# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 09:11:01 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: methyl (2~{S})-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-4-methylsulfanyl-butanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H](CCSC)N=Cc1c(O)c(C)ncc1CO[P](O)(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
 G06  G06  'methyl (2~{S})-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-4-methylsulfanyl-butanoate'  ligand  44  25  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G06
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
 G06  OAU  O  O      0  -0.874  35.9381   9.6739   -6.0133
 G06  PAT  P  P      0   1.254  36.0519   9.4350   -4.5039
 G06  OAV  O  OP    -1  -0.881  37.4729   9.3576   -3.9674
 G06  OAW  O  OP    -1  -0.889  35.0803   8.3880   -3.9709
 G06  OAS  O  O2     0  -0.649  35.5229  10.9126   -3.7973
 G06  CAR  C  CH2    0  -0.240  34.2020  11.2763   -4.0542
 G06  CAQ  C  C      0   0.002  34.0125  12.7449   -3.7882
 G06  CAX  C  C1     0  -0.164  33.1174  13.1457   -2.8138
 G06  NAY  N  N      0  -0.397  32.8848  14.4144   -2.4998
 G06  CAB  C  C      0   0.116  33.5364  15.3669   -3.1424
 G06  CAA  C  CH3    0  -0.789  33.2531  16.7902   -2.7589
 G06  CAC  C  C      0   0.251  34.4742  15.0702   -4.1494
 G06  OAD  O  OH1    0  -0.594  35.1113  16.0539   -4.8008
 G06  CAE  C  C      0   0.034  34.7315  13.7345   -4.4801
 G06  CAF  C  C1     0  -0.044  35.6839  13.3162   -5.5253
 G06  N    N  N      0  -0.343  36.6006  14.0781   -5.9553
 G06  CA   C  CH1    0  -0.224  37.4924  13.5984   -6.9909
 G06  C    C  C      0   0.584  36.7622  13.4732   -8.3222
 G06  O    O  O      0  -0.430  35.6683  12.9911   -8.4643
 G06  OAN  O  O2     0  -0.444  37.4954  13.9434   -9.3199
 G06  CAO  C  CH3    0  -0.425  36.9660  13.8325  -10.6415
 G06  CB   C  CH2    0  -0.492  38.1867  12.2707   -6.6411
 G06  CG   C  CH2    0  -0.573  39.2571  11.8225   -7.6254
 G06  SD   S  S2     0  -0.042  40.6003  13.0064   -7.9283
 G06  CE   C  CH3    0  -0.768  41.3959  13.0340   -6.3061
 G06  H3   H  HCH2   0   0.199  33.4911  10.7233   -3.4244
 G06  H4   H  HCH2   0   0.186  33.9096  11.0617   -5.0925
 G06  H5   H  H      0   0.249  32.5616  12.4013   -2.2527
 G06  H6   H  HCH3   0   0.271  32.5271  16.8109   -1.9498
 G06  H7   H  HCH3   0   0.257  34.1493  17.3112   -2.4121
 G06  H8   H  HCH3   0   0.255  32.8358  17.3698   -3.5872
 G06  H9   H  HOH1   0   0.483  34.7626  16.9153   -4.5446
 G06  H10  H  H      0   0.246  35.5487  12.2962   -5.8823
 G06  H11  H  HCH1   0   0.262  38.2708  14.3539   -7.1149
 G06  H12  H  HCH3   0   0.251  37.7104  14.2726  -11.2983
 G06  H13  H  HCH3   0   0.239  36.8086  12.7910  -10.9207
 G06  H14  H  HCH3   0   0.240  36.0280  14.3782  -10.7408
 G06  H15  H  HCH2   0   0.280  37.4555  11.4615   -6.5505
 G06  H16  H  HCH2   0   0.253  38.6287  12.3939   -5.6492
 G06  H17  H  HCH2   0   0.276  38.8370  11.6072   -8.6097
 G06  H18  H  HCH2   0   0.279  39.6991  10.8896   -7.2700
 G06  H19  H  HCH3   0   0.273  42.2957  13.6404   -6.3970
 G06  H20  H  HCH3   0   0.261  40.7579  13.4816   -5.5461
 G06  H21  H  HCH3   0   0.260  41.6830  12.0306   -5.9942

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
 G06  CAO  OAN  single    1.428  0.020  1.428
 G06  OAN  C    single    1.324  0.020  1.324
 G06  O    C    double    1.204  0.020  1.204
 G06  C    CA   single    1.523  0.020  1.523
 G06  CG   SD   single    1.816  0.020  1.816
 G06  CG   CB   single    1.522  0.020  1.522
 G06  CA   CB   single    1.539  0.020  1.539
 G06  CA   N    single    1.448  0.020  1.448
 G06  SD   CE   single    1.807  0.020  1.807
 G06  N    CAF  double    1.267  0.020  1.267
 G06  CAF  CAE  single    1.475  0.020  1.475
 G06  OAU  PAT  deloc     1.532  0.020  1.532
 G06  OAD  CAC  single    1.341  0.020  1.341
 G06  CAE  CAC  aromatic  1.400  0.020  1.400
 G06  CAE  CAQ  aromatic  1.405  0.020  1.405
 G06  CAC  CAB  aromatic  1.408  0.020  1.408
 G06  CAR  CAQ  single    1.505  0.020  1.505
 G06  CAR  OAS  single    1.394  0.020  1.394
 G06  CAQ  CAX  aromatic  1.383  0.020  1.383
 G06  PAT  OAW  deloc     1.525  0.020  1.525
 G06  PAT  OAS  single    1.721  0.020  1.721
 G06  PAT  OAV  deloc     1.521  0.020  1.521
 G06  CAB  CAA  single    1.501  0.020  1.501
 G06  CAB  NAY  aromatic  1.321  0.020  1.321
 G06  CAX  NAY  aromatic  1.328  0.020  1.328
 G06  CAR  H3   single    0.970  0.020  1.090
 G06  CAR  H4   single    0.970  0.020  1.090
 G06  CAX  H5   single    0.930  0.020  1.080
 G06  CAA  H6   single    0.970  0.020  1.090
 G06  CAA  H7   single    0.970  0.020  1.090
 G06  CAA  H8   single    0.970  0.020  1.090
 G06  OAD  H9   single    0.850  0.020  0.980
 G06  CAF  H10  single    0.930  0.020  1.080
 G06  CA   H11  single    0.970  0.020  1.090
 G06  CAO  H12  single    0.970  0.020  1.090
 G06  CAO  H13  single    0.970  0.020  1.090
 G06  CAO  H14  single    0.970  0.020  1.090
 G06  CB   H15  single    0.970  0.020  1.090
 G06  CB   H16  single    0.970  0.020  1.090
 G06  CG   H17  single    0.970  0.020  1.090
 G06  CG   H18  single    0.970  0.020  1.090
 G06  CE   H19  single    0.970  0.020  1.090
 G06  CE   H20  single    0.970  0.020  1.090
 G06  CE   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
 G06  OAS  PAT  OAW  104.49  3.000
 G06  OAS  PAT  OAV  100.72  3.000
 G06  OAW  PAT  OAV  115.92  3.000
 G06  OAV  PAT  OAU  115.14  3.000
 G06  OAS  PAT  OAU  104.34  3.000
 G06  OAW  PAT  OAU  113.83  3.000
 G06  CAR  OAS  PAT  116.08  3.000
 G06  H4   CAR  H3   105.72  3.000
 G06  H4   CAR  CAQ  108.90  3.000
 G06  H3   CAR  CAQ  107.96  3.000
 G06  H4   CAR  OAS  112.03  3.000
 G06  H3   CAR  OAS  112.09  3.000
 G06  CAQ  CAR  OAS  109.96  3.000
 G06  CAE  CAQ  CAX  118.30  3.000
 G06  CAX  CAQ  CAR  119.28  3.000
 G06  CAE  CAQ  CAR  122.41  3.000
 G06  H5   CAX  NAY  116.33  3.000
 G06  H5   CAX  CAQ  119.81  3.000
 G06  NAY  CAX  CAQ  123.86  3.000
 G06  CAB  NAY  CAX  119.19  3.000
 G06  CAC  CAB  CAA  120.55  3.000
 G06  CAA  CAB  NAY  117.80  3.000
 G06  CAC  CAB  NAY  121.65  3.000
 G06  H8   CAA  H7   107.49  3.000
 G06  H8   CAA  H6   107.38  3.000
 G06  H7   CAA  H6   107.59  3.000
 G06  H8   CAA  CAB  112.40  3.000
 G06  H7   CAA  CAB  112.23  3.000
 G06  H6   CAA  CAB  109.53  3.000
 G06  CAE  CAC  OAD  119.86  3.000
 G06  CAE  CAC  CAB  119.51  3.000
 G06  OAD  CAC  CAB  120.63  3.000
 G06  H9   OAD  CAC  110.77  3.000
 G06  CAF  CAE  CAC  123.84  3.000
 G06  CAC  CAE  CAQ  117.49  3.000
 G06  CAF  CAE  CAQ  118.66  3.000
 G06  H10  CAF  N    122.79  3.000
 G06  H10  CAF  CAE  114.70  3.000
 G06  N    CAF  CAE  122.49  3.000
 G06  CA   N    CAF  119.27  3.000
 G06  H11  CA   CB   107.53  3.000
 G06  H11  CA   C    107.42  3.000
 G06  CB   CA   C    110.12  3.000
 G06  H11  CA   N    106.92  3.000
 G06  CB   CA   N    113.64  3.000
 G06  C    CA   N    110.91  3.000
 G06  OAN  C    O    123.80  3.000
 G06  O    C    CA   124.86  3.000
 G06  OAN  C    CA   111.33  3.000
 G06  CAO  OAN  C    117.67  3.000
 G06  H14  CAO  H13  109.33  3.000
 G06  H14  CAO  H12  109.39  3.000
 G06  H13  CAO  H12  109.35  3.000
 G06  H14  CAO  OAN  111.38  3.000
 G06  H13  CAO  OAN  111.40  3.000
 G06  H12  CAO  OAN  105.91  3.000
 G06  H16  CB   H15  106.16  3.000
 G06  H16  CB   CG   109.62  3.000
 G06  H15  CB   CG   107.81  3.000
 G06  H16  CB   CA   106.95  3.000
 G06  H15  CB   CA   110.82  3.000
 G06  CG   CB   CA   115.12  3.000
 G06  H18  CG   H17  106.31  3.000
 G06  H18  CG   SD   108.17  3.000
 G06  H17  CG   SD   105.24  3.000
 G06  H18  CG   CB   109.02  3.000
 G06  H17  CG   CB   111.75  3.000
 G06  SD   CG   CB   115.86  3.000
 G06  CE   SD   CG   100.72  3.000
 G06  H21  CE   H20  109.48  3.000
 G06  H21  CE   H19  108.60  3.000
 G06  H20  CE   H19  108.28  3.000
 G06  H21  CE   SD   111.04  3.000
 G06  H20  CE   SD   112.02  3.000
 G06  H19  CE   SD   107.30  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
 G06  CONST_01  CAB  CAC  CAE  CAQ     0.00   0.0  0
 G06  CONST_02  CAB  NAY  CAX  CAQ     0.00   0.0  0
 G06  CONST_03  CAC  CAE  CAQ  CAX     0.00   0.0  0
 G06  CONST_04  CAC  CAB  NAY  CAX     0.00   0.0  0
 G06  CONST_05  CAE  CAC  CAB  NAY     0.00   0.0  0
 G06  CONST_06  CAE  CAQ  CAX  NAY     0.00   0.0  0
 G06  CONST_07  CAC  CAE  CAQ  CAR   180.00   0.0  0
 G06  CONST_08  NAY  CAX  CAQ  CAR   180.00   0.0  0
 G06  CONST_09  OAD  CAC  CAE  CAQ   180.00   0.0  0
 G06  CONST_10  CAF  CAE  CAQ  CAX   180.00   0.0  0
 G06  CONST_11  CAA  CAB  NAY  CAX   180.00   0.0  0
 G06  CONST_12  OAD  CAC  CAB  NAY   180.00   0.0  0
 G06  CONST_13  CAF  CAE  CAC  CAB   180.00   0.0  0
 G06  CONST_14  CAE  CAC  CAB  CAA   180.00   0.0  0
 G06  CONST_15  H5   CAX  NAY  CAB   180.00   0.0  0
 G06  Var_01    CAE  CAQ  CAR  OAS    60.28  30.0  2
 G06  Var_02    N    CAF  CAE  CAQ  -161.76  30.0  2
 G06  Var_03    H6   CAA  CAB  NAY     1.21  30.0  2
 G06  Var_04    CAQ  CAR  OAS  PAT  -161.21  30.0  2
 G06  Var_05    SD   CG   CB   CA     56.31  30.0  2
 G06  Var_06    H12  CAO  OAN  C     179.87  30.0  3
 G06  Var_07    H19  CE   SD   CG    173.99  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
 G06  chir_01  CA  C  CB  N  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
 G06  plan-1  CAR  0.020
 G06  plan-1  CAQ  0.020
 G06  plan-1  CAX  0.020
 G06  plan-1  NAY  0.020
 G06  plan-1  CAB  0.020
 G06  plan-1  CAA  0.020
 G06  plan-1  CAC  0.020
 G06  plan-1  OAD  0.020
 G06  plan-1  CAE  0.020
 G06  plan-1  CAF  0.020
 G06  plan-1  H5   0.020
 G06  plan-2  CA   0.020
 G06  plan-2  C    0.020
 G06  plan-2  O    0.020
 G06  plan-2  OAN  0.020
 G06  plan-3  CAE  0.020
 G06  plan-3  CAF  0.020
 G06  plan-3  N    0.020
 G06  plan-3  CA   0.020
 G06  plan-3  H10  0.020

