# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 08:58:26 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: [4-(dihydroxymethyl)-5-hydroxy-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(C(O)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
 P0P  P0P  '[4-(dihydroxymethyl)-5-hydroxy-6-methylpyridin-3-yl]methyl dihydrogen phosphate'  ligand  29  17  .  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_P0P
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
 P0P  O3    O  OH1   0  -0.633  21.5843  10.9078  21.3788
 P0P  N1    N  N     0  -0.402  21.6642   8.7932  18.5148
 P0P  C2    C  CR6   0   0.146  22.0361   9.5933  19.4965
 P0P  C2A   C  CH3   0  -0.720  23.4826   9.9595  19.6117
 P0P  C3    C  CR6   0   0.283  21.1038  10.1032  20.4199
 P0P  C4    C  CR6   0  -0.058  19.7558   9.7680  20.2919
 P0P  C4A   C  CH1   0   0.248  18.7201  10.3548  21.2332
 P0P  O4A   O  OH1   0  -0.660  18.2231  11.5689  20.7534
 P0P  O4B   O  OH1   0  -0.668  19.2501  10.5923  22.5155
 P0P  C5    C  CR6   0   0.014  19.3906   8.9084  19.2468
 P0P  C6    C  CR16  0  -0.141  20.3842   8.4583  18.3969
 P0P  C5A   C  CH2   0  -0.297  17.9829   8.4493  19.0075
 P0P  O4P   O  O2    0  -0.593  17.1970   9.5460  18.5247
 P0P  P     P  P     0   1.449  15.7555   9.9309  19.1150
 P0P  O1P   O  O     0  -0.714  15.3204   9.0946  20.2523
 P0P  O2P   O  OH1   0  -0.764  15.8834  11.4957  19.3609
 P0P  O3P   O  OH1   0  -0.726  14.7278   9.8404  17.9051
 P0P  HO3   H  HOH1  0   0.477  20.9025  11.0090  22.0713
 P0P  H2A1  H  HCH3  0   0.250  23.8927   9.6765  20.5825
 P0P  H2A2  H  HCH3  0   0.251  23.6329  11.0352  19.5042
 P0P  H2A3  H  HCH3  0   0.249  24.0543   9.4561  18.8352
 P0P  H4A   H  HCH1  0   0.245  17.8636   9.6826  21.3298
 P0P  H1    H  HOH1  0   0.483  18.9113  12.0755  20.3043
 P0P  H4B   H  HOH1  0   0.483  19.2097   9.7810  23.0369
 P0P  H6    H  HCR6  0   0.262  20.1331   7.7917  17.5783
 P0P  H5A1  H  HCH2  0   0.264  17.5423   8.0223  19.9101
 P0P  H5A2  H  HCH2  0   0.272  17.9803   7.6683  18.2464
 P0P  H2P   H  HOH1  0   0.501  16.6732  11.7136  19.9055
 P0P  H3P   H  HOH1  0   0.499  14.9226  10.3908  17.1348

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
 P0P  O3   C3    single    1.341  0.020  1.341
 P0P  O3   HO3   single    0.850  0.020  0.980
 P0P  N1   C2    aromatic  1.320  0.020  1.320
 P0P  N1   C6    aromatic  1.328  0.020  1.328
 P0P  C2   C2A   single    1.497  0.020  1.497
 P0P  C2   C3    aromatic  1.408  0.020  1.408
 P0P  C2A  H2A1  single    0.970  0.020  1.090
 P0P  C2A  H2A2  single    0.970  0.020  1.090
 P0P  C2A  H2A3  single    0.970  0.020  1.090
 P0P  C3   C4    aromatic  1.395  0.020  1.395
 P0P  C4   C4A   single    1.518  0.020  1.518
 P0P  C4   C5    aromatic  1.402  0.020  1.402
 P0P  C4A  O4A   single    1.397  0.020  1.397
 P0P  C4A  O4B   single    1.408  0.020  1.408
 P0P  C4A  H4A   single    0.970  0.020  1.090
 P0P  O4A  H1    single    0.850  0.020  0.980
 P0P  O4B  H4B   single    0.850  0.020  0.980
 P0P  C5   C6    aromatic  1.383  0.020  1.383
 P0P  C5   C5A   single    1.500  0.020  1.500
 P0P  C6   H6    single    0.930  0.020  1.080
 P0P  C5A  O4P   single    1.433  0.020  1.433
 P0P  C5A  H5A1  single    0.970  0.020  1.090
 P0P  C5A  H5A2  single    0.970  0.020  1.090
 P0P  O4P  P     single    1.605  0.020  1.605
 P0P  P    O1P   double    1.477  0.020  1.477
 P0P  P    O2P   single    1.589  0.020  1.589
 P0P  P    O3P   single    1.590  0.020  1.590
 P0P  O2P  H2P   single    0.850  0.020  0.980
 P0P  O3P  H3P   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
 P0P  HO3   O3   C3    108.60  3.000
 P0P  C6    N1   C2    119.36  3.000
 P0P  C3    C2   C2A   120.07  3.000
 P0P  C3    C2   N1    121.38  3.000
 P0P  C2A   C2   N1    118.55  3.000
 P0P  H2A3  C2A  H2A2  108.27  3.000
 P0P  H2A3  C2A  H2A1  108.51  3.000
 P0P  H2A2  C2A  H2A1  106.95  3.000
 P0P  H2A3  C2A  C2    109.87  3.000
 P0P  H2A2  C2A  C2    111.51  3.000
 P0P  H2A1  C2A  C2    111.61  3.000
 P0P  C4    C3   C2    119.52  3.000
 P0P  C4    C3   O3    123.79  3.000
 P0P  C2    C3   O3    116.68  3.000
 P0P  C5    C4   C4A   121.45  3.000
 P0P  C5    C4   C3    117.88  3.000
 P0P  C4A   C4   C3    120.64  3.000
 P0P  H4A   C4A  O4B   108.56  3.000
 P0P  H4A   C4A  O4A   106.62  3.000
 P0P  O4B   C4A  O4A   107.47  3.000
 P0P  H4A   C4A  C4    110.60  3.000
 P0P  O4B   C4A  C4    111.92  3.000
 P0P  O4A   C4A  C4    111.46  3.000
 P0P  H1    O4A  C4A   111.24  3.000
 P0P  H4B   O4B  C4A   109.54  3.000
 P0P  C5A   C5   C6    118.47  3.000
 P0P  C5A   C5   C4    123.45  3.000
 P0P  C6    C5   C4    118.08  3.000
 P0P  H6    C6   C5    119.82  3.000
 P0P  H6    C6   N1    116.41  3.000
 P0P  C5    C6   N1    123.76  3.000
 P0P  H5A2  C5A  H5A1  107.22  3.000
 P0P  H5A2  C5A  O4P   108.16  3.000
 P0P  H5A1  C5A  O4P   110.89  3.000
 P0P  H5A2  C5A  C5    109.44  3.000
 P0P  H5A1  C5A  C5    111.52  3.000
 P0P  O4P   C5A  C5    109.52  3.000
 P0P  P     O4P  C5A   123.53  3.000
 P0P  O3P   P    O2P   103.05  3.000
 P0P  O3P   P    O1P   111.30  3.000
 P0P  O2P   P    O1P   117.52  3.000
 P0P  O3P   P    O4P   106.68  3.000
 P0P  O2P   P    O4P   102.76  3.000
 P0P  O1P   P    O4P   114.33  3.000
 P0P  H2P   O2P  P     111.61  3.000
 P0P  H3P   O3P  P     116.34  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
 P0P  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 P0P  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 P0P  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 P0P  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 P0P  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 P0P  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 P0P  CONST_07  N1    C2   C3   O3    180.00   0.0  0
 P0P  CONST_08  C5    C4   C3   O3    180.00   0.0  0
 P0P  CONST_09  C5A   C5   C6   N1    180.00   0.0  0
 P0P  CONST_10  C4A   C4   C3   C2    180.00   0.0  0
 P0P  CONST_11  C6    N1   C2   C2A   180.00   0.0  0
 P0P  CONST_12  C4    C3   C2   C2A   180.00   0.0  0
 P0P  CONST_13  C5A   C5   C4   C3    180.00   0.0  0
 P0P  CONST_14  C6    C5   C4   C4A   180.00   0.0  0
 P0P  CONST_15  H6    C6   N1   C2    180.00   0.0  0
 P0P  Var_01    O4A   C4A  C4   C3     88.57  30.0  2
 P0P  Var_02    O4P   C5A  C5   C4     70.74  30.0  2
 P0P  Var_03    H2A1  C2A  C2   N1   -122.13  30.0  2
 P0P  Var_04    O1P   P    O4P  C5A     2.70  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
 P0P  plan-1  O3   0.020
 P0P  plan-1  N1   0.020
 P0P  plan-1  C2   0.020
 P0P  plan-1  C2A  0.020
 P0P  plan-1  C3   0.020
 P0P  plan-1  C4   0.020
 P0P  plan-1  C4A  0.020
 P0P  plan-1  C5   0.020
 P0P  plan-1  C6   0.020
 P0P  plan-1  C5A  0.020
 P0P  plan-1  H6   0.020

