# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 02:41:57 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: [5-hydroxy-4-(hydroxymethyl)-6-methylpyridin-3-yl]methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(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
 PXP  PXP  '[5-hydroxy-4-(hydroxymethyl)-6-methylpyridin-3-yl]methyl dihydrogen phosphate'  ligand  28  16  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PXP
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
 PXP  N1    N  N     0  -0.405   1.9828  -0.4030   1.9685
 PXP  C2    C  CR6   0   0.138   1.2775  -0.2086   3.0662
 PXP  C2A   C  CH3   0  -0.719   1.9658  -0.3412   4.3894
 PXP  C3    C  CR6   0   0.263  -0.0906   0.1098   3.0040
 PXP  O3    O  OH1   0  -0.621  -0.7038   0.2758   4.1901
 PXP  C4    C  CR6   0   0.039  -0.7151   0.2394   1.7679
 PXP  C4A   C  CH2   0  -0.252  -2.1770   0.5692   1.6330
 PXP  O4A   O  OH1   0  -0.654  -2.8483  -0.5787   1.1661
 PXP  C5    C  CR6   0  -0.062   0.0597   0.0157   0.6198
 PXP  C6    C  CR16  0  -0.136   1.3964  -0.3001   0.7785
 PXP  C5A   C  CH2   0  -0.196  -0.5740   0.1132  -0.7393
 PXP  O4P   O  O2    0  -0.592   0.4422   0.1293  -1.7375
 PXP  P     P  P     0   1.463   0.0298  -0.0123  -3.2749
 PXP  O1P   O  O     0  -0.708  -1.0041   0.9178  -3.7636
 PXP  O2P   O  OH1   0  -0.728   1.4992   0.1189  -3.8729
 PXP  O3P   O  OH1   0  -0.741  -0.4584  -1.5186  -3.4857
 PXP  H2A1  H  HCH3  0   0.247   1.8983   0.5768   4.9758
 PXP  H2A2  H  HCH3  0   0.248   1.5255  -1.1362   4.9941
 PXP  H2A3  H  HCH3  0   0.247   3.0176  -0.5719   4.2358
 PXP  HO3   H  HOH1  0   0.476  -1.6482   0.4357   4.0901
 PXP  H4A1  H  HCH2  0   0.214  -2.6061   0.9245   2.5775
 PXP  H4A2  H  HCH2  0   0.239  -2.2845   1.4121   0.9403
 PXP  HOA4  H  HOH1  0   0.463  -3.7292  -0.3144   0.8826
 PXP  H6    H  HCR6  0   0.257   2.0333  -0.4764  -0.0785
 PXP  H5A1  H  HCH2  0   0.261  -1.2507  -0.7323  -0.8890
 PXP  H5A2  H  HCH2  0   0.254  -1.1739   1.0248  -0.8143
 PXP  HOP2  H  HOH1  0   0.506   1.5271   0.1846  -4.8371
 PXP  HOP3  H  HOH1  0   0.497   0.1776  -2.2066  -3.2471

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
 PXP  N1   C2    aromatic  1.319  0.020  1.319
 PXP  N1   C6    aromatic  1.331  0.020  1.331
 PXP  C2   C2A   single    1.497  0.020  1.497
 PXP  C2   C3    aromatic  1.406  0.020  1.406
 PXP  C2A  H2A1  single    0.970  0.020  1.090
 PXP  C2A  H2A2  single    0.970  0.020  1.090
 PXP  C2A  H2A3  single    0.970  0.020  1.090
 PXP  C3   O3    single    1.346  0.020  1.346
 PXP  C3   C4    aromatic  1.391  0.020  1.391
 PXP  O3   HO3   single    0.850  0.020  0.980
 PXP  C4   C4A   single    1.505  0.020  1.505
 PXP  C4   C5    aromatic  1.403  0.020  1.403
 PXP  C4A  O4A   single    1.409  0.020  1.409
 PXP  C4A  H4A1  single    0.970  0.020  1.090
 PXP  C4A  H4A2  single    0.970  0.020  1.090
 PXP  O4A  HOA4  single    0.850  0.020  0.980
 PXP  C5   C6    aromatic  1.383  0.020  1.383
 PXP  C5   C5A   single    1.503  0.020  1.503
 PXP  C6   H6    single    0.930  0.020  1.080
 PXP  C5A  O4P   single    1.425  0.020  1.425
 PXP  C5A  H5A1  single    0.970  0.020  1.090
 PXP  C5A  H5A2  single    0.970  0.020  1.090
 PXP  O4P  P     single    1.598  0.020  1.598
 PXP  P    O1P   double    1.474  0.020  1.474
 PXP  P    O2P   single    1.592  0.020  1.592
 PXP  P    O3P   single    1.597  0.020  1.597
 PXP  O2P  HOP2  single    0.850  0.020  0.980
 PXP  O3P  HOP3  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
 PXP  C6    N1   C2    119.81  3.000
 PXP  C3    C2   C2A   120.42  3.000
 PXP  C3    C2   N1    121.13  3.000
 PXP  C2A   C2   N1    118.45  3.000
 PXP  H2A3  C2A  H2A2  108.29  3.000
 PXP  H2A3  C2A  H2A1  108.30  3.000
 PXP  H2A2  C2A  H2A1  106.86  3.000
 PXP  H2A3  C2A  C2    109.79  3.000
 PXP  H2A2  C2A  C2    111.63  3.000
 PXP  H2A1  C2A  C2    111.83  3.000
 PXP  C4    C3   O3    124.56  3.000
 PXP  C4    C3   C2    119.82  3.000
 PXP  O3    C3   C2    115.62  3.000
 PXP  HO3   O3   C3    112.08  3.000
 PXP  C5    C4   C4A   119.87  3.000
 PXP  C5    C4   C3    117.67  3.000
 PXP  C4A   C4   C3    122.43  3.000
 PXP  H4A2  C4A  H4A1  104.88  3.000
 PXP  H4A2  C4A  O4A   111.73  3.000
 PXP  H4A1  C4A  O4A   111.28  3.000
 PXP  H4A2  C4A  C4    108.69  3.000
 PXP  H4A1  C4A  C4    111.96  3.000
 PXP  O4A   C4A  C4    108.30  3.000
 PXP  HOA4  O4A  C4A   108.05  3.000
 PXP  C5A   C5   C6    121.76  3.000
 PXP  C5A   C5   C4    119.79  3.000
 PXP  C6    C5   C4    118.45  3.000
 PXP  H6    C6   C5    121.01  3.000
 PXP  H6    C6   N1    115.87  3.000
 PXP  C5    C6   N1    123.12  3.000
 PXP  H5A2  C5A  H5A1  107.20  3.000
 PXP  H5A2  C5A  O4P   109.49  3.000
 PXP  H5A1  C5A  O4P   110.76  3.000
 PXP  H5A2  C5A  C5    110.33  3.000
 PXP  H5A1  C5A  C5    109.56  3.000
 PXP  O4P   C5A  C5    109.49  3.000
 PXP  P     O4P  C5A   119.28  3.000
 PXP  O3P   P    O2P   108.08  3.000
 PXP  O3P   P    O1P   109.69  3.000
 PXP  O2P   P    O1P   118.09  3.000
 PXP  O3P   P    O4P   106.83  3.000
 PXP  O2P   P    O4P    96.66  3.000
 PXP  O1P   P    O4P   116.36  3.000
 PXP  HOP2  O2P  P     114.01  3.000
 PXP  HOP3  O3P  P     115.93  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
 PXP  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 PXP  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 PXP  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 PXP  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 PXP  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 PXP  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 PXP  CONST_07  O3    C3   C2   N1    180.00   0.0  0
 PXP  CONST_08  C5A   C5   C6   N1    180.00   0.0  0
 PXP  CONST_09  C4A   C4   C3   C2    180.00   0.0  0
 PXP  CONST_10  C6    N1   C2   C2A   180.00   0.0  0
 PXP  CONST_11  C4    C3   C2   C2A   180.00   0.0  0
 PXP  CONST_12  C5A   C5   C4   C3    180.00   0.0  0
 PXP  CONST_13  C5    C4   C3   O3    180.00   0.0  0
 PXP  CONST_14  C6    C5   C4   C4A   180.00   0.0  0
 PXP  CONST_15  H6    C6   N1   C2    180.00   0.0  0
 PXP  Var_01    O4A   C4A  C4   C3   -109.23  30.0  2
 PXP  Var_02    O4P   C5A  C5   C4    167.84  30.0  2
 PXP  Var_03    H2A1  C2A  C2   N1    121.54  30.0  2
 PXP  Var_04    O1P   P    O4P  C5A    52.30  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
 PXP  plan-1  N1   0.020
 PXP  plan-1  C2   0.020
 PXP  plan-1  C2A  0.020
 PXP  plan-1  C3   0.020
 PXP  plan-1  O3   0.020
 PXP  plan-1  C4   0.020
 PXP  plan-1  C4A  0.020
 PXP  plan-1  C5   0.020
 PXP  plan-1  C6   0.020
 PXP  plan-1  C5A  0.020
 PXP  plan-1  H6   0.020

