# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:21:44 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: 5-hydroxy-4-(hydroxymethyl)-6-methylpyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(C(O)=O)c(CO)c1O
#
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
 5PR  5PR  '5-hydroxy-4-(hydroxymethyl)-6-methylpyridine-3-carboxylic acid'  ligand  21  13  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5PR
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
 5PR  N1    N  N      0  -0.411  -1.3547   1.8839  -0.0755
 5PR  C2    C  CR6    0   0.126  -2.0289   0.7431  -0.1145
 5PR  C3    C  CR6    0   0.271  -1.3706  -0.4888  -0.0258
 5PR  O3    O  OH1    0  -0.649  -2.1310  -1.6005  -0.0240
 5PR  C4    C  CR6    0   0.009   0.0237  -0.5321   0.0729
 5PR  C5    C  CR6    0  -0.169   0.7164   0.6821   0.1151
 5PR  C6    C  CR16   0  -0.138  -0.0349   1.8504   0.0516
 5PR  C2A   C  CH3    0  -0.720  -3.5204   0.8016  -0.2421
 5PR  C4A   C  CH2    0  -0.237   0.7018  -1.8669   0.2419
 5PR  O4A   O  OH1    0  -0.679   0.0800  -2.8177  -0.6196
 5PR  O51   O  OC    -1  -0.588   2.6432   1.7249   0.9603
 5PR  O52   O  O      0  -0.588   2.9231   0.0605  -0.4949
 5PR  C5A   C  C      0   0.362   2.2333   0.8235   0.2081
 5PR  HO3   H  HOH1   0   0.471  -1.5441  -2.3583  -0.2256
 5PR  H6    H  HCR6   0   0.245   0.4652   2.8116   0.0897
 5PR  H2A   H  HCH3   0   0.242  -3.8766   0.2184  -1.0929
 5PR  H2AA  H  HCH3   0   0.243  -4.0200   0.4056   0.6447
 5PR  H2AB  H  HCH3   0   0.242  -3.8394   1.8334  -0.3759
 5PR  H4A   H  HCH2   0   0.255   1.7620  -1.7796   0.0175
 5PR  H4AA  H  HCH2   0   0.235   0.6036  -2.1766   1.2896
 5PR  HO4A  H  HOH1   0   0.476   0.3651  -3.6986  -0.3561

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
 5PR  N1   C2    aromatic  1.326  0.020  1.326
 5PR  N1   C6    aromatic  1.326  0.020  1.326
 5PR  C2   C3    aromatic  1.400  0.020  1.400
 5PR  C2   C2A   single    1.498  0.020  1.498
 5PR  C3   O3    single    1.347  0.020  1.347
 5PR  C3   C4    aromatic  1.398  0.020  1.398
 5PR  C4   C5    aromatic  1.399  0.020  1.399
 5PR  C4   C4A   single    1.507  0.020  1.507
 5PR  C5   C6    aromatic  1.390  0.020  1.390
 5PR  C5   C5A   single    1.526  0.020  1.526
 5PR  C4A  O4A   single    1.426  0.020  1.426
 5PR  O51  C5A   deloc     1.244  0.020  1.244
 5PR  O52  C5A   deloc     1.246  0.020  1.246
 5PR  O3   HO3   single    0.850  0.020  0.980
 5PR  C6   H6    single    0.930  0.020  1.080
 5PR  C2A  H2A   single    0.970  0.020  1.090
 5PR  C2A  H2AA  single    0.970  0.020  1.090
 5PR  C2A  H2AB  single    0.970  0.020  1.090
 5PR  C4A  H4A   single    0.970  0.020  1.090
 5PR  C4A  H4AA  single    0.970  0.020  1.090
 5PR  O4A  HO4A  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
 5PR  C6    N1   C2    119.15  3.000
 5PR  C2A   C2   C3    120.54  3.000
 5PR  C2A   C2   N1    118.37  3.000
 5PR  C3    C2   N1    121.09  3.000
 5PR  C4    C3   O3    122.49  3.000
 5PR  C4    C3   C2    120.05  3.000
 5PR  O3    C3   C2    117.46  3.000
 5PR  HO3   O3   C3    107.47  3.000
 5PR  C4A   C4   C5    122.88  3.000
 5PR  C4A   C4   C3    118.95  3.000
 5PR  C5    C4   C3    117.97  3.000
 5PR  C5A   C5   C6    117.51  3.000
 5PR  C5A   C5   C4    125.06  3.000
 5PR  C6    C5   C4    117.42  3.000
 5PR  H6    C6   C5    119.61  3.000
 5PR  H6    C6   N1    116.10  3.000
 5PR  C5    C6   N1    124.28  3.000
 5PR  H2AB  C2A  H2AA  108.03  3.000
 5PR  H2AB  C2A  H2A   108.37  3.000
 5PR  H2AA  C2A  H2A   106.86  3.000
 5PR  H2AB  C2A  C2    109.84  3.000
 5PR  H2AA  C2A  C2    111.84  3.000
 5PR  H2A   C2A  C2    111.75  3.000
 5PR  H4AA  C4A  H4A   107.89  3.000
 5PR  H4AA  C4A  O4A   110.48  3.000
 5PR  H4A   C4A  O4A   110.74  3.000
 5PR  H4AA  C4A  C4    108.48  3.000
 5PR  H4A   C4A  C4    110.15  3.000
 5PR  O4A   C4A  C4    109.07  3.000
 5PR  HO4A  O4A  C4A   108.41  3.000
 5PR  O52   C5A  O51   127.07  3.000
 5PR  O52   C5A  C5    117.33  3.000
 5PR  O51   C5A  C5    115.57  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
 5PR  CONST_01  C4   C3   C2  N1     0.00   0.0  0
 5PR  CONST_02  C4   C5   C6  N1     0.00   0.0  0
 5PR  CONST_03  C5   C6   N1  C2     0.00   0.0  0
 5PR  CONST_04  C5   C4   C3  C2     0.00   0.0  0
 5PR  CONST_05  C6   N1   C2  C3     0.00   0.0  0
 5PR  CONST_06  C6   C5   C4  C3     0.00   0.0  0
 5PR  CONST_07  O3   C3   C2  N1   180.00   0.0  0
 5PR  CONST_08  C5A  C5   C6  N1   180.00   0.0  0
 5PR  CONST_09  C4A  C4   C3  C2   180.00   0.0  0
 5PR  CONST_10  C5A  C5   C4  C3   180.00   0.0  0
 5PR  CONST_11  C5   C4   C3  O3   180.00   0.0  0
 5PR  CONST_12  C2A  C2   C3  C4   180.00   0.0  0
 5PR  CONST_13  C2A  C2   N1  C6   180.00   0.0  0
 5PR  CONST_14  C4A  C4   C5  C6   180.00   0.0  0
 5PR  CONST_15  H6   C6   N1  C2   180.00   0.0  0
 5PR  Var_01    O4A  C4A  C4  C3    41.96  30.0  2
 5PR  Var_02    O51  C5A  C5  C4  -139.68  30.0  2
 5PR  Var_03    H2A  C2A  C2  N1   125.34  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
 5PR  plan-1  N1   0.020
 5PR  plan-1  C2   0.020
 5PR  plan-1  C3   0.020
 5PR  plan-1  O3   0.020
 5PR  plan-1  C4   0.020
 5PR  plan-1  C5   0.020
 5PR  plan-1  C6   0.020
 5PR  plan-1  C2A  0.020
 5PR  plan-1  C4A  0.020
 5PR  plan-1  C5A  0.020
 5PR  plan-1  H6   0.020
 5PR  plan-2  C5   0.020
 5PR  plan-2  O51  0.020
 5PR  plan-2  O52  0.020
 5PR  plan-2  C5A  0.020

