# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 22:18:19 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-methionine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@H](N=Cc1c(O)c(C)ncc1CO[P](O)(O)=O)C(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
 AA5  AA5  (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-methionine  ligand  43  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AA5
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
 AA5  N     N  N     0  -0.452  79.6911  43.9584  -14.3343
 AA5  CA    C  CH1   0  -0.255  79.6918  44.0488  -12.8981
 AA5  C     C  C     0   0.564  78.7642  43.0133  -12.2798
 AA5  O1    O  O     0  -0.435  78.3684  43.0842  -11.1444
 AA5  CB    C  CH2   0  -0.422  79.3233  45.4678  -12.4559
 AA5  CG    C  CH2   0  -0.555  77.9533  45.9247  -12.9347
 AA5  SD    S  S2    0  -0.036  77.6879  47.6415  -12.4095
 AA5  CE    C  CH3   0  -0.763  76.0230  47.9100  -13.0544
 AA5  O2    O  OH1   0  -0.575  78.4881  42.0160  -13.0995
 AA5  C2    C  CR6   0   0.140  79.7333  43.9509  -18.5574
 AA5  C2A   C  CH3   0  -0.721  78.5074  44.2371  -19.3652
 AA5  C3    C  CR6   0   0.296  79.6621  43.9485  -17.1478
 AA5  C4    C  CR6   0  -0.020  80.8212  43.6894  -16.4058
 AA5  C4A   C  C1    0   0.086  80.7801  43.7268  -14.9461
 AA5  C5    C  CR6   0  -0.008  82.0079  43.4174  -17.1074
 AA5  C5A   C  CH2   0  -0.323  83.2930  43.0916  -16.4142
 AA5  C6    C  CR16  0  -0.145  81.9664  43.4330  -18.4849
 AA5  N1    N  N     0  -0.399  80.8643  43.7008  -19.1849
 AA5  O1P   O  O     0  -0.693  83.8374  39.8560  -14.3325
 AA5  O2P   O  OH1   0  -0.744  85.6115  41.2045  -15.5332
 AA5  O3P   O  OH1   0  -0.747  84.3077  42.3505  -13.6442
 AA5  O4P   O  O2    0  -0.583  83.1210  41.8355  -15.7416
 AA5  P     P  P     0   1.477  84.2138  41.2121  -14.7606
 AA5  HA    H  HCH1  0   0.299  80.6891  43.8247  -12.4893
 AA5  HB1   H  HCH2  0   0.261  79.3778  45.5157  -11.3676
 AA5  HB2   H  HCH2  0   0.263  80.0930  46.1405  -12.8396
 AA5  HG1   H  HCH2  0   0.261  77.8806  45.8747  -14.0221
 AA5  HG2   H  HCH2  0   0.266  77.1607  45.3030  -12.5130
 AA5  HE1   H  HCH3  0   0.274  75.7410  48.9341  -12.8169
 AA5  HE2   H  HCH3  0   0.261  75.9935  47.7832  -14.1358
 AA5  HE3   H  HCH3  0   0.262  75.3057  47.2341  -12.5914
 AA5  HO2   H  HOH1  0   0.487  77.9309  41.3621  -12.6497
 AA5  H2A1  H  HCH3  0   0.251  78.7500  44.2214  -20.4254
 AA5  H2A2  H  HCH3  0   0.252  77.7264  43.4975  -19.1793
 AA5  H2A3  H  HCH3  0   0.251  78.0853  45.2134  -19.1210
 AA5  H4A   H  H     0   0.255  81.7057  43.5626  -14.3921
 AA5  H5A1  H  HCH2  0   0.281  84.0948  43.0136  -17.1511
 AA5  H5A2  H  HCH2  0   0.266  83.5687  43.8737  -15.7022
 AA5  H6    H  HCR6  0   0.264  82.8630  43.2217  -19.0576
 AA5  H2P   H  HOH1  0   0.497  86.0603  42.0525  -15.6475
 AA5  HO3   H  HOH1  0   0.482  78.6099  44.1428  -15.5980
 AA5  H3P   H  HOH1  0   0.505  84.9066  42.1580  -12.9091
 AA5  O3    O  OH1   0  -0.624  78.4853  44.1937  -16.5855

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
 AA5  N    CA    single    1.439  0.020  1.439
 AA5  N    C4A   double    1.270  0.020  1.270
 AA5  CA   C     single    1.522  0.020  1.522
 AA5  CA   CB    single    1.531  0.020  1.531
 AA5  CA   HA    single    0.970  0.020  1.090
 AA5  C    O1    double    1.204  0.020  1.204
 AA5  C    O2    single    1.320  0.020  1.320
 AA5  CB   CG    single    1.521  0.020  1.521
 AA5  CB   HB1   single    0.970  0.020  1.090
 AA5  CB   HB2   single    0.970  0.020  1.090
 AA5  CG   SD    single    1.815  0.020  1.815
 AA5  CG   HG1   single    0.970  0.020  1.090
 AA5  CG   HG2   single    0.970  0.020  1.090
 AA5  SD   CE    single    1.806  0.020  1.806
 AA5  CE   HE1   single    0.970  0.020  1.090
 AA5  CE   HE2   single    0.970  0.020  1.090
 AA5  CE   HE3   single    0.970  0.020  1.090
 AA5  O2   HO2   single    0.850  0.020  0.980
 AA5  C2   C2A   single    1.496  0.020  1.496
 AA5  C2   C3    aromatic  1.411  0.020  1.411
 AA5  C2   N1    aromatic  1.317  0.020  1.317
 AA5  C2A  H2A1  single    0.970  0.020  1.090
 AA5  C2A  H2A2  single    0.970  0.020  1.090
 AA5  C2A  H2A3  single    0.970  0.020  1.090
 AA5  C3   C4    aromatic  1.400  0.020  1.400
 AA5  C3   O3    single    1.327  0.020  1.327
 AA5  C4   C4A   single    1.461  0.020  1.461
 AA5  C4   C5    aromatic  1.405  0.020  1.405
 AA5  C4A  H4A   single    0.930  0.020  1.080
 AA5  C5   C5A   single    1.496  0.020  1.496
 AA5  C5   C6    aromatic  1.378  0.020  1.378
 AA5  C5A  O4P   single    1.435  0.020  1.435
 AA5  C5A  H5A1  single    0.970  0.020  1.090
 AA5  C5A  H5A2  single    0.970  0.020  1.090
 AA5  C6   N1    aromatic  1.333  0.020  1.333
 AA5  C6   H6    single    0.930  0.020  1.080
 AA5  O1P  P     double    1.471  0.020  1.471
 AA5  O2P  P     single    1.597  0.020  1.597
 AA5  O2P  H2P   single    0.850  0.020  0.980
 AA5  O3   HO3   single    0.850  0.020  0.980
 AA5  O3P  P     single    1.597  0.020  1.597
 AA5  O3P  H3P   single    0.850  0.020  0.980
 AA5  O4P  P     single    1.595  0.020  1.595

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
 AA5  C4A   N    CA    119.45  3.000
 AA5  HA    CA   CB    107.43  3.000
 AA5  HA    CA   C     105.24  3.000
 AA5  CB    CA   C     111.50  3.000
 AA5  HA    CA   N     110.99  3.000
 AA5  CB    CA   N     110.26  3.000
 AA5  C     CA   N     111.26  3.000
 AA5  O2    C    O1    124.13  3.000
 AA5  O2    C    CA    112.91  3.000
 AA5  O1    C    CA    122.91  3.000
 AA5  HB2   CB   HB1   106.75  3.000
 AA5  HB2   CB   CG    109.83  3.000
 AA5  HB1   CB   CG    110.23  3.000
 AA5  HB2   CB   CA    107.44  3.000
 AA5  HB1   CB   CA    108.48  3.000
 AA5  CG    CB   CA    113.84  3.000
 AA5  HG2   CG   HG1   108.09  3.000
 AA5  HG2   CG   SD    108.71  3.000
 AA5  HG1   CG   SD    108.79  3.000
 AA5  HG2   CG   CB    111.16  3.000
 AA5  HG1   CG   CB    111.09  3.000
 AA5  SD    CG   CB    108.95  3.000
 AA5  CE    SD   CG     99.91  3.000
 AA5  HE3   CE   HE2   109.39  3.000
 AA5  HE3   CE   HE1   108.70  3.000
 AA5  HE2   CE   HE1   108.62  3.000
 AA5  HE3   CE   SD    111.30  3.000
 AA5  HE2   CE   SD    111.24  3.000
 AA5  HE1   CE   SD    107.51  3.000
 AA5  HO2   O2   C     109.97  3.000
 AA5  N1    C2   C3    121.24  3.000
 AA5  N1    C2   C2A   118.86  3.000
 AA5  C3    C2   C2A   119.89  3.000
 AA5  H2A3  C2A  H2A2  106.94  3.000
 AA5  H2A3  C2A  H2A1  108.50  3.000
 AA5  H2A2  C2A  H2A1  108.41  3.000
 AA5  H2A3  C2A  C2    111.55  3.000
 AA5  H2A2  C2A  C2    111.40  3.000
 AA5  H2A1  C2A  C2    109.93  3.000
 AA5  O3    C3   C4    122.94  3.000
 AA5  O3    C3   C2    117.88  3.000
 AA5  C4    C3   C2    119.19  3.000
 AA5  C5    C4   C4A   121.85  3.000
 AA5  C5    C4   C3    118.05  3.000
 AA5  C4A   C4   C3    120.09  3.000
 AA5  H4A   C4A  C4    118.66  3.000
 AA5  H4A   C4A  N     120.67  3.000
 AA5  C4    C4A  N     120.67  3.000
 AA5  C6    C5   C5A   119.44  3.000
 AA5  C6    C5   C4    118.13  3.000
 AA5  C5A   C5   C4    122.43  3.000
 AA5  H5A2  C5A  H5A1  107.79  3.000
 AA5  H5A2  C5A  O4P   110.56  3.000
 AA5  H5A1  C5A  O4P   109.98  3.000
 AA5  H5A2  C5A  C5    111.27  3.000
 AA5  H5A1  C5A  C5    109.49  3.000
 AA5  O4P   C5A  C5    107.75  3.000
 AA5  H6    C6   N1    116.45  3.000
 AA5  H6    C6   C5    120.04  3.000
 AA5  N1    C6   C5    123.51  3.000
 AA5  C6    N1   C2    119.86  3.000
 AA5  H2P   O2P  P     117.36  3.000
 AA5  H3P   O3P  P     115.19  3.000
 AA5  P     O4P  C5A   123.24  3.000
 AA5  O4P   P    O3P   101.04  3.000
 AA5  O4P   P    O2P   107.69  3.000
 AA5  O3P   P    O2P   106.86  3.000
 AA5  O4P   P    O1P   111.34  3.000
 AA5  O3P   P    O1P   117.95  3.000
 AA5  O2P   P    O1P   111.12  3.000
 AA5  HO3   O3   C3    107.42  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
 AA5  CONST_01  C5    C4   C3   C2      0.00   0.0  0
 AA5  CONST_02  C5    C6   N1   C2      0.00   0.0  0
 AA5  CONST_03  C6    N1   C2   C3      0.00   0.0  0
 AA5  CONST_04  C6    C5   C4   C3      0.00   0.0  0
 AA5  CONST_05  N1    C2   C3   C4      0.00   0.0  0
 AA5  CONST_06  N1    C6   C5   C4      0.00   0.0  0
 AA5  CONST_07  C4A   C4   C3   C2    180.00   0.0  0
 AA5  CONST_08  C4    C3   C2   C2A   180.00   0.0  0
 AA5  CONST_09  C6    N1   C2   C2A   180.00   0.0  0
 AA5  CONST_10  C5A   C5   C4   C3    180.00   0.0  0
 AA5  CONST_11  C6    C5   C4   C4A   180.00   0.0  0
 AA5  CONST_12  O3    C3   C4   C5    180.00   0.0  0
 AA5  CONST_13  N1    C6   C5   C5A   180.00   0.0  0
 AA5  CONST_14  O3    C3   C2   N1    180.00   0.0  0
 AA5  CONST_15  H6    C6   N1   C2    180.00   0.0  0
 AA5  CONST_16  HO2   O2   C    CA    180.00   0.0  0
 AA5  Var_01    C3    C4   C4A  N       1.87  30.0  1
 AA5  Var_02    O4P   C5A  C5   C4     65.82  30.0  2
 AA5  Var_03    H2A1  C2A  C2   C3    178.63  30.0  2
 AA5  Var_04    C4    C4A  N    CA   -177.23   0.0  2
 AA5  Var_05    SD    CG   CB   CA   -177.23  30.0  3
 AA5  Var_06    O1P   P    O4P  C5A  -173.74  30.0  3
 AA5  Var_07    HE1   CE   SD   CG   -179.03  30.0  3

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
 AA5  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
 AA5  plan-1  C2   0.020
 AA5  plan-1  C2A  0.020
 AA5  plan-1  C3   0.020
 AA5  plan-1  C4   0.020
 AA5  plan-1  C4A  0.020
 AA5  plan-1  C5   0.020
 AA5  plan-1  C5A  0.020
 AA5  plan-1  C6   0.020
 AA5  plan-1  N1   0.020
 AA5  plan-1  H6   0.020
 AA5  plan-1  O3   0.020
 AA5  plan-2  CA   0.020
 AA5  plan-2  C    0.020
 AA5  plan-2  O1   0.020
 AA5  plan-2  O2   0.020
 AA5  plan-2  HO2  0.020
 AA5  plan-3  N    0.020
 AA5  plan-3  CA   0.020
 AA5  plan-3  C4   0.020
 AA5  plan-3  C4A  0.020
 AA5  plan-3  H4A  0.020

