# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 09:56:20 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: (2E,3E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-5-phosphonopent-3-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN=C(\C=C\C[P](O)(O)=O)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
 HEN  HEN  '(2E,3E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-5-phosphonopent-3-enoic acid'  ligand  45  27  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HEN
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
 HEN  N1    N  N     0  -0.408  26.2165  170.1057  27.0977
 HEN  C2    C  CR6   0   0.134  25.9868  171.0427  26.1945
 HEN  C2A   C  CH3   0  -0.720  25.9049  170.6368  24.7556
 HEN  C3    C  CR6   0   0.251  25.8126  172.3937  26.5516
 HEN  O3    O  OH1   0  -0.645  25.5861  173.2571  25.5525
 HEN  C4    C  CR6   0   0.027  25.8780  172.7598  27.8965
 HEN  C4A   C  CH2   0  -0.357  25.6574  174.1681  28.3884
 HEN  C5    C  CR6   0   0.010  26.1298  171.7453  28.8307
 HEN  C6    C  CR16  0  -0.149  26.2873  170.4488  28.3786
 HEN  C5A   C  CH2   0  -0.304  26.2457  172.0218  30.2980
 HEN  OP4   O  O2    0  -0.583  24.9636  172.4352  30.8015
 HEN  P     P  P     0   1.459  24.8710  173.4574  32.0227
 HEN  OP1   O  OH1   0  -0.726  23.2947  173.3769  32.2320
 HEN  OP2   O  O     0  -0.694  25.4452  174.8072  31.8329
 HEN  OP3   O  OH1   0  -0.738  25.5295  172.6188  33.2142
 HEN  N4A   N  N     0  -0.452  25.7092  175.1539  27.3343
 HEN  CAI   C  C     0   0.231  25.5986  176.3924  27.5981
 HEN  CBC   C  C     0   0.504  25.7302  177.3180  26.4129
 HEN  O2B   O  OH1   0  -0.573  25.2239  176.7944  25.3146
 HEN  O3B   O  O     0  -0.415  26.2651  178.3933  26.4792
 HEN  CBI   C  C1    0  -0.311  25.4142  176.9467  28.9338
 HEN  CGI   C  C1    0  -0.187  25.0158  178.1895  29.2179
 HEN  CEI   C  CH2   0  -0.801  24.7771  178.6410  30.6182
 HEN  PG    P  P     0   1.367  26.0654  179.7927  31.1476
 HEN  OG1   O  OH1   0  -0.742  27.3405  178.8223  31.2601
 HEN  OG2   O  OH1   0  -0.743  25.5946  180.0997  32.6522
 HEN  OG3   O  O     0  -0.712  26.2754  180.9879  30.2941
 HEN  H2A1  H  HCH3  0   0.247  24.9305  170.8759  24.3255
 HEN  H2A2  H  HCH3  0   0.247  26.6528  171.1507  24.1489
 HEN  H2A3  H  HCH3  0   0.246  26.0663  169.5649  24.6632
 HEN  HO3   H  HOH1  0   0.474  25.6130  174.1689  25.9319
 HEN  H4A1  H  HCH2  0   0.291  24.6841  174.2191  28.8877
 HEN  H4A2  H  HCH2  0   0.273  26.4049  174.3945  29.1549
 HEN  HC6   H  HCR6  0   0.256  26.4819  169.6486  29.0854
 HEN  H5A1  H  HCH2  0   0.278  26.5558  171.1186  30.8256
 HEN  H5A2  H  HCH2  0   0.259  27.0026  172.7892  30.4876
 HEN  HP1O  H  HOH1  0   0.504  22.9079  174.1786  32.6082
 HEN  HP3O  H  HOH1  0   0.500  26.0081  173.1550  33.8597
 HEN  H2BO  H  HOH1  0   0.494  25.3696  177.3896  24.5627
 HEN  HBIC  H  H     0   0.301  25.5393  176.2581  29.7614
 HEN  HGIC  H  H     0   0.288  24.8410  178.9232  28.4411
 HEN  HCE1  H  HCH2  0   0.319  23.8259  179.1762  30.6828
 HEN  HCEC  H  HCH2  0   0.309  24.7393  177.7987  31.3120
 HEN  HG1O  H  HOH1  0   0.494  28.1885  179.2801  31.1829
 HEN  HG2O  H  HOH1  0   0.495  26.0307  180.8627  33.0558

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
 HEN  N1   C2    aromatic  1.322  0.020  1.322
 HEN  N1   C6    aromatic  1.328  0.020  1.328
 HEN  C2   C2A   single    1.497  0.020  1.497
 HEN  C2   C3    aromatic  1.408  0.020  1.408
 HEN  C2A  H2A1  single    0.970  0.020  1.090
 HEN  C2A  H2A2  single    0.970  0.020  1.090
 HEN  C2A  H2A3  single    0.970  0.020  1.090
 HEN  C3   O3    single    1.340  0.020  1.340
 HEN  C3   C4    aromatic  1.395  0.020  1.395
 HEN  O3   HO3   single    0.850  0.020  0.980
 HEN  C4   C4A   single    1.508  0.020  1.508
 HEN  C4   C5    aromatic  1.402  0.020  1.402
 HEN  C4A  N4A   single    1.444  0.020  1.444
 HEN  C4A  H4A1  single    0.970  0.020  1.090
 HEN  C4A  H4A2  single    0.970  0.020  1.090
 HEN  C5   C6    aromatic  1.382  0.020  1.382
 HEN  C5   C5A   single    1.498  0.020  1.498
 HEN  C6   HC6   single    0.930  0.020  1.080
 HEN  C5A  OP4   single    1.438  0.020  1.438
 HEN  C5A  H5A1  single    0.970  0.020  1.090
 HEN  C5A  H5A2  single    0.970  0.020  1.090
 HEN  OP4  P     single    1.595  0.020  1.595
 HEN  P    OP1   single    1.592  0.020  1.592
 HEN  P    OP2   double    1.479  0.020  1.479
 HEN  P    OP3   single    1.599  0.020  1.599
 HEN  OP1  HP1O  single    0.850  0.020  0.980
 HEN  OP3  HP3O  single    0.850  0.020  0.980
 HEN  N4A  CAI   double    1.271  0.020  1.271
 HEN  CAI  CBC   single    1.510  0.020  1.510
 HEN  CAI  CBI   single    1.458  0.020  1.458
 HEN  CBC  O2B   single    1.318  0.020  1.318
 HEN  CBC  O3B   double    1.203  0.020  1.203
 HEN  O2B  H2BO  single    0.850  0.020  0.980
 HEN  CBI  CGI   double    1.336  0.020  1.336
 HEN  CBI  HBIC  single    0.930  0.020  1.080
 HEN  CGI  CEI   single    1.491  0.020  1.491
 HEN  CGI  HGIC  single    0.930  0.020  1.080
 HEN  CEI  PG    single    1.807  0.020  1.807
 HEN  CEI  HCE1  single    0.970  0.020  1.090
 HEN  CEI  HCEC  single    0.970  0.020  1.090
 HEN  PG   OG1   single    1.606  0.020  1.606
 HEN  PG   OG2   single    1.606  0.020  1.606
 HEN  PG   OG3   double    1.484  0.020  1.484
 HEN  OG1  HG1O  single    0.850  0.020  0.980
 HEN  OG2  HG2O  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
 HEN  C6    N1   C2    119.03  3.000
 HEN  C3    C2   C2A   119.80  3.000
 HEN  C3    C2   N1    121.90  3.000
 HEN  C2A   C2   N1    118.30  3.000
 HEN  H2A3  C2A  H2A2  108.36  3.000
 HEN  H2A3  C2A  H2A1  108.35  3.000
 HEN  H2A2  C2A  H2A1  106.83  3.000
 HEN  H2A3  C2A  C2    109.91  3.000
 HEN  H2A2  C2A  C2    111.66  3.000
 HEN  H2A1  C2A  C2    111.60  3.000
 HEN  C4    C3   O3    123.89  3.000
 HEN  C4    C3   C2    119.36  3.000
 HEN  O3    C3   C2    116.75  3.000
 HEN  HO3   O3   C3    107.68  3.000
 HEN  C5    C4   C4A   118.99  3.000
 HEN  C5    C4   C3    117.44  3.000
 HEN  C4A   C4   C3    123.54  3.000
 HEN  H4A2  C4A  H4A1  106.15  3.000
 HEN  H4A2  C4A  N4A   110.22  3.000
 HEN  H4A1  C4A  N4A   109.44  3.000
 HEN  H4A2  C4A  C4    108.77  3.000
 HEN  H4A1  C4A  C4    108.80  3.000
 HEN  N4A   C4A  C4    113.21  3.000
 HEN  C5A   C5   C6    119.00  3.000
 HEN  C5A   C5   C4    122.23  3.000
 HEN  C6    C5   C4    118.77  3.000
 HEN  HC6   C6   C5    119.94  3.000
 HEN  HC6   C6   N1    116.56  3.000
 HEN  C5    C6   N1    123.49  3.000
 HEN  H5A2  C5A  H5A1  107.47  3.000
 HEN  H5A2  C5A  OP4   110.75  3.000
 HEN  H5A1  C5A  OP4   108.79  3.000
 HEN  H5A2  C5A  C5    110.65  3.000
 HEN  H5A1  C5A  C5    110.06  3.000
 HEN  OP4   C5A  C5    109.09  3.000
 HEN  P     OP4  C5A   120.26  3.000
 HEN  OP3   P    OP2   114.48  3.000
 HEN  OP3   P    OP1   106.45  3.000
 HEN  OP2   P    OP1   116.57  3.000
 HEN  OP3   P    OP4   102.15  3.000
 HEN  OP2   P    OP4   117.65  3.000
 HEN  OP1   P    OP4    97.22  3.000
 HEN  HP1O  OP1  P     113.92  3.000
 HEN  HP3O  OP3  P     114.26  3.000
 HEN  CAI   N4A  C4A   120.70  3.000
 HEN  CBI   CAI  CBC   119.82  3.000
 HEN  CBI   CAI  N4A   124.86  3.000
 HEN  CBC   CAI  N4A   115.27  3.000
 HEN  O3B   CBC  O2B   124.89  3.000
 HEN  O3B   CBC  CAI   122.93  3.000
 HEN  O2B   CBC  CAI   112.17  3.000
 HEN  H2BO  O2B  CBC   110.16  3.000
 HEN  HBIC  CBI  CGI   117.60  3.000
 HEN  HBIC  CBI  CAI   116.32  3.000
 HEN  CGI   CBI  CAI   125.90  3.000
 HEN  HGIC  CGI  CEI   116.29  3.000
 HEN  HGIC  CGI  CBI   121.74  3.000
 HEN  CEI   CGI  CBI   121.97  3.000
 HEN  HCEC  CEI  HCE1  108.06  3.000
 HEN  HCEC  CEI  PG    109.27  3.000
 HEN  HCE1  CEI  PG    106.91  3.000
 HEN  HCEC  CEI  CGI   111.64  3.000
 HEN  HCE1  CEI  CGI   110.07  3.000
 HEN  PG    CEI  CGI   110.74  3.000
 HEN  OG3   PG   OG2   115.24  3.000
 HEN  OG3   PG   OG1   114.50  3.000
 HEN  OG2   PG   OG1   106.41  3.000
 HEN  OG3   PG   CEI   116.47  3.000
 HEN  OG2   PG   CEI   100.79  3.000
 HEN  OG1   PG   CEI   101.62  3.000
 HEN  HG1O  OG1  PG    113.86  3.000
 HEN  HG2O  OG2  PG    114.18  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
 HEN  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 HEN  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 HEN  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 HEN  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 HEN  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 HEN  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 HEN  CONST_07  O3    C3   C2   N1    180.00   0.0  0
 HEN  CONST_08  C5A   C5   C6   N1    180.00   0.0  0
 HEN  CONST_09  C4A   C4   C3   C2    180.00   0.0  0
 HEN  CONST_10  C6    N1   C2   C2A   180.00   0.0  0
 HEN  CONST_11  C4    C3   C2   C2A   180.00   0.0  0
 HEN  CONST_12  C5A   C5   C4   C3    180.00   0.0  0
 HEN  CONST_13  C5    C4   C3   O3    180.00   0.0  0
 HEN  CONST_14  C6    C5   C4   C4A   180.00   0.0  0
 HEN  CONST_15  HC6   C6   N1   C2    180.00   0.0  0
 HEN  CONST_16  H2BO  O2B  CBC  CAI   180.00   0.0  0
 HEN  Var_01    N4A   C4A  C4   C3    -14.82  30.0  2
 HEN  Var_02    OP4   C5A  C5   C4     67.25  30.0  2
 HEN  Var_03    H2A1  C2A  C2   N1    119.66  30.0  2
 HEN  Var_04    CBC   CAI  N4A  C4A   177.45   0.0  2
 HEN  Var_05    CEI   CGI  CBI  CAI   176.25   0.0  2
 HEN  Var_06    OP1   P    OP4  C5A  -173.16  30.0  3
 HEN  Var_07    O2B   CBC  CAI  N4A    34.80  30.0  2
 HEN  Var_08    CGI   CBI  CAI  N4A  -164.83  30.0  2
 HEN  Var_09    PG    CEI  CGI  CBI   108.76  30.0  3
 HEN  Var_10    OG1   PG   CEI  CGI   -69.85  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
 HEN  plan-1  N1    0.020
 HEN  plan-1  C2    0.020
 HEN  plan-1  C2A   0.020
 HEN  plan-1  C3    0.020
 HEN  plan-1  O3    0.020
 HEN  plan-1  C4    0.020
 HEN  plan-1  C4A   0.020
 HEN  plan-1  C5    0.020
 HEN  plan-1  C6    0.020
 HEN  plan-1  C5A   0.020
 HEN  plan-1  HC6   0.020
 HEN  plan-2  CAI   0.020
 HEN  plan-2  CBC   0.020
 HEN  plan-2  O2B   0.020
 HEN  plan-2  O3B   0.020
 HEN  plan-2  H2BO  0.020
 HEN  plan-3  C4A   0.020
 HEN  plan-3  N4A   0.020
 HEN  plan-3  CAI   0.020
 HEN  plan-3  CBC   0.020
 HEN  plan-3  CBI   0.020
 HEN  plan-4  CAI   0.020
 HEN  plan-4  CBI   0.020
 HEN  plan-4  CGI   0.020
 HEN  plan-4  CEI   0.020
 HEN  plan-4  HBIC  0.020
 HEN  plan-4  HGIC  0.020

