# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 07:06:56 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: (6-but-3-ynyl-4-methyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(O)c(CCC#C)ncc1CO[P](O)(O)=O
#
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
 EOW  EOW  '(6-but-3-ynyl-4-methyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate'  ligand  32  18  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_EOW
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
 EOW  O3P  O  OH1   0  -0.741  -4.5570  -0.3652  -1.2389
 EOW  P    P  P     0   1.464  -4.0920   0.3268   0.1233
 EOW  O1P  O  OH1   0  -0.729  -4.3641   1.8904  -0.0009
 EOW  O2P  O  O     0  -0.708  -4.6777  -0.3907   1.2699
 EOW  O4P  O  O2    0  -0.593  -2.4969   0.4149   0.0713
 EOW  C5A  C  CH2   0  -0.207  -1.7156  -0.7658   0.2122
 EOW  C5   C  CR6   0  -0.075  -0.2681  -0.4392  -0.0279
 EOW  C6   C  CR16  0  -0.139   0.1593   0.8526  -0.2981
 EOW  N1   N  N     0  -0.404   1.4303   1.1681  -0.5137
 EOW  C4   C  CR6   0   0.062   0.6862  -1.4580   0.0253
 EOW  C4A  C  CH3   0  -0.791   0.3396  -2.8907   0.3116
 EOW  C3   C  CR6   0   0.274   2.0145  -1.1086  -0.2118
 EOW  O3   O  OH1   0  -0.622   3.0170  -2.0078  -0.1949
 EOW  C2   C  CR6   0   0.132   2.3547   0.2219  -0.4783
 EOW  C2A  C  CH2   0  -0.496   3.7806   0.6307  -0.7113
 EOW  C1   C  CH2   0  -0.575   4.5494   0.7885   0.6117
 EOW  C7   C  CSP   0   0.274   5.9273   1.2109   0.3996
 EOW  C8   C  CSP1  0  -0.555   7.0610   1.5625   0.2054
 EOW  H1   H  HOH1  0   0.497  -4.2730   0.0719  -2.0531
 EOW  H2   H  HOH1  0   0.505  -5.2750   2.1491   0.1936
 EOW  H3   H  HCH2  0   0.262  -1.8497  -1.1775   1.2168
 EOW  H4   H  HCH2  0   0.257  -2.0466  -1.5282  -0.5005
 EOW  H5   H  HCR6  0   0.257  -0.5459   1.6715  -0.3484
 EOW  H6   H  HCH3  0   0.273   0.5160  -3.5259  -0.5599
 EOW  H7   H  HCH3  0   0.267   0.9337  -3.2892   1.1371
 EOW  H8   H  HCH3  0   0.276  -0.7015  -3.0251   0.5911
 EOW  H9   H  HOH1  0   0.486   2.6890  -2.8993  -0.0346
 EOW  H10  H  HCH2  0   0.258   4.2983  -0.0907  -1.3455
 EOW  H11  H  HCH2  0   0.259   3.7802   1.5853  -1.2381
 EOW  H12  H  HCH2  0   0.277   4.0432   1.5226   1.2434
 EOW  H13  H  HCH2  0   0.278   4.5465  -0.1527   1.1659
 EOW  H14  H  H     0   0.279   8.0670   1.8713   0.0366

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
 EOW  O2P  P    double    1.474  0.020  1.474
 EOW  C6   N1   aromatic  1.327  0.020  1.327
 EOW  C6   C5   aromatic  1.387  0.020  1.387
 EOW  N1   C2   aromatic  1.323  0.020  1.323
 EOW  P    O3P  single    1.597  0.020  1.597
 EOW  P    O4P  single    1.598  0.020  1.598
 EOW  P    O1P  single    1.592  0.020  1.592
 EOW  C5A  O4P  single    1.423  0.020  1.423
 EOW  C5A  C5   single    1.503  0.020  1.503
 EOW  C5   C4   aromatic  1.397  0.020  1.397
 EOW  C2   C2A  single    1.502  0.020  1.502
 EOW  C2   C3   aromatic  1.399  0.020  1.399
 EOW  C2A  C1   single    1.538  0.020  1.538
 EOW  C1   C7   single    1.457  0.020  1.457
 EOW  C4   C3   aromatic  1.394  0.020  1.394
 EOW  C4   C4A  single    1.501  0.020  1.501
 EOW  C3   O3   single    1.347  0.020  1.347
 EOW  C7   C8   triple    1.203  0.020  1.203
 EOW  O3P  H1   single    0.832  0.020  0.971
 EOW  O1P  H2   single    0.832  0.020  0.971
 EOW  C5A  H3   single    0.939  0.020  1.096
 EOW  C5A  H4   single    0.939  0.020  1.096
 EOW  C6   H5   single    0.929  0.020  1.085
 EOW  C4A  H6   single    0.939  0.020  1.096
 EOW  C4A  H7   single    0.939  0.020  1.096
 EOW  C4A  H8   single    0.939  0.020  1.096
 EOW  O3   H9   single    0.832  0.020  0.971
 EOW  C2A  H10  single    0.939  0.020  1.096
 EOW  C2A  H11  single    0.939  0.020  1.096
 EOW  C1   H12  single    0.939  0.020  1.096
 EOW  C1   H13  single    0.939  0.020  1.096
 EOW  C8   H14  single    0.913  0.020  1.066

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
 EOW  H1   O3P  P    115.91  3.000
 EOW  O4P  P    O2P  116.66  3.000
 EOW  O4P  P    O1P   96.54  3.000
 EOW  O2P  P    O1P  118.09  3.000
 EOW  O1P  P    O3P  108.02  3.000
 EOW  O4P  P    O3P  106.66  3.000
 EOW  O2P  P    O3P  109.69  3.000
 EOW  H2   O1P  P    114.09  3.000
 EOW  C5A  O4P  P    119.93  3.000
 EOW  H4   C5A  H3   107.38  3.000
 EOW  H4   C5A  C5   109.79  3.000
 EOW  H3   C5A  C5   110.27  3.000
 EOW  H4   C5A  O4P  110.33  3.000
 EOW  H3   C5A  O4P  109.62  3.000
 EOW  C5   C5A  O4P  109.43  3.000
 EOW  C4   C5   C6   118.43  3.000
 EOW  C4   C5   C5A  119.55  3.000
 EOW  C6   C5   C5A  122.02  3.000
 EOW  H5   C6   N1   115.90  3.000
 EOW  H5   C6   C5   120.87  3.000
 EOW  N1   C6   C5   123.24  3.000
 EOW  C2   N1   C6   119.64  3.000
 EOW  C3   C4   C4A  119.45  3.000
 EOW  C4A  C4   C5   123.06  3.000
 EOW  C3   C4   C5   117.50  3.000
 EOW  H8   C4A  H7   106.36  3.000
 EOW  H8   C4A  H6   106.73  3.000
 EOW  H7   C4A  H6   107.62  3.000
 EOW  H8   C4A  C4   112.85  3.000
 EOW  H7   C4A  C4   111.51  3.000
 EOW  H6   C4A  C4   111.43  3.000
 EOW  C2   C3   O3   117.15  3.000
 EOW  O3   C3   C4   122.68  3.000
 EOW  C2   C3   C4   120.17  3.000
 EOW  H9   O3   C3   111.50  3.000
 EOW  C2A  C2   C3   121.30  3.000
 EOW  C3   C2   N1   121.02  3.000
 EOW  C2A  C2   N1   117.68  3.000
 EOW  H11  C2A  H10  107.34  3.000
 EOW  H11  C2A  C1   109.02  3.000
 EOW  H10  C2A  C1   109.30  3.000
 EOW  H11  C2A  C2   108.24  3.000
 EOW  H10  C2A  C2   111.15  3.000
 EOW  C1   C2A  C2   111.66  3.000
 EOW  H13  C1   H12  106.52  3.000
 EOW  H13  C1   C7   109.04  3.000
 EOW  H12  C1   C7   109.12  3.000
 EOW  H13  C1   C2A  110.28  3.000
 EOW  H12  C1   C2A  109.55  3.000
 EOW  C7   C1   C2A  112.17  3.000
 EOW  C8   C7   C1   180.00  3.000
 EOW  H14  C8   C7   180.00  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
 EOW  CONST_01  C2   N1   C6   C5      0.00   0.0  0
 EOW  CONST_02  C2   C3   C4   C5      0.00   0.0  0
 EOW  CONST_03  C3   C2   N1   C6      0.00   0.0  0
 EOW  CONST_04  C3   C4   C5   C6      0.00   0.0  0
 EOW  CONST_05  C4   C5   C6   N1      0.00   0.0  0
 EOW  CONST_06  C4   C3   C2   N1      0.00   0.0  0
 EOW  CONST_07  N1   C6   C5   C5A   180.00   0.0  0
 EOW  CONST_08  C3   C4   C5   C5A   180.00   0.0  0
 EOW  CONST_09  O3   C3   C4   C5    180.00   0.0  0
 EOW  CONST_10  C2A  C2   N1   C6    180.00   0.0  0
 EOW  CONST_11  C4A  C4   C5   C6    180.00   0.0  0
 EOW  CONST_12  O3   C3   C2   N1    180.00   0.0  0
 EOW  CONST_13  C2A  C2   C3   C4    180.00   0.0  0
 EOW  CONST_14  C2   C3   C4   C4A   180.00   0.0  0
 EOW  CONST_15  H5   C6   C5   C4    180.00   0.0  0
 EOW  Var_01    C6   C5   C5A  O4P     1.84  30.0  2
 EOW  Var_02    C1   C2A  C2   N1     98.90  30.0  2
 EOW  Var_03    H6   C4A  C4   C5    112.98  30.0  2
 EOW  Var_04    C5   C5A  O4P  P     173.61  30.0  3
 EOW  Var_05    C7   C1   C2A  C2   -178.86  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
 EOW  plan-1  C5A  0.020
 EOW  plan-1  C5   0.020
 EOW  plan-1  C6   0.020
 EOW  plan-1  N1   0.020
 EOW  plan-1  C4   0.020
 EOW  plan-1  C4A  0.020
 EOW  plan-1  C3   0.020
 EOW  plan-1  O3   0.020
 EOW  plan-1  C2   0.020
 EOW  plan-1  C2A  0.020
 EOW  plan-1  H5   0.020

