# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 21:58:32 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (2S,3S)-3-hydroxy-2-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-methylpentanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](O)[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
 FEJ  FEJ  '(2S,3S)-3-hydroxy-2-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-4-methylpentanoic acid (non-preferred name)'  ligand  46  25  .  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_FEJ
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
 FEJ  OAD  O  OH1   0  -0.727  -5.8591   0.8847   0.0022
 FEJ  PAP  P  P     0   1.467  -4.4361   1.5704  -0.1881
 FEJ  OAE  O  OH1   0  -0.741  -4.3502   2.1298  -1.6807
 FEJ  OAQ  O  O     0  -0.707  -4.0369   2.6240   0.7621
 FEJ  OAC  O  O2    0  -0.592  -3.5739   0.2220  -0.1494
 FEJ  CAB  C  CH2   0  -0.216  -2.1569   0.3011  -0.2102
 FEJ  CAM  C  CR6   0  -0.069  -1.5696  -1.0723  -0.0405
 FEJ  CAO  C  CR16  0  -0.145  -2.3523  -2.1847   0.1877
 FEJ  NAR  N  N     0  -0.396  -1.8478  -3.4098   0.3530
 FEJ  CAS  C  CR6   0   0.134  -0.5482  -3.6106   0.2996
 FEJ  CAA  C  CH3   0  -0.720  -0.0216  -4.9981   0.4912
 FEJ  CAT  C  CR6   0   0.299   0.3417  -2.5420   0.0658
 FEJ  OAU  O  OH1   0  -0.621   1.6395  -2.8124   0.0152
 FEJ  CAN  C  CR6   0  -0.013  -0.1760  -1.2518  -0.1027
 FEJ  CAL  C  C1    0   0.061   0.7250  -0.1283  -0.3343
 FEJ  N    N  N     0  -0.450   1.9829  -0.3012  -0.3914
 FEJ  CA   C  CH1   0  -0.270   2.8420   0.8314  -0.6031
 FEJ  C    C  C     0   0.565   3.6502   0.5857  -1.8672
 FEJ  O    O  O     0  -0.431   4.1722  -0.4671  -2.1261
 FEJ  OXT  O  OH1   0  -0.580   3.7197   1.6614  -2.6324
 FEJ  CB   C  CH1   0   0.059   3.8435   0.9458   0.5724
 FEJ  OG   O  OH1   0  -0.656   4.8300   1.8982   0.2621
 FEJ  CG   C  CH1   0  -0.271   3.1625   1.1866   1.9235
 FEJ  CD2  C  CH3   0  -0.650   4.1893   1.1058   3.0503
 FEJ  CD1  C  CH3   0  -0.683   2.3920   2.5027   1.9973
 FEJ  H1   H  HOH1  0   0.507  -6.5818   1.5126   0.1397
 FEJ  H2   H  HOH1  0   0.498  -4.6255   1.5191  -2.3779
 FEJ  H3   H  HCH2  0   0.264  -1.8487   0.7263  -1.1707
 FEJ  H4   H  HCH2  0   0.262  -1.7860   0.9631   0.5783
 FEJ  H5   H  HCR6  0   0.263  -3.4295  -2.1084   0.2438
 FEJ  H6   H  HCH3  0   0.249   0.5309  -5.3428  -0.3847
 FEJ  H7   H  HCH3  0   0.249   0.6617  -5.0545   1.3405
 FEJ  H8   H  HCH3  0   0.249  -0.8462  -5.6851   0.6683
 FEJ  H9   H  HOH1  0   0.475   2.1237  -1.9605  -0.1648
 FEJ  H10  H  H     0   0.265   0.2939   0.8666  -0.4614
 FEJ  H11  H  HCH1  0   0.269   2.2671   1.7608  -0.7086
 FEJ  H12  H  HOH1  0   0.485   4.2723   1.4843  -3.4094
 FEJ  H13  H  HCH1  0   0.251   4.3663  -0.0147   0.6296
 FEJ  H14  H  HOH1  0   0.450   4.4327   2.7758   0.2401
 FEJ  H15  H  HCH1  0   0.238   2.4509   0.3673   2.0658
 FEJ  H16  H  HCH3  0   0.222   4.9141   1.9179   2.9865
 FEJ  H17  H  HCH3  0   0.232   3.6964   1.1763   4.0205
 FEJ  H18  H  HCH3  0   0.229   4.7371   0.1620   3.0259
 FEJ  H19  H  HCH3  0   0.230   1.6155   2.5912   1.2358
 FEJ  H20  H  HCH3  0   0.248   1.8977   2.5876   2.9654
 FEJ  H21  H  HCH3  0   0.222   3.0495   3.3707   1.9060

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
 FEJ  CAA  CAS  single    1.496  0.020  1.496
 FEJ  CAS  NAR  aromatic  1.316  0.020  1.316
 FEJ  CAS  CAT  aromatic  1.410  0.020  1.410
 FEJ  OAU  CAT  single    1.327  0.020  1.327
 FEJ  NAR  CAO  aromatic  1.335  0.020  1.335
 FEJ  CAT  CAN  aromatic  1.400  0.020  1.400
 FEJ  O    C    double    1.203  0.020  1.203
 FEJ  CAO  CAM  aromatic  1.379  0.020  1.379
 FEJ  CAN  CAM  aromatic  1.406  0.020  1.406
 FEJ  CAN  CAL  single    1.459  0.020  1.459
 FEJ  C    OXT  single    1.322  0.020  1.322
 FEJ  C    CA   single    1.520  0.020  1.520
 FEJ  N    CAL  double    1.271  0.020  1.271
 FEJ  N    CA   single    1.437  0.020  1.437
 FEJ  CAM  CAB  single    1.503  0.020  1.503
 FEJ  CA   CB   single    1.549  0.020  1.549
 FEJ  OG   CB   single    1.406  0.020  1.406
 FEJ  CAB  OAC  single    1.421  0.020  1.421
 FEJ  OAQ  PAP  double    1.474  0.020  1.474
 FEJ  CB   CG   single    1.532  0.020  1.532
 FEJ  OAC  PAP  single    1.601  0.020  1.601
 FEJ  PAP  OAD  single    1.591  0.020  1.591
 FEJ  PAP  OAE  single    1.596  0.020  1.596
 FEJ  CG   CD1  single    1.527  0.020  1.527
 FEJ  CG   CD2  single    1.527  0.020  1.527
 FEJ  OAD  H1   single    0.850  0.020  0.980
 FEJ  OAE  H2   single    0.850  0.020  0.980
 FEJ  CAB  H3   single    0.970  0.020  1.090
 FEJ  CAB  H4   single    0.970  0.020  1.090
 FEJ  CAO  H5   single    0.930  0.020  1.080
 FEJ  CAA  H6   single    0.970  0.020  1.090
 FEJ  CAA  H7   single    0.970  0.020  1.090
 FEJ  CAA  H8   single    0.970  0.020  1.090
 FEJ  OAU  H9   single    0.850  0.020  0.980
 FEJ  CAL  H10  single    0.930  0.020  1.080
 FEJ  CA   H11  single    0.970  0.020  1.090
 FEJ  OXT  H12  single    0.850  0.020  0.980
 FEJ  CB   H13  single    0.970  0.020  1.090
 FEJ  OG   H14  single    0.850  0.020  0.980
 FEJ  CG   H15  single    0.970  0.020  1.090
 FEJ  CD2  H16  single    0.970  0.020  1.090
 FEJ  CD2  H17  single    0.970  0.020  1.090
 FEJ  CD2  H18  single    0.970  0.020  1.090
 FEJ  CD1  H19  single    0.970  0.020  1.090
 FEJ  CD1  H20  single    0.970  0.020  1.090
 FEJ  CD1  H21  single    0.970  0.020  1.090

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
 FEJ  H1   OAD  PAP  113.92  3.000
 FEJ  OAC  PAP  OAQ  116.14  3.000
 FEJ  OAC  PAP  OAE  106.78  3.000
 FEJ  OAQ  PAP  OAE  109.74  3.000
 FEJ  OAE  PAP  OAD  108.12  3.000
 FEJ  OAC  PAP  OAD   96.65  3.000
 FEJ  OAQ  PAP  OAD  118.24  3.000
 FEJ  H2   OAE  PAP  115.96  3.000
 FEJ  CAB  OAC  PAP  119.29  3.000
 FEJ  H4   CAB  H3   107.57  3.000
 FEJ  H4   CAB  CAM  109.81  3.000
 FEJ  H3   CAB  CAM  110.12  3.000
 FEJ  H4   CAB  OAC  109.93  3.000
 FEJ  H3   CAB  OAC  109.87  3.000
 FEJ  CAM  CAB  OAC  109.51  3.000
 FEJ  CAN  CAM  CAO  117.82  3.000
 FEJ  CAN  CAM  CAB  119.91  3.000
 FEJ  CAO  CAM  CAB  122.26  3.000
 FEJ  H5   CAO  NAR  115.76  3.000
 FEJ  H5   CAO  CAM  121.14  3.000
 FEJ  NAR  CAO  CAM  123.10  3.000
 FEJ  CAS  NAR  CAO  120.54  3.000
 FEJ  CAT  CAS  CAA  120.12  3.000
 FEJ  CAT  CAS  NAR  120.95  3.000
 FEJ  CAA  CAS  NAR  118.93  3.000
 FEJ  H8   CAA  H7   108.37  3.000
 FEJ  H8   CAA  H6   108.35  3.000
 FEJ  H7   CAA  H6   106.93  3.000
 FEJ  H8   CAA  CAS  109.86  3.000
 FEJ  H7   CAA  CAS  111.58  3.000
 FEJ  H6   CAA  CAS  111.61  3.000
 FEJ  CAN  CAT  OAU  123.01  3.000
 FEJ  CAN  CAT  CAS  119.00  3.000
 FEJ  OAU  CAT  CAS  117.98  3.000
 FEJ  H9   OAU  CAT  107.94  3.000
 FEJ  CAL  CAN  CAT  120.03  3.000
 FEJ  CAL  CAN  CAM  121.38  3.000
 FEJ  CAT  CAN  CAM  118.59  3.000
 FEJ  H10  CAL  N    120.64  3.000
 FEJ  H10  CAL  CAN  118.46  3.000
 FEJ  N    CAL  CAN  120.91  3.000
 FEJ  CA   N    CAL  119.40  3.000
 FEJ  H11  CA   CB   110.43  3.000
 FEJ  H11  CA   C    109.59  3.000
 FEJ  CB   CA   C    107.42  3.000
 FEJ  H11  CA   N    111.61  3.000
 FEJ  CB   CA   N    109.45  3.000
 FEJ  C    CA   N    108.23  3.000
 FEJ  OXT  C    O    124.38  3.000
 FEJ  OXT  C    CA   112.19  3.000
 FEJ  O    C    CA   123.43  3.000
 FEJ  H12  OXT  C    110.19  3.000
 FEJ  H13  CB   CG   107.70  3.000
 FEJ  H13  CB   OG   105.71  3.000
 FEJ  CG   CB   OG   113.58  3.000
 FEJ  H13  CB   CA   106.48  3.000
 FEJ  CG   CB   CA   113.18  3.000
 FEJ  OG   CB   CA   109.65  3.000
 FEJ  H14  OG   CB   109.44  3.000
 FEJ  H15  CG   CD1  108.11  3.000
 FEJ  H15  CG   CD2  107.56  3.000
 FEJ  CD1  CG   CD2  110.45  3.000
 FEJ  H15  CG   CB   106.62  3.000
 FEJ  CD2  CG   CB   110.10  3.000
 FEJ  CD1  CG   CB   113.73  3.000
 FEJ  H18  CD2  H17  107.62  3.000
 FEJ  H18  CD2  H16  108.01  3.000
 FEJ  H17  CD2  H16  107.71  3.000
 FEJ  H18  CD2  CG   111.52  3.000
 FEJ  H17  CD2  CG   110.44  3.000
 FEJ  H16  CD2  CG   111.37  3.000
 FEJ  H21  CD1  H20  106.57  3.000
 FEJ  H21  CD1  H19  107.78  3.000
 FEJ  H20  CD1  H19  106.89  3.000
 FEJ  H21  CD1  CG   112.15  3.000
 FEJ  H20  CD1  CG   109.81  3.000
 FEJ  H19  CD1  CG   113.29  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
 FEJ  CONST_01  CAS  NAR  CAO  CAM     0.00   0.0  0
 FEJ  CONST_02  CAS  CAT  CAN  CAM     0.00   0.0  0
 FEJ  CONST_03  CAT  CAS  NAR  CAO     0.00   0.0  0
 FEJ  CONST_04  CAT  CAN  CAM  CAO     0.00   0.0  0
 FEJ  CONST_05  CAN  CAT  CAS  NAR     0.00   0.0  0
 FEJ  CONST_06  CAN  CAM  CAO  NAR     0.00   0.0  0
 FEJ  CONST_07  NAR  CAO  CAM  CAB   180.00   0.0  0
 FEJ  CONST_08  CAT  CAN  CAM  CAB   180.00   0.0  0
 FEJ  CONST_09  OAU  CAT  CAN  CAM   180.00   0.0  0
 FEJ  CONST_10  CAA  CAS  NAR  CAO   180.00   0.0  0
 FEJ  CONST_11  CAL  CAN  CAM  CAO   180.00   0.0  0
 FEJ  CONST_12  OAU  CAT  CAS  NAR   180.00   0.0  0
 FEJ  CONST_13  CAL  CAN  CAT  CAS   180.00   0.0  0
 FEJ  CONST_14  CAN  CAT  CAS  CAA   180.00   0.0  0
 FEJ  CONST_15  H5   CAO  NAR  CAS   180.00   0.0  0
 FEJ  CONST_16  H12  OXT  C    CA    180.00   0.0  0
 FEJ  Var_01    CAO  CAM  CAB  OAC    -2.26  30.0  1
 FEJ  Var_02    N    CAL  CAN  CAM  -179.87  30.0  2
 FEJ  Var_03    H6   CAA  CAS  NAR   119.65  30.0  2
 FEJ  Var_04    CAM  CAB  OAC  PAP   175.21  30.0  1
 FEJ  Var_05    H19  CD1  CG   CB     58.01  30.0  3
 FEJ  Var_06    H16  CD2  CG   CB     66.04  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
 FEJ  chir_01  CA  C   N   CB  negativ
 FEJ  chir_02  CB  OG  CA  CG  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
 FEJ  plan-1  CAB  0.020
 FEJ  plan-1  CAM  0.020
 FEJ  plan-1  CAO  0.020
 FEJ  plan-1  NAR  0.020
 FEJ  plan-1  CAS  0.020
 FEJ  plan-1  CAA  0.020
 FEJ  plan-1  CAT  0.020
 FEJ  plan-1  OAU  0.020
 FEJ  plan-1  CAN  0.020
 FEJ  plan-1  CAL  0.020
 FEJ  plan-1  H5   0.020
 FEJ  plan-2  CA   0.020
 FEJ  plan-2  C    0.020
 FEJ  plan-2  O    0.020
 FEJ  plan-2  OXT  0.020
 FEJ  plan-2  H12  0.020
 FEJ  plan-3  CAN  0.020
 FEJ  plan-3  CAL  0.020
 FEJ  plan-3  N    0.020
 FEJ  plan-3  CA   0.020
 FEJ  plan-3  H10  0.020

