# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 16:21:54 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-(2-hydroxyethyl)-2-methylpyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(C[n+]2cccc(CCO)c2C)c(N)n1
#
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
 218  218  1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-(2-hydroxyethyl)-2-methylpyridinium  ligand  38  19  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_218
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
 218  CM2   C  CH3   0  -0.728   4.6241   2.0440   1.2521
 218  C2A   C  CR6   0   0.364   3.6435   1.2596   0.4415
 218  N1A   N  N     0  -0.437   3.1255   1.8471  -0.6329
 218  C6A   C  CR16  0  -0.065   2.1918   1.1569  -1.2781
 218  C5A   C  CR6   0  -0.038   1.7652  -0.1009  -0.9111
 218  C7A   C  CH2   0  -0.483   0.6823  -0.8044  -1.6647
 218  N3    N  NR6   1  -0.442  -0.5176  -1.0817  -0.8304
 218  C2    C  CR16  0   0.045  -0.7701  -2.3703  -0.5440
 218  C1    C  CR16  0  -0.338  -1.8160  -2.7287   0.2615
 218  C6    C  CR16  0  -0.110  -2.6102  -1.7256   0.7874
 218  C5    C  CR6   0  -0.027  -2.3669  -0.3946   0.4785
 218  CM6   C  CH2   0  -0.580  -3.2842   0.6576   1.0330
 218  CM7   C  CH2   0  -0.129  -4.4679   0.8869   0.0992
 218  OM7   O  OH1   0  -0.665  -5.2897   1.8756   0.6682
 218  C4    C  CR6   0   0.412  -1.3048  -0.0791  -0.3703
 218  CM4   C  CH3   0  -0.759  -1.0188   1.3254  -0.7781
 218  C4A   C  CR6   0   0.471   2.4477  -0.6701   0.1863
 218  N4A   N  NH2   0  -0.822   2.1981  -1.9205   0.6231
 218  N3A   N  N     0  -0.457   3.3528   0.0376   0.8615
 218  HM21  H  HCH3  0   0.262   4.1079   2.5326   2.0818
 218  HM22  H  HCH3  0   0.252   5.3894   1.3988   1.6790
 218  HM23  H  HCH3  0   0.251   5.0941   2.8192   0.6514
 218  H6A   H  HCR6  0   0.276   1.7516   1.6403  -2.1456
 218  H7A1  H  HCH2  0   0.335   0.3723  -0.2246  -2.5324
 218  H7A2  H  HCH2  0   0.328   1.0140  -1.7679  -2.0502
 218  H2    H  HCR6  0   0.349  -0.1180  -3.1053  -0.9904
 218  H1    H  HCR6  0   0.314  -1.9940  -3.7719   0.4725
 218  H6    H  HCR6  0   0.304  -3.4348  -1.9767   1.4425
 218  HM61  H  HCH2  0   0.281  -3.6519   0.3180   2.0030
 218  HM62  H  HCH2  0   0.274  -2.7558   1.5951   1.2095
 218  HM71  H  HCH2  0   0.204  -4.1015   1.1847  -0.8925
 218  HM72  H  HCH2  0   0.210  -5.0020  -0.0629  -0.0344
 218  HOM7  H  HOH1  0   0.459  -6.0354   2.0210   0.0788
 218  HM41  H  HCH3  0   0.300  -0.2468   1.7677  -0.1472
 218  HM42  H  HCH3  0   0.284  -0.6973   1.4030  -1.8139
 218  HM43  H  HCH3  0   0.298  -1.9076   1.9397  -0.6803
 218  H4A1  H  HNH2  0   0.401   1.8636  -2.6161  -0.0215
 218  H4A2  H  HNH2  0   0.404   2.8199  -2.2822   1.3294

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
 218  CM2  C2A   single    1.495  0.020  1.495
 218  CM2  HM21  single    0.970  0.020  1.090
 218  CM2  HM22  single    0.970  0.020  1.090
 218  CM2  HM23  single    0.970  0.020  1.090
 218  C2A  N1A   aromatic  1.330  0.020  1.330
 218  C2A  N3A   aromatic  1.324  0.020  1.324
 218  N1A  C6A   aromatic  1.328  0.020  1.328
 218  C6A  C5A   aromatic  1.378  0.020  1.378
 218  C6A  H6A   single    0.930  0.020  1.080
 218  C5A  C7A   single    1.495  0.020  1.495
 218  C5A  C4A   aromatic  1.412  0.020  1.412
 218  C7A  N3    single    1.488  0.020  1.488
 218  C7A  H7A1  single    0.970  0.020  1.090
 218  C7A  H7A2  single    0.970  0.020  1.090
 218  N3   C2    aromatic  1.344  0.020  1.344
 218  N3   C4    aromatic  1.355  0.020  1.355
 218  C2   C1    aromatic  1.368  0.020  1.368
 218  C2   H2    single    0.930  0.020  1.080
 218  C1   C6    aromatic  1.383  0.020  1.383
 218  C1   H1    single    0.930  0.020  1.080
 218  C6   C5    aromatic  1.388  0.020  1.388
 218  C6   H6    single    0.930  0.020  1.080
 218  C5   CM6   single    1.502  0.020  1.502
 218  C5   C4    aromatic  1.396  0.020  1.396
 218  CM6  CM7   single    1.525  0.020  1.525
 218  CM6  HM61  single    0.970  0.020  1.090
 218  CM6  HM62  single    0.970  0.020  1.090
 218  CM7  OM7   single    1.406  0.020  1.406
 218  CM7  HM71  single    0.970  0.020  1.090
 218  CM7  HM72  single    0.970  0.020  1.090
 218  OM7  HOM7  single    0.850  0.020  0.980
 218  C4   CM4   single    1.490  0.020  1.490
 218  CM4  HM41  single    0.970  0.020  1.090
 218  CM4  HM42  single    0.970  0.020  1.090
 218  CM4  HM43  single    0.970  0.020  1.090
 218  C4A  N4A   single    1.348  0.020  1.348
 218  C4A  N3A   aromatic  1.333  0.020  1.333
 218  N4A  H4A1  single    0.890  0.020  1.040
 218  N4A  H4A2  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
 218  HM23  CM2  HM22  109.59  3.000
 218  HM23  CM2  HM21  107.75  3.000
 218  HM22  CM2  HM21  107.43  3.000
 218  HM23  CM2  C2A   110.99  3.000
 218  HM22  CM2  C2A   111.28  3.000
 218  HM21  CM2  C2A   109.67  3.000
 218  N3A   C2A  N1A   125.34  3.000
 218  N3A   C2A  CM2   117.14  3.000
 218  N1A   C2A  CM2   117.51  3.000
 218  C6A   N1A  C2A   115.90  3.000
 218  H6A   C6A  C5A   119.57  3.000
 218  H6A   C6A  N1A   116.20  3.000
 218  C5A   C6A  N1A   124.23  3.000
 218  C4A   C5A  C7A   123.51  3.000
 218  C4A   C5A  C6A   115.17  3.000
 218  C7A   C5A  C6A   121.30  3.000
 218  H7A2  C7A  H7A1  106.00  3.000
 218  H7A2  C7A  N3    106.22  3.000
 218  H7A1  C7A  N3    108.46  3.000
 218  H7A2  C7A  C5A   111.96  3.000
 218  H7A1  C7A  C5A   110.94  3.000
 218  N3    C7A  C5A   112.91  3.000
 218  C4    N3   C2    121.86  3.000
 218  C4    N3   C7A   121.41  3.000
 218  C2    N3   C7A   116.73  3.000
 218  H2    C2   C1    121.81  3.000
 218  H2    C2   N3    116.83  3.000
 218  C1    C2   N3    121.35  3.000
 218  H1    C1   C6    122.14  3.000
 218  H1    C1   C2    119.64  3.000
 218  C6    C1   C2    118.22  3.000
 218  H6    C6   C5    119.39  3.000
 218  H6    C6   C1    119.94  3.000
 218  C5    C6   C1    120.67  3.000
 218  C4    C5   CM6   122.07  3.000
 218  C4    C5   C6    119.05  3.000
 218  CM6   C5   C6    118.85  3.000
 218  HM62  CM6  HM61  106.67  3.000
 218  HM62  CM6  CM7   110.24  3.000
 218  HM61  CM6  CM7   109.23  3.000
 218  HM62  CM6  C5    111.47  3.000
 218  HM61  CM6  C5    108.41  3.000
 218  CM7   CM6  C5    110.69  3.000
 218  HM72  CM7  HM71  106.68  3.000
 218  HM72  CM7  OM7   111.92  3.000
 218  HM71  CM7  OM7   111.70  3.000
 218  HM72  CM7  CM6   108.79  3.000
 218  HM71  CM7  CM6   109.55  3.000
 218  OM7   CM7  CM6   108.16  3.000
 218  HOM7  OM7  CM7   108.15  3.000
 218  CM4   C4   C5    121.70  3.000
 218  CM4   C4   N3    119.53  3.000
 218  C5    C4   N3    118.77  3.000
 218  HM43  CM4  HM42  106.72  3.000
 218  HM43  CM4  HM41  107.34  3.000
 218  HM42  CM4  HM41  108.23  3.000
 218  HM43  CM4  C4    110.60  3.000
 218  HM42  CM4  C4    112.62  3.000
 218  HM41  CM4  C4    111.09  3.000
 218  N3A   C4A  N4A   117.02  3.000
 218  N3A   C4A  C5A   120.52  3.000
 218  N4A   C4A  C5A   122.43  3.000
 218  H4A2  N4A  H4A1  113.96  3.000
 218  H4A2  N4A  C4A   116.47  3.000
 218  H4A1  N4A  C4A   119.71  3.000
 218  C4A   N3A  C2A   118.58  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
 218  CONST_01  C5A   C6A  N1A  C2A     0.00   0.0  0
 218  CONST_02  C5A   C4A  N3A  C2A     0.00   0.0  0
 218  CONST_03  C4A   N3A  C2A  N1A     0.00   0.0  0
 218  CONST_04  C4A   C5A  C6A  N1A     0.00   0.0  0
 218  CONST_05  N3A   C2A  N1A  C6A     0.00   0.0  0
 218  CONST_06  N3A   C4A  C5A  C6A     0.00   0.0  0
 218  CONST_07  C6    C1   C2   N3      0.00   0.0  0
 218  CONST_08  C6    C5   C4   N3      0.00   0.0  0
 218  CONST_09  C5    C4   N3   C2      0.00   0.0  0
 218  CONST_10  C5    C6   C1   C2      0.00   0.0  0
 218  CONST_11  C4    N3   C2   C1      0.00   0.0  0
 218  CONST_12  C4    C5   C6   C1      0.00   0.0  0
 218  CONST_13  C6A   N1A  C2A  CM2   180.00   0.0  0
 218  CONST_14  C4A   N3A  C2A  CM2   180.00   0.0  0
 218  CONST_15  N4A   C4A  N3A  C2A   180.00   0.0  0
 218  CONST_16  C7A   C5A  C6A  N1A   180.00   0.0  0
 218  CONST_17  N4A   C4A  C5A  C6A   180.00   0.0  0
 218  CONST_18  N3A   C4A  C5A  C7A   180.00   0.0  0
 218  CONST_19  C1    C2   N3   C7A   180.00   0.0  0
 218  CONST_20  C5    C4   N3   C7A   180.00   0.0  0
 218  CONST_21  CM6   C5   C4   N3    180.00   0.0  0
 218  CONST_22  CM4   C4   N3   C2    180.00   0.0  0
 218  CONST_23  CM6   C5   C6   C1    180.00   0.0  0
 218  CONST_24  CM4   C4   C5   C6    180.00   0.0  0
 218  CONST_25  H6A   C6A  N1A  C2A   180.00   0.0  0
 218  CONST_26  H1    C1   C2   N3    180.00   0.0  0
 218  CONST_27  H6    C6   C1   C2    180.00   0.0  0
 218  CONST_28  H2    C2   C1   C6    180.00   0.0  0
 218  CONST_30  H4A2  N4A  C4A  C5A   180.00   0.0  0
 218  Var_01    N3    C7A  C5A  C6A  -117.79  30.0  2
 218  Var_02    C2    N3   C7A  C5A  -111.74  30.0  2
 218  Var_03    CM7   CM6  C5   C6    -88.17  30.0  2
 218  Var_04    HM21  CM2  C2A  N1A    95.26  30.0  2
 218  Var_05    HM41  CM4  C4   N3    -83.49  30.0  2
 218  Var_06    OM7   CM7  CM6  C5    179.90  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
 218  plan-1  CM2   0.020
 218  plan-1  C2A   0.020
 218  plan-1  N1A   0.020
 218  plan-1  C6A   0.020
 218  plan-1  C5A   0.020
 218  plan-1  C7A   0.020
 218  plan-1  C4A   0.020
 218  plan-1  N4A   0.020
 218  plan-1  N3A   0.020
 218  plan-1  H6A   0.020
 218  plan-2  C7A   0.020
 218  plan-2  N3    0.020
 218  plan-2  C2    0.020
 218  plan-2  C1    0.020
 218  plan-2  C6    0.020
 218  plan-2  C5    0.020
 218  plan-2  CM6   0.020
 218  plan-2  C4    0.020
 218  plan-2  CM4   0.020
 218  plan-2  H2    0.020
 218  plan-2  H1    0.020
 218  plan-2  H6    0.020
 218  plan-3  C4A   0.020
 218  plan-3  N4A   0.020
 218  plan-3  H4A1  0.020
 218  plan-3  H4A2  0.020

