# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 08:32:58 2021
#   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  46  25  .  2022-03-18  2022-11-17
;
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  -0.705  36.3283   9.3047   -5.4941
 G06  PAT  P  P     0   1.472  36.5412   9.7532   -4.1029
 G06  OAV  O  OH1   0  -0.728  38.0143  10.1906   -3.6840
 G06  OAW  O  OH1   0  -0.738  36.0658   8.7038   -2.9934
 G06  OAS  O  O2    0  -0.581  35.8222  11.1090   -3.6618
 G06  CAR  C  CH2   0  -0.299  34.4168  11.2739   -3.8970
 G06  CAQ  C  CR6   0   0.005  34.0791  12.7233   -3.7343
 G06  CAX  C  CR16  0  -0.146  33.1765  13.1017   -2.7591
 G06  NAY  N  N     0  -0.400  32.8108  14.3609   -2.5537
 G06  CAB  C  CR6   0   0.129  33.3363  15.3186   -3.2963
 G06  CAA  C  CH3   0  -0.791  32.8979  16.7295   -3.0416
 G06  CAC  C  CR6   0   0.263  34.2829  15.0398   -4.3007
 G06  OAD  O  OH1   0  -0.593  34.8038  16.0150   -5.0547
 G06  CAE  C  CR6   0   0.043  34.6620  13.7171   -4.5334
 G06  CAF  C  C1    0  -0.041  35.6074  13.3313   -5.5968
 G06  N    N  N     0  -0.320  36.5866  14.0585   -5.9244
 G06  CA   C  CH1   0  -0.231  37.4623  13.6269   -6.9940
 G06  C    C  C     0   0.594  36.7742  13.8265   -8.3379
 G06  O    O  O     0  -0.433  35.6237  13.5504   -8.5597
 G06  OAN  O  O2    0  -0.443  37.6085  14.3074   -9.2436
 G06  CAO  C  CH3   0  -0.429  37.1153  14.4686  -10.5760
 G06  CB   C  CH2   0  -0.477  37.9466  12.1735   -6.8671
 G06  CG   C  CH2   0  -0.574  39.0404  11.7735   -7.8472
 G06  SD   S  S2    0  -0.035  40.5651  12.7499   -7.7267
 G06  CE   C  CH3   0  -0.771  41.2106  12.1364   -6.1536
 G06  H1   H  HOH1  0   0.503  38.7010   9.5614   -3.9425
 G06  H2   H  HOH1  0   0.500  35.8199   7.8398   -3.3487
 G06  H3   H  HCH2  0   0.277  33.8484  10.6792   -3.1792
 G06  H4   H  HCH2  0   0.264  34.1553  10.9200   -4.8986
 G06  H5   H  HCR6  0   0.264  32.7243  12.3546   -2.1154
 G06  H6   H  HCH3  0   0.276  32.1709  16.7476   -2.2338
 G06  H7   H  HCH3  0   0.264  33.7329  17.3725   -2.7521
 G06  H8   H  HCH3  0   0.260  32.4245  17.1784   -3.9190
 G06  H9   H  HOH1  0   0.487  34.3979  16.8644   -4.8476
 G06  H10  H  H     0   0.236  35.3924  12.3676   -6.0636
 G06  H11  H  HCH1  0   0.274  38.3433  14.2707   -6.9679
 G06  H12  H  HCH3  0   0.255  37.9455  14.8617  -11.1546
 G06  H13  H  HCH3  0   0.242  36.7977  13.5161  -10.9995
 G06  H14  H  HCH3  0   0.244  36.2846  15.1727  -10.6082
 G06  H15  H  HCH2  0   0.261  37.1180  11.4733   -6.9916
 G06  H16  H  HCH2  0   0.259  38.3053  12.0418   -5.8436
 G06  H17  H  HCH2  0   0.281  38.7101  11.8618   -8.8830
 G06  H18  H  HCH2  0   0.282  39.2921  10.7226   -7.6930
 G06  H19  H  HCH3  0   0.278  42.1285  12.6811   -5.9407
 G06  H20  H  HCH3  0   0.259  40.5133  12.3116   -5.3354
 G06  H21  H  HCH3  0   0.262  41.4404  11.0732   -6.2117

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    1.430  0.020  1.430
 G06  OAN  C    single    1.322  0.020  1.322
 G06  O    C    double    1.204  0.020  1.204
 G06  C    CA   single    1.523  0.020  1.523
 G06  CG   SD   single    1.815  0.020  1.815
 G06  CG   CB   single    1.522  0.020  1.522
 G06  CA   CB   single    1.537  0.020  1.537
 G06  CA   N    single    1.448  0.020  1.448
 G06  SD   CE   single    1.808  0.020  1.808
 G06  N    CAF  double    1.263  0.020  1.263
 G06  CAF  CAE  single    1.474  0.020  1.474
 G06  OAU  PAT  double    1.477  0.020  1.477
 G06  OAD  CAC  single    1.338  0.020  1.338
 G06  CAE  CAC  aromatic  1.396  0.020  1.396
 G06  CAE  CAQ  aromatic  1.402  0.020  1.402
 G06  CAC  CAB  aromatic  1.408  0.020  1.408
 G06  CAR  CAQ  single    1.497  0.020  1.497
 G06  CAR  OAS  single    1.434  0.020  1.434
 G06  CAQ  CAX  aromatic  1.382  0.020  1.382
 G06  PAT  OAW  single    1.599  0.020  1.599
 G06  PAT  OAS  single    1.597  0.020  1.597
 G06  PAT  OAV  single    1.593  0.020  1.593
 G06  CAB  CAA  single    1.499  0.020  1.499
 G06  CAB  NAY  aromatic  1.321  0.020  1.321
 G06  CAX  NAY  aromatic  1.327  0.020  1.327
 G06  OAV  H1   single    0.850  0.020  0.980
 G06  OAW  H2   single    0.850  0.020  0.980
 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  103.39  3.000
 G06  OAS  PAT  OAV   96.35  3.000
 G06  OAW  PAT  OAV  105.83  3.000
 G06  OAV  PAT  OAU  117.67  3.000
 G06  OAS  PAT  OAU  116.94  3.000
 G06  OAW  PAT  OAU  114.28  3.000
 G06  H1   OAV  PAT  114.07  3.000
 G06  H2   OAW  PAT  114.04  3.000
 G06  CAR  OAS  PAT  119.57  3.000
 G06  H4   CAR  H3   107.53  3.000
 G06  H4   CAR  CAQ  111.03  3.000
 G06  H3   CAR  CAQ  109.79  3.000
 G06  H4   CAR  OAS  110.31  3.000
 G06  H3   CAR  OAS  109.86  3.000
 G06  CAQ  CAR  OAS  108.33  3.000
 G06  CAE  CAQ  CAX  118.67  3.000
 G06  CAX  CAQ  CAR  119.29  3.000
 G06  CAE  CAQ  CAR  122.04  3.000
 G06  H5   CAX  NAY  116.53  3.000
 G06  H5   CAX  CAQ  120.16  3.000
 G06  NAY  CAX  CAQ  123.30  3.000
 G06  CAB  NAY  CAX  119.42  3.000
 G06  CAC  CAB  CAA  120.27  3.000
 G06  CAA  CAB  NAY  118.07  3.000
 G06  CAC  CAB  NAY  121.66  3.000
 G06  H8   CAA  H7   107.57  3.000
 G06  H8   CAA  H6   107.46  3.000
 G06  H7   CAA  H6   107.72  3.000
 G06  H8   CAA  CAB  112.13  3.000
 G06  H7   CAA  CAB  112.04  3.000
 G06  H6   CAA  CAB  109.73  3.000
 G06  CAE  CAC  OAD  119.41  3.000
 G06  CAE  CAC  CAB  119.30  3.000
 G06  OAD  CAC  CAB  121.28  3.000
 G06  H9   OAD  CAC  110.93  3.000
 G06  CAF  CAE  CAC  122.86  3.000
 G06  CAC  CAE  CAQ  117.63  3.000
 G06  CAF  CAE  CAQ  119.49  3.000
 G06  H10  CAF  N    123.36  3.000
 G06  H10  CAF  CAE  114.39  3.000
 G06  N    CAF  CAE  122.25  3.000
 G06  CA   N    CAF  119.26  3.000
 G06  H11  CA   CB   107.54  3.000
 G06  H11  CA   C    107.97  3.000
 G06  CB   CA   C    109.82  3.000
 G06  H11  CA   N    107.13  3.000
 G06  CB   CA   N    114.29  3.000
 G06  C    CA   N    109.84  3.000
 G06  OAN  C    O    124.09  3.000
 G06  O    C    CA   124.35  3.000
 G06  OAN  C    CA   111.53  3.000
 G06  CAO  OAN  C    117.49  3.000
 G06  H14  CAO  H13  109.34  3.000
 G06  H14  CAO  H12  109.47  3.000
 G06  H13  CAO  H12  109.40  3.000
 G06  H14  CAO  OAN  111.31  3.000
 G06  H13  CAO  OAN  111.36  3.000
 G06  H12  CAO  OAN  105.88  3.000
 G06  H16  CB   H15  106.18  3.000
 G06  H16  CB   CG   109.61  3.000
 G06  H15  CB   CG   107.66  3.000
 G06  H16  CB   CA   107.14  3.000
 G06  H15  CB   CA   110.97  3.000
 G06  CG   CB   CA   114.94  3.000
 G06  H18  CG   H17  106.38  3.000
 G06  H18  CG   SD   108.35  3.000
 G06  H17  CG   SD   105.90  3.000
 G06  H18  CG   CB   109.13  3.000
 G06  H17  CG   CB   111.88  3.000
 G06  SD   CG   CB   114.81  3.000
 G06  CE   SD   CG   100.09  3.000
 G06  H21  CE   H20  109.40  3.000
 G06  H21  CE   H19  108.73  3.000
 G06  H20  CE   H19  108.21  3.000
 G06  H21  CE   SD   111.11  3.000
 G06  H20  CE   SD   111.75  3.000
 G06  H19  CE   SD   107.55  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    60.25  30.0  2
 G06  Var_02    N    CAF  CAE  CAQ  -146.75  30.0  3
 G06  Var_03    H6   CAA  CAB  NAY     0.08  30.0  2
 G06  Var_04    CAQ  CAR  OAS  PAT  -165.25  30.0  1
 G06  Var_05    SD   CG   CB   CA     59.68  30.0  1
 G06  Var_06    H12  CAO  OAN  C    -179.57  30.0  3
 G06  Var_07    H19  CE   SD   CG   -177.95  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

