# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 07:56:23 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: (6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1c(C=O)c(CO[P](O)(O)=O)cnc1C#C
#
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
 EM2  EM2  '(6-ethynyl-4-methanoyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate'  ligand  25  17  .  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_EM2
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
 EM2  N1   N  N     0  -0.380  -1.8862  -1.6757  -0.0689
 EM2  C2   C  CR6   0   0.013  -2.9219  -0.8542  -0.0387
 EM2  C2A  C  CSP   0   0.275  -4.2417  -1.3935  -0.1116
 EM2  C3   C  CR6   0   0.306  -2.7680   0.5381   0.0629
 EM2  O3   O  OH1   0  -0.585  -3.8105   1.3618   0.0898
 EM2  C4   C  CR6   0  -0.035  -1.4739   1.0674   0.1325
 EM2  C4A  C  C1    0   0.124  -1.3217   2.5338   0.2294
 EM2  C5   C  CR6   0  -0.041  -0.3861   0.1806   0.1027
 EM2  C6   C  CR16  0  -0.129  -0.6616  -1.1808   0.0006
 EM2  C5A  C  CH2   0  -0.189   1.0336   0.6677   0.1828
 EM2  O4P  O  O2    0  -0.596   1.9069  -0.4562   0.2248
 EM2  P    P  P     0   1.463   3.4594  -0.2505  -0.1012
 EM2  O1P  O  O     0  -0.706   4.1153   0.8973   0.5500
 EM2  O2P  O  OH1   0  -0.727   3.9266  -1.7164   0.3050
 EM2  O3P  O  OH1   0  -0.737   3.5802  -0.1108  -1.6871
 EM2  C1   C  CSP1  0  -0.523  -5.3791  -1.7836  -0.1622
 EM2  H1   H  HOH1  0   0.489  -4.6467   0.8751   0.0509
 EM2  H2   H  H     0   0.234  -2.2547   3.1084   0.2969
 EM2  H5   H  HCR6  0   0.280   0.1382  -1.9062  -0.0281
 EM2  H6   H  HCH2  0   0.265   1.2511   1.3003  -0.6822
 EM2  H7   H  HCH2  0   0.274   1.1795   1.2734   1.0784
 EM2  H8   H  HOH1  0   0.506   4.8838  -1.8501   0.2735
 EM2  H9   H  HOH1  0   0.497   3.2150  -0.8417  -2.2041
 EM2  H10  H  H     0   0.290  -6.3827  -2.1419  -0.2102
 EM2  O1   O  O     0  -0.371  -0.2549   3.1027   0.2359

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
 EM2  O1P  P    double    1.474  0.020  1.474
 EM2  C6   N1   aromatic  1.323  0.020  1.323
 EM2  C6   C5   aromatic  1.393  0.020  1.393
 EM2  N1   C2   aromatic  1.322  0.020  1.322
 EM2  P    O3P  single    1.597  0.020  1.597
 EM2  P    O4P  single    1.600  0.020  1.600
 EM2  P    O2P  single    1.591  0.020  1.591
 EM2  C5A  O4P  single    1.424  0.020  1.424
 EM2  C5A  C5   single    1.503  0.020  1.503
 EM2  C5   C4   aromatic  1.404  0.020  1.404
 EM2  C2   C2A  single    1.428  0.020  1.428
 EM2  C2   C3   aromatic  1.404  0.020  1.404
 EM2  C2A  C1   triple    1.203  0.020  1.203
 EM2  C4   C3   aromatic  1.400  0.020  1.400
 EM2  C4   C4A  single    1.477  0.020  1.477
 EM2  C3   O3   single    1.329  0.020  1.329
 EM2  O3   H1   single    0.832  0.020  0.971
 EM2  C4A  H2   single    0.930  0.020  1.086
 EM2  C6   H5   single    0.929  0.020  1.085
 EM2  C5A  H6   single    0.939  0.020  1.096
 EM2  C5A  H7   single    0.939  0.020  1.096
 EM2  O2P  H8   single    0.832  0.020  0.971
 EM2  O3P  H9   single    0.832  0.020  0.971
 EM2  C1   H10  single    0.913  0.020  1.066
 EM2  C4A  O1   double    1.209  0.020  1.209

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
 EM2  C6   N1   C2   119.44  3.000
 EM2  C3   C2   C2A  118.65  3.000
 EM2  C3   C2   N1   122.12  3.000
 EM2  C2A  C2   N1   119.23  3.000
 EM2  C1   C2A  C2   180.00  3.000
 EM2  C4   C3   O3   119.33  3.000
 EM2  O3   C3   C2   122.00  3.000
 EM2  C4   C3   C2   118.67  3.000
 EM2  H1   O3   C3   111.42  3.000
 EM2  C5   C4   C4A  123.27  3.000
 EM2  C4A  C4   C3   118.28  3.000
 EM2  C5   C4   C3   118.45  3.000
 EM2  O1   C4A  H2   120.22  3.000
 EM2  O1   C4A  C4   123.93  3.000
 EM2  H2   C4A  C4   115.85  3.000
 EM2  C5A  C5   C6   120.50  3.000
 EM2  C5A  C5   C4   121.74  3.000
 EM2  C6   C5   C4   117.76  3.000
 EM2  H5   C6   C5   120.80  3.000
 EM2  H5   C6   N1   115.65  3.000
 EM2  C5   C6   N1   123.55  3.000
 EM2  H7   C5A  H6   107.56  3.000
 EM2  H7   C5A  O4P  109.39  3.000
 EM2  H6   C5A  O4P  110.98  3.000
 EM2  H7   C5A  C5   110.48  3.000
 EM2  H6   C5A  C5   109.46  3.000
 EM2  O4P  C5A  C5   108.97  3.000
 EM2  P    O4P  C5A  119.18  3.000
 EM2  O3P  P    O2P  108.17  3.000
 EM2  O2P  P    O1P  118.29  3.000
 EM2  O3P  P    O1P  109.70  3.000
 EM2  O2P  P    O4P   96.57  3.000
 EM2  O3P  P    O4P  106.69  3.000
 EM2  O1P  P    O4P  116.24  3.000
 EM2  H8   O2P  P    114.18  3.000
 EM2  H9   O3P  P    115.88  3.000
 EM2  H10  C1   C2A  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
 EM2  CONST_01  C4   C5   C6   N1      0.00   0.0  0
 EM2  CONST_02  C4   C3   C2   N1      0.00   0.0  0
 EM2  CONST_03  C5   C6   N1   C2      0.00   0.0  0
 EM2  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 EM2  CONST_05  C6   N1   C2   C3      0.00   0.0  0
 EM2  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 EM2  CONST_07  C5A  C5   C6   N1    180.00   0.0  0
 EM2  CONST_08  O3   C3   C2   N1    180.00   0.0  0
 EM2  CONST_09  C4A  C4   C3   C2    180.00   0.0  0
 EM2  CONST_10  C6   N1   C2   C2A   180.00   0.0  0
 EM2  CONST_11  C4   C3   C2   C2A   180.00   0.0  0
 EM2  CONST_12  C5A  C5   C4   C3    180.00   0.0  0
 EM2  CONST_13  C5   C4   C3   O3    180.00   0.0  0
 EM2  CONST_14  C6   C5   C4   C4A   180.00   0.0  0
 EM2  CONST_15  H5   C6   N1   C2    180.00   0.0  0
 EM2  Var_01    O1   C4A  C4   C3   -176.62  30.0  2
 EM2  Var_02    O4P  C5A  C5   C4    175.94  30.0  3
 EM2  Var_03    O1P  P    O4P  C5A    45.96  30.0  1

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
 EM2  plan-1  N1   0.020
 EM2  plan-1  C2   0.020
 EM2  plan-1  C2A  0.020
 EM2  plan-1  C3   0.020
 EM2  plan-1  O3   0.020
 EM2  plan-1  C4   0.020
 EM2  plan-1  C4A  0.020
 EM2  plan-1  C5   0.020
 EM2  plan-1  C6   0.020
 EM2  plan-1  C5A  0.020
 EM2  plan-1  C1   0.020
 EM2  plan-1  H5   0.020
 EM2  plan-2  C4   0.020
 EM2  plan-2  C4A  0.020
 EM2  plan-2  H2   0.020
 EM2  plan-2  O1   0.020

