1  108.82  3.000
 1MI  C3   C   C1  110.64  3.000
 1MI  C2   C   C1  111.16  3.000
 1MI  H11  O1  C3  108.10  3.000
 1MI  H12  O   C2  108.14  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
 1MI  Var_01  O    C2  C   C1    63.51  30.0  3
 1MI  Var_02  O1   C3  C   C1  -172.51  30.0  2
 1MI  Var_03  C4   C1  C   C2  -147.01  30.0  2
 1MI  Var_04  O1   C3  C   C2    64.23  30.0  2
 1MI  Var_05  O    C2  C   C3  -173.54  30.0  3
 1MI  Var_06  C4   C1  C   C3    90.35  30.0  2
 1MI  Var_07  C    C1  C4  O2   -64.20  30.0  1
 1MI  Var_08  H3   C2  C   C1   -58.19  30.0  3
 1MI  Var_09  H4   C2  C   C1  -174.74  30.0  3
 1MI  Var_10  H5   C3  C   C1    65.57  30.0  2
 1MI  Var_11  H6   C3  C   C1   -50.42  30.0  2
 1MI  Var_12  H1   C1  C   C2    88.01  30.0  2
 1MI  Var_13  H2   C1  C   C2   -27.70  30.0  2
 1MI  Var_14  H5   C3  C   C2   -57.69  30.0  2
 1MI  Var_15  H6   C3  C   C2  -173.68  30.0  2
 1MI  Var_16  H3   C2  C   C3    64.77  30.0  3
 1MI  Var_17  H4   C2  C   C3   -51.79  30.0  3
 1MI  Var_18  H1   C1  C   C3   -34.63  30.0  2
 1MI  Var_19  H2   C1  C   C3  -150.34  30.0  2
 1MI  Var_20  H10  C   C1  C4   -28.38  30.0  3
 1MI  Var_21  H1   C1  C4  O2    60.89  30.0  1
 1MI  Var_22  H2   C1  C4  O2   174.57  30.0  1
 1MI  Var_23  H7   C4  C1  C    173.70  30.0  3
 1MI  Var_24  H8   C4  C1  C     58.14  30.0  3
 1MI  Var_25  H10  C   C3  O1   -53.39  30.0  3
 1MI  Var_26  H10  C   C2  O    -55.71  30.0  3

