# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 21:57:57 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: 4-(aminomethyl)-5-(hydroxymethyl)-2-methylpyridin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO)c(CN)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
 PXM  PXM  4-(aminomethyl)-5-(hydroxymethyl)-2-methylpyridin-3-ol  ligand  24  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_PXM
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
 PXM  N1    N  N     0  -0.410   1.9739  -0.0983   0.8287
 PXM  C2    C  CR6   0   0.121   0.9293  -0.1291   1.6395
 PXM  C2A   C  CH3   0  -0.719   1.1706  -0.2685   3.1117
 PXM  C3    C  CR6   0   0.271  -0.3801  -0.0251   1.1449
 PXM  O3    O  OH1   0  -0.654  -1.3946  -0.0476   2.0202
 PXM  C4    C  CR6   0   0.018  -0.5865   0.1094  -0.2305
 PXM  C5    C  CR6   0  -0.061   0.5333   0.1352  -1.0673
 PXM  C5A   C  CH2   0  -0.203   0.3704   0.2857  -2.5567
 PXM  O5    O  OH1   0  -0.667   1.6274   0.2881  -3.1807
 PXM  C6    C  CR16  0  -0.154   1.7857   0.0272  -0.4823
 PXM  C4A   C  CH2   0  -0.346  -1.9882   0.2765  -0.7647
 PXM  N4    N  NH2   0  -0.830  -2.9434  -0.5159   0.0090
 PXM  H2A1  H  HCH3  0   0.242   0.8270   0.6094   3.6629
 PXM  H2A2  H  HCH3  0   0.241   0.6415  -1.1280   3.5271
 PXM  H2A3  H  HCH3  0   0.242   2.2344  -0.3946   3.3035
 PXM  HO3   H  HOH1  0   0.473  -2.2227  -0.2291   1.4766
 PXM  H5A1  H  HCH2  0   0.220  -0.1798   1.2132  -2.7676
 PXM  H5A2  H  HCH2  0   0.219  -0.2580  -0.5353  -2.9314
 PXM  HO5   H  HOH1  0   0.463   1.4878   0.3831  -4.1269
 PXM  H6    H  HCR6  0   0.250   2.6814   0.0418  -1.0895
 PXM  H4A1  H  HCH2  0   0.249  -2.0314   0.0442  -1.8314
 PXM  H4A2  H  HCH2  0   0.272  -2.2740   1.3278  -0.6703
 PXM  HN41  H  HNH2  0   0.387  -3.8904  -0.2218  -0.1902
 PXM  HN42  H  HNH2  0   0.379  -2.8779  -1.4941  -0.2447

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
 PXM  N1   C2    aromatic  1.323  0.020  1.323
 PXM  N1   C6    aromatic  1.330  0.020  1.330
 PXM  C2   C2A   single    1.498  0.020  1.498
 PXM  C2   C3    aromatic  1.404  0.020  1.404
 PXM  C2A  H2A1  single    0.970  0.020  1.090
 PXM  C2A  H2A2  single    0.970  0.020  1.090
 PXM  C2A  H2A3  single    0.970  0.020  1.090
 PXM  C3   O3    single    1.340  0.020  1.340
 PXM  C3   C4    aromatic  1.397  0.020  1.397
 PXM  O3   HO3   single    0.850  0.020  0.980
 PXM  C4   C5    aromatic  1.398  0.020  1.398
 PXM  C4   C4A   single    1.509  0.020  1.509
 PXM  C5   C5A   single    1.506  0.020  1.506
 PXM  C5   C6    aromatic  1.387  0.020  1.387
 PXM  C5A  O5    single    1.403  0.020  1.403
 PXM  C5A  H5A1  single    0.970  0.020  1.090
 PXM  C5A  H5A2  single    0.970  0.020  1.090
 PXM  O5   HO5   single    0.850  0.020  0.980
 PXM  C6   H6    single    0.930  0.020  1.080
 PXM  C4A  N4    single    1.463  0.020  1.463
 PXM  C4A  H4A1  single    0.970  0.020  1.090
 PXM  C4A  H4A2  single    0.970  0.020  1.090
 PXM  N4   HN41  single    0.890  0.020  1.040
 PXM  N4   HN42  single    0.890  0.020  1.040

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
 PXM  C6    N1   C2    119.64  3.000
 PXM  C3    C2   C2A   120.23  3.000
 PXM  C3    C2   N1    121.27  3.000
 PXM  C2A   C2   N1    118.51  3.000
 PXM  H2A3  C2A  H2A2  108.40  3.000
 PXM  H2A3  C2A  H2A1  108.16  3.000
 PXM  H2A2  C2A  H2A1  106.76  3.000
 PXM  H2A3  C2A  C2    109.96  3.000
 PXM  H2A2  C2A  C2    111.66  3.000
 PXM  H2A1  C2A  C2    111.74  3.000
 PXM  C4    C3   O3    122.19  3.000
 PXM  C4    C3   C2    119.46  3.000
 PXM  O3    C3   C2    118.35  3.000
 PXM  HO3   O3   C3    105.84  3.000
 PXM  C4A   C4   C5    122.00  3.000
 PXM  C4A   C4   C3    119.75  3.000
 PXM  C5    C4   C3    118.20  3.000
 PXM  C6    C5   C5A   121.52  3.000
 PXM  C6    C5   C4    118.00  3.000
 PXM  C5A   C5   C4    120.48  3.000
 PXM  H5A2  C5A  H5A1  106.17  3.000
 PXM  H5A2  C5A  O5    111.20  3.000
 PXM  H5A1  C5A  O5    111.21  3.000
 PXM  H5A2  C5A  C5    108.92  3.000
 PXM  H5A1  C5A  C5    109.17  3.000
 PXM  O5    C5A  C5    110.07  3.000
 PXM  HO5   O5   C5A   107.93  3.000
 PXM  H6    C6   C5    120.65  3.000
 PXM  H6    C6   N1    115.92  3.000
 PXM  C5    C6   N1    123.43  3.000
 PXM  H4A2  C4A  H4A1  106.16  3.000
 PXM  H4A2  C4A  N4    107.73  3.000
 PXM  H4A1  C4A  N4    112.06  3.000
 PXM  H4A2  C4A  C4    108.58  3.000
 PXM  H4A1  C4A  C4    111.02  3.000
 PXM  N4    C4A  C4    111.06  3.000
 PXM  HN42  N4   HN41  106.98  3.000
 PXM  HN42  N4   C4A   110.40  3.000
 PXM  HN41  N4   C4A   110.48  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
 PXM  CONST_01  C4    C3   C2   N1     0.00   0.0  0
 PXM  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 PXM  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 PXM  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 PXM  CONST_05  C6    N1   C2   C3     0.00   0.0  0
 PXM  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 PXM  CONST_07  O3    C3   C2   N1   180.00   0.0  0
 PXM  CONST_08  C5A   C5   C6   N1   180.00   0.0  0
 PXM  CONST_09  C4A   C4   C3   C2   180.00   0.0  0
 PXM  CONST_10  C6    N1   C2   C2A  180.00   0.0  0
 PXM  CONST_11  C4    C3   C2   C2A  180.00   0.0  0
 PXM  CONST_12  C5A   C5   C4   C3   180.00   0.0  0
 PXM  CONST_13  C5    C4   C3   O3   180.00   0.0  0
 PXM  CONST_14  C4A   C4   C5   C6   180.00   0.0  0
 PXM  CONST_15  H6    C6   N1   C2   180.00   0.0  0
 PXM  Var_01    N4    C4A  C4   C3   -36.09  30.0  2
 PXM  Var_02    O5    C5A  C5   C4   179.84  30.0  2
 PXM  Var_03    H2A1  C2A  C2   N1   116.36  30.0  2
 PXM  Var_04    HN41  N4   C4A  C4   165.33  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
 PXM  plan-1  N1   0.020
 PXM  plan-1  C2   0.020
 PXM  plan-1  C2A  0.020
 PXM  plan-1  C3   0.020
 PXM  plan-1  O3   0.020
 PXM  plan-1  C4   0.020
 PXM  plan-1  C5   0.020
 PXM  plan-1  C5A  0.020
 PXM  plan-1  C6   0.020
 PXM  plan-1  C4A  0.020
 PXM  plan-1  H6   0.020

