# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 21:59:19 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: 3-hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carbaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO)c(C=O)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
 PXL  PXL  3-hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carbaldehyde  ligand  21  12  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PXL
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
 PXL  OP4   O  OH1   0  -0.663   0.6008  -0.0463  -3.5078
 PXL  C5A   C  CH2   0  -0.207  -0.4260  -0.0343  -2.5553
 PXL  C5    C  CR6   0  -0.035   0.1644  -0.0455  -1.1700
 PXL  C6    C  CR16  0  -0.145   1.5277  -0.0266  -0.9622
 PXL  N1    N  N     0  -0.389   2.0842  -0.0346   0.2534
 PXL  C2    C  CR6   0   0.141   1.3399  -0.0600   1.3366
 PXL  C3    C  CR6   0   0.310  -0.0672  -0.0791   1.2394
 PXL  C4    C  CR6   0  -0.088  -0.6605  -0.0719  -0.0280
 PXL  C4A   C  C1    0   0.157  -2.1174  -0.0907  -0.1375
 PXL  O4A   O  O     0  -0.417  -2.8630  -0.1151   0.8280
 PXL  O3    O  OH1   0  -0.608  -0.7622  -0.1029   2.3695
 PXL  C2A   C  CH3   0  -0.719   2.0032  -0.0694   2.6776
 PXL  HP4   H  HOH1  0   0.467   0.1963  -0.0152  -4.3794
 PXL  H5A1  H  HCH2  0   0.229  -1.0865  -0.9040  -2.6685
 PXL  H5A2  H  HCH2  0   0.231  -1.0616   0.8550  -2.6614
 PXL  H6    H  HCR6  0   0.267   2.2184  -0.0051  -1.7934
 PXL  H4A   H  H     0   0.236  -2.5456  -0.0807  -1.1484
 PXL  HO3   H  HOH1  0   0.480  -1.7173  -0.1146   2.1495
 PXL  H2A1  H  HCH3  0   0.251   1.7075   0.7929   3.2775
 PXL  H2A2  H  HCH3  0   0.251   1.7391  -0.9605   3.2492
 PXL  H2A3  H  HCH3  0   0.252   3.0836  -0.0480   2.5548

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
 PXL  OP4  C5A   single    1.401  0.020  1.401
 PXL  OP4  HP4   single    0.850  0.020  0.980
 PXL  C5A  C5    single    1.506  0.020  1.506
 PXL  C5A  H5A1  single    0.970  0.020  1.090
 PXL  C5A  H5A2  single    0.970  0.020  1.090
 PXL  C5   C6    aromatic  1.379  0.020  1.379
 PXL  C5   C4    aromatic  1.409  0.020  1.409
 PXL  C6   N1    aromatic  1.337  0.020  1.337
 PXL  C6   H6    single    0.930  0.020  1.080
 PXL  N1   C2    aromatic  1.314  0.020  1.314
 PXL  C2   C3    aromatic  1.411  0.020  1.411
 PXL  C2   C2A   single    1.496  0.020  1.496
 PXL  C3   C4    aromatic  1.399  0.020  1.399
 PXL  C3   O3    single    1.327  0.020  1.327
 PXL  C4   C4A   single    1.461  0.020  1.461
 PXL  C4A  O4A   double    1.220  0.020  1.220
 PXL  C4A  H4A   single    0.930  0.020  1.080
 PXL  O3   HO3   single    0.850  0.020  0.980
 PXL  C2A  H2A1  single    0.970  0.020  1.090
 PXL  C2A  H2A2  single    0.970  0.020  1.090
 PXL  C2A  H2A3  single    0.970  0.020  1.090

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
 PXL  HP4   OP4  C5A   107.92  3.000
 PXL  H5A2  C5A  H5A1  106.46  3.000
 PXL  H5A2  C5A  C5    108.78  3.000
 PXL  H5A1  C5A  C5    108.96  3.000
 PXL  H5A2  C5A  OP4   111.44  3.000
 PXL  H5A1  C5A  OP4   111.35  3.000
 PXL  C5    C5A  OP4   109.76  3.000
 PXL  C4    C5   C6    117.18  3.000
 PXL  C4    C5   C5A   121.07  3.000
 PXL  C6    C5   C5A   121.74  3.000
 PXL  H6    C6   N1    115.68  3.000
 PXL  H6    C6   C5    121.07  3.000
 PXL  N1    C6   C5    123.25  3.000
 PXL  C2    N1   C6    120.91  3.000
 PXL  C2A   C2   C3    120.26  3.000
 PXL  C2A   C2   N1    119.19  3.000
 PXL  C3    C2   N1    120.55  3.000
 PXL  O3    C3   C4    123.33  3.000
 PXL  O3    C3   C2    117.64  3.000
 PXL  C4    C3   C2    119.03  3.000
 PXL  C4A   C4   C3    119.38  3.000
 PXL  C4A   C4   C5    121.55  3.000
 PXL  C3    C4   C5    119.07  3.000
 PXL  H4A   C4A  O4A   119.37  3.000
 PXL  H4A   C4A  C4    117.25  3.000
 PXL  O4A   C4A  C4    123.38  3.000
 PXL  HO3   O3   C3    108.62  3.000
 PXL  H2A3  C2A  H2A2  108.41  3.000
 PXL  H2A3  C2A  H2A1  108.41  3.000
 PXL  H2A2  C2A  H2A1  106.96  3.000
 PXL  H2A3  C2A  C2    109.82  3.000
 PXL  H2A2  C2A  C2    111.55  3.000
 PXL  H2A1  C2A  C2    111.57  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
 PXL  CONST_01  C2    N1   C6   C5     0.00   0.0  0
 PXL  CONST_02  C2    C3   C4   C5     0.00   0.0  0
 PXL  CONST_03  C3    C4   C5   C6     0.00   0.0  0
 PXL  CONST_04  C3    C2   N1   C6     0.00   0.0  0
 PXL  CONST_05  C4    C5   C6   N1     0.00   0.0  0
 PXL  CONST_06  C4    C3   C2   N1     0.00   0.0  0
 PXL  CONST_07  N1    C6   C5   C5A  180.00   0.0  0
 PXL  CONST_08  C3    C4   C5   C5A  180.00   0.0  0
 PXL  CONST_09  O3    C3   C4   C5   180.00   0.0  0
 PXL  CONST_10  C4A   C4   C5   C6   180.00   0.0  0
 PXL  CONST_11  C2A   C2   N1   C6   180.00   0.0  0
 PXL  CONST_12  O3    C3   C2   N1   180.00   0.0  0
 PXL  CONST_13  C4A   C4   C3   C2   180.00   0.0  0
 PXL  CONST_14  C2A   C2   C3   C4   180.00   0.0  0
 PXL  CONST_15  H6    C6   N1   C2   180.00   0.0  0
 PXL  Var_01    C6    C5   C5A  OP4    1.86  30.0  2
 PXL  Var_02    O4A   C4A  C4   C5   179.92  30.0  2
 PXL  Var_03    H2A1  C2A  C2   N1   120.49  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
 PXL  plan-1  C5A  0.020
 PXL  plan-1  C5   0.020
 PXL  plan-1  C6   0.020
 PXL  plan-1  N1   0.020
 PXL  plan-1  C2   0.020
 PXL  plan-1  C3   0.020
 PXL  plan-1  C4   0.020
 PXL  plan-1  C4A  0.020
 PXL  plan-1  O3   0.020
 PXL  plan-1  C2A  0.020
 PXL  plan-1  H6   0.020
 PXL  plan-2  C4   0.020
 PXL  plan-2  C4A  0.020
 PXL  plan-2  O4A  0.020
 PXL  plan-2  H4A  0.020

