# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 10:45:57 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: methyl (2~{S})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-4-methylsulfanyl-butanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H](CCSC)NCc1c(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
 G03  G03  'methyl (2~{S})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-4-methylsulfanyl-butanoate'  ligand  46  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_G03
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
 G03  OAU  O  OP    -1  -0.859  -32.5806   9.5449  -21.9795
 G03  PAT  P  P      0   1.247  -32.6202   9.6674  -23.5095
 G03  OAV  O  O      0  -0.878  -33.9467  10.1461  -24.0784
 G03  OAW  O  OP    -1  -0.887  -31.9669   8.4927  -24.2299
 G03  OAS  O  O2     0  -0.650  -31.6080  11.0092  -23.8694
 G03  CAR  C  CH2    0  -0.235  -30.2608  10.8866  -23.5181
 G03  CAQ  C  CR6    0  -0.014  -29.6622  12.2394  -23.2431
 G03  CAX  C  CR16   0  -0.170  -28.6107  12.7058  -24.0157
 G03  NAY  N  N      0  -0.409  -28.0184  13.8816  -23.8358
 G03  CAB  C  CR6    0   0.122  -28.4431  14.6748  -22.8643
 G03  CAA  C  CH3    0  -0.720  -27.7635  15.9963  -22.6719
 G03  CAC  C  CR6    0   0.255  -29.5088  14.3007  -22.0309
 G03  OAD  O  OH1    0  -0.649  -29.9002  15.1575  -21.0750
 G03  CAE  C  CR6    0   0.028  -30.1345  13.0667  -22.2203
 G03  CAF  C  CH2    0  -0.369  -31.3115  12.6811  -21.3633
 G03  N    N  NH1    0  -0.660  -31.1175  13.1153  -19.9768
 G03  CA   C  CH1    0  -0.158  -32.3199  13.0014  -19.1635
 G03  C    C  C      0   0.591  -32.1073  13.8058  -17.8965
 G03  O    O  O      0  -0.440  -31.0559  13.8781  -17.3129
 G03  OAN  O  O2     0  -0.447  -33.2202  14.3978  -17.4923
 G03  CAO  C  CH3    0  -0.425  -33.1675  15.1409  -16.2726
 G03  CB   C  CH2    0  -0.473  -32.6921  11.5492  -18.8180
 G03  CG   C  CH2    0  -0.569  -34.0500  11.3676  -18.1518
 G03  SD   S  S2     0  -0.049  -35.4579  11.9311  -19.1511
 G03  CE   C  CH3    0  -0.791  -35.5522  10.6021  -20.3759
 G03  H3   H  HCH2   0   0.183  -30.1279  10.2623  -22.6233
 G03  H4   H  HCH2   0   0.196  -29.6737  10.4045  -24.3130
 G03  H5   H  HCR6   0   0.239  -28.2254  12.0916  -24.8242
 G03  H6   H  HCH3   0   0.241  -26.9564  16.1079  -23.3931
 G03  H7   H  HCH3   0   0.240  -28.4548  16.8312  -22.8028
 G03  H8   H  HCH3   0   0.240  -27.3423  16.0903  -21.6692
 G03  H9   H  HOH1   0   0.469  -30.4464  14.6233  -20.4313
 G03  H10  H  HCH2   0   0.255  -32.2000  13.1976  -21.7420
 G03  H11  H  HCH1   0   0.271  -33.1425  13.4459  -19.7293
 G03  H12  H  HCH3   0   0.252  -34.1718  15.5211  -16.1122
 G03  H13  H  HCH3   0   0.240  -32.8810  14.5084  -15.4329
 G03  H14  H  HCH3   0   0.241  -32.4723  15.9766  -16.3480
 G03  H15  H  HCH2   0   0.278  -32.6612  10.9554  -19.7346
 G03  H16  H  HCH2   0   0.247  -31.9237  11.1318  -18.1585
 G03  H17  H  HCH2   0   0.278  -34.2007  10.3136  -17.9117
 G03  H18  H  HCH2   0   0.277  -34.1161  11.9116  -17.2092
 G03  H19  H  HCH3   0   0.267  -36.3436  10.8663  -21.0756
 G03  H20  H  HCH3   0   0.276  -34.6223  10.4809  -20.9305
 G03  H21  H  HCH3   0   0.254  -35.8131   9.6576  -19.8991
 G03  H22  H  HCH2   0   0.293  -31.5243  11.6149  -21.4445
 G03  H23  H  HNH1   0   0.373  -30.3640  12.5794  -19.5568

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
 G03  OAV  PAT  deloc     1.521  0.020  1.521
 G03  NAY  CAX  aromatic  1.329  0.020  1.329
 G03  NAY  CAB  aromatic  1.324  0.020  1.324
 G03  CAX  CAQ  aromatic  1.386  0.020  1.386
 G03  OAS  PAT  single    1.719  0.020  1.719
 G03  OAS  CAR  single    1.398  0.020  1.398
 G03  CAA  CAB  single    1.498  0.020  1.498
 G03  OAW  PAT  deloc     1.525  0.020  1.525
 G03  CAB  CAC  aromatic  1.404  0.020  1.404
 G03  PAT  OAU  deloc     1.535  0.020  1.535
 G03  CAQ  CAR  single    1.505  0.020  1.505
 G03  CAQ  CAE  aromatic  1.398  0.020  1.398
 G03  CAC  CAE  aromatic  1.396  0.020  1.396
 G03  CAC  OAD  single    1.342  0.020  1.342
 G03  CAE  CAF  single    1.506  0.020  1.506
 G03  CAF  N    single    1.466  0.020  1.466
 G03  CE   SD   single    1.810  0.020  1.810
 G03  N    CA   single    1.456  0.020  1.456
 G03  CB   CA   single    1.538  0.020  1.538
 G03  CB   CG   single    1.523  0.020  1.523
 G03  SD   CG   single    1.816  0.020  1.816
 G03  CA   C    single    1.516  0.020  1.516
 G03  C    O    double    1.205  0.020  1.205
 G03  C    OAN  single    1.324  0.020  1.324
 G03  OAN  CAO  single    1.429  0.020  1.429
 G03  CAR  H3   single    0.970  0.020  1.090
 G03  CAR  H4   single    0.970  0.020  1.090
 G03  CAX  H5   single    0.930  0.020  1.080
 G03  CAA  H6   single    0.970  0.020  1.090
 G03  CAA  H7   single    0.970  0.020  1.090
 G03  CAA  H8   single    0.970  0.020  1.090
 G03  OAD  H9   single    0.850  0.020  0.980
 G03  CAF  H10  single    0.970  0.020  1.090
 G03  CA   H11  single    0.970  0.020  1.090
 G03  CAO  H12  single    0.970  0.020  1.090
 G03  CAO  H13  single    0.970  0.020  1.090
 G03  CAO  H14  single    0.970  0.020  1.090
 G03  CB   H15  single    0.970  0.020  1.090
 G03  CB   H16  single    0.970  0.020  1.090
 G03  CG   H17  single    0.970  0.020  1.090
 G03  CG   H18  single    0.970  0.020  1.090
 G03  CE   H19  single    0.970  0.020  1.090
 G03  CE   H20  single    0.970  0.020  1.090
 G03  CE   H21  single    0.970  0.020  1.090
 G03  CAF  H22  single    0.970  0.020  1.090
 G03  N    H23  single    0.890  0.020  1.040

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
 G03  OAS  PAT  OAW  104.49  3.000
 G03  OAW  PAT  OAV  116.07  3.000
 G03  OAS  PAT  OAV  100.93  3.000
 G03  OAW  PAT  OAU  113.47  3.000
 G03  OAS  PAT  OAU  104.82  3.000
 G03  OAV  PAT  OAU  114.86  3.000
 G03  CAR  OAS  PAT  116.52  3.000
 G03  H4   CAR  H3   105.96  3.000
 G03  H4   CAR  CAQ  108.30  3.000
 G03  H3   CAR  CAQ  108.29  3.000
 G03  H4   CAR  OAS  111.80  3.000
 G03  H3   CAR  OAS  111.78  3.000
 G03  CAQ  CAR  OAS  110.52  3.000
 G03  CAE  CAQ  CAX  117.72  3.000
 G03  CAE  CAQ  CAR  122.11  3.000
 G03  CAX  CAQ  CAR  120.17  3.000
 G03  H5   CAX  NAY  116.30  3.000
 G03  H5   CAX  CAQ  119.60  3.000
 G03  NAY  CAX  CAQ  124.10  3.000
 G03  CAB  NAY  CAX  119.10  3.000
 G03  CAC  CAB  CAA  120.21  3.000
 G03  CAC  CAB  NAY  121.30  3.000
 G03  CAA  CAB  NAY  118.49  3.000
 G03  H8   CAA  H7   106.77  3.000
 G03  H8   CAA  H6   108.29  3.000
 G03  H7   CAA  H6   108.17  3.000
 G03  H8   CAA  CAB  111.64  3.000
 G03  H7   CAA  CAB  111.83  3.000
 G03  H6   CAA  CAB  109.98  3.000
 G03  CAE  CAC  OAD  122.01  3.000
 G03  OAD  CAC  CAB  118.30  3.000
 G03  CAE  CAC  CAB  119.68  3.000
 G03  H9   OAD  CAC  106.08  3.000
 G03  CAF  CAE  CAC  119.95  3.000
 G03  CAF  CAE  CAQ  121.93  3.000
 G03  CAC  CAE  CAQ  118.09  3.000
 G03  H22  CAF  H10  106.08  3.000
 G03  H22  CAF  N    112.71  3.000
 G03  H10  CAF  N    107.15  3.000
 G03  H22  CAF  CAE  111.13  3.000
 G03  H10  CAF  CAE  108.45  3.000
 G03  N    CAF  CAE  111.04  3.000
 G03  H23  N    CA   109.91  3.000
 G03  H23  N    CAF  109.45  3.000
 G03  CA   N    CAF  113.32  3.000
 G03  H11  CA   CB   108.55  3.000
 G03  H11  CA   C    108.81  3.000
 G03  CB   CA   C    110.31  3.000
 G03  H11  CA   N    107.50  3.000
 G03  C    CA   N    108.03  3.000
 G03  CB   CA   N    113.52  3.000
 G03  OAN  C    O    123.98  3.000
 G03  OAN  C    CA   112.00  3.000
 G03  O    C    CA   124.00  3.000
 G03  CAO  OAN  C    117.52  3.000
 G03  H14  CAO  H13  109.32  3.000
 G03  H14  CAO  H12  109.38  3.000
 G03  H13  CAO  H12  109.43  3.000
 G03  H14  CAO  OAN  111.30  3.000
 G03  H13  CAO  OAN  111.44  3.000
 G03  H12  CAO  OAN  105.90  3.000
 G03  H16  CB   H15  106.15  3.000
 G03  H16  CB   CG   108.46  3.000
 G03  H15  CB   CG   109.10  3.000
 G03  H16  CB   CA   108.98  3.000
 G03  H15  CB   CA   108.52  3.000
 G03  CG   CB   CA   115.24  3.000
 G03  H18  CG   H17  106.46  3.000
 G03  H18  CG   SD   105.89  3.000
 G03  H17  CG   SD   108.28  3.000
 G03  H18  CG   CB   111.87  3.000
 G03  H17  CG   CB   109.54  3.000
 G03  SD   CG   CB   114.42  3.000
 G03  CE   SD   CG   100.65  3.000
 G03  H21  CE   H20  109.31  3.000
 G03  H21  CE   H19  108.51  3.000
 G03  H20  CE   H19  108.68  3.000
 G03  H21  CE   SD   110.66  3.000
 G03  H20  CE   SD   112.44  3.000
 G03  H19  CE   SD   107.13  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
 G03  CONST_01  CAB  NAY  CAX  CAQ     0.00   0.0  0
 G03  CONST_02  CAB  CAC  CAE  CAQ     0.00   0.0  0
 G03  CONST_03  CAC  CAB  NAY  CAX     0.00   0.0  0
 G03  CONST_04  CAC  CAE  CAQ  CAX     0.00   0.0  0
 G03  CONST_05  CAE  CAQ  CAX  NAY     0.00   0.0  0
 G03  CONST_06  CAE  CAC  CAB  NAY     0.00   0.0  0
 G03  CONST_07  NAY  CAX  CAQ  CAR   180.00   0.0  0
 G03  CONST_08  CAC  CAE  CAQ  CAR   180.00   0.0  0
 G03  CONST_09  OAD  CAC  CAE  CAQ   180.00   0.0  0
 G03  CONST_10  CAA  CAB  NAY  CAX   180.00   0.0  0
 G03  CONST_11  CAF  CAE  CAQ  CAX   180.00   0.0  0
 G03  CONST_12  OAD  CAC  CAB  NAY   180.00   0.0  0
 G03  CONST_13  CAF  CAE  CAC  CAB   180.00   0.0  0
 G03  CONST_14  CAE  CAC  CAB  CAA   180.00   0.0  0
 G03  CONST_15  H5   CAX  NAY  CAB   180.00   0.0  0
 G03  Var_01    CAX  CAQ  CAR  OAS  -118.44  30.0  1
 G03  Var_02    N    CAF  CAE  CAQ   143.04  30.0  2
 G03  Var_03    H6   CAA  CAB  NAY    -1.17  30.0  2
 G03  Var_04    CAQ  CAR  OAS  PAT  -152.21  30.0  3
 G03  Var_05    CA   N    CAF  CAE   168.89  30.0  3
 G03  Var_06    SD   CG   CB   CA     60.52  30.0  3
 G03  Var_07    H12  CAO  OAN  C    -178.79  30.0  3
 G03  Var_08    H19  CE   SD   CG   -176.94  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
 G03  chir_01  CA  N  CB  C  negativ

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
 G03  plan-1  CAR  0.020
 G03  plan-1  CAQ  0.020
 G03  plan-1  CAX  0.020
 G03  plan-1  NAY  0.020
 G03  plan-1  CAB  0.020
 G03  plan-1  CAA  0.020
 G03  plan-1  CAC  0.020
 G03  plan-1  OAD  0.020
 G03  plan-1  CAE  0.020
 G03  plan-1  CAF  0.020
 G03  plan-1  H5   0.020
 G03  plan-2  CA   0.020
 G03  plan-2  C    0.020
 G03  plan-2  O    0.020
 G03  plan-2  OAN  0.020

