# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 03:02:53 2021
#   Inital geometry file: a 96 line input string
#   Ligand name: (2~{R})-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-sulfanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C=N[C@@H](CS)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
 E1O  E1O  '(2~{R})-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-sulfanyl-propanoic acid'  ligand  37  22  .  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_E1O
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
 E1O  C6   C  CR16  0  -0.144  -0.7841  -7.9285  -2.8607
 E1O  C5   C  CR6   0  -0.005  -0.4677  -7.3311  -1.6596
 E1O  N1   N  N     0  -0.399  -0.2352  -7.5770  -4.0233
 E1O  C2   C  CR6   0   0.138   0.6643  -6.6145  -4.0621
 E1O  C4   C  CR6   0  -0.024   0.4832  -6.2971  -1.6675
 E1O  CB   C  CH2   0  -0.569   3.4315  -4.9413   1.3415
 E1O  CA   C  CH1   0  -0.226   2.2254  -4.1599   0.7800
 E1O  C    C  C     0   0.555   2.6394  -2.7186   0.5276
 E1O  OXT  O  OH1   0  -0.588   2.8397  -2.0773   1.6686
 E1O  N    N  N     0  -0.445   1.8026  -4.7429  -0.4554
 E1O  O3P  O  OH1   0  -0.744  -1.3986  -6.5612   2.4758
 E1O  P    P  P     0   1.479  -2.6539  -6.7249   1.5020
 E1O  O1P  O  O     0  -0.693  -3.6990  -5.6907   1.5842
 E1O  O2P  O  OH1   0  -0.741  -3.0322  -8.2225   1.8970
 E1O  C5A  C  CH2   0  -0.319  -1.1320  -7.7959  -0.4011
 E1O  C2A  C  CH3   0  -0.722   1.2635  -6.2411  -5.3808
 E1O  C3   C  CR6   0   0.298   1.0671  -5.9403  -2.8892
 E1O  O3   O  OH1   0  -0.622   1.9855  -4.9897  -3.0016
 E1O  C4A  C  C1    0   0.098   0.8789  -5.6154  -0.4391
 E1O  H1   H  HCR6  0   0.263  -1.5122  -8.7316  -2.8943
 E1O  H2   H  HSH1  0   0.229   2.3564  -6.4154   2.8760
 E1O  H3   H  HCH2  0   0.301   4.2251  -4.9829   0.5950
 E1O  H4   H  HCH2  0   0.306   3.8259  -4.4436   2.2247
 E1O  H5   H  HCH1  0   0.284   1.4303  -4.1624   1.5374
 E1O  H6   H  HOH1  0   0.489   3.1325  -1.1693   1.4980
 E1O  H7   H  HOH1  0   0.503  -1.3063  -5.6703   2.8375
 E1O  H8   H  HOH1  0   0.504  -3.7697  -8.5977   1.3971
 E1O  H9   H  HCH2  0   0.279  -1.6656  -8.7292  -0.5877
 E1O  H10  H  HCH2  0   0.254  -0.3898  -7.9891   0.3788
 E1O  H11  H  HCH3  0   0.251   0.8323  -6.8522  -6.1704
 E1O  H12  H  HCH3  0   0.251   1.0839  -5.1912  -5.6191
 E1O  H13  H  HCH3  0   0.252   2.3452  -6.3864  -5.3850
 E1O  H14  H  HOH1  0   0.476   2.1706  -4.6345  -2.0880
 E1O  H15  H  H     0   0.238   0.3560  -5.8659   0.4826
 E1O  O    O  O     0  -0.416   2.7811  -2.2284  -0.5598
 E1O  SG   S  S2    0  -0.208   3.0431  -6.6615   1.7537
 E1O  O4P  O  O2    0  -0.584  -2.0626  -6.7848   0.0146

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
 E1O  C2A  C2   single    1.496  0.020  1.496
 E1O  C2   N1   aromatic  1.318  0.020  1.318
 E1O  C2   C3   aromatic  1.412  0.020  1.412
 E1O  N1   C6   aromatic  1.333  0.020  1.333
 E1O  O3   C3   single    1.327  0.020  1.327
 E1O  C3   C4   aromatic  1.400  0.020  1.400
 E1O  C6   C5   aromatic  1.378  0.020  1.378
 E1O  C4   C5   aromatic  1.405  0.020  1.405
 E1O  C4   C4A  single    1.459  0.020  1.459
 E1O  C5   C5A  single    1.497  0.020  1.497
 E1O  C4A  N    double    1.271  0.020  1.271
 E1O  O    C    double    1.201  0.020  1.201
 E1O  C5A  O4P  single    1.436  0.020  1.436
 E1O  N    CA   single    1.430  0.020  1.430
 E1O  O4P  P    single    1.602  0.020  1.602
 E1O  C    CA   single    1.521  0.020  1.521
 E1O  C    OXT  single    1.324  0.020  1.324
 E1O  CA   CB   single    1.543  0.020  1.543
 E1O  O1P  P    double    1.473  0.020  1.473
 E1O  CB   SG   single    1.811  0.020  1.811
 E1O  P    O2P  single    1.594  0.020  1.594
 E1O  P    O3P  single    1.597  0.020  1.597
 E1O  C6   H1   single    0.930  0.020  1.080
 E1O  SG   H2   single    1.200  0.020  1.300
 E1O  CB   H3   single    0.970  0.020  1.090
 E1O  CB   H4   single    0.970  0.020  1.090
 E1O  CA   H5   single    0.970  0.020  1.090
 E1O  OXT  H6   single    0.850  0.020  0.980
 E1O  O3P  H7   single    0.850  0.020  0.980
 E1O  O2P  H8   single    0.850  0.020  0.980
 E1O  C5A  H9   single    0.970  0.020  1.090
 E1O  C5A  H10  single    0.970  0.020  1.090
 E1O  C2A  H11  single    0.970  0.020  1.090
 E1O  C2A  H12  single    0.970  0.020  1.090
 E1O  C2A  H13  single    0.970  0.020  1.090
 E1O  O3   H14  single    0.850  0.020  0.980
 E1O  C4A  H15  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
 E1O  H1   C6   N1   116.41  3.000
 E1O  H1   C6   C5   120.14  3.000
 E1O  N1   C6   C5   123.46  3.000
 E1O  C5A  C5   C4   122.25  3.000
 E1O  C5A  C5   C6   119.74  3.000
 E1O  C4   C5   C6   118.01  3.000
 E1O  C2   N1   C6   119.96  3.000
 E1O  C3   C2   C2A  119.93  3.000
 E1O  C3   C2   N1   121.27  3.000
 E1O  C2A  C2   N1   118.79  3.000
 E1O  C4A  C4   C3   120.15  3.000
 E1O  C4A  C4   C5   121.51  3.000
 E1O  C3   C4   C5   118.34  3.000
 E1O  H4   CB   H3   108.02  3.000
 E1O  H4   CB   CA   110.32  3.000
 E1O  H3   CB   CA   109.82  3.000
 E1O  H4   CB   SG   109.12  3.000
 E1O  H3   CB   SG   106.00  3.000
 E1O  CA   CB   SG   113.34  3.000
 E1O  H5   CA   N    112.39  3.000
 E1O  H5   CA   C    108.29  3.000
 E1O  N    CA   C    108.88  3.000
 E1O  H5   CA   CB   108.29  3.000
 E1O  C    CA   CB   109.12  3.000
 E1O  N    CA   CB   109.82  3.000
 E1O  O    C    OXT  124.37  3.000
 E1O  OXT  C    CA   110.93  3.000
 E1O  O    C    CA   124.69  3.000
 E1O  H6   OXT  C    110.35  3.000
 E1O  C4A  N    CA   118.94  3.000
 E1O  H7   O3P  P    113.45  3.000
 E1O  O4P  P    O2P  106.41  3.000
 E1O  O2P  P    O1P  118.52  3.000
 E1O  O4P  P    O1P  109.88  3.000
 E1O  O2P  P    O3P   97.57  3.000
 E1O  O1P  P    O3P  116.86  3.000
 E1O  O4P  P    O3P  106.25  3.000
 E1O  H8   O2P  P    114.67  3.000
 E1O  H10  C5A  H9   107.62  3.000
 E1O  H10  C5A  O4P  110.97  3.000
 E1O  H9   C5A  O4P  109.57  3.000
 E1O  H10  C5A  C5   110.68  3.000
 E1O  H9   C5A  C5   109.80  3.000
 E1O  O4P  C5A  C5   108.20  3.000
 E1O  H13  C2A  H12  106.87  3.000
 E1O  H13  C2A  H11  108.37  3.000
 E1O  H12  C2A  H11  108.47  3.000
 E1O  H13  C2A  C2   111.54  3.000
 E1O  H12  C2A  C2   111.51  3.000
 E1O  H11  C2A  C2   109.94  3.000
 E1O  O3   C3   C4   123.03  3.000
 E1O  C4   C3   C2   118.97  3.000
 E1O  O3   C3   C2   118.00  3.000
 E1O  H14  O3   C3   107.82  3.000
 E1O  H15  C4A  N    121.19  3.000
 E1O  H15  C4A  C4   118.34  3.000
 E1O  N    C4A  C4   120.47  3.000
 E1O  H2   SG   CB    97.25  3.000
 E1O  C5A  O4P  P    122.31  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
 E1O  CONST_01  C3   C2   N1  C6      0.00   0.0  0
 E1O  CONST_02  C3   C4   C5  C6      0.00   0.0  0
 E1O  CONST_03  C2   N1   C6  C5      0.00   0.0  0
 E1O  CONST_04  C2   C3   C4  C5      0.00   0.0  0
 E1O  CONST_05  C4   C3   C2  N1      0.00   0.0  0
 E1O  CONST_06  C4   C5   C6  N1      0.00   0.0  0
 E1O  CONST_07  C2A  C2   N1  C6    180.00   0.0  0
 E1O  CONST_08  C4A  C4   C5  C6    180.00   0.0  0
 E1O  CONST_09  O3   C3   C4  C5    180.00   0.0  0
 E1O  CONST_10  O3   C3   C2  N1    180.00   0.0  0
 E1O  CONST_11  C5A  C5   C6  N1    180.00   0.0  0
 E1O  CONST_12  C4A  C4   C3  C2    180.00   0.0  0
 E1O  CONST_13  C2A  C2   C3  C4    180.00   0.0  0
 E1O  CONST_14  C3   C4   C5  C5A   180.00   0.0  0
 E1O  CONST_15  H1   C6   N1  C2    180.00   0.0  0
 E1O  CONST_16  H6   OXT  C   CA    180.00   0.0  0
 E1O  Var_01    O4P  C5A  C5  C6   -107.93  30.0  2
 E1O  Var_02    N    C4A  C4  C5    175.44  30.0  2
 E1O  Var_03    H11  C2A  C2  N1      0.66  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 E1O  chir_01  CA  N  C  CB  positiv

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
 E1O  plan-1  C6   0.020
 E1O  plan-1  C5   0.020
 E1O  plan-1  N1   0.020
 E1O  plan-1  C2   0.020
 E1O  plan-1  C4   0.020
 E1O  plan-1  C5A  0.020
 E1O  plan-1  C2A  0.020
 E1O  plan-1  C3   0.020
 E1O  plan-1  O3   0.020
 E1O  plan-1  C4A  0.020
 E1O  plan-1  H1   0.020
 E1O  plan-2  CA   0.020
 E1O  plan-2  C    0.020
 E1O  plan-2  OXT  0.020
 E1O  plan-2  H6   0.020
 E1O  plan-2  O    0.020
 E1O  plan-3  C4   0.020
 E1O  plan-3  CA   0.020
 E1O  plan-3  N    0.020
 E1O  plan-3  C4A  0.020
 E1O  plan-3  H15  0.020

