# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 20:51:59 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 4-(aminomethyl)-3-hydroxy-1,2-dimethyl-5-[(phosphonooxy)methyl]pyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(O)c(CN)c(CO[P](O)(O)=O)c[n+]1C
#
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
 NPL  NPL  4-(aminomethyl)-3-hydroxy-1,2-dimethyl-5-[(phosphonooxy)methyl]pyridinium  ligand  33  17  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NPL
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
 NPL  N1    N  NR6   1  -0.404  25.8578  3.9679  -13.8859
 NPL  C1    C  CH3   0  -0.524  26.3031  2.5748  -13.9897
 NPL  C2    C  CR6   0   0.131  26.3673  4.8862  -14.7232
 NPL  C2A   C  CH3   0  -0.686  27.3701  4.4774  -15.7443
 NPL  C3    C  CR6   0   0.373  25.9420  6.2155  -14.5956
 NPL  O3    O  OH1   0  -0.624  26.4526  7.1086  -15.4246
 NPL  C4    C  CR6   0   0.137  24.9941  6.5612  -13.6233
 NPL  C4A   C  CH2   0  -0.387  24.5985  8.0023  -13.4190
 NPL  N4    N  NH2   0  -0.782  24.8562  8.8156  -14.6046
 NPL  C5    C  CR6   0  -0.123  24.4903  5.5573  -12.7970
 NPL  C5A   C  CH2   0  -0.276  23.4977  5.8891  -11.7160
 NPL  O4P   O  O2    0  -0.535  23.1000  4.6933  -11.0703
 NPL  P     P  P     0   1.352  22.5361  4.5979   -9.5856
 NPL  O1P   O  O     0  -0.818  22.1214  3.2321   -9.2284
 NPL  O2P   O  OH1   0  -0.702  21.3997  5.7146   -9.6200
 NPL  O3P   O  OH1   0  -0.554  23.7250  5.2068   -8.7043
 NPL  C6    C  CR16  0   0.070  24.9448  4.2704  -12.9513
 NPL  H11   H  HCH3  0   0.328  25.8675  2.0030  -13.1785
 NPL  H12   H  HCH3  0   0.281  25.9802  2.1529  -14.9381
 NPL  H13   H  HCH3  0   0.279  27.3856  2.5246  -13.9162
 NPL  H21   H  HCH3  0   0.305  27.5299  5.2781  -16.4692
 NPL  H22   H  HCH3  0   0.240  28.3318  4.2529  -15.2780
 NPL  H23   H  HCH3  0   0.269  27.0524  3.5893  -16.2890
 NPL  HO3   H  HOH1  0   0.474  25.8522  7.9367  -15.3563
 NPL  H41   H  HCH2  0   0.262  23.5570  8.0730  -13.0978
 NPL  H42   H  HCH2  0   0.286  25.2014  8.3982  -12.5974
 NPL  HN41  H  HNH2  0   0.381  24.9755  9.7854  -14.3442
 NPL  HN42  H  HNH2  0   0.333  24.0774  8.7684  -15.2496
 NPL  H51   H  HCH2  0   0.314  23.9554  6.5912  -11.0130
 NPL  H52   H  HCH2  0   0.248  22.6205  6.3763  -12.1482
 NPL  HOP2  H  HOH1  0   0.515  20.9744  5.8609   -8.7637
 NPL  HOP3  H  HOH1  0   0.489  23.8466  4.7648   -7.8576
 NPL  H6    H  HCR6  0   0.347  24.6043  3.4491  -12.3300

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
 NPL  N1   C1    single    1.466  0.020  1.466
 NPL  N1   C2    aromatic  1.343  0.020  1.343
 NPL  N1   C6    aromatic  1.341  0.020  1.341
 NPL  C1   H11   single    0.970  0.020  1.090
 NPL  C1   H12   single    0.970  0.020  1.090
 NPL  C1   H13   single    0.970  0.020  1.090
 NPL  C2   C2A   single    1.488  0.020  1.488
 NPL  C2   C3    aromatic  1.401  0.020  1.401
 NPL  C2A  H21   single    0.970  0.020  1.090
 NPL  C2A  H22   single    0.970  0.020  1.090
 NPL  C2A  H23   single    0.970  0.020  1.090
 NPL  C3   O3    single    1.321  0.020  1.321
 NPL  C3   C4    aromatic  1.401  0.020  1.401
 NPL  O3   HO3   single    0.850  0.020  0.980
 NPL  C4   C4A   single    1.508  0.020  1.508
 NPL  C4   C5    aromatic  1.394  0.020  1.394
 NPL  C4A  N4    single    1.461  0.020  1.461
 NPL  C4A  H41   single    0.970  0.020  1.090
 NPL  C4A  H42   single    0.970  0.020  1.090
 NPL  N4   HN41  single    0.890  0.020  1.040
 NPL  N4   HN42  single    0.890  0.020  1.040
 NPL  C5   C5A   single    1.505  0.020  1.505
 NPL  C5   C6    aromatic  1.373  0.020  1.373
 NPL  C5A  O4P   single    1.416  0.020  1.416
 NPL  C5A  H51   single    0.970  0.020  1.090
 NPL  C5A  H52   single    0.970  0.020  1.090
 NPL  O4P  P     single    1.591  0.020  1.591
 NPL  P    O1P   double    1.471  0.020  1.471
 NPL  P    O2P   single    1.594  0.020  1.594
 NPL  P    O3P   single    1.600  0.020  1.600
 NPL  O2P  HOP2  single    0.850  0.020  0.980
 NPL  O3P  HOP3  single    0.850  0.020  0.980
 NPL  C6   H6    single    0.930  0.020  1.080

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
 NPL  C6    N1   C2    122.58  3.000
 NPL  C6    N1   C1    118.06  3.000
 NPL  C2    N1   C1    119.35  3.000
 NPL  H13   C1   H12   109.70  3.000
 NPL  H13   C1   H11   108.99  3.000
 NPL  H12   C1   H11   109.21  3.000
 NPL  H13   C1   N1    109.99  3.000
 NPL  H12   C1   N1    109.89  3.000
 NPL  H11   C1   N1    109.04  3.000
 NPL  C3    C2   C2A   121.83  3.000
 NPL  C3    C2   N1    118.46  3.000
 NPL  C2A   C2   N1    119.71  3.000
 NPL  H23   C2A  H22   107.62  3.000
 NPL  H23   C2A  H21   107.97  3.000
 NPL  H22   C2A  H21   107.78  3.000
 NPL  H23   C2A  C2    111.74  3.000
 NPL  H22   C2A  C2    110.91  3.000
 NPL  H21   C2A  C2    110.66  3.000
 NPL  C4    C3   O3    122.00  3.000
 NPL  C4    C3   C2    120.17  3.000
 NPL  O3    C3   C2    117.83  3.000
 NPL  HO3   O3   C3    106.14  3.000
 NPL  C5    C4   C4A   120.86  3.000
 NPL  C5    C4   C3    118.55  3.000
 NPL  C4A   C4   C3    120.48  3.000
 NPL  H42   C4A  H41   106.34  3.000
 NPL  H42   C4A  N4    108.12  3.000
 NPL  H41   C4A  N4    111.77  3.000
 NPL  H42   C4A  C4    107.65  3.000
 NPL  H41   C4A  C4    110.60  3.000
 NPL  N4    C4A  C4    112.07  3.000
 NPL  HN42  N4   HN41  107.43  3.000
 NPL  HN42  N4   C4A   110.82  3.000
 NPL  HN41  N4   C4A   110.23  3.000
 NPL  C6    C5   C5A   120.37  3.000
 NPL  C6    C5   C4    119.24  3.000
 NPL  C5A   C5   C4    120.35  3.000
 NPL  H52   C5A  H51   107.70  3.000
 NPL  H52   C5A  O4P   109.36  3.000
 NPL  H51   C5A  O4P   111.50  3.000
 NPL  H52   C5A  C5    110.11  3.000
 NPL  H51   C5A  C5    109.10  3.000
 NPL  O4P   C5A  C5    109.06  3.000
 NPL  P     O4P  C5A   125.15  3.000
 NPL  O3P   P    O2P   105.96  3.000
 NPL  O3P   P    O1P   115.40  3.000
 NPL  O2P   P    O1P   117.05  3.000
 NPL  O3P   P    O4P   103.17  3.000
 NPL  O2P   P    O4P   100.99  3.000
 NPL  O1P   P    O4P   112.46  3.000
 NPL  HOP2  O2P  P     113.60  3.000
 NPL  HOP3  O3P  P     113.79  3.000
 NPL  H6    C6   C5    122.77  3.000
 NPL  H6    C6   N1    116.24  3.000
 NPL  C5    C6   N1    120.99  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
 NPL  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 NPL  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 NPL  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 NPL  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 NPL  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 NPL  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 NPL  CONST_07  O3    C3   C2   N1    180.00   0.0  0
 NPL  CONST_08  C5A   C5   C6   N1    180.00   0.0  0
 NPL  CONST_09  C3    C2   N1   C1    180.00   0.0  0
 NPL  CONST_10  C5    C6   N1   C1    180.00   0.0  0
 NPL  CONST_11  C4A   C4   C3   C2    180.00   0.0  0
 NPL  CONST_12  C6    N1   C2   C2A   180.00   0.0  0
 NPL  CONST_13  C4    C3   C2   C2A   180.00   0.0  0
 NPL  CONST_14  C5A   C5   C4   C3    180.00   0.0  0
 NPL  CONST_15  C5    C4   C3   O3    180.00   0.0  0
 NPL  CONST_16  C6    C5   C4   C4A   180.00   0.0  0
 NPL  CONST_17  H6    C6   N1   C2    180.00   0.0  0
 NPL  Var_01    N4    C4A  C4   C3     22.89  30.0  2
 NPL  Var_02    O4P   C5A  C5   C4    177.19  30.0  2
 NPL  Var_03    H21   C2A  C2   N1    168.35  30.0  2
 NPL  Var_04    H11   C1   N1   C2    174.29  30.0  2
 NPL  Var_05    HN41  N4   C4A  C4   -155.35  30.0  3
 NPL  Var_06    O1P   P    O4P  C5A   176.01  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
 NPL  plan-1  N1   0.020
 NPL  plan-1  C1   0.020
 NPL  plan-1  C2   0.020
 NPL  plan-1  C2A  0.020
 NPL  plan-1  C3   0.020
 NPL  plan-1  O3   0.020
 NPL  plan-1  C4   0.020
 NPL  plan-1  C4A  0.020
 NPL  plan-1  C5   0.020
 NPL  plan-1  C5A  0.020
 NPL  plan-1  C6   0.020
 NPL  plan-1  H6   0.020

