# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 09:49:28 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCc1c(O)c(C)ncc1CO
#
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
 GT0  GT0  5-(hydroxymethyl)-4-(methoxymethyl)-2-methylpyridin-3-ol  ligand  26  13  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GT0
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
 GT0  C8   C  CR16  0  -0.148   1.1890   1.8011   0.0112
 GT0  N1   N  N     0  -0.408   2.2406   1.0023   0.1725
 GT0  C7   C  CR6   0   0.130   2.0718  -0.3086   0.1852
 GT0  C4   C  CR6   0   0.264   0.7990  -0.8771   0.0282
 GT0  C6   C  CR6   0  -0.005  -0.3086  -0.0491  -0.1453
 GT0  C2   C  CR6   0  -0.056  -0.1055   1.3350  -0.1533
 GT0  C1   C  CH2   0  -0.193  -1.6704  -0.6437  -0.3889
 GT0  O3   O  O2    0  -0.509  -1.8373  -1.7949   0.4130
 GT0  C3   C  CH3   0  -0.397  -3.0556  -2.4647   0.1612
 GT0  C5   C  CH2   0  -0.206  -1.2648   2.2765  -0.3450
 GT0  O2   O  OH1   0  -0.665  -0.8172   3.6049  -0.3173
 GT0  C9   C  CH3   0  -0.721   3.2740  -1.1839   0.3658
 GT0  O1   O  OH1   0  -0.641   0.7162  -2.2190   0.0366
 GT0  H1   H  HCR6  0   0.255   1.3968   2.8630   0.0148
 GT0  H2   H  HCH2  0   0.244  -2.4640   0.0768  -0.1664
 GT0  H3   H  HCH2  0   0.247  -1.7700  -0.8999  -1.4538
 GT0  H4   H  HCH3  0   0.247  -3.1026  -3.3261   0.8237
 GT0  H5   H  HCH3  0   0.223  -3.9117  -1.8143   0.3648
 GT0  H6   H  HCH3  0   0.220  -3.1208  -2.8084  -0.8758
 GT0  H7   H  HCH2  0   0.223  -1.7625   2.0425  -1.2957
 GT0  H8   H  HCH2  0   0.222  -2.0081   2.0889   0.4432
 GT0  H9   H  HOH1  0   0.464  -1.5713   4.1751  -0.4910
 GT0  H10  H  HCH3  0   0.245   3.4058  -1.8705  -0.4725
 GT0  H11  H  HCH3  0   0.245   4.1697  -0.5716   0.4476
 GT0  H12  H  HCH3  0   0.245   3.1948  -1.7959   1.2664
 GT0  H13  H  HOH1  0   0.474  -0.2195  -2.4669   0.1624

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
 GT0  C9  C7   single    1.498  0.020  1.498
 GT0  O1  C4   single    1.344  0.020  1.344
 GT0  C7  C4   aromatic  1.403  0.020  1.403
 GT0  C7  N1   aromatic  1.322  0.020  1.322
 GT0  C4  C6   aromatic  1.394  0.020  1.394
 GT0  N1  C8   aromatic  1.330  0.020  1.330
 GT0  C6  C1   single    1.506  0.020  1.506
 GT0  C6  C2   aromatic  1.399  0.020  1.399
 GT0  C1  O3   single    1.413  0.020  1.413
 GT0  C8  C2   aromatic  1.386  0.020  1.386
 GT0  C2  C5   single    1.506  0.020  1.506
 GT0  O3  C3   single    1.413  0.020  1.413
 GT0  C5  O2   single    1.402  0.020  1.402
 GT0  C8  H1   single    0.930  0.020  1.080
 GT0  C1  H2   single    0.970  0.020  1.090
 GT0  C1  H3   single    0.970  0.020  1.090
 GT0  C3  H4   single    0.970  0.020  1.090
 GT0  C3  H5   single    0.970  0.020  1.090
 GT0  C3  H6   single    0.970  0.020  1.090
 GT0  C5  H7   single    0.970  0.020  1.090
 GT0  C5  H8   single    0.970  0.020  1.090
 GT0  O2  H9   single    0.850  0.020  0.980
 GT0  C9  H10  single    0.970  0.020  1.090
 GT0  C9  H11  single    0.970  0.020  1.090
 GT0  C9  H12  single    0.970  0.020  1.090
 GT0  O1  H13  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
 GT0  H1   C8  C2   120.66  3.000
 GT0  H1   C8  N1   115.92  3.000
 GT0  C2   C8  N1   123.42  3.000
 GT0  C7   N1  C8   119.72  3.000
 GT0  C9   C7  C4   120.32  3.000
 GT0  C4   C7  N1   121.11  3.000
 GT0  C9   C7  N1   118.57  3.000
 GT0  O1   C4  C6   123.01  3.000
 GT0  C6   C4  C7   119.62  3.000
 GT0  O1   C4  C7   117.37  3.000
 GT0  C1   C6  C2   121.40  3.000
 GT0  C2   C6  C4   118.24  3.000
 GT0  C1   C6  C4   120.28  3.000
 GT0  C5   C2  C6   120.50  3.000
 GT0  C5   C2  C8   121.61  3.000
 GT0  C6   C2  C8   117.89  3.000
 GT0  H3   C1  H2   106.53  3.000
 GT0  H3   C1  O3   110.43  3.000
 GT0  H2   C1  O3   109.59  3.000
 GT0  H3   C1  C6   109.30  3.000
 GT0  H2   C1  C6   111.28  3.000
 GT0  O3   C1  C6   109.68  3.000
 GT0  C3   O3  C1   112.76  3.000
 GT0  H6   C3  H5   108.44  3.000
 GT0  H6   C3  H4   109.01  3.000
 GT0  H5   C3  H4   108.88  3.000
 GT0  H6   C3  O3   111.66  3.000
 GT0  H5   C3  O3   111.09  3.000
 GT0  H4   C3  O3   107.70  3.000
 GT0  H8   C5  H7   106.13  3.000
 GT0  H8   C5  O2   111.30  3.000
 GT0  H7   C5  O2   111.33  3.000
 GT0  H8   C5  C2   108.82  3.000
 GT0  H7   C5  C2   109.02  3.000
 GT0  O2   C5  C2   110.12  3.000
 GT0  H9   O2  C5   107.94  3.000
 GT0  H12  C9  H11  108.25  3.000
 GT0  H12  C9  H10  106.84  3.000
 GT0  H11  C9  H10  108.19  3.000
 GT0  H12  C9  C7   111.65  3.000
 GT0  H11  C9  C7   109.93  3.000
 GT0  H10  C9  C7   111.83  3.000
 GT0  H13  O1  C4   108.25  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
 GT0  CONST_01  C4   C7  N1  C8     0.00   0.0  0
 GT0  CONST_02  C4   C6  C2  C8     0.00   0.0  0
 GT0  CONST_03  C6   C4  C7  N1     0.00   0.0  0
 GT0  CONST_04  C6   C2  C8  N1     0.00   0.0  0
 GT0  CONST_05  C2   C6  C4  C7     0.00   0.0  0
 GT0  CONST_06  C2   C8  N1  C7     0.00   0.0  0
 GT0  CONST_07  C9   C7  N1  C8   180.00   0.0  0
 GT0  CONST_08  C1   C6  C2  C8   180.00   0.0  0
 GT0  CONST_09  O1   C4  C7  N1   180.00   0.0  0
 GT0  CONST_10  C5   C2  C8  N1   180.00   0.0  0
 GT0  CONST_11  C1   C6  C4  C7   180.00   0.0  0
 GT0  CONST_12  C5   C2  C6  C4   180.00   0.0  0
 GT0  CONST_13  C9   C7  C4  C6   180.00   0.0  0
 GT0  CONST_14  O1   C4  C6  C2   180.00   0.0  0
 GT0  CONST_15  H1   C8  N1  C7   180.00   0.0  0
 GT0  Var_01    O2   C5  C2  C8    -0.39  30.0  2
 GT0  Var_02    O3   C1  C6  C4    39.13  30.0  2
 GT0  Var_03    H10  C9  C7  N1  -121.27  30.0  2
 GT0  Var_04    H4   C3  O3  C1  -179.51  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
 GT0  plan-1  C8  0.020
 GT0  plan-1  N1  0.020
 GT0  plan-1  C7  0.020
 GT0  plan-1  C4  0.020
 GT0  plan-1  C6  0.020
 GT0  plan-1  C2  0.020
 GT0  plan-1  C1  0.020
 GT0  plan-1  C5  0.020
 GT0  plan-1  C9  0.020
 GT0  plan-1  O1  0.020
 GT0  plan-1  H1  0.020

